%%: Begin bibliography entries
@Article{SCI:Abd2013a,
author = "A. Abdul-Rahman and J. Lein and K. Coles and E.
Maguire and M.D. Meyer and M. Wynne and C.R.
Johnson and A. Trefethen and M. Chen",
title = "Rule-based Visual Mappings - with a Case Study on
Poetry Visualization",
journal = "Proceedings of the 2013 Eurographics Conference on
Visualization (EuroVis)",
volume = "32",
number = "3",
pages = "381--390",
year = "2013",
month = "June",
url = "http://www.sci.utah.edu/publications/Abd2013a/Rahman_EuroVis2013.pdf",
}
@Article{SCI:Abd2018a,
author = "O. Abdullah and L. Dai and J. Tippetts and B.
Zimmerman and A. Van Hoek and S. Joshi and E.
Hsu",
title = "High resolution and high field diffusion MRI in
the visual system of primates (P3.086)",
journal = "Neurology",
volume = "90",
number = "15 Supplement",
year = "2018",
publisher = "Wolters Kluwer Health, Inc",
issn = "0028-3878",
}
@Article{SCI:Abr2013a,
author = "C.L. Abraham and S.A. Maas and J.A. Weiss and B.J.
Ellis and C.L. Peters and A.E. Anderson",
title = "A new discrete element analysis method for
predicting hip joint contact stresses",
journal = "Journal of Biomechanics",
volume = "46",
number = "6",
pages = "1121--1127",
year = "2013",
doi = "10.1016/j.jbiomech.2013.01.012",
url = "http://www.sci.utah.edu/publications/abraham13/Abraham_jbme_2013.pdf",
}
@Article{SCI:Ada2017a,
author = "M. Adamaszek and H. Adams and E. Gasparovic and M.
Gommel and E. Purvine and R. Sazdanovic and B. Wang
and Y. Wang and L. Ziegelmeier",
title = "Vietoris-Rips and Cech Complexes of Metric
Gluings",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Ada2017a/1712.06224.pdf",
}
@InProceedings{SCI:Ade94a,
author = "S. Adelson and C.D. Hansen",
title = "Fast Stereoscopic Images with Ray-Traced Volume
Rendering",
booktitle = "Symposium on Volume Visualization",
pages = "3--9",
year = "1994",
month = "October",
location = "Washington, DC.",
keywords = "volume rendering",
}
@InProceedings{SCI:Adl2006a,
author = "G. Adluru and E.V.R. DiBella and R.T. Whitaker",
title = "Automatic Segmentation of Cardiac Short Axis
Slices in Perfusion {MRI}",
booktitle = c-ISBI2006,
pages = "133--136",
year = "2006",
keywords = "ip image processing signal processing,
segmentation, cardiac heart, ncrr, ip gp image
processing goemetry processing",
url = "http://www.sci.utah.edu/publications/adluru06/Adluru_ISBI_06.pdf",
}
@InProceedings{SCI:Adl2006b,
author = "G. Adluru and E.V.R. DiBella",
title = "Segmentation Based Registration of Myocardium in
Cardiac Perfusion Images",
booktitle = c-ISMRM2006,
volume = "14",
pages = "1223",
year = "2006",
keywords = "ip image processing signal processing,
segmentation, cardiac heart, ncrr, ip gp image
processing goemetry processing",
url = "http://www.sci.utah.edu/publications/adluru06/Adluru_ISMRM_06.pdf",
}
@Article{SCI:Adl2006d,
author = "G. Adluru and E.V.R. DiBella and M.C. Schabel",
title = "Model-Based Registration for Dynamic Cardiac
Perfusion {MRI}",
journal = "Journal of Magnetic Resonance Imaging",
volume = "24",
number = "5",
pages = "1062--1070",
year = "2006",
publisher = "Wiley Subscription Services, Inc., A Wiley
Company",
doi = "10.1002/jmri.20756",
url = "http://www.sci.utah.edu/publications/Adl2006d/Adluru_JMRI_06.pdf",
}
@Article{SCI:Adl2007a,
author = "G. Adluru and S.P. Awate and T. Tasdizen and R.T.
Whitaker and E.V.R. DiBella",
title = "Temporally Constrained Reconstruction of Dynamic
Cardiac Perfusion MRI",
journal = "Magnetic Resonance in Medicine",
volume = "57",
pages = "1027--1036",
year = "2007",
keywords = "ncrr",
url = "http://www.sci.utah.edu/publications/adluru07/Adluru_MRM_07.pdf",
}
@InProceedings{SCI:Adl2007b,
author = "G. Adluru and R.T. Whitaker and E.V.R. DiBella",
title = "Spatio-Temporal Constrained Reconstruction of
Sparse Dynamic Contrast Enhanced Radial {MRI}
Data",
booktitle = "Proceedings of the {IEEE} International Symposium
on Biomedical Imaging",
pages = "109--112",
year = "2007",
keywords = "ncrr",
url = "http://www.sci.utah.edu/publications/adluru07/Adluru_ISBI_07.pdf",
}
@InProceedings{SCI:Adl2007c,
author = "G. Adluru and E. Hsu and E.V.R. DiBella",
title = "Constrained Reconstruction of Sparse Cardiac MR
DTI Data",
booktitle = "Proceedings of FIMH 2007",
number = "4466",
pages = "91--99",
year = "2007",
series = "LNCS",
keywords = "tensor field methods, diffusion tensor imaging,
cardiac heart",
url = "http://www.sci.utah.edu/publications/adluru07/Adluru_FIMH_07.pdf",
}
@InProceedings{SCI:Adl2008a,
author = "G. Adluru and E.V.R. DiBella and C.J. McGann",
title = "Data Acquisition and Reconstruction of
Undersampled Radial MR Myocardial Perfusion",
booktitle = "Proceedings of the 11th Annual Scientific Sessions
of the Society for Cardiovascular Magnetic
Resonance (SCMR) 2008",
pages = "215",
year = "2008",
url = "http://www.sci.utah.edu/publications/adluru08/Adluru_SCMR_08.pdf",
}
@InProceedings{SCI:Adl2008b,
author = "G. Adluru and E.V.R. DiBella",
title = "A Comparison of {L1} and {L2} Norms as Temporal
Constraints for Reconstruction of Undersampled
Dynamic Contrast Enhanced Cardiac Scans with
Respiratory Motion",
booktitle = "Proceedings of the 16th Scientific Meeting and
Exhibition of the International Society for
Magnetic Resonance in Medicine ({ISMRM}) 2008",
pages = "340",
year = "2008",
url = "http://www.sci.utah.edu/publications/adluru08/Adluru_ISMRM_08_a.pdf",
}
@InProceedings{SCI:Adl2008c,
author = "G. Adluru and E.V.R. DiBella",
title = "Data Reordering for Improved Constrained
Reconstruction from Undersampled k-space Data",
booktitle = "Proceedings of the 16th Scientific Meeting and
Exhibition of the International Society for
Magnetic Resonance in Medicine ({ISMRM}) 2008",
pages = "3153",
year = "2008",
url = "http://www.sci.utah.edu/publications/adluru08/Adluru_ISMRM_08_b.pdf",
}
@Article{SCI:Adl2010a,
author = "G. Adluru and T. Tasdizen and M.C. Schabel and
E.V.R. DiBella",
title = "Reconstruction of 3D Dynamic Contrast-Enhanced
Magnetic Resonance Imaging Using Nonlocal Means",
journal = "Journal of Magnetic Resonance Imaging",
volume = "32",
pages = "1217--1227",
year = "2010",
doi = "10.1002/jmri.22358",
url = "http://www.sci.utah.edu/publications/adluru10/Adluru_JMRI_10.pdf",
}
@InProceedings{SCI:Adl2010b,
author = "G. Adluru and T. Tasdizen and R. Whitaker and E.
DiBella",
title = "Improving Undersampled MRI Reconstruction Using
Non-Local Means",
booktitle = "Proceedings of the 2010 International Conference
on Pattern Recognition",
pages = "4000--4003",
year = "2010",
doi = "10.1109/ICPR.2010.973",
url = "http://www.sci.utah.edu/publications/adluru10/Adluru_ICPR_10.PDF",
}
@InProceedings{SCI:Adl2014a,
author = "G. Adluru and Y. Gur and J. Anderson and L.
Richards and N. Adluru and E. DiBella",
title = "Assessment of white matter microstructure in
stroke patients using {NODDI}",
booktitle = "Proceedings of the 2014 {IEEE} Int. Conf.
Engineering and Biology Society ({EMBC})",
year = "2014",
url = "http://www.sci.utah.edu/publications/Adl2014a/Adluru_NODDIwithStroke.pdf",
}
@Unpublished{SCI:Ahe2011a,
author = "S. Ahern and A. Shoshani and K.L. Ma and A.
Choudhary and T. Critchlow and S. Klasky and V.
Pascucci",
title = "Scientific Discovery at the Exascale: Report from
the (DOE) (ASCR) 2011 Workshop on Exascale Data
Management, Analysis, and Visualization",
year = "2011",
month = "January",
note = "Office of Scientific and Technical Information
(OSTI)",
doi = "10.2172/1011053",
url = "http://www.sci.utah.edu/publications/Ahe2011a/Exascale-ASCR-Analysis2011.pdf",
}
@Article{SCI:Ahm2001a,
author = "I. Ahmad and M. Berzins",
title = "MOL Solvers for Hyperbolic PDEs with Source
Terms",
journal = "Mathematics and Computers in Simulation",
volume = "56",
pages = "1115--1125",
year = "2001",
url = "http://www.sci.utah.edu/publications/ahmad01/Ahmad_MOL-solvers.pdf",
}
@Article{SCI:Ahm97a,
author = "I. Ahmad and M. Berzins",
title = "An Algorithm for {ODE}s from Atmospheric
Dispersion Problems",
journal = "Applied Numerical Mathematics",
volume = "25",
pages = "137--149",
year = "1997",
url = "http://www.sci.utah.edu/publications/ahmad97/amsterp.pdf",
}
@Article{SCI:Ahn2012a,
author = "Y.-J. Ahn and C. Hoffmann and P. Rosen",
title = "A Note on Circle Packing",
journal = "Journal of Zhejiang University SCIENCE C",
volume = "13",
number = "8",
pages = "559--564",
year = "2012",
keywords = "Circle packing, Algorithm performance, Parallel
computation, Graphics processing unit (GPU)",
url = "http://www.sci.utah.edu/publications/ahn12/Ahn_JZUS2012.pdf",
}
@InProceedings{SCI:Ahr95a,
author = "J. Ahrens and C.D. Hansen",
title = "Cost-Effective Data-Parallel Load Balancing",
booktitle = "International Conference on Parallel Processing",
pages = "14--18",
year = "1995",
month = "August",
location = "Oconomowoc, Wi.",
}
@Article{SCI:Aie2018a,
author = "K. A. Aiello and S. P. Ponnapalli and O. Alter",
title = "Mathematically universal and biologically
consistent astrocytoma genotype encodes for
transformation and predicts survival phenotype",
journal = "APL Bioengineering",
volume = "2",
number = "3",
pages = "031909",
year = "2018",
publisher = "AIP Publishing",
month = "September",
doi = "10.1063/1.5037882",
url = "http://www.sci.utah.edu/publications/Aie2018a/1.5037882.pdf",
}
@Article{SCI:Ako2011a,
author = "N. Akoum and M. Daccarett and C. McGann and N.
Segerson and G. Vergara and S. Kuppahally and T.
Badger and N. Burgon and T. Haslam and E.
Kholmovski and R.S. MacLeod and N.F. Marrouche",
title = "Atrial fibrosis helps select the appropriate
patient and strategy in catheter ablation of atrial
fibrillation: a {DE-MRI} guided approach",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "22",
number = "1",
pages = "16--22",
year = "2011",
doi = "10.1111/j.1540-8167.2010.01876.x",
pmid = "20807271",
url = "http://www.sci.utah.edu/publications/akoum11/Akoum_JCE2011.pdf",
}
@Article{SCI:Ako2012a,
author = "N.W. Akoum and C.J. McGann and G. Vergara and T.
Badger and R. Ranjan and C. Mahnkopf and E.G.
Kholmovski and R.S. Macleod and N.F. Marrouche",
title = "Atrial Fibrosis Quantified Using Late Gadolinium
Enhancement {MRI} is AssociatedWith Sinus Node
Dysfunction Requiring Pacemaker Implant",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "23",
number = "1",
pages = "44--50",
year = "2012",
doi = "10.1111/j.1540-8167.2011.02140.x",
url = "http://www.sci.utah.edu/publications/akoum12/Akoum_JCE2012.pdf",
}
@Article{SCI:Ale2003a,
author = "M. Alexa and J. Behr and D. Cohen-Or and S.
Fleishman and C.T. Silva and D. Levin",
title = "Computing and Rendering Point Set Surfaces",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "9",
number = "1",
pages = "3--15",
year = "2003",
issn = "1077-2626",
url = "http://www.sci.utah.edu/publications/alexa03/tvcg2003acr.pdf",
}
@Article{SCI:Ale2005a,
author = "Y. Alexeev and B.A. Allan and R.C. Armstrong and
D.E. Bernholdt and T.L. Dahlgren and D. Gannon and
C.L. Janssen and J.P. Kenny and M. Krishnan and
J.A. Kohl and G. Kumfert and L.C. McInnes and J.
Nieplocha and S.G. Parker and C. Rasmussen and T.L.
Windus",
title = "Component-Based Software for High-Performance
Scientific Computing",
journal = "Journal of Physics: Conference Series",
volume = "16",
pages = "536--540",
year = "2005",
publisher = "IOP Publishing",
month = "January",
doi = "10.1088/1742-6596/16/1/073",
url = "http://www.sci.utah.edu/publications/Ale2005a/jpconf5_16_073.pdf",
}
@TechReport{SCI:Alt1990a,
author = "O. Alter and O. Zachar",
title = "Achilles and the Turtle in the Maze of the Weak
Measurement",
number = "TAUP 90-1832",
year = "1990",
institution = "Tel Aviv University",
type = "Tel Aviv University Report",
url = "http://www.sci.utah.edu/publications/alter90/Alter_Achilles1990.pdf",
}
@Article{SCI:Alt1995a,
author = "O. Alter and Y. Yamamoto",
title = "Inhibition of the Measurement of the Wave Function
of a Single Quantum System in Repeated Weak Quantum
Nondemolition Measurements",
journal = "Physical Review Letters",
volume = "74",
number = "21",
pages = "4106--4109",
year = "1995",
publisher = "American Physical Society",
month = "May",
doi = "10.1103/PhysRevLett.74.4106",
url = "http://www.sci.utah.edu/publications/alter95/Alter_PhysRevLett.74.4106.pdf",
}
@InCollection{SCI:Alt1995b,
author = "O. Alter and Y. Yamamoto",
title = "Can We Measure the Wave Function of a Single Wave
Packet of Light?: Brownian Motion and Continuous
Wave Packet Collapse in Repeated Weak Quantum
Non-Demolition Measurements",
booktitle = "Fundamental Problems in Quantum Theory",
volume = "755",
pages = "103--109",
year = "1995",
editor = "D.M. Greenberger and A. Zeilinger",
publisher = "New York Academy of Sciences, New York, NY",
doi = "10.1111/j.1749-6632.1995.tb38960.x",
url = "http://www.sci.utah.edu/publications/Alt1995b/Alter_FPQT1995.pdf",
}
@Article{SCI:Alt1996a,
author = "O. Alter and Y. Yamamoto",
title = "Protective Measurement of the Wave Function of a
Single Squeezed Harmonic Oscillator State",
journal = "Physical Review A",
volume = "53",
number = "5",
pages = "R2911--R2914",
year = "1996",
month = "May",
doi = "10.1103/PhysRevA.53.R2911",
url = "http://www.sci.utah.edu/publications/Alt1996a/Alter_PhysRevA.53.R2911.pdf",
}
@InCollection{SCI:Alt1996b,
author = "O. Alter and Y. Yamamoto",
title = "Inhibition of the Measurement of the Wavefunction
of a Single Quantum System and the Projection
Postulate",
booktitle = "Quantum Physics, Chaos Theory and Cosmology",
pages = "151--172",
year = "1996",
editor = "M. Namiki and I. Ohba and K. Maeda and Y.
Aizawa",
publisher = "American Institute of Physics",
doi = "10.1103/PhysRevLett.74.4106",
url = "http://www.sci.utah.edu/publications/Alt1996b/Alter_QPCTC1996.pdf",
}
@InCollection{SCI:Alt1996c,
author = "O. Alter and Y. Yamamoto",
title = "The Quantum Zeno Effect of a Single System is
Equivalent to the Indetermination of the Quantum
State of a Single System",
booktitle = "Quantum Interferometry",
pages = "539--544",
year = "1996",
editor = "F. De Martini and G. Denardo and Y. Shih",
publisher = "VCH",
doi = "10.1103/PhysRevA.55.R2499",
url = "http://www.sci.utah.edu/publications/Alt1996c/Alter_QuantumZeno1996.pdf",
}
@InCollection{SCI:Alt1996d,
author = "O. Alter and Y. Yamamoto",
title = "The Unknown Wavefunction of a Single System Cannot
Be Inferred Using Repeated Quantum Measurements",
booktitle = "Quantum Coherence and Decoherence",
pages = "31--34",
year = "1996",
editor = "K. Fujikawa and Y. A. Ono",
publisher = "Elsevier Science, Amsterdam, Netherlands",
url = "http://www.sci.utah.edu/publications/alter96/Alter_QuantumCohere1996.pdf",
}
@Article{SCI:Alt1997a,
author = "O. Alter and Y. Yamamoto",
title = "Reply to the Comment on 'Protective Measurement of
the Wave Function of a Single Squeezed Harmonic
Oscillator State'",
journal = "Physical Review A",
volume = "56",
number = "1",
pages = "1057--1059",
year = "1997",
month = "July",
doi = "10.1103/PhysRevA.56.1057",
url = "http://www.sci.utah.edu/publications/Alt1997a/Alter_PhysRevA.56.1057.pdf",
}
@Article{SCI:Alt1997b,
author = "O. Alter and Y. Yamamoto",
title = "Quantum Zeno Effect and the Impossibility of
Determining the Quantum State of a Single System",
journal = "Physical Review A",
volume = "55",
number = "4",
pages = "R2499--R2502",
year = "1997",
month = "April",
doi = "10.1103/PhysRevA.55.R2499",
url = "http://www.sci.utah.edu/publications/Alt1997b/Alter_PhysRevA.55.R2499.pdf",
}
@Article{SCI:Alt1998a,
author = "O. Alter and Y. Yamamoto",
title = "Impossibility of Determining the Unknown
Wavefunction of a Single Quantum System: Quantum
Non-Demolition Measurements, Measurements without
Entanglement and Adiabatic Measurements",
journal = "Fortschritte der Physik",
volume = "46",
number = "6-8",
pages = "817--827",
year = "1998",
month = "November",
url = "http://www.sci.utah.edu/publications/Alt1998a/Alter_Fortchritte1998.pdf",
}
@Article{SCI:Alt1999a,
author = "O. Alter and Y. Yamamoto",
title = "Fundamental Quantum Limit to External Force
Detection via Monitoring a Single Harmonic
Oscillator or Free Mass",
journal = "Physics Letters A",
volume = "236",
number = "4-6",
pages = "226--231",
year = "1999",
doi = "10.1016/S0375-9601(99)00743-4",
url = "http://www.sci.utah.edu/publications/alter99/Alter_PhysLettersA1999.pdf",
}
@Article{SCI:Alt2000a,
author = "O. Alter and P.O. Brown and D. Botstein",
title = "Singular Value Decomposition for Genome-Wide
Expression Data Processing and Modeling",
title_url = "http://www.alterlab.org/SVD/PNAS_2000/",
journal = "Proceedings of the National Academy of Sciences",
volume = "97",
number = "18",
pages = "10101--10106",
year = "2000",
publisher = "Proceedings of the National Academy of Sciences",
month = "August",
doi = "10.1073/pnas.97.18.10101",
url = "http://www.sci.utah.edu/publications/Alt2000a/Alter_PNAS2000.pdf",
url = "http://www.sci.utah.edu/publications/Alt2000a/Alter_PNAS2000-appendix.pdf",
}
@Book{SCI:Alt2001a,
author = "O. Alter and Y. Yamamoto",
title = "Quantum Measurement of a Single System",
title_url =
"http://www.alterlab.org/publications/Alter_Yamamoto_Wiley-Interscience_2001.pdf",
year = "2001",
publisher = "Wiley-Blackwell",
month = "May",
isbn = "9780471283089",
doi = "10.1002/9783527617128",
}
@Article{SCI:Alt2001b,
author = "O. Alter and P.O. Brown and D. Botstein",
title = "Processing and Modeling Genome-Wide Expression
Data Using Singular Value Decomposition",
title_url = "http://www.alterlab.org/SVD/SPIE_2001/",
journal = "Microarrays: Optical Technologies and
Informatics",
volume = "4266",
pages = "171--186",
year = "2001",
editor = "M.L. Bittner and Y. Chen and A.N. Dorsel and E.R.
Dougherty (International Society for Optical
Engineering Bellingham)",
url = "http://www.sci.utah.edu/publications/alter01/Alter_SPIE2001.pdf",
url = "http://www.sci.utah.edu/publications/alter01/Alter_SPIE2001-appendix.pdf",
}
@Article{SCI:Alt2003a,
author = "O. Alter and P.O. Brown and D. Botstein",
title = "Generalized Singular Value Decomposition for
Comparative Analysis of Genome-Scale Expression
Datasets of Two Different Organisms",
journal = "Proceedings of the National Academy of Sciences",
volume = "100",
number = "6",
pages = "3351--3356",
year = "2003",
publisher = "Proceedings of the National Academy of Sciences",
month = "March",
doi = "10.1073/pnas.0530258100",
url = "http://www.sci.utah.edu/publications/Alt2003a/Alter_PNAS2003.pdf",
}
@Article{SCI:Alt2004a,
author = "O. Alter and G.H. Golub",
title = "Integrative Analysis of Genome-Scale Data by Using
Pseudoinverse Projection Predicts Novel Correlation
Between DNA Replication and RNA Transcription",
title_url = "http://www.alterlab.org/pseudoinverse/",
journal = "Proceedings of the National Academy of Sciences",
volume = "101",
number = "47",
pages = "16577--16582",
year = "2004",
publisher = "Proceedings of the National Academy of Sciences",
month = "November",
doi = "10.1073/pnas.0406767101",
url = "http://www.sci.utah.edu/publications/Alt2004a/Alter_PNAS2004.pdf",
}
@InProceedings{SCI:Alt2004b,
author = "O. Alter and G.H. Golub and P.O. Brown and D.
Botstein",
title = "Novel Genome-Scale Correlation Between DNA
Replication and {RNA} Transcription During the Cell
Cycle in Yeast is Predicted by Data-Driven
Models",
booktitle = "Proceedings of the Miami Nature Biotechnology
Winter Symposium on the Cell Cycle, Chromosomes and
Cancer",
volume = "15",
year = "2004",
editor = "M.P. Deutscher and S. Black and P.E. Boehmer and
G. D'Urso and T. Fletcher and F. Huijing and A.
Marshall and B. Pulverer and B. Renault and J.D.
Rosenblatt and J.M. Slingerland and W.J. Whelan",
url = "http://www.sci.utah.edu/publications/alter04/Alter_MNBWS2004.pdf",
}
@Article{SCI:Alt2005a,
author = "O. Alter and G.H. Golub",
title = "Reconstructing the Pathways of a Cellular System
from Genome-Scale Signals by Using Matrix and
Tensor Computations",
title_url = "http://www.alterlab.org/network_decomposition/",
journal = "Proceedings of the National Academy of Sciences",
volume = "102",
number = "49",
pages = "17559--17564",
year = "2005",
publisher = "Proceedings of the National Academy of Sciences",
month = "November",
doi = "10.1073/pnas.0509033102",
url = "http://www.sci.utah.edu/publications/Alt2005a/Alter_PNAS2005.pdf",
url = "http://www.sci.utah.edu/publications/Alt2005a/Alter_PNAS2005-appendix.pdf",
}
@Article{SCI:Alt2006a,
author = "I. Altintas and O. Barney and Z. Cheng and T.
Critchlow and B. Ludaescher and S.G. Parker and A.
Shoshani and M. Vouk",
title = "Accelerating the Scientific Exploration Process
with Scientific Workflows",
journal = "J. Phys. : Conf. Ser.",
volume = "46",
pages = "468--478",
year = "2006",
keywords = "SciDAC Scientific Data Management (SDM) Center, ,
scidac scientific data management (sdm) center",
url = "http://www.sci.utah.edu/publications/altintas06/jpconf6_46_065.pdf",
}
@Article{SCI:Alt2006b,
author = "O. Alter",
title = "Discovery of Principles of Nature from
Mathematical Modeling of DNA Microarray Data",
journal = "Proceedings of the National Academy of Sciences",
volume = "103",
number = "44",
pages = "16063--16064",
year = "2006",
publisher = "Proceedings of the National Academy of Sciences",
month = "October",
doi = "10.1073/pnas.0607650103",
url = "http://www.sci.utah.edu/publications/Alt2006b/PNAS-2006-Alter-16063-4.pdf",
}
@Article{SCI:Alt2006c,
author = "O. Alter and G. H. Golub",
title = "Singular Value Decomposition of Genome-Scale mRNA
Lengths Distribution Reveals Asymmetry in RNA Gel
Electrophoresis Band Broadening",
title_url = "http://www.alterlab.org/harmonic_oscillator/",
journal = "Proceedings of the National Academy of Sciences",
volume = "103",
number = "32",
pages = "11828--11833",
year = "2006",
publisher = "Proceedings of the National Academy of Sciences",
month = "July",
doi = "10.1073/pnas.0604756103",
url = "http://www.sci.utah.edu/publications/Alt2006c/Alter_PNAS2006.pdf",
}
@Article{SCI:Alt2007a,
author = "O. Alter",
title = "Genomic Signal Processing: From Matrix Algebra to
Genetic Networks",
journal = "Microarray Data Analysis: Methods in Molecular
Biology",
volume = "377",
pages = "17--59",
year = "2007",
editor = "M.J. Korenberg",
publisher = "Humana Press, Totowa",
doi = "10.1007/978-1-59745-390-5_2",
url = "http://www.sci.utah.edu/publications/alter07/Alter_Humana2007.pdf",
}
@Article{SCI:Alt2011a,
author = "I. Altrogge and T. Preusser and T. Kroeger and S.
Haase and T. Paetz and R.M. Kirby",
title = "Sensitivity Analysis for the Optimization of
Radiofrequency Ablation in the Presence of Material
Parameter Uncertainty",
journal = "International Journal for Uncertainty
Quantification",
year = "2011",
keywords = "netl, stochastic sensitivity analysis, stochastic
partial dierential equations, stochastic nite
element method, adaptive sparse grid, heat
transfer, multiscale modeling, representation of
uncertainty",
url = "http://www.sci.utah.edu/publications/altrogge11/Altrogge_IJUQ2011.pdf",
}
@InProceedings{SCI:Ame2004a,
author = "S. Amer-Yahia and F. Du and J. Freire",
title = "A Comprehensive Solution to the XML-to-Relational
Mapping Problem",
booktitle = "Proceedings of the 6th Annual ACM International
Workshop on Web Information and Data Management",
pages = "31--38",
year = "2004",
location = "Washington DC, USA",
isbn = "1-58113-978-0",
url = "http://www.sci.utah.edu/publications/amer-yahia04/Amer-yahia_WIDM2004.pdf",
}
@Article{SCI:And1992a,
author = "D.R. Anderson and J.A. Weiss and S. Takai and K.J.
Ohland and S.L-Y. Woo",
title = "Healing of the Medial Collateral Ligament
Following a Triad Injury: A Biomechanical and
Histological Study of the Knee in Rabbits",
journal = "Journal of Orthopaedic Research",
volume = "10",
pages = "485--495",
year = "1992",
}
@InProceedings{SCI:And2004a,
author = "A.E. Anderson and C.L. Peters and B.D. Tuttle and
J.A. Weiss",
title = "Development and Validation of a Subject-Specific
Finite Element Model of the Pelvis: Assessment of
Model Sensitivity",
booktitle = c-CMBBE2004,
pages = "(6 pages)",
year = "2004",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational mechanics, computational
biomechanics, ip image processing signal
processing, segmentation, surface processing",
url = "http://www.sci.utah.edu/publications/anderson04/25B.pdf",
}
@InProceedings{SCI:And2004b,
author = "A.E. Anderson and C.L. Peters and B.D. Tuttle and
J.A. Weiss",
title = "A Subject-Specific Finite Element Model of the
Pelvis Accurately Predicts Cortical Strains Under
Acetabular Loading",
booktitle = c-ORS2004,
volume = "29",
pages = "1334",
year = "2004",
month = "March",
location = "San Francisco, {CA}",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational mechanics, computational
biomechanics, segmentation, surface processing",
}
@Article{SCI:And2005a,
author = "A.E. Anderson and C.L. Peters and B.D. Tuttle and
J.A. Weiss",
title = "A Subject-Specific Finite Element Model of the
Pelvis: Development, Validation and Sensitivity
Studies",
journal = j-JBE,
volume = "127",
number = "3",
pages = "364--373",
year = "2005",
keywords = "finite elements, computational mechanics,
computational biomechanics",
url = "http://www.sci.utah.edu/publications/anderson05/Anderson_JBME_2005.pdf",
}
@TechReport{SCI:And2006a,
author = "E.W. Anderson and S.P. Callahan and G.T.Y. Chen
and J. Freire and E. Santos and C.E. Scheidegger
and C.T. Silva and H.T. Vo",
title = "Visualization in Radiation Oncology: Towards
Replacing the Laboratory Notebook",
number = "UUSCI-2006-017",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scalar field methods",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-017.pdf",
}
@Article{SCI:And2006b,
author = "A.E. Anderson and B.J. Ellis and J.A. Weiss",
title = "Verification, Validation and Sensitivity Studies
in Computational Biomechanics",
journal = "Computer Methods in Biomechanics and Biomedical
Engineering",
pages = "(in press)",
year = "2006",
keywords = "mrl, computational mechanics, computational
biomechanics",
url = "http://www.sci.utah.edu/publications/anderson06/anderson_cmbbe_2007.pdf",
}
@InProceedings{SCI:And2007b,
author = "E.W. Anderson and S.P. Callahan and C.E.
Scheidegger and J.M. Schriener and C.T. Silva",
title = "Hardware-Assisted Point-Based Volume Rendering of
Tetrahedral Meshes",
booktitle = "Proceedings of SIBGRAPI 2007",
pages = "163--170",
year = "2007",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/anderson07/pbvr.pdf",
}
@InProceedings{SCI:And2007c,
author = "E.W. Anderson and G.A. Preston and C.T. Silva",
title = "Towards Development of a Circuit Based Treatment
for Impaired Memory: A Multidisciplinary
Approach",
booktitle = "Proceedings of {IEEE} {EMBS} Neural Engineering
2007",
pages = "163--172",
year = "2007",
keywords = "neuro brain",
url = "http://www.sci.utah.edu/publications/anderson07/embs2007_neuro.pdf",
}
@Article{SCI:And2007d,
author = "A.E. Anderson and B.J. Ellis and J.A. Weiss",
title = "Verification, Validation and Sensitivity Studies
in Computational Biomechanics",
journal = "Computer Methods in Biomechanics and Biomedical
Engineering",
volume = "10",
number = "3",
pages = "171--184",
year = "2007",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/anderson07/anderson_cmbbe_2007.pdf",
}
@InProceedings{SCI:And2007e,
author = "E.W. Anderson and S.P. Callahan and D.A. Koop and
E. Santos and C.E. Scheidegger and H.T. Vo and J.
Freire and C.T. Silva",
title = "VisTrails: Using Provenance to Streamline Data
Exploration",
booktitle = "Poster Proceedings of the International Workshop
on Data Integration in the Life Sciences (DILS)
2007",
year = "2007",
note = "Poster presentation",
keywords = "vistrails",
}
@Article{SCI:And2008a,
author = "A.E. Anderson and B.J. Ellis and C.L. Peters and
J.A. Weiss",
title = "Cartilage Thickness: Factors Influencing
Multidetector CT Measurements in a Phantom Study",
journal = "Radiology",
volume = "246",
number = "1",
pages = "133-141",
year = "2008",
pmid = "18982614",
keywords = "bioengineering, MRL",
url = "http://www.sci.utah.edu/publications/anderson08/Anderson_Radiology_2008.pdf",
}
@Article{SCI:And2008b,
author = "A.E. Anderson and B.J. Ellis and S.A. Maas and
C.L. Peters and J.A. Weiss",
title = "Validation of Finite Element Predictions of
Cartilage Contact Pressure in the Human Hip
Joint",
journal = "ASME Journal of Biomechanical Engineering",
volume = "130",
number = "3",
pages = "051008-1--10",
year = "2008",
month = "May",
keywords = "bioengineering, MRL",
url = "http://www.sci.utah.edu/publications/anderson08/anderson_jbme_2008.pdf",
}
@Article{SCI:And2008c,
author = "E.W. Anderson and J. Ahrens and K. Heitmann and S.
Habib and C.T. Silva",
title = "Provenance in Comparative Analysis: A Study in
Cosmology",
journal = "Computing in Science and Engineering",
volume = "10",
number = "3",
pages = "30--37",
year = "2008",
keywords = "astronomy, cosmology, astrophysics, big bang,
vistrails, workflows, provenance",
url = "http://www.sci.utah.edu/publications/anderson08/cise2008c.pdf",
}
@Article{SCI:And2008d,
author = "A.E. Anderson and B.J. Ellis and C.L. Peters and
J.A. Weiss",
title = "Factors Influencing Cartilage Thickness
Measurements with Multi-Detector CT: A Phantom
Study",
journal = "Radiology",
volume = "246",
number = "1",
pages = "144-141",
year = "2008",
keywords = "mrl",
}
@Article{SCI:And2009a,
author = "J.R. Anderson and B.W. Jones and J.-H. Yang and
M.V. Shaw and C.B. Watt and P. Koshevoy and J.
Spaltenstein and E. Jurrus and Kannan U.V. and R.T.
Whitaker and D. Mastronarde and T. Tasdizen and
R.E. Marc",
title = "A Computational Framework for Ultrastructural
Mapping of Neural Circuitry",
title_url =
"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000074",
journal = "PLoS Biology",
volume = "7",
number = "3",
pages = "e74",
year = "2009",
pmid = "19855814",
keywords = "ucnia, crcns, ir-tweak, ir-tools, ncr toolset,
neural circuit reconstruction, electron microscopy
registration",
url = "http://www.sci.utah.edu/publications/anderson09/Anderson_PLoSBio2009.pdf",
}
@InProceedings{SCI:And2009b,
author = "J. Anderson and B. Jones and J. Yang and M. Shaw
and C. Watt and P. Koshevoy and J. Spaltenstein and
E. Jurrus and Kannan U.V. and R.T. Whitaker and D.
Mastronarde and T. Tasdizen and R. Marc",
title = "Ultra Structural Mapping of Neural Circuitry: A
Computational Framework",
booktitle = "{IEEE} International Symposium on Biomedical
Engineering ({ISBI} 2009)",
pages = "1135--1137",
year = "2009",
doi = "10.1109/ISBI.2009.5193257",
keywords = "crcns, neural circuitry",
url = "http://www.sci.utah.edu/publications/anderson09/Anderson_ISBI2009.pdf",
}
@Article{SCI:And2010a,
author = "A.E. Anderson and B.J. Ellis and S.A. Maas and
J.A. Weiss",
title = "Effects of idealized joint geometry on finite
element predictions of cartilage contact stresses
in the hip",
journal = "Journal of Biomechanics",
volume = "43",
number = "7",
pages = "1351--1357",
year = "2010",
month = "May",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/And2010a/anderson_jbiomech_2010.pdf",
}
@Article{SCI:And2010b,
author = "E.W. Anderson and G.A. Preston and C.T. Silva",
title = "Using Python for Signal Processing and
Visualization",
journal = "IEEE Computing in Science and Engineering",
volume = "12",
number = "4",
pages = "90--95",
year = "2010",
url = "http://www.sci.utah.edu/publications/anderson10/Anderson_python_processing2010.pdf",
}
@Article{SCI:And2010c,
author = "J.R. Anderson and B.C. Grimm and S. Mohammed and
B.W. Jones and T. Tasdizen and J. Spaltenstein and
P. Koshevoy and R.T. Whitaker and R.E. Marc",
title = "The Viking Viewer: Scalable Multiuser Annotation
and Summarization of Large Volume Datasets",
journal = "Journal of Microscopy",
volume = "241",
number = "1",
pages = "13--28",
year = "2010",
doi = "10.1111/j.1365-2818.2010.03402.x",
url = "http://www.sci.utah.edu/publications/anderson10/Anderson_JMicro2010.pdf",
}
@Article{SCI:And2011a,
author = "J.R. Anderson and B.W. Jones and C.B. Watt and
M.V. Shaw and J.-H. Yang and D. DeMill and J.S.
Lauritzen and Y. Lin and K.D. Rapp and D.
Mastronarde and P. Koshevoy and B. Grimm and T.
Tasdizen and R.T. Whitaker and R.E. Marc",
title = "Exploring the Retinal Connectome",
journal = "Molecular Vision",
volume = "17",
pages = "355--379",
year = "2011",
pmid = "21311605",
keywords = "neuroscience, retina, vision, blindness, visus,
crcns",
url = "http://www.sci.utah.edu/publications/anderson11/Anderson_MolVis2011.pdf",
}
@Article{SCI:And2011b,
author = "E.W. Anderson and K.C. Potter and L.E. Matzen and
J.F. Shepherd and G.A. Preston and C.T. Silva",
title = "A User Study of Visualization Effectiveness Using
{EEG} and Cognitive Load",
journal = "Computer Graphics Forum",
volume = "30",
number = "3",
pages = "791--800",
year = "2011",
editor = "H. Hauser and H. Pfister and J.J. van Wijk",
month = "June",
note = "Awarded 2nd Best Paper!",
doi = "10.1111/j.1467-8659.2011.01928.x",
url = "http://www.sci.utah.edu/publications/And2011b/Anderson_eurovis2011.pdf",
}
@InProceedings{SCI:And2011c,
author = "N. Andrysco and P. Rosen and V. Popescu and B.
Benes and K.R. Gurney",
title = "Experiences in Disseminating Educational
Visualizations",
booktitle = "Lecture Notes in Computer Science (7th
International Symposium on Visual Computing)",
volume = "2",
pages = "239--248",
year = "2011",
month = "September",
doi = "10.1007/978-3-642-24031-7_24",
url = "http://www.sci.utah.edu/publications/andrysco11/Andrysco.2011.ISVC.pdf",
}
@Article{SCI:And2011d,
author = "J.S. Anderson and J.A. Nielsen and A.L. Froehlich
and M.B. DuBray and T.J. Druzgal and A.N. Cariello
and J.R. Cooperrider and B.A. Zielinski and C.
Ravichandran and P.T. Fletcher and A.L. Alexander
and E.D. Bigler and N. Lange and J.E. Lainhart",
title = "Functional connectivity magnetic resonance imaging
classification of autism",
journal = "Brain",
pages = "(published online)",
year = "2011",
doi = "10.1093/brain/awr263",
pmid = "22006979",
url = "http://www.sci.utah.edu/publications/anderson11/Anderson_Brain2011.pdf",
}
@Article{SCI:And2011e,
author = "J.R. Anderson and S. Mohammed and B.C. Grimm and
B.W. Jones and P. Koshevoy and T. Tasdizen and R.T.
Whitaker and R.E. Marc",
title = "The Viking viewer for connectomics: scalable
multi-user annotation and summarization of large
volume data sets",
journal = "Journal of Microscopy",
volume = "241",
number = "1",
pages = "13--28",
year = "2011",
doi = "10.1111/j.1365-2818.2010.03402.x",
keywords = "Annotation, automated electron microscopy, citizen
science, computational methods, connectome,
networks, visualization",
url = "http://www.sci.utah.edu/publications/anderson11/Anderson_JM2011.pdf",
}
@InProceedings{SCI:And2013a,
author = "E.W. Anderson and C. Chong and G.A. Preston and
C.T. Silva",
title = "Discovering and Visualizing Patterns in {EEG}
Data",
booktitle = "Proceedings of the 2013 {IEEE} Pacific
Visualization Symposium ({PacificVis})",
pages = "105--112",
year = "2013",
url = "http://www.sci.utah.edu/publications/anderson13/EGI_Anderson_PacVis.pdf",
}
@Article{SCI:And2013b,
author = "J.S. Anderson and J.A. Nielsen and M.A. Ferguson
and M.C. Burback and E.T. Cox and L. Dai and G.
Gerig and J.O. Edgin and J.R. Korenberg",
title = "Abnormal brain synchrony in Down Syndrome",
title_url =
"http://www.sciencedirect.com/science/article/pii/S2213158213000624",
journal = "NeuroImage: Clinical",
volume = "2",
pages = "703--715",
year = "2013",
issn = "2213-1582",
doi = "10.1016/j.nicl.2013.05.006",
url = "http://www.sci.utah.edu/publications/anderson13/Anderson_NeuroImageClinical2013.pdf",
}
@Article{SCI:And2018a,
author = "D. N. Anderson and B. Osting and J. Vorwerk and A.
D Dorval and C. R Butson",
title = "Optimized programming algorithm for cylindrical
and directional deep brain stimulation
electrodes",
journal = "Journal of Neural Engineering",
volume = "15",
number = "2",
pages = "026005",
year = "2018",
url = "http://www.sci.utah.edu/publications/And2018a/Anderson_2018_J._Neural_Eng._15_026005.pdf",
}
@Article{SCI:And2018b,
author = "D. N. Anderson and G. Duffley and J. Vorwerk and
A. Dorval and C. R. Butson",
title = "Anodic Stimulation Misunderstood: Preferential
Activation of Fiber Orientations with Anodic
Waveforms in Deep Brain Stimulation",
journal = "Journal of Neural Engineering",
year = "2018",
publisher = "IOP Publishing",
month = "Oct",
doi = "10.1088/1741-2552/aae590",
url = "http://www.sci.utah.edu/publications/And2018b/Anderson_2018_J_Neural_Eng.pdf",
}
@Article{SCI:And2019a,
author = "D.N. Anderson and G. Duffley and J. Vorwerk and
A.D. Dorval and C.R. Butson",
title = "Anodic stimulation misunderstood: preferential
activation of fiber orientations with anodic
waveforms in deep brain stimulation",
journal = "Journal of Neural Engineering",
volume = "16",
number = "1",
pages = "016026",
year = "2019",
publisher = "IOP Publishing",
month = "Jan",
doi = "10.1088/1741-2552/aae590",
url = "http://www.sci.utah.edu/publications/And2019a/Anderson_2019_J._Neural_Eng._16_016026.pdf",
}
@Article{SCI:And2019b,
author = "C.J. Anderson and D.N. Anderson and S.M. Pulst and
C.R. Butson and A.D. Dorval",
title = "Neural Selectivity, Efficiency, and Dose
Equivalence in Deep Brain Stimulation through Pulse
Width Tuning and Segmented Electrodes",
journal = "bioRxiv",
year = "2019",
publisher = "Cold Spring Harbor Laboratory",
month = "April",
doi = "10.1101/613133",
url = "http://www.sci.utah.edu/publications/And2019b/613133.full.pdf",
}
@Article{SCI:And2019c,
author = "D. N. Anderson and C. Anderson and N. Lanka and R.
Sharma and C. R. Butson and B. W. Baker and A. D.
Dorval",
title = "The μDBS: Multiresolution, Directional Deep Brain
Stimulation for Improved Targeting of Small
Diameter Fibers",
journal = "Frontiers in Neuroscience",
volume = "13",
year = "2019",
month = "October",
doi = "10.3389/fnins.2019.01152",
url = "http://www.sci.utah.edu/publications/And2019c/fnins-13-01152.pdf",
}
@Article{SCI:Ape2000a,
author = "Th. Apel and M. Berzins and P.K. Jimack and G.
Kunert and A. Plaks and I. Tsukerman and M.
Walkley",
title = "Mesh Shape and Anistropic Elements: Theory and
Practice",
journal = "The Mathematics of Finite Elements and
Applications X",
pages = "367--376",
year = "2000",
editor = "J.R. Whiteman",
publisher = "Elsevier",
keywords = "finite elements, meshing",
url = "http://www.sci.utah.edu/publications/apel00/ABJKPTW99.pdf",
}
@Article{SCI:Aqu2019a,
author = "C. C. Aquino and G. Duffley and D. M. Hedges and
J. Vorwerk and P. A. House and H. B. Ferraz and J.
D. Rolston and C. R. Butson and L. E. Schrock",
title = "Interleaved deep brain stimulation for dyskinesia
management in Parkinson's disease",
journal = "Movement Disorders",
year = "2019",
doi = "10.1002/mds.27839",
url = "http://www.sci.utah.edu/publications/Aqu2019a/mds.27839.pdf",
}
@Article{SCI:Ara2015a,
author = "K.K. Aras and W. Good and J. Tate and B.M. Burton
and D.H. Brooks and J. Coll-Font and O. Doessel and
W. Schulze and D. Patyogaylo and L. Wang and P. Van
Dam and and R.S. MacLeod",
title = "Experimental Data and Geometric Analysis
Repository: EDGAR",
journal = "Journal of Electrocardiology",
year = "2015",
url = "http://www.sci.utah.edu/publications/Ara2015a/aras-j-electrocardio15-2.pdf",
}
@Article{SCI:Ara2016a,
author = "K. Aras B. Burton and D. Swenson and R.S.
MacLeod",
title = "Spatial organization of acute myocardial
ischemia",
journal = "Journal of Electrocardiology",
volume = "49",
number = "3",
pages = "323–336",
year = "2016",
publisher = "Elsevier",
month = "May",
url = "http://www.sci.utah.edu/publications/Ara2016a/macleod_spatial.pdf",
}
@Article{SCI:Arc2009a,
author = "R. Archibald and A. Gelb and R. Saxena and D.
Xiu",
title = "Discontinuity Detection in Multivariate Space for
Stochastic Simulations",
journal = "Journal of Computational Physics",
volume = "228",
number = "7",
pages = "2676--2689",
year = "2009",
doi = "10.1016/j.jcp.2009.01.001",
keywords = "Stochastic partial differential equations,
Multivariate edge detection, Generalized polynomial
chaos method",
url = "http://www.sci.utah.edu/publications/archibald09/Archibald_JCP2009.pdf",
}
@Article{SCI:Arm2006a,
author = "R. Armstrong and G. Kumfert and L.C. McInnes and
S.G. Parker and B. Allan and M. Sottile and T.
Epperly and T. Dahlgren",
title = "The {CCA} Component Model for High-Performance
Scientific Computing",
journal = "Concurrency and Computation: Practice \&
Experience",
volume = "18",
number = "2",
pages = "215--229",
year = "2006",
publisher = "John Wiley and Sons Ltd.",
address = "Chichester, UK",
issn = "1532-0626",
keywords = "ncrr, Common Component Architecture, CCA",
}
@InProceedings{SCI:Arm99a,
author = "R. Armstrong and D. Gannon and A. Geist and K.
Keahey and S. Kohn and L. McInnes and S.G. Parker
and B. Smolinksi",
title = "Toward a Common Component Architecture for
High-Performance Scientific Computing",
booktitle = "Proceedings of the 8th {IEEE} International
Symposium on High Performance Distributed
Computation ({HPDC})",
year = "1999",
month = "August",
keywords = "scirun, CCA",
url = "http://www.sci.utah.edu/publications/hpdc99/cca.ps.gz",
url = "http://www.sci.utah.edu/publications/hpdc99/cca.pdf",
}
@Article{SCI:Ate2006a,
author = "G.A. Ateshian and B.J. Ellis and J.A. Weiss",
title = "Equivalence Between Instantaneous Biphasic and
Incompressible Elastic Material Response",
journal = "Journal of Biomechanical Engineering",
pages = "(in press)",
year = "2006",
month = "November",
keywords = "mrl, computational biomechanics",
url = "http://www.sci.utah.edu/publications/ateshian06/ateshian_jbme_2007.pdf",
}
@Article{SCI:Ate2007a,
author = "G.A. Ateshian and B.J. Ellis and J.A. Weiss",
title = "Equivalence Between Short-Time Biphasic and
Incompressible Elastic Material Response",
journal = "Journal of Biomechanical Engineering",
volume = "129",
number = "3",
pages = "405--412",
year = "2007",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/ateshian07/ateshian_jbme_2007.pdf",
}
@Article{SCI:Ate2010a,
author = "G.A. Ateshian and S.A. Maas and J.A. Weiss",
title = "Finite element algorithm for frictionless contact
of porous permeable media under finite deformation
and sliding",
journal = "Journal of Biomechanical Engineering",
volume = "132",
number = "6",
year = "2010",
note = "Cover article",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/ateshian10/ateshian_jbme_2010.pdf",
}
@Article{SCI:Ate2011a,
author = "G.A. Ateshian and M.B. Albro and S.A. Maas and
J.A. Weiss",
title = "{F}inite element implementation of mechanochemical
phenomena in neutral deformable porous media under
finite deformation",
journal = "Journal of Biomechanical Engineering",
volume = "133",
number = "8",
year = "2011",
doi = "10.1115/1.4004810",
url = "http://www.sci.utah.edu/publications/ateshian11/Ateshian_JBE2011.pdf",
}
@Article{SCI:Ate2012a,
author = "G.A. Ateshian and S.A. Maas and J.A. Weiss",
title = "Solute transport across a contact interface in
deformable porous media",
journal = "Journal of Biomechanics",
volume = "45",
number = "6",
pages = "1023-–1027",
year = "2012",
doi = "10.1016/j.jbiomech.2012.01.003",
keywords = "FEBio, Finite element modeling, Contact mechanics,
Solute transport, Porous media, Biphasic theory",
}
@Article{SCI:Ate2018a,
author = "G.A. Ateshian and J.J. Shim and S.A. Maas and J.A.
Weiss",
title = "Finite Element Framework for Computational Fluid
Dynamics in FEBio",
title_url =
"https://biomechanical.asmedigitalcollection.asme.org/article.aspx?articleID=2666594",
journal = "Journal of Biomechanical Engineering",
volume = "140",
number = "2",
pages = "021001",
year = "2018",
publisher = "ASME International",
month = "Jan",
doi = "10.1115/1.4038716",
}
@Article{SCI:Ath2018a,
author = "T. M. Athawale and K. A. Johnson and C. R. Butson
and C. R. Johnson",
title = "A statistical framework for quantification and
visualisation of positional uncertainty in deep
brain stimulation electrodes",
title_url =
"https://www.tandfonline.com/doi/full/10.1080/21681163.2018.1523750",
journal = "Computer Methods in Biomechanics and Biomedical
Engineering: Imaging \& Visualization",
pages = "1-12",
year = "2018",
publisher = "Taylor \& Francis",
doi = "doi:10.1080/21681163.2018.1523750",
url = "http://www.sci.utah.edu/publications/Ath2018a/athawale2019.pdf",
url = "http://www.sci.utah.edu/publications/Ath2018a/athawale2019.pdf",
}
@Article{SCI:Ath2019a,
author = "T. Athawale and C. R. Johnson",
title = "Probabilistic Asymptotic Decider for Topological
Ambiguity Resolution in Level-Set Extraction for
Uncertain 2D Data",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "25",
number = "1",
pages = "1163-1172",
year = "2019",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/TVCG.2018.2864505",
url = "http://www.sci.utah.edu/publications/Ath2019a/08440034.pdf",
}
@Article{SCI:Ath2019b,
author = "T. M. Athawale and K. A. Johnson and C. R. Butson
and C. R. Johnson",
title = "A statistical framework for quantification and
visualisation of positional uncertainty in deep
brain stimulation electrodes",
title_url =
"https://www.tandfonline.com/doi/full/10.1080/21681163.2018.1523750",
journal = "Computer Methods in Biomechanics and Biomedical
Engineering: Imaging \& Visualization",
volume = "7",
number = "4",
pages = "438-449",
year = "2019",
publisher = "Taylor \& Francis",
doi = "10.1080/21681163.2018.1523750",
}
@Article{SCI:Atk2016a,
author = "P.R. Atkins and S.Y. Elhabian and P. Agrawal and
M.D. Harris and R.T. Whitaker and J.A. Weiss and
C.L. Peters and A.E. Anderson",
title = "Quantitative comparison of cortical bone thickness
using correspondence-based shape modeling in
patients with cam femoroacetabular impingement",
journal = "Journal of Orthopaedic Research",
year = "2016",
publisher = "Wiley-Blackwell",
month = "Nov",
doi = "10.1002/jor.23468",
url = "http://www.sci.utah.edu/publications/Atk2016a/Atkins_et_al-2016-Journal_of_Orthopaedic_Research.pdf",
}
@Article{SCI:Atk2019a,
author = "P. R. Atkins and Y. Shin and P. Agrawal and S. Y.
Elhabian and R. T. Whitaker and J. A. Weiss and S.
K. Aoki and C. L. Peters and A. E. Anderson",
title = "Which Two-dimensional Radiographic Measurements of
Cam Femoroacetabular Impingement Best Describe the
Three-dimensional Shape of the Proximal Femur?",
journal = "Clinical Orthopaedics and Related Research",
volume = "477",
number = "1",
year = "2019",
url = "http://www.sci.utah.edu/publications/Atk2019a/abjs-477-242.pdf",
}
@Article{SCI:Att2006a,
author = "L. Atty and N. Holzschuch and M. Lapierre and
J.-M. Hasenfratz and C.D. Hansen and F.X.
Sillion",
title = "Soft Shadow Maps: Efficient Sampling of Light
Source Visibility",
journal = "Computer Graphics Forum",
volume = "25",
number = "4",
pages = "725--741",
year = "2006",
url = "http://www.sci.utah.edu/publications/atty06/Soft_Shadow_Maps.pdf",
}
@TechReport{SCI:Awa2005a,
author = "S.P. Awate and T. Tasdizen and R.T. Whitaker",
title = "Nonparametric Statistics of Image Neighborhoods
for Unsupervised Texture Segmentation",
number = "UUSCI-2005-003",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "segmentation",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-003.pdf",
}
@TechReport{SCI:Awa2005b,
author = "S.P. Awate and R.T. Whitaker",
title = "Higher-Order Image Statistics for Unsupervised,
Information-Theoretic, Adaptive, Image Filtering",
number = "UUSCI-2005-004",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-004.pdf",
}
@TechReport{SCI:Awa2005c,
author = "S.P. Awate and R.T. Whitaker",
title = "Nonparametric Neighborhood Statistics for {MRI}
Denoising",
number = "UUSCI-2005-005",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-005.pdf",
}
@InProceedings{SCI:Awa2005e,
author = "S.P. Awate and R.T. Whitaker",
title = "Nonparametric Neighborhood Statistics for {MRI}
Denoising",
booktitle = "In Proc. Int. Conf. Information Processing in
Medical Imaging ({IPMI}), 2005. Lecture Notes in
Computer Science",
volume = "3565",
pages = "677--688",
year = "2005",
month = "July",
keywords = "ip image processing signal processing, ncrr",
url = "http://www.sci.utah.edu/publications/awate05/Awate_nonparametric_neighborhood.pdf",
}
@InProceedings{SCI:Awa2005f,
author = "S.P. Awate and R.T. Whitaker",
title = "Higher-Order Image Statistics for Unsupervised,
Information-Theoretic, Adaptive, Image Filtering",
booktitle = "Proceedings of the {IEEE} Int. Conf. Computer
Vision and Pattern Recognition ({CVPR})",
pages = "44--51",
year = "2005",
keywords = "ip image processing signal processing, ncrr",
url = "http://www.sci.utah.edu/publications/awate05/Awate_UINTA_CVPR.pdf",
}
@Article{SCI:Awa2005g,
author = "S.P. Awate and R.T. Whitaker",
title = "Unsupervised, Information-Theoretic, Adaptive
Image Filtering for Image Restoration",
journal = j-PAMI,
volume = "28",
number = "3",
pages = "364--376",
year = "2005",
keywords = "ip image processing signal processing, ncrr",
url = "http://www.sci.utah.edu/publications/awate05/Awate_JPAMI05.pdf",
}
@TechReport{SCI:Awa2006a,
author = "S.P. Awate and T. Tasdizen and N. Foster and R.T.
Whitaker",
title = "Adaptive, Nonparametric Markov Modeling for
Unsupervised, MRI Brain-Tissue Classification",
number = "UUSCI-2006-008",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-008.pdf",
}
@InProceedings{SCI:Awa2006b,
author = "S.P. Awate and T. Tasdizen and R.T. Whitaker",
title = "Unsupervised Texture Segmentation with
Nonparametric Neighborhood Statistics",
booktitle = "Proceedings of The European Conference on Computer
Vision (ECCV) 2006 Springer, Lecture Notes in
Computer Science",
pages = "494--507",
year = "2006",
keywords = "segmentation, ip image processing signal
processing, crcns",
url = "http://www.sci.utah.edu/publications/awate06/Awate_ECCV_SegmentTextures.pdf",
}
@TechReport{SCI:Awa2006c,
author = "S.P. Awate and T. Tasdizen and R.T. Whitaker",
title = "Unsupervised Texture Segmentation with
Nonparametric Neighborhood Statistics",
number = "UUSCI-2006-011",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing,
segmentation",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-011.pdf",
}
@Article{SCI:Awa2006d,
author = "S.P. Awate and R.T. Whitaker",
title = "Unsupervised, Information-Theoretic, Adaptive
Image Filtering for Image Restoration",
journal = j-PAMI,
volume = "28",
number = "3",
pages = "364--376",
year = "2006",
month = "March",
pmid = "16526423",
keywords = "ip image processing signal processing, ncrr",
url = "http://www.sci.utah.edu/publications/suyash06/Awate_UINTA_PAMI.pdf",
}
@TechReport{SCI:Awa2006e,
author = "S.P. Awate and R.T. Whitaker",
title = "Adaptive Markov Models for Information-Theoretic
Empirical-Bayesian MRI Denoising",
number = "UUSCI-2006-030",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-030.pdf",
}
@PhdThesis{SCI:Awa2006f,
author = "S.P. Awate",
title = "Adaptive, Nonparametric Markov Models and
Information-Theoretic Methods for Image Restoration
and Segmentation",
year = "2006",
school = "School of Computing, University of Utah",
month = "December",
note = "PhD Thesis",
keywords = "ip image processing signal processing,
segmentation",
url = "http://www.sci.utah.edu/publications/suyash06/Awate_Dissertation.pdf",
}
@InProceedings{SCI:Awa2006g,
author = "S.P. Awate and E.V.R. DiBella and T. Tasdizen and
R.T. Whitaker",
title = "Model-Based Image Reconstruction for Dynamic
Cardiac Perfusion MRI from Sparse Data",
booktitle = "Proceedings of the 2006 {IEEE} Int. Conf.
Engineering and Biology Society ({EMBC})",
pages = "936--941",
year = "2006",
url = "http://www.sci.utah.edu/publications/suyash06/Awate_ModelBasedCardiacPerfusionReconstruct.pdf",
}
@Article{SCI:Awa2006h,
author = "S.P. Awate and T. Tasdizen and N.L. Foster and
R.T. Whitaker",
title = "Adaptive, Nonparametric Markov Modeling for
Unsupervised, MRI Brain-Tissue Classification",
journal = "Medical Image Analysis (MEDIA)",
volume = "10",
number = "5",
pages = "726--739",
year = "2006",
url = "http://www.sci.utah.edu/publications/suyash06/Awate_MRI_Segmentation.pdf",
}
@Article{SCI:Awa2007a,
author = "S. Awate and R.T. Whitaker",
title = "Feature-Preserving {MRI} Denoising: A
Nonparametric Empirical-{B}ayes Approach",
journal = "IEEE Transactions on Medical Imaging",
volume = "26",
number = "9",
pages = "1242--1255",
year = "2007",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/awate07/Awate_MRI_Denoising_TMI.pdf",
}
@Article{SCI:Awa2010a,
author = "S.P. Awate and P.A. Yushkevich and Z. Song and
D.J. Licht and J.C. Gee",
title = "Cerebral cortical folding analysis with
multivariate modeling and testing: Studies on
gender differences and neonatal development",
journal = "NeuroImage",
volume = "53",
number = "2",
pages = "450--459",
year = "2010",
pmid = "20630489",
url = "http://www.sci.utah.edu/publications/awate10/Awate_NeuroImage2010.pdf",
}
@InProceedings{SCI:Awa2012a,
author = "S.P. Awate and P. Zhu and R.T. Whitaker",
title = "How Many Templates Does It Take for a Good
Segmentation?: Error Analysis in Multiatlas
Segmentation as a Function of Database Size",
booktitle = "Int. Workshop Multimodal Brain Image Analysis
(MBIA) at Int. Conf. MICCAI",
volume = "2",
pages = "103--114",
year = "2012",
series = "Lecture Notes in Computer Science (LNCS)",
note = "Recieved Best Paper Award",
pmid = "24501720",
pmcid = "PMC3910563",
url = "http://www.sci.utah.edu/publications/awate12/Awate_MICCAI2012.pdf",
}
@Article{SCI:Awa2014a,
author = "S.P. Awate and R.T. Whitaker",
title = "Multiatlas Segmentation as Nonparametric
Regression",
journal = "{IEEE} Trans Med Imaging",
year = "2014",
month = "April",
pmid = "24802528",
}
@InProceedings{SCI:Awa2014b,
author = "S.P. Awate and Y.-Y. Yu and R.T. Whitaker",
title = "Kernel Principal Geodesic Analysis",
booktitle = "Proceedings of the European Conference on Machine
Learning and Principles and Practice of Knowledge
Discovery in Databases ({ECML} {PKDD})",
year = "2014",
publisher = "Springer {LNAI}",
}
@InProceedings{SCI:Aya1988a,
author = "N. Ayache and C.D. Hansen",
title = "Rectification of Images for Binocular and
Trinocular Stereovision",
booktitle = "Proceedings of the 9th International Conference on
Pattern Recognition",
volume = "1",
pages = "11--16",
year = "1988",
month = "November",
location = "Rome, Italy",
doi = "10.1109/ICPR.1988.28160",
}
@InProceedings{SCI:Ayy2018a,
author = "D. Ayyagari and N. Ramesh and D. Yatsenko and T.
Tasdizen and C. Atria",
title = "Image reconstruction using priors from deep
learning",
booktitle = "Medical Imaging 2018: Image Processing",
year = "2018",
publisher = "SPIE",
month = "March",
url = "http://www.sci.utah.edu/publications/Ayy2018a/1805.07632.pdf",
}
@Article{SCI:Bad2009a,
author = "T.J. Badger and R.S. Oakes and M. Daccarett and
N.S. Burgon and N. Akoum and E.N. Fish and J.J.
Blauer and S.N. Rao and Y. Adjei-Poku and E.G.
Kholmovski and S. Vijayakumar and E.V. Di Bella and
R.S. MacLeod and N.F. Marrouche",
title = "Temporal Left Atrial Lesion Formation After
Ablation of Atrial Fibrillation",
journal = "Heart Rhythm",
volume = "6",
number = "2",
pages = "161--168",
year = "2009",
month = "February",
url = "http://www.sci.utah.edu/publications/badger09/TemporalLeftAtrialLession.pdf",
}
@Article{SCI:Bad2009b,
author = "T.J. Badger and Y.A. Adjei-Poku and N.S. Burgon
and S. Kalvaitis and A. Shaaban and D.N. Sommers
and J.J.E. Blauer and E.N. Fish N. Akoum and T.S.
Haslem and E.G. Kholmovski and R.S. MacLeod and
D.G. Adler and N.F. Marrouche",
title = "Initial Experience of Assessing Esophageal Tissue
Injury and Recovery Using Delayed-Enhancement MRI
After Atrial Fibrillation Ablation",
journal = "Circulation: Arrhythmia and Electrophysiology",
volume = "2",
pages = "620--625",
year = "2009",
url = "http://www.sci.utah.edu/publications/badger09/Badger_CAE2009a.pdf",
}
@Article{SCI:Bad2010a,
author = "T.J. Badger and M. Daccarett and N.W. Akoum and
Y.A. Adjei-Poku and N.S. Burgon and T.S. Haslam and
S. Kalvaitis and S. Kuppahally and G. Vergara and
L. McMullen and P.A. Anderson and E. Kholmovski and
R.S. Macleod and N.F. Marrouche",
title = "Evaluation of left atrial lesions after initial
and repeat atrial fibrillation ablation: lessons
learned from delayed-enhancement MRI in repeat
ablation procedures",
journal = "Circulation. Arrhythmia and Electrophysiology",
volume = "3",
number = "3",
pages = "249--259",
year = "2010",
pmid = "20335558",
keywords = "cibc",
url = "http://www.sci.utah.edu/publications/badger10/Badger_CircArrhythmElectrophysiol2010.pdf",
}
@Article{SCI:Bag1993a,
author = "C.M. Bagi and M. Mecham and J.A. Weiss and S.C.
Miller",
title = "Comparative Morphometric Changes in Rat Cortical
Bone Following Ovariectomy and/or Immobilization",
journal = "Bone",
volume = "14",
pages = "877--883",
year = "1993",
}
@Article{SCI:Bah2007a,
author = "A.N. Bahadur and I.Q. Wu and D.M. Weinstein and
M.D. Davis and D.A. Lewis and P. Kochunov and C.
Keller",
title = "Multimodality Chamber for Coregistered Anatomical
and Molecular Imaging of Small Animals",
journal = "Lab Animal",
volume = "36",
number = "8",
pages = "29--35",
year = "2007",
}
@InProceedings{SCI:Baj1996a,
author = "C.L. Bajaj and V. Pascucci and D.R. Schikore",
title = "Fast Isocontouring for Improved Interactivity",
booktitle = "1996 Volume Visualization Symposium",
pages = "39--46",
year = "1996",
organization = "IEEE Computer Society",
month = "October",
isbn = "0-89791-741-3",
}
@InProceedings{SCI:Baj1996b,
author = "C.L. Bajaj and V. Pascucci",
title = "Splitting a Complex of Convex Polytopes in any
Dimension",
booktitle = "Proceedings of the Twelfth Annual Symposium On
Computational Geometry ({ISG} '96)",
pages = "88--97",
year = "1996",
publisher = "ACM Press",
address = "New York",
month = "May",
isbn = "0-89791-832-0",
}
@InProceedings{SCI:Baj1996c,
author = "C.L. Bajaj and F. Bernardini and V. Pascucci and
D.R. Schikore",
title = "Interrogative Visualization of the Visible Human
Datasets",
booktitle = "Proceedings of the The Visible Human Project
Conference",
year = "1996",
}
@InProceedings{SCI:Baj1997a,
author = "C.L. Bajaj and V. Pascucci and D.R. Schikore",
title = "The Contour Spectrum",
booktitle = "Proceedings of the 8th Annual {IEEE} Conference on
Visualization ({VIS}-97)",
pages = "167--175",
year = "1997",
editor = "Roni Yagel and Hans Hagen",
organization = "IEEE Computer Society",
month = "November",
}
@InProceedings{SCI:Baj1997b,
author = "C. Bajaj and H.Y. Lee and R. Merkert and V.
Pascucci",
title = "{NURBS} based {B}-rep Models for Macromolecules
and their Properties",
booktitle = "Proceedings of the 4th Symposium on Solid Modeling
and Applications",
pages = "217--228",
year = "1997",
editor = "Christoph Hoffmann and Wim Bronsvort",
publisher = "ACM Press",
address = "New York",
month = "May",
isbn = "0-89791-946-7",
}
@InProceedings{SCI:Baj1997d,
author = "C.L. Bajaj and V. Pascucci and D.R. Schikore",
title = "Fast Isocontouring for Structured and Unstructured
Meshes in Any Dimension",
booktitle = "Late Breaking Hot Topics Proceedings of the 8th
Annual {IEEE} Conference on Visualization
({VIS}-97)",
pages = "25--28",
year = "1997",
editor = "Amitabj Varshney and David S. Ebert",
organization = "IEEE Computer Society",
month = "November",
}
@InProceedings{SCI:Baj1998a,
author = "C.L. Bajaj and V. Pascucci and R.J. Holt and A.N.
Netravali",
title = "Dynamic Maintenance and Visualization of Molecular
Surfaces",
booktitle = "Proceedings of the 10th Canadian Conference on
Computational Geometry ({CCCG})",
pages = "68--69",
year = "1998",
editor = "Mike Soss",
publisher = "School of Computer Science, McGill University",
month = "August",
location = "Montreal, Quebec, Canada",
}
@InProceedings{SCI:Baj1998b,
author = "C.L. Bajaj and V. Pascucci and G. Rabbiolo and
D.R. Schikore",
title = "Hypervolume Visualization: A Challenge in
Simplicity",
booktitle = "Proceedings of the 1998 {IEEE} Symposium on Volume
Visualization",
pages = "95--102",
year = "1998",
}
@InProceedings{SCI:Baj1998c,
author = "C.L. Bajaj and V. Pascucci and D.R. Schikore",
title = "Visualization of Scalar Topology for Structural
Enhancement",
booktitle = "Proceedings of the 9th Annual {IEEE} Conference on
Visualization ({VIS}-98)",
pages = "51--58",
year = "1998",
organization = "IEEE Computer Society",
address = "New York",
month = "October",
isbn = "1-58113-106-2",
}
@Article{SCI:Baj1999a,
author = "C.L. Bajaj and C. Baldazzi and S. Cutchin and A.
Paoluzzi and V. Pascucci and M. Vicentino",
title = "A Programming Approach for Complex Animations",
journal = "Computer Aided Design",
volume = "31",
number = "11",
pages = "695--710",
year = "1999",
}
@Article{SCI:Baj1999b,
author = "C.L. Bajaj and V. Pascucci and G. Zhuang",
title = "Single Resolution Compression of Arbitrary
Triangular Meshes with Properties",
journal = "Computational Geometry: Theory and Applications",
volume = "14",
number = "1--3",
pages = "167--186",
year = "1999",
issn = "0925-7721",
doi = "10.1016/S0925-7721(99)00026-7",
}
@InBook{SCI:Baj1999c,
author = "C.L. Bajaj and V. Pascucci and D.R. Schikore",
title = "Data Visualization Techniques",
volume = "6",
pages = "31--47",
year = "1999",
chapter = "3: Accelerated IsoContouring of Scalar Fields",
series = "Trends in Software",
publisher = "John Wiley \& Sons",
}
@InProceedings{SCI:Baj1999d,
author = "C.L. Bajaj and V. Pascucci and G. Zhuang",
title = "Progressive Compression and Transmission of
Arbitrary Triangular Meshes",
booktitle = "Proceedings of the 10th Annual {IEEE} Conference
on Visualization ({VIS}-99)",
pages = "307--316",
year = "1999",
month = "October 24-29",
location = "San Francisco, CA",
}
@InProceedings{SCI:Baj1999e,
author = "C.L. Bajaj and V. Pascucci and D. Thompson and
X.Y. Zhang",
title = "Parallel Accelerated Isocontouring for Out-Of-Core
Visualization",
booktitle = "Proceedings of First Parallel Visualization and
Graphics Symposium 1999",
year = "1999",
organization = "IEEE Computer Society",
month = "October",
location = "San Francisco, CA",
}
@InProceedings{SCI:Baj1999f,
author = "C.L. Bajaj and V. Pascucci and G. Zhuang",
title = "Single Resolution Compression of Arbitrary
Triangular Meshes with Properties",
booktitle = "Proceedings of DCC: Data Compression Conference
1999",
year = "1999",
organization = "IEEE Computer Society",
address = "Snowbird, Utah",
month = "March",
}
@InProceedings{SCI:Baj1999g,
author = "C.L. Bajaj and S. Cutchin and V. Pascucci and A.
Paoluzzi and C. Morgia",
title = "Web Based Collaborative {CAAD}",
booktitle = "Proceedings of the 5th Symposium on Solid Modeling
and Applications",
year = "1999",
}
@InProceedings{SCI:Baj1999h,
author = "C. Bajaj and V. Pascucci and E. Petajan and G.
Zhuang",
title = "Polygonal Model Coding Evaluation for Low bit-rate
Communication",
booktitle = "Proceedings of the International Workshop on
Synthetic - Natural Hybrid Coding and Three
Dimensional Imaging",
year = "1999",
month = "September",
}
@Article{SCI:Bak2016a,
author = "J.L. Baker and J. Ryou and X.F. Wei and C.R.
Butson and N.D. Schiff and K.P. Purpura",
title = "Robust modulation of arousal regulation,
performance, and frontostriatal activity through
central thalamic deep brain stimulation in healthy
nonhuman primates",
journal = "Journal of Neurophysiology",
volume = "116",
number = "5",
pages = "2383--2404",
year = "2016",
publisher = "American Physiological Society",
month = "Aug",
doi = "10.1152/jn.01129.2015",
url = "http://www.sci.utah.edu/publications/Bak2016a/Butson 2016 J of Neurophsiology.pdf",
}
@InProceedings{SCI:Ban1995a,
author = "A. Banerjee and G.E. Christensen and J. Haller and
S. Joshi and M.E. Raichle and M.I. Miller",
title = "Accommodating anatomical variability in functional
imaging via deformable templates",
booktitle = "Proc. 33rd Annual Allerton Conference on
Communication, Control and Computing",
pages = "275--284",
year = "1995",
}
@InProceedings{SCI:Bap2003a,
author = "A. Baptista and T. Leen and Y. Zhang and A. Chawla
and D. Maier and Wu-chang Feng and Wu-chi Feng and
J. Walpole and C.T. Silva and J. Freire",
title = "Environmental Observation and Forecasting Systems:
Vision, Challenges and Successes of a Prototype",
booktitle = "Proceedings of the International Society for
Environmental Information Sciences Annual
Conference (ISEIS '2003) on Systems Science and
Information Technology for Environmental
Applications",
year = "2003",
month = "July",
location = "Regina, Sask, Canada",
}
@Article{SCI:Bap2008a,
author = "A. Baptista and B. Howe and J. Freire and D. Maier
and C.T. Silva",
title = "Scientific Exploration in the Era of Ocean
Observatories",
journal = "Computing in Science and Engineering",
volume = "10",
number = "3",
pages = "53--58",
year = "2008",
keywords = "oceanography, vistrails, provenance",
url = "http://www.sci.utah.edu/publications/baptista08/cise2008b.pdf",
}
@Article{SCI:Bar2004a,
author = "D. Barbosa and J. Freire and A. Mendelzon",
title = "Information Preservation in XML-to-Relational
Mappings",
journal = "Database and XML Technologies",
volume = "3186/2004",
pages = "66--81",
year = "2004",
series = "Lecture Notes in Computer Science (LNCS)",
isbn = "978-3-540-22969-8",
url = "http://www.sci.utah.edu/publications/barbosa04/Barbosa_LNCS2004.pdf",
}
@InProceedings{SCI:Bar2005a,
author = "L. Barbosa and A.C. Salgado and F. de Carvalho and
J. Robin and J. Freire",
title = "Looking at both the Present and the Past to
Efficiently Update Replicas of Web Content",
booktitle = "Proceedings of the 7th Annual ACM International
Workshop on Web Information and Data Management",
pages = "75--80",
year = "2005",
url = "http://www.sci.utah.edu/publications/barbosa05/Barbosa_WWIDM2005a.pdf",
}
@InProceedings{SCI:Bar2005b,
author = "D. Barbosa and J. Freire and A. Mendelzon",
title = "Designing Information-Preserving Mapping Schemes
for XML",
booktitle = "Proceedings of the 31st International Conference
on Very Large Data Bases",
pages = "109--120",
year = "2005",
location = "Trondheim, Norway",
url = "http://www.sci.utah.edu/publications/barbosa05/Barbosa_VLDB2005.pdf",
}
@InProceedings{SCI:Bar2006a,
author = "L. Barbosa and J. Freire",
title = "Automatically Constructing Collections of Online
Databases",
booktitle = "Proceedings of the 15th ACM International
Conference on Information and Knowledge Management
(CIKM)",
pages = "796--797",
year = "2006",
location = "Arlington",
url = "http://www.sci.utah.edu/publications/barbosa06/Barbosa_CIKM2006a.pdf",
}
@InProceedings{SCI:Bar2007a,
author = "L. Barbosa and J. Freire",
title = "An Adaptive Crawler for Locating Hidden-Web Entry
Points",
booktitle = "Proceedings of the 16th international conference
on World Wide Web (WWW)",
pages = "441--450",
year = "2007",
month = "May",
location = "Banff, Alberta, Canada",
url = "http://www.sci.utah.edu/publications/barbosa07/Barbosa_WWW2007a.pdf",
}
@InProceedings{SCI:Bar2007b,
author = "L. Barbosa and J. Freire",
title = "Combining Classifiers to Identify Online
Databases",
booktitle = "Proceedings of the 16th International Conference
on World Wide Web (WWW)",
pages = "431--440",
year = "2007",
month = "May",
location = "Banff, Alberta, Canada",
url = "http://www.sci.utah.edu/publications/barbosa07/Barbosa_WWW2007b.pdf",
}
@InProceedings{SCI:Bar2007c,
author = "L. Barbosa and J. Freire and A. Silva",
title = "Organizing Hidden-Web Databases by Clustering
Visible Web Documents",
booktitle = "Proceedings of the {IEEE} 23rd International
Conference on Data Engineering, 2007. ({ICDE}
2007)",
pages = "326--335",
year = "2007",
location = "Istanbul",
url = "http://www.sci.utah.edu/publications/barbosa07/Barbosa_ICDE2007.pdf",
}
@Article{SCI:Bar2007d,
author = "L. Barbosa and S. Tandon and J. Freire",
title = "Automatically Constructing a Directory of
Molecular Biology Databases",
journal = "Data Integration in the Life Sciences",
volume = "4544/2007",
pages = "6--16",
year = "2007",
series = "Lecture Notes in Computer Science (LNCS)",
isbn = "978-3-540-73254-9",
url = "http://www.sci.utah.edu/publications/barbosa07/Barbosa_LNCS2007.pdf",
}
@Article{SCI:Bar2012a,
author = "A. Barg and N. Knupp and H.B. Henninger and L.
Zwicky and B. Hintermann",
title = "Total ankle replacement using {HINTEGRA}, an
unconstrained, three-component system: surgical
technique and pitfalls",
journal = "Foot and Ankle Clinics",
volume = "17",
number = "4",
pages = "607--635",
year = "2012",
doi = "10.1016/j.fcl.2012.08.006",
keywords = "Total ankle replacement, Three-component total
ankle prosthesis, HINTEGRA prosthesis, Valgus
osteoarthritic ankle, Varus osteoarthritic ankle,
Functional outcome",
url = "http://www.sci.utah.edu/publications/barg12/Barg_FAC2012a.pdf",
}
@Article{SCI:Bar2012b,
author = "A. Barg and G.I. Pagenstert and A.G. Leumann and
A.M. M{\"u}ller and H.B. Henninger and V.
Valderrabano",
title = "Treatment of the Arthritic Valgus Ankle",
journal = "Foot and Ankle Clinics",
volume = "17",
number = "4",
pages = "647--663",
year = "2012",
doi = "10.1016/j.fcl.2012.08.007",
keywords = "Total ankle replacement, Ankle alignment,
Arthritic valgus ankle, Valgus deformity,
Realignment surgery for arthritic valgus ankle,
Total ankle replacement for arthritic valgus
angle",
url = "http://www.sci.utah.edu/publications/barg12/Barg_FAC2012b.pdf",
}
@Article{SCI:Bar2012c,
author = "A. Barg and M.D. Harris and H.B. Henninger and
R.L. Amendola and C.L. Saltzman and B. Hintermann
and A.E. Anderson",
title = "Medial distal tibial angle: comparison between
weightbearing mortise view and hindfoot alignment
view",
journal = "Foot \& Ankle International",
volume = "33",
number = "8",
pages = "655--661",
year = "2012",
doi = "10.3113/FAI.2012.0655",
}
@Article{SCI:Bar2015a,
author = "I. Arganda-Carreras and S.C. Turaga and D.R.
Berger and D. Ciresan and A. Giusti and L.M.
Gambardella and J. Schmidhuber and D. Laptev and S.
Dwivedi and J. Buhmann and T. Liu and M.
Seyedhosseini and T. Tasdizen and L. Kamentsky and
R. Burget and V. Uher and X. Tan and C. Sun and
T.D. Pham and E. Bas and M.G. Uzunbas and A.
Cardona and J. Schindelin and H.S. Seung",
title = "Crowdsourcing the creation of image segmentation
algorithms for connectomics",
journal = "Frontiers in Neuroanatomy",
volume = "9",
year = "2015",
publisher = "Frontiers Media SA",
month = "Nov",
doi = "10.3389/fnana.2015.00142",
url = "http://www.sci.utah.edu/publications/Bar2015a/fnana-09-00142.pdf",
}
@Article{SCI:Bar2016a,
author = "M. Barjatia and T. Tasdizen and B. Song and K.M.
Golden",
title = "Network modeling of Arctic melt ponds",
journal = "Cold Regions Science and Technology",
volume = "124",
pages = "40--53",
year = "2016",
publisher = "Elsevier BV",
month = "April",
doi = "10.1016/j.coldregions.2015.11.019",
url = "http://www.sci.utah.edu/publications/Bar2016a/1-s2.0-S0165232X15002992-main.pdf",
}
@InProceedings{SCI:Bas2006a,
author = "S. Basu and P.T. Fletcher and R.T. Whitaker",
title = "Rician Noise Removal in Diffusion Tensor MRI",
booktitle = "Medical Image Computing and Computer Assisted
Intervention (MICCAI)",
volume = "LNCS 4190",
pages = "117--125",
year = "2006",
month = "October",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/basu06/BasuDTIFilteringMICCAI2006.pdf",
}
@InProceedings{SCI:Bav2005a,
author = "L. Bavoil and S.P. Callahan and P.J. Crossno and
J. Freire and C.E. Scheidegger and C.T. Silva and
H.T. Vo",
title = "Vistrails: Enabling Interactive Multiple-View
Visualizations",
booktitle = c-VIS2005,
pages = "18",
year = "2005",
keywords = "scientific visualization, pses",
url = "http://www.sci.utah.edu/publications/bavoil05/vistrails.pdf",
}
@TechReport{SCI:Bav2006a,
author = "L. Bavoil and S.P. Callahan and C.T. Silva",
title = "Robust Soft Shadow Mapping with Depth Peeling",
number = "UUSCI-2006-028",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-028.pdf",
}
@TechReport{SCI:Bav2006b,
author = "L. Bavoil and S.P. Callahan and A. Lefohn and
J.L.D. Comba and C.T. Silva",
title = "Multi-Fragment Effects on the GPU using the
k-Buffer",
number = "UUSCI-2006-032",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-032.pdf",
}
@InProceedings{SCI:Bav2007a,
author = "L. Bavoil and S.P. Callahan and A. Lefohn and
J.L.D. Comba and C.T. Silva",
title = "Multi-Fragment Effects on the GPU using the
k-Buffer",
booktitle = "{ACM} Symposium on Interactive {3D} Graphics and
Games (i3D)",
pages = "97--104",
year = "2007",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/bavoil07/kbuffer_preprint.pdf",
}
@Article{SCI:Bav2008a,
author = "L. Bavoil and S.P. Callahan and and C.T. Silva",
title = "Robust Soft Shadow Mapping with Depth Peeling",
journal = "Journal of Graphics Tools",
volume = "13",
number = "1",
pages = "19--30",
year = "2008",
url = "http://www.sci.utah.edu/publications/bavoil08/jgt08.pdf",
}
@InProceedings{SCI:Bea96a,
author = "D.M. Beazley",
title = "Using SWIG to control, prototype, and debug C
programs with Python",
booktitle = "4th International Python Conference",
year = "1996",
}
@Article{SCI:Bea97,
author = "D.M. Beazley",
title = "Using SWIG to control, prototype, and debug C
program with Python",
journal = "4th International Python Conference",
year = "1997",
keywords = ", swig. python",
}
@Proceedings{SCI:Beb2006a,
title = "Advances in Visual Computing, Second International
Symposium, {ISVC} 2006, Lake Tahoe, {NV}, {USA},
November 6-8, 2006 Proceedings, Part {I}",
booktitle = "ISVC (1)",
volume = "4291",
year = "2006",
editor = "George Bebis and Richard Boyle and Bahram Parvin
and Darko Koracin and Paolo Remagnino and Ara V.
Nefian and Meenakshisundaram Gopi and Valerio
Pascucci and Jiri Zara and Jose Molineros and
Holger Theisel and Thomas Malzbender",
series = "Lecture Notes in Computer Science",
publisher = "Springer",
isbn = "3-540-48628-3",
}
@Article{SCI:Bec2013a,
author = "J. Beckvermit and J. Peterson and T. Harman and S.
Bardenhagen and C. Wight and Q. Meng and M.
Berzins",
title = "Multiscale Modeling of Accidental Explosions and
Detonations",
journal = "Computing in Science and Engineering",
volume = "15",
number = "4",
pages = "76--86",
year = "2013",
doi = "10.1109/MCSE.2013.89",
keywords = "uintah, c-safe, accidents, explosions, military
computing, risk analysis",
url = "http://www.sci.utah.edu/publications/Bec2013a/Beckvermit_ModelingExplosiveswithUintah2013_2.pdf",
}
@TechReport{SCI:Bec2016a,
author = "J. Beckvermit and T. Harman and C. Wight and M.
Berzins",
title = "Physical Mechanisms of DDT in an Array of PBX 9501
Cylinders Initiation Mechanisms of DDT",
year = "2016",
institution = "SCI Institute",
month = "April",
url = "http://www.sci.utah.edu/publications/Bec2016a/SCI-TR-2016-001.pdf",
}
@Article{SCI:Bec2016b,
author = "J. Beckvermit and T. Harman and C. Wight and and
M. Berzins",
title = "Packing Configurations of PBX-9501 Cylinders to
Reduce the Probability of a Deflagration to
Detonation Transition (DDT)",
journal = "Propellants, Explosives, Pyrotechnics",
year = "2016",
issn = "1521-4087",
doi = "10.1002/prep.201500331",
url = "http://www.sci.utah.edu/publications/Bec2016b/Preprint-Packi-49870.pdf",
}
@InProceedings{SCI:Bee2012a,
author = "J. Beezley and M. Martin and P. Rosen and J.
Mandel and A. Kochanski",
title = "Data management and analysis with {WRF} and
{SFIRE}",
booktitle = "Proceedings of the {IEEE} International Geoscience
and Remote Sensing Symposium",
year = "2012",
note = "UCD CCM Report 312",
url = "http://www.sci.utah.edu/publications/beezley12/Beezley_IGRSS2012.pdf",
}
@Article{SCI:Bel2007a,
author = "M.K. Belmonte and J.C. Mazziotta and N.J. Minshew
and A.C. Evans and E. Courchesne and S.R. Dager and
S.Y. Bookheimer and E.H. Aylward and D.G. Amaral
and R.M. Cantor and D.C. Chugani and A.M. Dale and
C. Davatzikos and G. Gerig and M.R. Herbert and
J.E. Lainhart and D.G. Murphy and J. Piven and A.L.
Reiss and R.T. Schultz and T.A. Zeffiro and S.
Levi-Pearl and C. Lajonchere and S.A. Colamarino",
title = "Offering to Share: How to Put Heads Together in
Autism Neuroimaging",
journal = "Journal of Autism and Developmental Disorders
JADD",
volume = "38",
pages = "2--13",
year = "2007",
url = "http://www.sci.utah.edu/publications/belmonte08/Belmonte_JADD2007.pdf",
}
@InProceedings{SCI:Ben2002a,
author = "M. Benedikt and J. Freire and P. Godefroid",
title = "VeriWeb: Automatically Testing Dynamic Web
Sites",
booktitle = "In Proceedings of 11th International World Wide
Web Conference 2002",
year = "2002",
url = "http://www.sci.utah.edu/publications/benedikt02/veriweb-www2002.pdf",
}
@InProceedings{SCI:Ben2003a,
author = "M. Benedikt and C.Y. Chan and W. Fan and J. Freire
and R. Rastogi",
title = "Capturing Both Types and Constraints in Data
Integration",
booktitle = "Proceedings of the 2003 ACM SIGMOD International
Conference on Management of Data",
pages = "277--288",
year = "2003",
isbn = "1-58113-634-X",
url = "http://www.sci.utah.edu/publications/benedikt03/Benedikt_SIGMOD2003.pdf",
}
@Article{SCI:Ben2006a,
author = "C. Benthin and I. Wald and P. Slusallek",
title = "Techniques for Interactive Ray Tracing of Bezier
Surfaces",
journal = "Journal of Graphics Tools",
volume = "11",
number = "2",
pages = "1--16",
year = "2006",
keywords = "rtcenter",
}
@InProceedings{SCI:Ben2006b,
author = "C. Benthin and I. Wald and M. Scherbaum and H.
Friedrich",
title = "Ray Tracing on the {CELL} Processor",
booktitle = "Proceedings of the 2006 {IEEE} Symposium on
Interactive Ray Tracing",
pages = "25--32",
year = "2006",
keywords = "rtcenter",
url = "http://www.sci.utah.edu/publications/benthin06/cell.pdf",
}
@TechReport{SCI:Ben2007a,
author = "C. Benthin and S. Boulos and D. Lacewell and I.
Wald",
title = "Packet-based Ray Tracing of Catmull-Clark
Subdivision Surfaces",
number = "UUSCI-2007-011",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "interactive rt distributed interactive ray tracing
dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-011.pdf",
}
@InProceedings{SCI:Ben2007b,
author = "J. Bennett and V. Pascucci and K.I. Joy",
title = "Genus Oblivious Cross Parameterization: Robust
Topological Management of Intersurface Maps",
booktitle = "Proceedings of Pacific Graphics 2007",
year = "2007",
}
@Article{SCI:Ben2011a,
author = "J.C. Bennett and V. Krishnamoorthy and S. Liu and
R.W. Grout and E.R. Hawkes and J.H. Chen and J.
Shepherd and V. Pascucci and P.-T. Bremer",
title = "Feature-Based Statistical Analysis of Combustion
Simulation Data",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics, Proceedings of the 2011 {IEEE}
Visualization Conference",
volume = "17",
number = "12",
pages = "1822--1831",
year = "2011",
url = "http://www.sci.utah.edu/publications/bennett11/Bennett_VIS2011.pdf",
}
@InProceedings{SCI:Ben2012a,
author = "J.C. Bennett and H. Abbasi and P. Bremer and R.W.
Grout and A. Gyulassy and T. Jin and S. Klasky and
H. Kolla and M. Parashar and V. Pascucci and P.
Pbay and D. Thompson and H. Yu and F. Zhang and J.
Chen",
title = "Combining In-Situ and In-Transit Processing to
Enable Extreme-Scale Scientific Analysis",
booktitle = "{ACM/IEEE} International Conference for High
Performance Computing, Networking, Storage, and
Analysis ({SC})",
year = "2012",
month = "November",
location = "Salt Lake City, Utah, U.S.A.",
url = "http://www.sci.utah.edu/publications/bennett12/Bennett_ICHPCNSA2012.pdf",
}
@Book{SCI:Ben2015a,
author = "J. Bennett and F. Vivodtzev and V. Pascucci
(Eds.)",
title = "Topological and Statistical Methods for Complex
Data",
title_url =
"http://link.springer.com/book/10.1007/978-3-662-44900-4",
subtitle = "Tackling Large-Scale, High-Dimensional, and
Multivariate Data Spaces",
year = "2015",
series = "Mathematics and Visualization",
publisher = "Springer Berlin Heidelberg",
isbn = "978-3-662-44899-1",
}
@Unpublished{SCI:Ben2015b,
author = "J. Bennett and R. Clay and G. Baker and M. Gamell
and D. Hollman and S. Knight and H. Kolla and G.
Sjaardema and N. Slattengren and K. Teranishi and
J. Wilke and M. Bettencourt and S. Bova and K.
Franko and P. Lin and R. Grant and S. Hammond and
S. Olivier",
title = "ASC ATDM Level 2 Milestone #5325",
subtitle = "Asynchronous Many-Task Runtime System Analysis and
Assessment for Next Generation Platforms",
year = "2015",
note = "Sandia Report",
url = "http://www.sci.utah.edu/publications/Ben2015b/Sandia2015_AMT_RTS_L2-2.pdf",
}
@TechReport{SCI:Ben2015c,
author = "J. Bennett and R. Clay and G. Baker and M. Gamell
and D. Hollman and S. Knight and H. Kolla and G.
Sjaardema and N. Slattengren and K. Teranishi and
J. Wilke and M. Bettencourt and S. Bova and K.
Franko and P. Lin and R. Grant and S. Hammond and
S. Olivier and L. Kale and N. Jain and E. Mikida
and A. Aiken and M. Bauer and W. Lee and E.
Slaughter and S. Treichler and M. Berzins and T.
Harman and A. Humphrey and J. Schmidt and D.
Sunderland and P. McCormick and S. Gutierrez and M.
Schulz and A. Bhatele and D. Boehme and P. Bremer
and T. Gamblin",
title = "ASC ATDM level 2 milestone #5325: Asynchronous
many-task runtime system analysis and assessment
for next generation platforms",
year = "2015",
institution = "Sandia National Laboratories",
url = "http://www.sci.utah.edu/publications/Ben2015c/ATDM-AMT-L2-Final-SAND2015-8312.pdf",
}
@Article{SCI:Ber1980a,
author = "M. Berzins and P.M. Dew",
title = "A note on the extension of the Chebyshev method to
quasi-linear parabolic {P.D.E}.s.",
journal = "International Journal on Computer Mathematics",
volume = "8",
pages = "249--263",
year = "1980",
url = "http://www.sci.utah.edu/publications/Ber1980a/Berzins_IJCM1980.pdf",
}
@Article{SCI:Ber1981a,
author = "M. Berzins and P.M. Dew",
title = "A Generalized Chebyshev Method for Non-linear
Parabolic Equations in One Space Variable",
journal = "I.M.A. Journal on Numerical Analysis",
volume = "1",
pages = "469--487",
year = "1981",
url = "http://www.sci.utah.edu/publications/Ber1981a/Berzins_JNA1981.pdf",
}
@Article{SCI:Ber1983a,
author = "M. Berzins and P.M. Dew and R.M. Furzeland",
title = "Software for time-dependent problems",
journal = "{P.D.E.} Software: Modules, Interfaces and
Systems; Proc. of 1983 {IFIPS} Conference",
year = "1983",
editor = "B. Engquist and J. Rice",
location = "North Holland",
url = "http://www.sci.utah.edu/publications/Ber1983a/Berzins_PDESoftware1983.pdf",
}
@Article{SCI:Ber1986a,
author = "M. Berzins",
title = "A C1 Interpolant for Codes Based on Backward
Differentiation Formulae",
journal = "Applied Numerical Mathematics",
volume = "2",
pages = "109--118",
year = "1986",
url = "http://www.sci.utah.edu/publications/Ber1986a/Berzins_Apnumv2C1interp.pdf",
}
@Article{SCI:Ber1987a,
author = "M. Berzins and P.M. Dew",
title = "A Note on C0 Chebyshev Methods for Parabolic
Equations",
journal = "I.M.A. Journal of Numerical Analysis",
volume = "7",
pages = "15--37",
year = "1987",
url = "http://www.sci.utah.edu/publications/Ber1987a/Berzins_JNA1987_W_Correction.pdf",
}
@Article{SCI:Ber1988b,
author = "M. Berzins",
title = "Global Error Estimation in the Method of Lines for
Parabolic Equations",
journal = "{SIAM} Journal on Scientific Computing",
volume = "9",
pages = "687--703",
year = "1988",
url = "http://www.sci.utah.edu/publications/Ber1988b/Berzins_JSC1988.pdf",
}
@Article{SCI:Ber1988c,
author = "M. Berzins and R. Brankin and I. Gladwell",
title = "Design of Stiff Integrators in the {N.A.G.}
Library",
journal = "Signum Bulletin",
volume = "23",
number = "2",
pages = "16--24",
year = "1988",
month = "April",
url = "http://www.sci.utah.edu/publications/Ber1988c/Berzins_SignumBull1988.pdf",
}
@Article{SCI:Ber1989a,
author = "M. Berzins",
title = "Developments in {NAG} Library Software for
Parabolic Equations",
journal = "Scientific Software Systems",
pages = "59--72",
year = "1989",
editor = "J.C. Mason and M.G. Cox",
publisher = "Chapman and Hall",
month = "July",
isbn = "0412345706",
url = "http://www.sci.utah.edu/publications/Ber1989a/Berzins_SciSoftSys1989.pdf",
}
@Article{SCI:Ber1989b,
author = "M. Berzins and P.M. Dew and R.M. Furzeland",
title = "Developing Software for Time-Dependent Problems
Using the Method of Lines and Differential
Algebraic Integrators",
journal = "Applied Numerical Mathematics",
volume = "5",
pages = "375--397",
year = "1989",
url = "http://www.sci.utah.edu/publications/Ber1989b/Berzins_Apnumv5SPRINT.pdf",
}
@Article{SCI:Ber1990a,
author = "M. Berzins and A.J. Preston and P.M. Dew",
title = "Integration Algorithms for the Dynamic Simulation
of Production Processes",
journal = "Proc of Third European Conference for Mathematics
in Industry",
pages = "265--271",
year = "1990",
editor = "J. Manley et al.",
publisher = "Kluwer Academic Publishers, Stuttgart.",
url = "http://www.sci.utah.edu/publications/Ber1990a/Berzins_ECMI1990.pdf",
}
@Article{SCI:Ber1991a,
author = "M. Berzins and P. Baehmann and J.E. Flaherty and
J. Lawson",
title = "Towards An Automated Finite Element Solver for
Time-Dependent Fluid-Flow Problems",
journal = "MAFELAP 90",
pages = "181--188",
year = "1991",
editor = "J.R. Whiteman",
publisher = "Academic Press",
url = "http://www.sci.utah.edu/publications/Ber1991a/Berzins_MAFELAP1991.pdf",
}
@Article{SCI:Ber1991b,
author = "M. Berzins and P.M. Dew",
title = "Chebyshev Polynomial Software for
Elliptic-Parabolic Systems of {P.D.E.}s",
journal = "{A.C.M.} Transactions on Mathematical Software",
volume = "17",
number = "2",
pages = "178--206",
year = "1991",
month = "June",
url = "http://www.sci.utah.edu/publications/Ber1991b/Berzins_Chebyshev1991.pdf",
}
@Unpublished{SCI:Ber1991c,
author = "M. Berzins",
title = "Balancing Space and Time Errors for Spectral
Methods used with the Method of Lines for Parabolic
equations",
year = "1991",
url = "http://www.sci.utah.edu/publications/Ber1991c/4219_001.pdf",
}
@InProceedings{SCI:Ber1992b,
author = "M. Berzins and A.J. Preston and P.M. Dew and L.E.
Scales",
title = "Towards Efficient {D.A.E.} Solvers for the
Solution of Dynamic Simulation Problems",
booktitle = "Proc of {I.M.A.} 1989 {O.D.E.} Conference",
pages = "299--308",
year = "1992",
editor = "I. Gladwell and J. Cash and A. Iserles",
publisher = "Oxford University Press",
isbn = "0-19-853659-3",
url = "http://www.sci.utah.edu/publications/Ber1992b/1926_001-2.pdf",
}
@Article{SCI:Ber1992c,
author = "M. Berzins and R.M. Furzeland",
title = "An Adaptive Theta Method for the Solution of Stiff
and Non-stiff Differential Equations",
journal = "Applied Numerical Mathematics",
volume = "9",
pages = "1--19",
year = "1992",
url = "http://www.sci.utah.edu/publications/Ber1992c/Berzins_Appnumv9theta.pdf",
}
@InProceedings{SCI:Ber1993a,
author = "F. Bernardini and V. Ferrucci and A. Paoluzzi and
V. Pascucci",
title = "Product Operator on Cell Complexes",
booktitle = "SMA '93: Proceedings of the Second Symposium on
Solid Modeling and Applications",
pages = "43--52",
year = "1993",
organization = "ACM",
month = "May",
note = "held May 19-21, 1993 in Montreal, Quebec,
Canada",
}
@Article{SCI:Ber1993b,
author = "M. Berzins and J.M. Ware",
title = "Reliable Finite Volume Methods for Time-Dependent
Partial Differential Equations",
journal = "{MAFELAP} 1993 Highlights",
pages = "299--306",
year = "1993",
editor = "J.R. Whiteman and John Wiley",
url = "http://www.sci.utah.edu/publications/Ber1993b/Berzins_MAFELAP1993.pdf",
}
@InCollection{SCI:Ber1994a,
author = "M. Berzins and J.M. Ware",
title = "Reliable Finite Volume Methods for the Navier
Stokes Equations.",
booktitle = "Numerical methods for the Navier-Stokes
equations",
number = "47",
pages = "1-8",
year = "1994",
editor = "F.K. Hebeker and R. Rannacher and G. Wittum",
series = "Notes on Numerical Fluid Mechanics",
publisher = "Springer",
doi = "10.1007/978-3-663-14007-8_1",
url = "http://www.sci.utah.edu/publications/Ber1994a/heidelb.pdf",
}
@Article{SCI:Ber1995a,
author = "M. Berzins and J.M. Ware",
title = "Positive Cell Centered Finite Volume
Discretisation Methods for Hyperbolic Equations on
Irregular Meshes",
journal = "Applied Numerical Mathematics",
volume = "16",
pages = "417--438",
year = "1995",
url = "http://www.sci.utah.edu/publications/Ber1995a/Berzins_Apnumv16FVol.pdf",
}
@Article{SCI:Ber1995d,
author = "M. Berzins and P. Gaskell and A. Sleigh and A.S.
Tomlin and J. Ware",
title = "An adaptive CFD solver for time-dependent
environmental flow problems",
journal = "Proceedings of the Institute of Computational
Fluid Dynamics Conference",
pages = "311-317",
year = "1995",
editor = "K.W. Morton, M.J. Baines",
publisher = "Oxford University Press",
url = "http://www.sci.utah.edu/publications/Ber1995d/2453_001.pdf",
}
@Article{SCI:Ber1996c,
author = "M. Berzins and T.H.C. Childs and G.R. Ryder",
title = "The Selective Laser Sintering of Polycarbonate",
journal = "CIRP Annals",
volume = "45",
number = "1",
pages = "187--190",
year = "1996",
issn = "0007-8506",
doi = "10.1016/S0007-8506(07)63044-3",
url = "http://www.sci.utah.edu/publications/berzins96/MBTHCGRR96.pdf",
}
@Article{SCI:Ber1997b,
author = "M. Berzins and S.V. Pennington and P.R. Pratt and
J.M. Ware",
title = "{SPRINT2D} Software for Convection Dominated
{PDE}s",
journal = "Modern Software Tools in Scientific Computing",
year = "1997",
editor = "E. Arge and A.M. Bruaset and H.P. Langtangen",
publisher = "Birkhauser Press",
url = "http://www.sci.utah.edu/publications/Ber1997b/Berzins_SPRINT2D.pdf",
}
@Article{SCI:Ber1997c,
author = "M. Berzins and P.J. Capon and P.K. Jimack",
title = "On Spatial Adaptivity and Interpolation when Using
the Method of Lines",
journal = "Applied Numerical Mathematics: Transactions of
IMACS",
volume = "26",
number = "1--2",
pages = "117--133",
year = "1997",
url = "http://www.sci.utah.edu/publications/berzins97/berzins91spatial.pdf",
}
@InProceedings{SCI:Ber1999a,
author = "M. Berzins and L.J.K. Durbeck",
title = "Unstructured Mesh Methods Applied to Hyperbolic
{PDE}s with Source Terms: Error Estimates and Mesh
Quality",
booktitle = "Godunov Methods: Theory and Applications
Conference and Short Course",
year = "1999",
publisher = "Oxford. numeritek Ltd.URL",
month = "October",
keywords = "computational pde pdes computational partial
differential equations evaporation, adaptive mesh
generation, evaporation, scirun, atmospherics
weather meterology",
url = "http://www.sci.utah.edu/publications/berzins99/unstructured-mesh-methods-applied.pdf",
}
@Article{SCI:Ber1999c,
author = "M. Berzins and J. Nash and P. Selwood",
title = "Parallel Solution of Reacting Flow Problems using
Unstructured Tetrahedral Meshes",
journal = "Proceedings of 9th {SIAM} Parallel Processing for
Scientific Computing",
year = "1999",
location = "Philadelphia, PA",
isbn = "0-89871-435-4",
url = "http://www.sci.utah.edu/publications/Ber1999c/Berzins_PPSC1999.pdf",
}
@InCollection{SCI:Ber1999e,
author = "M. Berzins",
title = "A Solution Based H1 Norm Triangular Mesh Quality
Indicator",
booktitle = "Grid Generation and Adaptive Algorithms",
booktitle_url =
"http://www.springer.com/us/book/9781461271918",
pages = "77-88",
year = "1999",
editor = "Marshal W. Bern, Joseph E. Flaherty, Mitchell
Luskin",
publisher = "Springer",
url = "http://www.sci.utah.edu/publications/Ber1999e/2210_001.pdf",
}
@InCollection{SCI:Ber2000a,
author = "M. Berzins and L. Durbeck and P.K. Jimack and M.
Walkley",
title = "Mesh Quality and Moving and Meshes for 2D and 3D
Unstructured Mesh Solvers",
booktitle = "Von Karman Institute for Fluid Mechanics 31st
Lecture Series on Computational Fluid Mechanics",
year = "2000",
editor = "N.P. Weatherill and H. Deconinck",
publisher = "Von Karman Institute",
month = "March",
issn = "0377-8312",
keywords = "computational pde pdes computational partial
differential equations evaporation, adaptive mesh
generation, evaporation, atmospherics weather
meterology, scientific computing",
url = "http://www.sci.utah.edu/publications/Ber2000a/vki_00.ps",
url = "http://www.sci.utah.edu/publications/Ber2000a/vki_00.pdf",
}
@Article{SCI:Ber2000b,
author = "M. Berzins",
title = "An Introduction to Mesh Quality",
journal = "Lectures notes for 31st Lecture Series on
Computational Fluid Mechanics",
pages = "21 pages",
year = "2000",
editor = "N.P. Weatherill and H. Deconink",
institution = "Von Karman Institute for Fluid Mechanics",
month = "March",
location = "Rhode st Genessee, Brussels, Belgium",
issn = "0377-8312",
url = "http://www.sci.utah.edu/publications/berzins00/vkione.pdf",
}
@Article{SCI:Ber2000d,
author = "M. Berzins",
title = "Solution-Based Mesh Quality Indicators for
Triangular and Tetrahedral Meshes",
journal = "International Journal of Computational Geometry
and Applications",
volume = "10",
number = "3",
pages = "333-346",
year = "2000",
month = "June",
url = "http://www.sci.utah.edu/publications/berzins00/CompG.pdf",
}
@Article{SCI:Ber2000e,
author = "M. Berzins",
title = "A New Metric for Dynamic Load Balancing",
journal = "Applied Mathematical Modelling",
volume = "25",
pages = "141--151",
year = "2000",
note = "Special issue on dynamic load balancing",
url = "http://www.sci.utah.edu/publications/berzins00/apmathmodv2.pdf",
}
@Article{SCI:Ber2000g,
author = "M. Berzins",
title = "A Data-Bounded Quadratic Interpolant on Triangles
and Tetrahedra",
journal = "{SIAM} Journal on Scientific Computing",
volume = "22",
number = "1",
pages = "177--197",
year = "2000",
url = "http://www.sci.utah.edu/publications/berzins00/finalout.pdf",
}
@InProceedings{SCI:Ber2001a,
author = "M. Bertram and D. Laney and M. Duchaineau and C.D.
Hansen and B. Hamann and K. Joy",
title = "Wavelet Representation of Contour Sets",
booktitle = c-VIS2001,
pages = "303--310, 566",
year = "2001",
keywords = "computational pde pdes computational partial
differential equations evaporation, ip image
processing signal processing, surface processing",
url = "http://www.sci.utah.edu/publications/bertram01/vis01-bertram.pdf",
}
@InCollection{SCI:Ber2001b,
author = "M. Berzins and A.S. Tomlin and S. Ghorai and I.
Ahmad J.Ware",
title = "Unstructured Mesh Adaptive Mesh {MOL} Solvers for
Atmospheric Reacting Flow Problems",
booktitle = "The Adaptive Method of Lines",
pages = "317--351",
year = "2001",
editor = "A. Vande Wouwer and Ph. Saucez and W. Schiesser",
publisher = "{CRC} Press, Boca Raton, Florida, {USA}.",
note = "invited chapter",
isbn = "1-58488-231-X",
url = "http://www.sci.utah.edu/publications/berzins01/mbmolch.pdf",
}
@InCollection{SCI:Ber2001c,
author = "M. Berzins and L. Durbeck",
title = "Unstructured Mesh Solvers for Hyperbolic PDEs with
Source Terms: Error Estimates and Mesh Quality",
booktitle = "Godunonv Methods: Theory and Applications",
pages = "117--124",
year = "2001",
editor = "E. Toro et al.",
publisher = "Kluwer Academic/Plenum",
note = "Proc. of Godunov Conf. October 18-22, Oxford UK",
url = "http://www.sci.utah.edu/publications/berzins01/mbgodunov.pdf",
}
@Article{SCI:Ber2001d,
author = "M. Berzins",
title = "Modified Mass Matrices and Positivity Preservation
for Hyperbolic and Parabolic {PDE}s",
journal = "Communications in Numerical Methods in
Engineering",
volume = "17",
pages = "659--666",
year = "2001",
url = "http://www.sci.utah.edu/publications/berzins01/austpapv3.pdf",
}
@Article{SCI:Ber2003b,
author = "M. Berzins and A.G. Wilson",
title = "Spatial Interaction Models and Fisher Information
Theory A New Calibration Model",
journal = "Environment and Planning",
volume = "35",
pages = "2161--2176",
year = "2003",
url = "http://www.sci.utah.edu/publications/berzins03/MBAGWFINALDRAFT.pdf",
}
@InProceedings{SCI:Ber2003c,
author = "M. Bertram and X. Tricoche and H. Hagen",
title = "Adaptive Smooth Scattered Data Approximation for
Largescale Terrain Visualization",
booktitle = "Proceedings of the Joint Eurographics-{IEEE}
{TCVG} Symposium on Visualization: Data
Visualization 2003",
pages = "177--184",
year = "2003",
url = "http://www.sci.utah.edu/publications/bertram03/terrain.pdf",
}
@TechReport{SCI:Ber2004a,
author = "F.F. Bernardon and C.A. Pagot and J.L.D. Comba and
C.T. Silva",
title = "{GPU}-based Tiled Ray Casting using Depth
Peeling",
number = "UUSCI-2004-006",
year = "2004",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2004-006.pdf",
}
@Article{SCI:Ber2004b,
author = "M. Berzins",
title = "Variable Order Finite Elements and Positivity
Preservation for Hyperbolic PDEs",
journal = "Applied Numerical Mathematics",
volume = "48",
number = "3-4",
pages = "253--439",
year = "2004",
month = "March",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational pde pdes computational partial
differential equations",
url = "http://www.sci.utah.edu/publications/berzins04/HPhyp.pdf",
}
@InProceedings{SCI:Ber2005a,
author = "F. Bertrand and R. Bramley and K. Damevski and D.
Bernholdt and J. Kohl and J. Larson and A.
Sussman",
title = "Data Redistribution and Remote Method Invocation
in Parallel Component Architectures",
booktitle = c-IPDPS2005,
volume = "1",
pages = "40--42",
year = "2005",
note = "Awarded Best Paper",
}
@TechReport{SCI:Ber2005b,
author = "F.F. Bernardon and S.P. Callahan and J.L.D. Comba
and C.T. Silva",
title = "Volume Rendering of Time-Varying Scalar Fields on
Unstructured Meshes",
number = "UUSCI-2005-006",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scalar field methods, volume rendering",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-006.pdf",
}
@InProceedings{SCI:Ber2005c,
author = "M. Berzins and R.M. Kirby and C.R. Johnson",
title = "Integrating Teaching and Research in HPC:
Experiences and Opportunities",
booktitle = c-ICCS2005,
pages = "36--43",
year = "2005",
location = "Atlanta, GA",
url = "http://www.sci.utah.edu/publications/berzins05/Teaching_and_Research_HPC.pdf",
}
@Article{SCI:Ber2005d,
author = "M. Berzins",
title = "Preserving Positivity for Hyperbolic PDEs Using
Variable-Order Finite Elements with Bounded
Polynomials",
journal = "Applied Numerical Mathematics",
volume = "52",
number = "2-3",
pages = "197--217",
year = "2005",
month = "February",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational pde pdes computational partial
differential equations",
url = "http://www.sci.utah.edu/publications/berzins05/GENhp.pdf",
}
@InProceedings{SCI:Ber2006a,
author = "F.F. Bernardon and S.P. Callahan and J.L.D. Comba
and C.T. Silva",
title = "Interactive Volume Rendering of Unstructured Grids
with Time-Varying Scalar Fields",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "51--58",
year = "2006",
keywords = "scalar field methods, volume rendering",
url = "http://www.sci.utah.edu/publications/bernardon06/egpgv2006.pdf",
}
@TechReport{SCI:Ber2006b,
author = "M. Berzins",
title = "Is there Still More to Science than Simulation?",
number = "UUSCI-2006-031",
year = "2006",
institution = "SCI Institute, University of Utah",
month = "November",
url = "http://www.sci.utah.edu/publications/Ber2006b/UUSCI-2006-031.pdf",
}
@TechReport{SCI:Ber2006c,
author = "M. Berzins",
title = "Adaptive Polynomial Interpolation on Evenly Spaced
Meshes",
number = "UUSCI-2006-033",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-033.pdf",
}
@Article{SCI:Ber2007a,
author = "F.F. Bernardon and S.P Callahan and J.L.D. Comba
and C.T. Silva",
title = "An Adaptive Framework for Visualizing Unstructured
Grids with Time-Varying Scalar Fields",
journal = "Journal on Parallel Computing",
volume = "33",
number = "6",
pages = "391--405",
year = "2007",
keywords = "vacet",
url = "http://www.sci.utah.edu/publications/bernardon07/parco07.pdf",
}
@TechReport{SCI:Ber2007b,
author = "F.F. Bernardon and L.K. Ha and S.P. Callahan and
J.L.D. Comba and C.T. Silva",
title = "Interactive Transfer Function Specification for
Direct Volume Rendering of Disparate Volumes",
number = "UUSCI-2007-007",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "volume rendering, transfer functions",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-007.pdf",
}
@Article{SCI:Ber2007c,
author = "M. Berzins",
title = "Is there Still More to Science than
Computation?",
journal = "Computing in Science and Engineering",
volume = "9",
number = "1",
pages = "98--101",
year = "2007",
keywords = "scientific computing",
url = "http://www.sci.utah.edu/publications/berzins07/CISEPAPER.pdf",
}
@Article{SCI:Ber2007d,
author = "M. Berzins",
title = "Adaptive Polynomial Interpolation on Evenly Spaced
Meshes.",
journal = "SIAM Review",
volume = "49",
number = "4",
pages = "604-627",
year = "2007",
url = "http://www.sci.utah.edu/publications/berzins07/SIpapv4.pdf",
}
@TechReport{SCI:Ber2009a,
author = "M. Berzins",
title = "Data Bounded Polynomials and Preserving Positivity
in High Order ENO and WENO Methods",
number = "UUSCI-2009-003",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2009-003.pdf",
}
@Article{SCI:Ber2010a,
author = "M. Berger and L.G. Nonato and V. Pascucci and C.T.
Silva",
title = "Fiedler Trees for Multiscale Surface Analysis",
journal = "Computer \& Graphics",
volume = "34",
number = "3",
pages = "272--281",
year = "2010",
month = "June",
note = "Special Issue of Sha",
doi = "10.1016/j.cag.2010.03.009",
url = "http://www.sci.utah.edu/publications/Ber2010a/Berger_htpaper2010.pdf",
}
@InProceedings{SCI:Ber2010b,
author = "M. Berzins and J. Luitjens and Q. Meng and T.
Harman and C.A. Wight and J.R. Peterson",
title = "Uintah: A Scalable Framework for Hazard
Analysis",
booktitle = "Proceedings of the Teragrid 2010 Conference, TG
10",
pages = "(published online)",
year = "2010",
month = "July",
note = "Awarded Best Paper in the Science Track!",
isbn = "978-1-60558-818-6",
doi = "10.1145/1838574.1838577",
keywords = "Uintah, csafe",
url = "http://www.sci.utah.edu/publications/Ber2010b/Tgrid10PAPPSv4.pdf",
}
@Article{SCI:Ber2010c,
author = "M. Berzins",
title = "Nonlinear Data-Bounded Polynomial Approximations
and their Applications in ENO Methods",
journal = "Numerical Algorithms",
volume = "55",
number = "2",
pages = "171",
year = "2010",
keywords = "Data bounded polynomials, Essentially
non-oscillatory methods",
url = "http://www.sci.utah.edu/publications/berzins10/Berzins_NA1020a.pdf",
}
@TechReport{SCI:Ber2011a,
author = "M. Berger and J.A. Levine and L.G. Nonato and G.
Taubin and C.T. Silva",
title = "An End-to-End Framework for Evaluating Surface
Reconstruction",
number = "UUSCI-2011-001",
year = "2011",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2011-001.pdf",
}
@Article{SCI:Ber2011c,
author = "M.L. Berlanga and S. Phan and E.A. Bushong and S.
Lamont and S. Wu and O. Kwon and B.S. Phung and M.
Terada and T. Tasdizen and E. Martone and M.H.
Ellisman",
title = "Three-dimensional reconstruction of serial mouse
brain sections using high-resolution large-scale
mosaics",
journal = "Frontiers in Neuroscience Methods",
volume = "5",
pages = "(published online)",
year = "2011",
month = "March",
doi = "10.3389/fnana.2011.00017",
url = "http://www.sci.utah.edu/publications/berlanga11/fnana-05-00017.pdf",
}
@TechReport{SCI:Ber2012a,
author = "M. Berzins",
title = "Status of Release of the Uintah Computational
Framework",
number = "UUSCI-2012-001",
year = "2012",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2012-001.pdf",
}
@InProceedings{SCI:Ber2012b,
author = "M. Berzins and Q. Meng and J. Schmidt and J.C.
Sutherland",
title = "{DAG-Based} Software Frameworks for PDEs",
booktitle = "Proceedings of {Euro-Par} 2011 Workshops, Part
{I}",
pages = "324--333",
year = "2012",
series = "Lecture Notes in Computer Science ({LNCS}) 7155",
publisher = "Springer-Verlag Berlin Heidelberg",
month = "August",
keywords = "DOD, Uintah, CSAFE",
url = "http://www.sci.utah.edu/publications/berzins12/Berzins_HPSS2012.pdf",
}
@InProceedings{SCI:Ber2013a,
author = "M. Berzins and J. Schmidt and Q. Meng and A.
Humphrey",
title = "Past, Present, and Future Scalability of the
Uintah Software",
booktitle = "Proceedings of the Blue Waters Extreme Scaling
Workshop 2012",
pages = "Article No.: 6",
year = "2013",
keywords = "netl, Uintah, parallelism, scalability, adaptive
mesh refinement, linear equations",
url = "http://www.sci.utah.edu/publications/berzins12/BerzinsBWW2012.pdf",
}
@Article{SCI:Ber2013b,
author = "M. Berzins",
title = "Data and Range-Bounded Polynomials in ENO
Methods",
journal = "Journal of Computational Science",
volume = "4",
number = "1-2",
pages = "62--70",
year = "2013",
doi = "10.1016/j.jocs.2012.04.006",
url = "http://www.sci.utah.edu/publications/berzins12/Berzins_ammcs11v7.pdf",
}
@Article{SCI:Ber2013c,
author = "N.M. Bertagnolli and J.A. Drake and J.M. Tennessen
and O. Alter",
title = "{SVD} Identifies Transcript Length Distribution
Functions from {DNA} Microarray Data and Reveals
Evolutionary Forces Globally Affecting {GBM}
Metabolism",
journal = "Public Library of Science (PLoS) One",
volume = "8",
number = "11",
pages = "article e78913",
year = "2013",
month = "November",
doi = "10.1371/journal.pone.0078913",
url = "http://www.sci.utah.edu/publications/bertagnolli13/Bertagnolli_PLoSOne2013.pdf",
}
@Article{SCI:Ber2016a,
author = "M. Berzins and J. Beckvermit and T. Harman and A.
Bezdjian and A. Humphrey and Q. Meng and J. Schmidt
and and C. Wight",
title = "Extending the Uintah Framework through the
Petascale Modeling of Detonation in Arrays of High
Explosive Devices",
journal = "SIAM Journal on Scientific Computing (Accepted)",
year = "2016",
url = "http://www.sci.utah.edu/publications/Ber2015a/detonationsiam16-2.pdf",
}
@Unpublished{SCI:Ber2017a,
author = "M. Berzins and D. A. Bonnell and Jr. Cizewski and
K. M. Heeger and A.J.G. Hey and C. J. Keane and B.
A. Ramsey and K. A. Remington and J.L. Rempe",
title = "Department of Energy, Advanced Scientific
Computing Advisory Committee (ASCAC), Subcommittee
on LDRD Review Final Report",
year = "2017",
month = "May",
url = "http://www.sci.utah.edu/publications/Ber2017a/REPORTLDRDMay09.pdf",
}
@InProceedings{SCI:Ber2017b,
author = "M. Berzins",
title = "Nonlinear Stability of the MPM Method",
booktitle = "V International Conference on Particle-based
Methods – Fundamentals and Applications.
PARTICLES 2017",
booktitle_url =
"http://congress.cimne.com/particles2017/frontal/doc/Ebook%20PARTICLES%202017.pdf",
pages = "671--682",
year = "2017",
editor = "P. Wriggers, M. Bischoff, E. O˜nate, D.R.J. Owen,
\& T. Zohdi",
url = "http://www.sci.utah.edu/publications/Ber2017b/mpmstabParticles.pdf",
}
@Article{SCI:Ber2018a,
author = "M. Berzins",
title = "Nonlinear stability and time step selection for
the MPM method",
journal = "Computational Particle Mechanics",
year = "2018",
month = "Jan",
issn = "2196-4386",
doi = "10.1007/s40571-018-0182-y",
url = "http://www.sci.utah.edu/publications/Ber2018a/mpmstabSpringer2.pdf",
}
@InProceedings{SCI:Ber2019a,
author = "M. Berzins",
title = "Time Integration Errors and Energy Conservation
Properties of the Stormer Verlet Method Applied to
MPM",
booktitle = "Proceedings of VI International Conference on
Particle-based Methods – Fundamentals and
Applications",
booktitle_url =
"https://congress.cimne.com/particles2019/frontal/doc/Ebook_Particles_2019.pdf",
pages = "555-566",
year = "2019",
editor = "E. O nate, M. Bischoff, D.R.J. Owen, P.
Wriggers \& T. Zohdi",
organization = "PARTICLES 2019",
month = "October",
location = "Barcelona",
isbn = "978-84-121101-1-1",
url = "http://www.sci.utah.edu/publications/Ber2019a/Ebook_Particles_2019.pdf",
}
@Article{SCI:Ber84a,
author = "M. Berzins and T.F. Buckley and P.M. Dew",
title = "Path Pascal Simulation of Multi-Processor Lattice
Architectures for Numerical Computations",
journal = "Progress in the Use of Vector and Array
processors",
year = "1984",
editor = "D.J. Paddon and J.D. Pryce",
publisher = "Academic Press",
}
@Article{SCI:Ber92d,
author = "M. Berzins and P.M. Dew and S. Hillen",
title = "Exploiting Parallelism for Adaptive {CFD}
Software",
journal = "Parallelogram",
pages = "14--16",
year = "1992",
month = "February",
}
@InProceedings{SCI:Ber95a,
author = "M. Berzins and T.H.C. Childs and K.W. Dalgarno and
G.R. Ryder and G. Stein",
title = "Densification and Distortion in Selective Laser
Sintering of Polycarbonate",
booktitle = "Proc 6th Symposium on Solid Free Form
Fabrication",
pages = "196--203",
year = "1995",
editor = "J.W. Barlow et al.",
location = "University of Texas at Austin",
url = "http://www.sci.utah.edu/publications/berzins95/1995-24-Berzins.pdf",
}
@Article{SCI:Ber95c,
author = "M. Berzins",
title = "Temporal Error Control in the Method of Lines for
Convection Dominated Equations",
journal = "{SIAM} Journal on Scientific Computing",
volume = "16",
pages = "558--580",
year = "1995",
url = "http://www.sci.utah.edu/publications/berzins95/SIAMhypbal4.pdf",
}
@Article{SCI:Ber96a,
author = "M. Berzins and J.M. Ware",
title = "Solving Convection and Convection Reaction
Problems Using the M.O.L.",
journal = "Applied Numerical Mathematics",
volume = "20",
pages = "83--99",
year = "1996",
url = "http://www.sci.utah.edu/publications/berzins96/molpap.pdf",
}
@Article{SCI:Ber98b,
author = "M. Berzins and P.J. Capon and P.K. Jimack",
title = "On Spatial Adaptivity and Interpolation When Using
the Method of Lines",
journal = "Applied Numerical Mathematics",
volume = "26",
pages = "117--134",
year = "1998",
url = "http://www.sci.utah.edu/publications/berzins98/berzins91spatial.pdf",
}
@Article{SCI:Ber98c,
author = "M. Berzins",
title = "A Solution-Based Triangular and Tetrahedral Mesh
Quality Indicator",
journal = "{SIAM} Journal on Scientific Computing",
volume = "19",
pages = "2051--2060",
year = "1998",
url = "http://www.sci.utah.edu/publications/berzins98/SISC19.pdf",
}
@Article{SCI:Ber98d,
author = "M. Berzins and R. Fairlie and S.V. Pennington and
J.M. Ware and L.E. Scales",
title = "{SPRINT2D}: Adaptive Software for {PDE}s",
journal = "{ACM} Transactions on Mathematical Software",
volume = "24",
number = "4",
pages = "475--499",
year = "1998",
month = "December",
keywords = "computational pde pdes computational partial
differential equations",
url = "http://www.sci.utah.edu/publications/berzins98/berzins98sprintd.pdf",
}
@Article{SCI:Ber99d,
author = "M. Berzins",
title = "Mesh Quality - Geometry, Error Estimates or
Both?",
journal = "Engineering and Computers",
volume = "15",
pages = "236--247",
year = "1999",
url = "http://www.sci.utah.edu/publications/berzins99/MESHQUALITY.pdf",
url = "http://www.sci.utah.edu/publications/berzins99/Engwcomp.pdf",
}
@Article{SCI:Bet2006a,
author = "W. Bethel and C.R. Johnson and C.D. Hansen and
S.G. Parker and A.R. Sanderson and C.T. Silva and
X. Tricoche and V. Pascucci and H. Childs and J.
Cohen and M. Duchaineau and D. Laney and P.
Lindstrom and S. Ahern and J. Meredith and G.
Ostrouchov and K. Joy and B. Hamann",
title = "VACET: Proposed SciDAC2 Visualization and
Analytics Center for Enabling Technologies",
journal = "J. Phys.: Conf. Ser.",
volume = "46",
pages = "561--569",
year = "2006",
keywords = "VACET, SciDAC",
url = "http://www.sci.utah.edu/publications/bethel06/jpconf6_46_078.pdf",
}
@Article{SCI:Bet2007a,
author = "E.W. Bethel and C.R. Johnson and K. Joy and S.
Ahern and V. Pascucci and H. Childs and J. Cohen
and M. Duchaineau and B. Hamann and C.D. Hansen and
D. Laney and P. Lindstrom and J. Meredith and G.
Ostrouchov and S.G. Parker and C.T. Silva and A.R.
Sanderson and X. Tricoche",
title = "SciDAC Visualization and Analytics Center for
Enabling Technology",
journal = "Journal of Physics",
volume = "78",
number = "012032",
pages = "(published online)",
year = "2007",
series = "Conference Series",
keywords = "vacet",
url = "http://www.sci.utah.edu/publications/bethel07/VACET-Paper07-Final.pdf",
}
@Article{SCI:Bet2007b,
author = "E.W. Bethel and C.R. Johnson and C. Aragon and
Prabhat and O. R{\"u}bel and G. Weber and V.
Pascucci and H. Childs and P.-T. Bremer and B.
Whitlock and S. Ahern and J. Meredith and G.
Ostrouchov and K. Joy and B. Hamann and C. Garth
and M. Cole and C.D. Hansen and S.G. Parker and
A.R. Sanderson and C.T. Silva and X. Tricoche",
title = "DOE's SciDAC Visualization and Analytics Center
for Enabling Technologies - Strategy for Petascale
Visual Data Analysis Success",
journal = "CTWatch Quarterly",
volume = "3",
number = "4",
year = "2007",
}
@InCollection{SCI:Bet2008a,
author = "E.W. Bethel and H. Childs and A. Mascarenhas and
V. Pascucci and Prabhat",
title = "Scientific Data Management Challenges in High
Performance Visual Data Analysis",
booktitle = "Scientific Data Management: Challenges, Existing
Technology, and Deployment",
year = "2008",
publisher = "Chapman Hall/CRC Press",
keywords = "vacet, data management",
}
@Article{SCI:Bet2009a,
author = "E.W. Bethel and C.R. Johnson and S. Ahern and J.
Bell and P.-T. Bremer and H. Childs and E.
Cormier-Michel and M. Day and E. Deines and P.T.
Fogal and C. Garth and C.G.R. Geddes and H. Hagen
and B. Hamann and C.D. Hansen and J. Jacobsen and
K.I. Joy and J. Kr{\"u}ger and J. Meredith and P.
Messmer and G. Ostrouchov and V. Pascucci and K.
Potter and Prabhat and D. Pugmire and O. Rubel and
A.R. Sanderson and C.T. Silva and D. Ushizima and
G.H. Weber and B. Whitlock and K. Wu",
title = "Occam's Razor and Petascale Visual Data
Analysis",
journal = "Journal of Physics: Conference Series",
volume = "180",
number = "012084",
pages = "(published online)",
year = "2009",
series = "Journal of Physics: Conference Series",
doi = "10.1088/1742-6596/180/1/012084",
url = "http://www.sci.utah.edu/publications/Bet2009a/Bethel_IOPScience2009.pdf",
}
@InProceedings{SCI:Bha2011a,
author = "H. Bhatia and S. Jadhav and P.-T. Bremer and G.
Chen and J.A. Levine and L.G. Nonato and V.
Pascucci",
title = "Edge Maps: Representing Flow with Bounded Error",
booktitle = "Proceedings of {IEEE} Pacific Visualization
Symposium 2011",
pages = "75--82",
year = "2011",
month = "March",
location = "Hong Kong, China",
note = "Won Best Paper Award!",
doi = "10.1109/PACIFICVIS.2011.5742375",
url = "http://www.sci.utah.edu/publications/bhatia11/Bhatia_vfmaps_pacvis11.pdf",
}
@Article{SCI:Bha2011b,
author = "H. Bhatia and S. Jadhav and P.-T. Bremer and G.
Chen and J.A. Levine and L.G. Nonato and V.
Pascucci",
title = "Flow Visualization with Quantified Spatial and
Temporal Errors using Edge Maps",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "18",
number = "9",
pages = "1383--1396",
year = "2011",
publisher = "{IEEE} Society",
doi = "10.1109/TVCG.2011.265",
url = "http://www.sci.utah.edu/publications/bhatia11/Bhatia_TVCG2011_EdgeMaps.pdf",
}
@InProceedings{SCI:Bha2012b,
author = "A. Bhatele and T. Gamblin and S.H. Langer and
P.-T. Bremer and E.W. Draeger and B. Hamann and
K.E. Isaacs and A.G. Landge and J.A. Levine and V.
Pascucci and M. Schulz and C.H. Still",
title = "Mapping applications with collectives over
sub-communicators on torus networks",
booktitle = "Proceedings of Supercomputing 2012",
pages = "1--11",
year = "2012",
doi = "10.1109/SC.2012.75",
url = "http://www.sci.utah.edu/publications/bhatele12/Bhatele_SC2012.pdf",
}
@Article{SCI:Bha2013a,
author = "H. Bhatia and G. Norgard and V. Pascucci and P.-T.
Bremer",
title = "The Helmholtz-Hodge Decomposition - A Survey",
journal = "IEEE Transactions on Visualization and Computer
Graphics (TVCG)",
volume = "19",
number = "8",
pages = "1386--1404",
year = "2013",
note = "Selected as Spotlight paper for August 2013
issue",
doi = "10.1109/TVCG.2012.316",
url = "http://www.sci.utah.edu/publications/Bha2013a/Bhatia_TVCG2013.pdf",
}
@Article{SCI:Bha2013c,
author = "H. Bhatia and G. Norgard and V. Pascucci and P.-T.
Bremer",
title = "Comments on the “Meshless Helmholtz-Hodge
decomposition”",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "19",
number = "3",
pages = "527--528",
year = "2013",
doi = "10.1109/TVCG.2012.62",
url = "http://www.sci.utah.edu/publications/bhatia12/Bhatia_TVCG2012.pdf",
}
@Article{SCI:Bha2014a,
author = "H. Bhatia and V. Pascucci and R.M. Kirby and P.-T.
Bremer",
title = "Extracting Features from Time-Dependent Vector
Fields Using Internal Reference Frames",
journal = "Computer Graphics Forum",
volume = "33",
number = "3",
pages = "21--30",
year = "2014",
month = "June",
doi = "10.1111/cgf.12358",
url = "http://www.sci.utah.edu/publications/Bha2014a/Bhatia_EuroVis2014.pdf",
}
@InCollection{SCI:Bha2014b,
author = " H. Bhatia and A. Gyulassy and H. Wang and P.-T.
Bremer and V. Pascucci ",
title = "Robust Detection of Singularities in Vector
Fields",
booktitle = "Topological Methods in Data Analysis and
Visualization III",
pages = "3--18",
year = "2014",
series = "Mathematics and Visualization",
publisher = "Springer International Publishing",
month = "March",
doi = "10.1007/978-3-319-04099-8_1",
url = "http://www.sci.utah.edu/publications/Bha2014b/Bhatia_TopoInVis2014.pdf",
}
@Article{SCI:Bha2014c,
author = "H. Bhatia and V. Pascucci and P.-T. Bremer",
title = "The Natural Helmholtz-Hodge Decomposition For
Open-Boundary Flow Analysis",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "99",
pages = "1566--1578",
year = "2014",
doi = "10.1109/TVCG.2014.2312012",
url = "http://www.sci.utah.edu/publications/Bha2014c/Bhatia_TVCG2014.pdf",
}
@Article{SCI:Bha2015a,
author = "H. Bhatia and Bei Wang and G. Norgard and V.
Pascucci and P. T. Bremer",
title = "Local, Smooth, and Consistent Jacobi Set
Simplification",
journal = "Computational Geometry",
volume = "48",
number = "4",
pages = "311-332",
year = "2015",
publisher = "Elsevier",
month = "May",
doi = "10.1016/j.comgeo.2014.10.009",
url = "http://www.sci.utah.edu/publications/Bha2015a/JacobiSetSimplification_BeiWang_2015.pdf",
}
@Article{SCI:Bha2017a,
author = "A. Bhaduri and Y. He and M.D. Shields and L.
Graham-Brady and R.M. Kirby",
title = "Stochastic collocation approach with adaptive mesh
refinement for parametric uncertainty analysis",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Bha2017a/1709.04584.pdf",
}
@InProceedings{SCI:Bha2017b,
author = "A. Bhatele and J. Yeom and N. Jain and C. J.
Kuhlman and Y. Livnat and K. R. Bisset and L. V.
Kale and M. V. Marathe",
title = "Massively Parallel Simulations of Spread of
Infectious Diseases over Realistic Social
Networks",
booktitle = "2017 17th IEEE/ACM International Symposium on
Cluster, Cloud and Grid Computing (CCGRID)",
year = "2017",
month = "May",
doi = "10.1109/ccgrid.2017.141",
url = "http://www.sci.utah.edu/publications/Bha2017b/ccgrid2017a.pdf",
}
@Article{SCI:Bha2018a,
author = "H. Bhatia and A.G. Gyulassy and V. Lordi and J.E.
Pask and V. Pascucci and P.T. Bremer",
title = "TopoMS: Comprehensive topological exploration for
molecular and condensed‐matter systems",
journal = "Journal of Computational Chemistry",
volume = "39",
number = "16",
pages = "936--952",
year = "2018",
publisher = "Wiley",
month = "March",
doi = "10.1002/jcc.25181",
url = "http://www.sci.utah.edu/publications/Bha2018a/2018_JCC_TopoMS.pdf",
}
@InProceedings{SCI:Bha2019a,
author = "R. Bhalodia and S. Y. Elhabian and L. Kavan and R.
T. Whitaker",
title = "A Cooperative Autoencoder for Population-Based
Regularization of CNN Image Registration",
booktitle = "Medical Image Computing and Computer Assisted
Intervention -- MICCAI 2019",
journal = "Medical Image Computing and Computer Assisted
Intervention – MICCAI 2019",
pages = "391--400",
year = "2019",
publisher = "Springer International Publishing",
url = "http://www.sci.utah.edu/publications/Bha2019a/1908.05825.pdf",
}
@TechReport{SCI:Big2006a,
author = "J. Bigler and A.J. Stephens and S.G. Parker",
title = "Design for Parallel Interactive Ray Tracing
Systems",
number = "UUSCI-2006-027",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "rtrt real-time ray tracing, parallel
visualization, interactive rt distributed
interactive ray tracing dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-027.pdf",
}
@InProceedings{SCI:Big2006b,
author = "J. Bigler and J. Guilkey and C. Gribble and C.D.
Hansen and S.G. Parker",
title = "A Case Study: Visualizing Material Point Method
Data",
booktitle = "Proceedings of Euro Vis 2006",
pages = "299--306, 377",
year = "2006",
month = "May",
keywords = "mpm material point method, csafe c-safe",
url = "http://www.sci.utah.edu/publications/bigler06/mpmvis-electronic.pdf",
}
@InProceedings{SCI:Big2006c,
author = "J. Bigler and A.J. Stephens and S.G. Parker",
title = "Design for Parallel Interactive Ray Tracing
Systems",
booktitle = "Proceedings of The {IEEE} {S}ymposium on
{I}nteractive {R}ay {T}racing",
pages = "187--196",
year = "2006",
keywords = "rtrt real-time ray tracing, parallel
visualization, interactive rt distributed
interactive ray tracing dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/bigler06/manta-rt06.pdf",
}
@InProceedings{SCI:Big2014a,
author = "A. Bigelow and S. Drucker and D. Fisher and M.D.
Meyer",
title = "Reflections on How Designers Design With Data",
booktitle = "Proceedings of the ACM International Conference on
Advanced Visual Interfaces ({AVI})",
year = "2014",
note = "Awarded Best Paper!",
keywords = "Visualization, infographics, design practice",
url = "http://www.sci.utah.edu/publications/Big2014a/Bigelow_AVI2014.pdf",
}
@Article{SCI:Big2016a,
author = "A. Bigelow and R. Choudhury and J. Baumes",
title = "Resonant Laboratory and Candela: Spreading Your
Visualization Ideas to the Masses",
journal = "Proceedings of Workshop on Visualization in
Practice (VIP '16)",
year = "2016",
note = "Best Paper Award ",
url = "http://www.sci.utah.edu/publications/Big2016a/2016_vip_resonant_lab.pdf",
}
@InCollection{SCI:Bla2010a,
author = "J.J.E. Blauer and J. Cates and C.J. McGann and
E.G. Kholmovski and A. Alexander and M.W. Prastawa
and S. Joshi and N.F. Marrouche and R.S. MacLeod",
title = "MRI Based Injury Characterization Immediately
Following Ablation of Atrial Fibrillation",
booktitle = "Computing in Cardiology",
volume = "37",
pages = "165--168",
year = "2010",
issn = "0276−6574",
url = "http://www.sci.utah.edu/publications/Bla2010a/Blauer_CinC2010.pdf",
}
@Article{SCI:Bla2014a,
author = "J.J.E. Blauer and D. Swenson and K. Higuchi and G.
Plank and R. Ranjan and N. Marrouche and and R.S.
MacLeod",
title = "Sensitivity and Specificity of Substrate Mapping:
An In Silico Framework for the Evaluation of
Electroanatomical Substrate Mapping Strategies",
booktitle = "Journal of Cardiovascular Electrophysiology",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "25",
number = "7",
pages = "774--780",
year = "2014",
month = "May",
note = "Featured on journal cover.",
keywords = "arrhythmia, computer-based model,
electroanatomical mapping, voltage mapping, bipolar
electrogram",
url = "http://www.sci.utah.edu/publications/Bla2014a/Blauer_JCE2014-BPA_Modeling-formatted.pdf",
url = "http://www.sci.utah.edu/publications/Bla2014a/Blauer_JCE2014-OnlineSupplement-formatted.pdf",
}
@Article{SCI:Boc2018a,
author = "A. Bock and E. Axelsson and C. Emmart and M.
Kuznetsova and C. Hansen and A. Ynnerman",
title = "OpenSpace: Changing the Narrative of Public
Dissemination in Astronomical Visualization from
What to How",
journal = "IEEE Computer Graphics and Applications",
volume = "38",
number = "3",
pages = "44--57",
year = "2018",
publisher = "IEEE",
month = "May",
doi = "10.1109/mcg.2018.032421653",
url = "http://www.sci.utah.edu/publications/Boc2018a/08370192.pdf",
}
@InProceedings{SCI:Boh2002a,
author = "P. Bohannon and J. Freire and J. Haritsa and M.
Ramanath and P. Roy and J. Simeon",
title = "LegoDB: Customizing Relational Storage for XML
Documents",
booktitle = "Proceedings of the 28th international conference
on Very Large Data Bases",
pages = "1091--1094",
year = "2002",
location = "Hong Kong, China",
keywords = "xml, relational storage, legodb",
url = "http://www.sci.utah.edu/publications/bohannon02/Bohannon_LegoDB2002.pdf",
}
@Article{SCI:Boh2002b,
author = "P. Bohannon and J. Freire and P. Roy and J.
Sim{\'e}on",
title = "From XML Schema to Relations: A Cost-Based
Approach to XML Storage",
journal = "International Conference on Data Engineering",
pages = "64",
year = "2002",
publisher = "IEEE Computer Society",
address = "Los Alamitos, CA, USA",
isbn = "0-7695-1531-2",
url = "http://www.sci.utah.edu/publications/bohannon02/Bohannon_icde2002.pdf",
}
@Article{SCI:Boh2003a,
author = "P. Bohannon and J. Freire and J. Haritsa and M.
Ramanath and P. Roy and J. Simeon",
title = "Bridging the XML-Relational Divide with LegoDB: A
Demonstration",
journal = "International Conference on Data Engineering",
pages = "759",
year = "2003",
issn = "1063-6382",
url = "http://www.sci.utah.edu/publications/bohannon03/Bohannon_ICDE2003.pdf",
}
@Article{SCI:Bon2005a,
author = "C. Bonifasi-Lista and S.P. Lake and M. Small and
J.A. Weiss",
title = "Viscoelastic Properties of the Human Medial
Collateral Ligament Under Longitudinal, Transverse
and Shear Loading",
journal = j-OR,
volume = "23",
number = "1",
pages = "67--76",
year = "2005",
month = "January",
keywords = "computational mechanics, computational
biomechanics, angiogenesis",
url = "http://www.sci.utah.edu/publications/lista05/bonifasi_jor_2005.pdf",
}
@InCollection{SCI:Bon2014a,
author = "G.P. Bonneau and H.C. Hege and C.R. Johnson and
M.M. Oliveira and K. Potter and P. Rheingans and T.
Schultz",
title = "Overview and State-of-the-Art of Uncertainty
Visualization",
booktitle = "Scientific Visualization: Uncertainty, Multifield,
Biomedical, and Scalable Visualization",
pages = "3--27",
year = "2014",
editor = "M. Chen and H. Hagen and C.D. Hansen and C.R.
Johnson and A. Kauffman",
publisher = "Springer-Verlag",
isbn = "978-1-4471-6496-8",
issn = "1612-3786",
doi = "10.1007/978-1-4471-6497-5_1",
url = "http://www.sci.utah.edu/publications/Bon2014a/Overview-Uncertainty-Visualization-2015.pdf",
}
@InProceedings{SCI:Bor2003a,
author = "R. Borgo and R. Scopigno and P. Cignoni and V.
Pascucci",
title = "A Progressive Subdivision Paradigm ({PSP})",
booktitle = "Proceedings of the Conference on Vision, Modeling
and Visualization 2003 ({VMV}-03)",
pages = "441--450",
year = "2003",
editor = "T. Ertl and B. Girod and G. Greiner and H. Niemann
and H.-P. Seidel and E. Steinbach and R.
Westermann",
publisher = "Aka GmbH",
address = "Berlin, Germany",
month = "Nov",
note = "UCRL-PROC-208557",
}
@InProceedings{SCI:Bor2004a,
author = "R. Borgo and V. Pascucci and R. Scopigno",
title = "Massive Data Pre-Processing with a Cluster Based
Approach",
booktitle = "Proceedings of the 2004 Eurographics Symposium on
Parallel Graphics and Visualization
({EG}-{PGV}-04)",
pages = "67--74",
year = "2004",
publisher = "Eurographics Association",
address = "Aire-la-Ville, Switzerland",
month = "June",
note = "UCRL-PROC-208678",
}
@Article{SCI:Bos2017a,
author = "L. Bos and A. Narayan and N. Levenberg and F.
Piazzon",
title = "An Orthogonality Property of the Legendre
Polynomials",
journal = "Constructive Approximation",
volume = "45",
number = "1",
pages = "65--81",
year = "2017",
month = "Feb",
issn = "0176-4276, 1432-0940",
doi = "10.1007/s00365-015-9321-3",
url = "http://www.sci.utah.edu/publications/Bos2017a/1505.06635.pdf",
}
@Unpublished{SCI:Bot1999a,
author = "D. Botstein and L. Smarr and D. Agard and M.
Levitt and D. Lippman and D. Herrington and C.R.
Johnson and G Rose and G. Rubin and A. Levison and
M. Spence and H. Smith and C. Peskin and G.
Jacobs",
title = "{NIH} Biomedical Information Science and
Technology Initiative ({BISTI})",
year = "1999",
publisher = "National Institutes of Health",
month = "July",
note = "Prepared by the Working Group on Biomedical
Computing Advisory Committee to the Director",
url = "http://www.sci.utah.edu/publications/botstein99/BISTI_1999.pdf",
}
@TechReport{SCI:Bou2006a,
author = "S. Boulos and D. Edwards and J.D. Lacewell and
J.M. Kniss and J. Kautz and P. Shirley and I.
Wald",
title = "Interactive Distribution Ray Tracing",
number = "UUSCI-2006-022",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "rtrt real-time ray tracing, parallel
visualization, interactive rt distributed
interactive ray tracing dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-022.pdf",
}
@TechReport{SCI:Bou2006b,
author = "S. Boulos and I. Wald and P. Shirley",
title = "Geometric and Arithmetic Culling Methods for
Entire Ray Packets",
number = "UUCS-06-010",
year = "2006",
institution = "School of Computing, University of Utah",
type = "School of Computing Technical Report",
keywords = "rtcenter",
url = "http://www.sci.utah.edu/publications/boulos06/UUCS-06-10.pdf",
}
@InProceedings{SCI:Bou2007a,
author = "S. Boulos and D. Edwards and J.D. Lacewell and J.
Kniss and J. Kautz and I. Wald and P. Shirley",
title = "Packet-based Whitted and Distribution Ray
Tracing",
booktitle = "Proceedings of Graphics Interface 2007",
volume = "234",
pages = "177--184",
year = "2007",
keywords = "rtcenter",
url = "http://www.sci.utah.edu/publications/boulos07/packetdrt.pdf",
}
@InProceedings{SCI:Bow1998a,
author = "A.E. Bowden and R.D. Rabbitt and J.A. Weiss",
title = "Anatomical Registration and Segmentation by
Warping Template Finite Element Models",
booktitle = "Proc. {SPIE} (Laser-Tissue Interaction IX)",
volume = "3254",
pages = "469--476",
year = "1998",
url = "http://www.sci.utah.edu/publications/bowden98/spie98_anton.pdf",
}
@InCollection{SCI:Bra2000a,
author = "R. Bramley and C.R. Johnson and D. Gannon and J.
Reynders and T. Hewett and J. Rice",
title = "Workshop on Scientific Knowledge, Information and
Computing, SIDEKIC 98",
booktitle = "Enabling Technologies for Computational Science",
pages = "19-32",
year = "2000",
publisher = "Springer",
doi = "10.1007/978-1-4615-4541-5_2",
url = "http://www.sci.utah.edu/publications/Bra2000a/SIDEKIC98.pdf",
}
@InProceedings{SCI:Bra2008a,
author = "D. Brayford and M. Turner and W.T. Hewitt",
title = "A Physical Model for the Polarized Scattering of
Light",
booktitle = "Proceedings of The sixth Theory and Practice of
Computer Graphics 2008 Conference ({TPCG08})",
year = "2008",
month = "June",
location = "University of Manchester, UK",
note = "Best Paper Award",
url = "http://www.sci.utah.edu/publications/brayford08/eg_uk_DavidBrayford.pdf",
}
@InProceedings{SCI:Bre2000a,
author = "J.D. Brederson and M. Ikits and C.R. Johnson and
C.D. Hansen and J.M. Hollerbach",
title = "The Visual Haptic Workbench",
booktitle = "Proceedings of the Fifth PHANToM Users Group
Workshop",
pages = "46--49",
year = "2000",
month = "October",
keywords = "vr virtual reality haptics, uve, scientific
visualization, haptics",
url = "http://www.sci.utah.edu/publications/jdb00/pug00.pdf",
url = "http://www.sci.utah.edu/publications/jdb00/pug00.ps.gz",
url = "http://www.sci.utah.edu/publications/jdb00/pug00.ps",
}
@InProceedings{SCI:Bre2001a,
author = "J.D. Brederson and M. Ikits and C.R. Johnson and
C.D. Hansen",
title = "A Prototype System For Synergistic Data Display",
booktitle = "{IEEE} Virtual Reality 2001",
year = "2001",
keywords = "vector field methods, visual haptic workbench,
scientific visualization",
url = "http://www.sci.utah.edu/publications/jdb01/vr01-wk.ps",
url = "http://www.sci.utah.edu/publications/jdb01/vr01-wk.ps.gz",
url = "http://www.sci.utah.edu/publications/jdb01/vr01-wk.pdf",
}
@Article{SCI:Bre2001b,
author = "D. Breen and R.T. Whitaker",
title = "A Level-Set Approach for the Metamorphosis of
Solid Models",
journal = j-TVCG,
volume = "7",
number = "2",
pages = "173--192",
year = "2001",
keywords = "ip image processing signal processing,
segmentation, imaging, level-set methods,
level-sets",
url = "http://www.sci.utah.edu/publications/breen01/breen_whitaker_2001.pdf",
}
@InProceedings{SCI:Bre2003a,
author = "P.-T. Bremer and H. Edelsbrunner and B. Hamann and
V. Pascucci",
title = "A Multi-resolution Data Structure for
Two-dimensional {Morse} Functions",
booktitle = "Proceedings of {IEEE} Conference on Visualization
({VIS}-03)",
pages = "139--146",
year = "2003",
month = "October",
note = "UCRL-JC-154014",
}
@Article{SCI:Bre2004a,
author = "P.-T. Bremer and H. Edelsbrunner and B. Hamann and
V. Pascucci",
title = "A Topological Hierarchy for Functions on
Triangulated Surfaces",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "10",
number = "4",
pages = "385-396",
year = "2004",
month = "July/August",
note = "UCRL-JRNL-208700",
}
@InProceedings{SCI:Bre2004c,
author = "P.-T. Bremer and V. Pascucci and B. Hamann",
title = "Maximizing adaptivity in hierarchical topological
models",
booktitle = "Trends in Software",
pages = "121--130",
year = "2004",
editor = "T. Moeller and B. Hamann and B. Russell",
publisher = "Springer",
month = "January",
note = "UCRL-BOOK-200013",
}
@InProceedings{SCI:Bre2005b,
author = "P.-T. Bremer and V. Pascucci and B. Hamann",
title = "Maximizing Adaptivity in Hierarchical Topological
Models",
booktitle = "International Conference on Shape Modeling and
Applications 2005",
year = "2005",
publisher = "IEEE",
doi = "10.1109/smi.2005.28",
}
@InProceedings{SCI:Bre2006b,
author = "P.-T. Bremer and W. Cabot and A. Cook and D. Laney
and A. Mascarenhas and P. Miller and V. Pascucci",
title = "Understanding the Structure of the Turbulent
Mixing Layer in Hydrodynamic Instabilities",
booktitle = "Proceedings of SciDAC 2006 -- Scientific Discovery
Through Advanced Computing",
volume = "46",
pages = "556--560",
year = "2006",
publisher = "Journal of Physics Conference Series",
month = "June",
location = "Denver, CO, USA",
}
@InProceedings{SCI:Bre2007a,
author = "P.-T. Bremer and E.M. Bringa and M.A. Duchaineau
and A. Gyulassy and D. Laney and A. Mascarenhas and
V. Pascucci",
title = "Topological Feature Extraction and Tracking",
booktitle = "Proceedings of SciDAC 2007 -- Scientific Discovery
Through Advanced Computing",
volume = "78",
pages = "012032 (5pp)",
year = "2007",
publisher = "Journal of Physics Conference Series",
month = "June",
location = "Boston, MA, USA",
}
@InCollection{SCI:Bre2007b,
author = "P.-T. Bremer and V. Pascucci",
title = "A Practical Approach to Two-Dimensional Scalar
Topology",
booktitle = "Mathematics and Visualization",
pages = "151--169",
year = "2007",
publisher = "Springer Verlag",
isbn = " Online ISBN 978-3-540-70823-0 Series Title
Mathematics and Visualization Series ISSN
1",
doi = "10.1007/978-3-540-70823-0_11",
url = "http://www.sci.utah.edu/publications/Bre2007b/Bremer_TopologyBasedMethInVis2006.pdf",
}
@Book{SCI:Bre2014a,
title = "Topological Methods in Data Analysis and
Visualization III",
year = "2014",
editor = "Peer-Timo Bremer and Ingrid Hotz and Valerio
Pascucci and Ronald Peikert",
publisher = "Springer International Publishing",
isbn = "978-3-319-04099-8",
}
@Article{SCI:Bre2015a,
author = "P. T. Bremer and D. Maljovec and A. Saha and Bei
Wang and J. Gaffney and B. K. Spears and V.
Pascucci",
title = "ND2AV: N-Dimensional Data Analysis and
Visualization -- Analysis for the National Ignition
Campaign",
journal = "Computing and Visualization in Science",
year = "2015",
url = "http://www.sci.utah.edu/publications/Bre2015a/NIC_BeiWang_2014.pdf",
}
@Article{SCI:Bre2015b,
author = "T. Bregman and R. Reznikov and M. Diwan and R.
Raymond and C. R.Butson and J. N.Nobrega and C.
Hamani",
title = "Antidepressant-like Effects of Medial Forebrain
Bundle Deep Brain Stimulation in Rats are not
Associated With Accumbens Dopamine Release",
journal = "Brain Stimulation",
volume = "8",
number = "4",
pages = "708--713",
year = "2015",
url = "http://www.sci.utah.edu/publications/Bre2015b/1-s2.0-S1935861X15008876-main.pdf",
}
@TechReport{SCI:Bre99,
author = "J.D. Brederson",
title = "The I3Stick: An Inexpensive, Immersive,
Interaction Device",
number = "UUCS-99-014",
year = "1999",
institution = "University of Utah",
type = "School of Computing Technical Report",
month = "November",
keywords = "vector field methods, vr virtual reality
haptics",
url = "http://www.sci.utah.edu/publications/jdb99/UUCS-99-016.ps",
url = "http://www.sci.utah.edu/publications/jdb99/UUCS-99-016.ps.gz",
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}
@Article{SCI:Bro1992a,
author = "K.W. Brodlie and M. Berzins and P.M. Dew and A.
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title = "Visualization and its Use in Scientific
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@Article{SCI:Bro1999a,
author = "D.H. Brooks and G.F. Ahmad and R.S. MacLeod and
G.M. Maratos",
title = "Inverse Electrocardiography by Simultaneous
Imposition of Multiple Constraints",
journal = j-BME,
volume = "46",
number = "1",
pages = "3--18",
year = "1999",
keywords = "forward problems inverse problems forward
simulation inverse solutions, cardiac heart,
ncrr",
url = "http://www.sci.utah.edu/publications/brooks99/brooks-tmbe-1999.pdf",
}
@InProceedings{SCI:Bro2004b,
author = "D.H. Brooks and A. Ghodrati and Y. Zhang and G.
Tadmor and R.S. MacLeod",
title = "Inverse Electrocardiography in the Framework of
Dynamic Imaging Problems",
booktitle = c-EMBS2004,
pages = "3565--3568",
year = "2004",
month = "September",
location = "San Francisco, CA",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions, cardiac heart",
url = "http://www.sci.utah.edu/publications/brooks04/EMBS04_DanaBrooks.pdf",
}
@Article{SCI:Bro2006a,
author = "S. Browd and L.J. Healy and G. Dobie and J.T.
Johnson III and G.M. Jones and L.F. Rodriguez and
D.L. Brockmeyer",
title = "Morphometric and Qualitative Analysis of
Congenital Occipitocervical Instability in
Children: Implications for Down Syndrome
Patients",
journal = "Journal of Neurosurgery: Pediatrics",
volume = "105",
number = "1 ",
pages = "50--54",
year = "2006",
publisher = "Journal of Neurosurgery Publishing Group",
month = "July",
doi = "10.3171/ped.2006.105.1.50",
}
@InProceedings{SCI:Bro2007a,
author = "D.H. Brooks and A. Keely and A. Ghodrati and G.
Tadmor and R.S. MacLeod",
title = "Some Spatio-Temporal Approaches to Inverse
Electrocardiography",
booktitle = "Proc. Asilomar Conf. on Signals, Systems, and
Computers",
year = "2007",
month = "November",
location = "Pacific Grove, CA",
doi = "10.1109/ACSSC.2007.4487316",
keywords = "inverse eeg, ncrr, cibc",
url = "http://www.sci.utah.edu/publications/brooks07/Brooks_SSC2007.pdf",
}
@Article{SCI:Bro2009a,
author = "J. Brouillat and C. Bouville and B. Loos and C.D.
Hansen and K. Bouatouch",
title = "A Bayesian Monte Carlo Approach to Global
Illumination",
journal = "Computer Graphics Forum Journal, Early View",
volume = "28",
number = "8",
pages = "2315--2329",
year = "2009",
month = "October",
url = "http://www.sci.utah.edu/publications/brouillat09/Brouillat_CGF2009.pdf",
}
@InProceedings{SCI:Bro2010a,
author = "C. Brownlee and V. Pegoraro and S. Shankar and P.
McCormick and C.D. Hansen",
title = "Physically-Based Interactive Schlieren Flow
Visualization",
booktitle = "Proceedings of {IEEE} Pacific Visualization
2010",
year = "2010",
note = "Won Best Paper Award!",
url = "http://www.sci.utah.edu/publications/brownlee10/Brownlee_PacVis2010.pdf",
}
@InCollection{SCI:Bro2010c,
author = "J.R. Bronson and J.A. Levine and R.T. Whitaker",
title = "Particle Systems for Adaptive, Isotropic Meshing
of {CAD} Models",
booktitle = "Proceedings of the 19th International Meshing
Roundtable",
pages = "279-296",
year = "2010",
publisher = "Springer",
note = "Awarded Best Paper",
doi = "10.1007/978-3-642-15414-0_17",
url = "http://www.sci.utah.edu/publications/Bro2010c/Bronson_IMR2010.pdf",
}
@Article{SCI:Bro2011a,
author = "C. Brownlee and V. Pegoraro and S. Shankar and
P.S. McCormick and C.D. Hansen",
title = "Physically-Based Interactive Flow Visualization
Based on Schlieren and Interferometry Experimental
Techniques",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "17",
number = "11",
pages = "1574--1586",
year = "2011",
keywords = "uintah, c-safe",
url = "http://www.sci.utah.edu/publications/brownlee11/Brownlee_TVCG2011.pdf",
}
@Article{SCI:Bro2011b,
author = "C. Brownlee and V. Pegoraro and S. Shankar and
P.S. McCormick and C.D. Hansen",
title = "Physically-Based Interactive Flow Visualization
Based on Schlieren and Interferometry Experimental
Techniques",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "17",
number = "11",
pages = "1574--1586",
year = "2011",
series = "IEEE Transactions on Visualization and Computer
Graphics",
publisher = "IEEE",
month = "November",
doi = "10.1109/tvcg.2010.255",
keywords = "Scalar Field Data, GPUs and Multi-core
Architectures, Flow Visualization",
url = "http://www.sci.utah.edu/publications/Bro2011b/brownlee_tvcg10.pdf",
}
@InProceedings{SCI:Bro2012a,
author = "C. Brownlee and T. Fogal and C.D. Hansen",
title = "{GLuRay:} Ray Tracing in Scientific Visualization
Applications using {OpenGL} Interception",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization (2012)",
pages = "41--50",
year = "2012",
editor = "H. Childs and T. Kuhlen and F. Marton",
doi = "10.2312/EGPGV/EGPGV12/041-050",
keywords = "kaust, scidac",
url = "http://www.sci.utah.edu/publications/brownlee12/Brownlee_gluray-EGPGV2012.pdf",
}
@InProceedings{SCI:Bro2012b,
author = "C. Brownlee and J. Patchett and L.-T. Lo and D.
DeMarle and C. Mitchell and J. Ahrens and C.D.
Hansen",
title = "A Study of Ray Tracing Large-scale Scientific Data
in Parallel Visualization Applications",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization (2012)",
pages = "51--60",
year = "2012",
editor = "H. Childs and T. Kuhlen and F. Marton",
keywords = "kaust, scidac",
url = "http://www.sci.utah.edu/publications/brownlee12/Brownlee_scaling-EGPGV2012.pdf",
}
@InProceedings{SCI:Bro2012c,
author = "J.R. Bronson and J.A. Levine and R.T. Whitaker",
title = "Lattice Cleaving: Conforming Tetrahedral Meshes of
Multimaterial Domains with Bounded Quality",
booktitle = "Proceedings of the 21st International Meshing
Roundtable",
pages = "191--209",
year = "2012",
url = "http://www.sci.utah.edu/publications/bronson12/Bronson_cleaving2012.pdf",
}
@Article{SCI:Bro2012d,
author = "J.R. Bronson and J.A. Levine and R.T. Whitaker",
title = "Particle Systems for Adaptive, Isotropic Meshing
of {CAD} Models",
journal = "Engineering with Computers",
volume = "28",
number = "4",
pages = "331--344",
year = "2012",
pmid = "23162181",
pmcid = "PMC3499137",
url = "http://www.sci.utah.edu/publications/bronson12/Bronson_EngComp2012.pdf",
}
@InProceedings{SCI:Bro2013a,
author = "C. Brownlee and T. Ize and C.D. Hansen",
title = "Image-parallel Ray Tracing using OpenGL
Interception",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization ({EGPGV}
2013)",
pages = "65--72",
year = "2013",
url = "http://www.sci.utah.edu/publications/brownlee13/Brownlee_ESPGV2013.pdf",
}
@Article{SCI:Bro2014a,
author = "J. Bronson and J.A. Levine and R.T. Whitaker",
title = "Lattice cleaving: a multimaterial tetrahedral
meshing algorithm with guarantees",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
pages = "223--237",
year = "2014",
doi = "10.1109/TVCG.2013.115",
pmid = "24356365",
url = "http://www.sci.utah.edu/publications/Bro2014a/Bronson_TVCG2014.pdf",
}
@Article{SCI:Bro2017a,
author = "A. Brown and B. Wang",
title = "Sheaf-Theoretic Stratification Learning",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Bro2017a/1712.07734.pdf",
}
@InProceedings{SCI:Bue2008a,
author = "K. Buerger and P. Kondratieva and J. Kr{\"u}ger and
R. Westermann",
title = "Importance-Driven Particle Techniques for Flow
Visualization",
booktitle = "Proceedings of {IEEE} {VGTC} PacificVis 2008",
pages = "71--78",
year = "2008",
keywords = "particle systems, flow visualization, vacet",
url = "http://www.sci.utah.edu/publications/Bue2008a/pvis08.pdf",
}
@Article{SCI:Bul2004a,
author = "E. Bullitt and M.G. Ewend and S. Aylward and W.
Lin and G. Gerig and S. Joshi and I. Jung and K.
Muller and J. Smith",
title = "Abnormal Vessel Tortuosity as a Marker of
Treatment Response of Malignant Gliomas:
Preliminary Report",
journal = "Technol Cancer Res Treat",
volume = "3",
number = "6",
pages = "577--584",
year = "2004",
month = "December",
url = "http://www.sci.utah.edu/publications/bullitt04/B_TCRT_3_6_577.pdf",
}
@Article{SCI:Bul2005a,
author = "E. Bullitt and D. Zeng and G. Gerig and S. Aylward
and S. Joshi and J.K. Smith and W. Lin and M.
Ewend",
title = "Vessel Tortuosity and Brain Tumor Malignancy: A
Blinded Study",
journal = "Acad Radiol",
volume = "12",
number = "10",
pages = "1232--1240",
year = "2005",
month = "October",
}
@InProceedings{SCI:Bur2011a,
author = "B.M. Burton and J.D. Tate and B. Erem and D.J.
Swenson and D.F. Wang and D.H. Brooks and P.M. van
Dam and R.S. MacLeod",
title = "A Toolkit for Forward/Inverse Problems in
Electrocardiography within the {SCIRun} Problem
Solving Environment",
booktitle = "Proceedings of the 2011 {IEEE} Int. Conf.
Engineering and Biology Society ({EMBC})",
pages = "267--270",
year = "2011",
doi = "10.1109/IEMBS.2011.6090052",
pmid = "22254301",
pmcid = "PMC3337752",
url = "http://www.sci.utah.edu/publications/burton11/Burton_2011BMB_EMBC.pdf",
}
@InProceedings{SCI:Bur2013a,
author = "B. Burton and B. Erem and K. Potter and P. Rosen
and C.R. Johnson and D. Brooks and R.S. Macleod",
title = "Uncertainty Visualization in Forward and Inverse
Cardiac Models",
booktitle = "Computing in Cardiology {CinC}",
pages = "57--60",
year = "2013",
issn = "2325-8861",
url = "http://www.sci.utah.edu/publications/burton13/Burton_CinC2013.pdf",
}
@Article{SCI:Bur2018a,
author = "B.M. Burton and K.K. Aras and W.W. Good and J.D.
Tate and B. Zenger and R.S. MacLeod",
title = "A Framework for Image-Based Modeling of Acute
Myocardial Ischemia Using Intramurally Recorded
Extracellular Potentials",
journal = "Annals of Biomedical Engineering",
year = "2018",
publisher = "Springer Nature",
month = "May",
doi = "10.1007/s10439-018-2048-0",
url = "http://www.sci.utah.edu/publications/Bur2018a/s10439-018-2048-0.pdf",
}
@Article{SCI:Bur2018b,
author = "B.M. Burton and K.K. Aras and W.W. Good and J.D.
Tate and B. Zenger and R.S. MacLeod",
title = "Image-Based Modeling of Acute Myocardial Ischemia
Using Experimentally Derived Ischemic Zone Source
Representations",
journal = "Journal of Electrocardiology",
volume = "51",
number = "4",
pages = "725--733",
year = "2018",
publisher = "Elsevier BV",
month = "July",
doi = "10.1016/j.jelectrocard.2018.05.005",
url = "http://www.sci.utah.edu/publications/Bur2018b/1-s2.0-S0022073618301559-main.pdf",
}
@InProceedings{SCI:But2001a,
author = "C.R. Butson",
title = "From Action Potentials to Surface Potentials",
booktitle = "Multilevel Neuronal Modeling Workshop",
year = "2001",
month = "May",
location = "Edinburgh, Scotland",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
forward simulation, scalar field methods, bipolar
stimulation, neuron potential simulation, ncrr",
}
@InProceedings{SCI:But2001b,
author = "C.R. Butson and G.A. Clark",
title = "Random Noise Confers a Paradoxical Improvement in
the Ability of a Simulated Hermissenda
Photoreceptor Network to Encode Light Intensity",
booktitle = "Society for Neuroscience Conference",
year = "2001",
month = "November",
keywords = "bipolar stimulation, neuron potential
simulation",
}
@Article{SCI:But2005a,
author = "C.R. Butson and C.C. McIntyre",
title = "Tissue and electrode capacitance reduce neural
activation volumes during deep brain stimulation",
journal = "Clinical Neurophysiology",
volume = "116",
number = "10",
pages = "2490--500",
year = "2005",
month = "October",
doi = "10.1016/j.clinph.2005.06.023",
pmid = "16125463",
keywords = "Algorithms, Axons, Axons: physiology, Computer
Simulation, Deep Brain Stimulation, Electric
Capacitance, Electrodes, Extracellular Space,
Extracellular Space: physiology, Finite Element
Analysis, Implanted, Models, Myelinated,
Myelinated: physiology, Nerve Fibers, Neurological,
Neurons, Neurons: physiology, Poisson Distribution,
Statistical",
url = "http://www.sci.utah.edu/publications/But2005a/Butson_ClinNeurophys2005.pdf",
}
@Article{SCI:But2006a,
author = "C.R. Butson and C.B. Maks and C.C. McIntyre",
title = "Sources and effects of electrode impedance during
deep brain stimulation",
journal = "Clinical Neurophysiology",
volume = "117",
number = "2",
pages = "447--454",
year = "2006",
doi = "10.1016/j.clinph.2005.10.007",
pmid = "16376143",
keywords = "Brain, Brain: physiology, Computer Simulation,
Deep Brain Stimulation, Electric Conductivity,
Electric Impedance, Electrodes, Humans, Imaging,
Models, Neurological, Three-Dimensional",
url = "http://www.sci.utah.edu/publications/But2006a/Butson_ClinNeurophys2006.pdf",
}
@Article{SCI:But2006b,
author = "C.R. Butson and C.C. McIntyre",
title = "Role of electrode design on the volume of tissue
activated during deep brain stimulation",
journal = "Journal of Neural Engineering",
volume = "3",
number = "1",
pages = "1--8",
year = "2006",
month = "March",
issn = "1741-2560",
doi = "10.1088/1741-2560/3/1/001",
pmid = "16510937",
keywords = "Animals, Brain, Brain: physiology, Computer
Simulation, Computer-Aided Design, Deep Brain
Stimulation, Deep Brain Stimulation:
instrumentation, Deep Brain Stimulation: methods,
Electrodes, Equipment Design, Equipment Design:
methods, Equipment Failure Analysis, Equipment
Failure Analysis: methods, Humans, Implanted,
Microelectrodes, Models, Neurological, Neurons,
Neurons: physiology, Organ Size, Organ Size:
physiology",
url = "http://www.sci.utah.edu/publications/But2006b/Butson_JNeuralEng2006.pdf",
}
@InProceedings{SCI:But2007a,
author = "L. Butler and A.J. Stephens",
title = "Bullet Ray Vision",
booktitle = "Proceedings of the {IEEE} Symposium on Interactive
Ray Tracing",
pages = "167--170",
year = "2007",
keywords = "interactive rt distributed interactive ray tracing
dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/butler07/BulletRayVision.pdf",
}
@Article{SCI:But2007b,
author = "C.R. Butson and C.C. McIntyre",
title = "Differences among implanted pulse generator
waveforms cause variations in the neural response
to deep brain stimulation",
journal = "Clinical Neurophysiology",
volume = "118",
pages = "1889--1894",
year = "2007",
month = "August",
issn = "1388-2457",
doi = "10.1016/j.clinph.2007.05.061",
url = "http://www.sci.utah.edu/publications/But2007b/Butson_ClinNeurophys2007.pdf",
}
@Article{SCI:But2007c,
author = "C.R. Butson and S.E. Cooper and J.M. Henderson and
C.C. McIntyre",
title = "Patient-specific analysis of the volume of tissue
activated during deep brain stimulation",
journal = "NeuroImage",
volume = "34",
number = "2",
pages = "661--670",
year = "2007",
month = "January",
issn = "1053-8119",
doi = "10.1016/j.neuroimage.2006.09.034",
pmid = "17113789",
keywords = "Deep Brain Stimulation, Finite Element Analysis,
Humans, Imaging, Three-Dimensional, Magnetic
Resonance Imaging, Models, Neurological, Parkinson
Disease, Parkinson Disease: therapy, Pyramidal
Tracts, Pyramidal Tracts: physiology, Subthalamic
Nucleus, Subthalamic Nucleus: physiology",
url = "http://www.sci.utah.edu/publications/But2007c/Butson_NeuroImage2007.pdf",
}
@Article{SCI:But2008a,
author = "C.R. Butson and G.A. Clark",
title = "Mechanisms of noise-induced improvement in
light-intensity encoding in Hermissenda
photoreceptor network",
journal = "Journal of Neurophysiology",
volume = "99",
number = "1",
pages = "155--165",
year = "2008",
month = "January",
issn = "0022-3077",
doi = "10.1152/jn.01250.2006",
pmid = "18003872",
keywords = "Action Potentials, Action Potentials: physiology,
Animals, Artifacts, Computer Simulation, Eye, Eye:
cytology, Hermissenda, Hermissenda: physiology,
Invertebrate, Invertebrate: physiology, Nerve Net,
Nerve Net: physiology, Neurons, Neurons:
physiology, Ocular, Ocular Physiological Phenomena,
Ocular: physiology, Photic Stimulation,
Photoreceptor Cells, Reaction Time, Reaction Time:
physiology, Sensory Thresholds, Sensory Thresholds:
physiology, Synaptic Transmission, Synaptic
Transmission: physiology, Vision",
url = "http://www.sci.utah.edu/publications/But2008a/Butson_JNeurophys2007b.pdf",
}
@Article{SCI:But2008b,
author = "C.R. Butson and G.A. Clark",
title = "Random noise paradoxically improves
light-intensity encoding in Hermissenda
photoreceptor network",
journal = "Journal of Neurophysiology",
volume = "99",
number = "1",
pages = "146--154",
year = "2008",
month = "January",
issn = "0022-3077",
doi = "10.1152/jn.01247.2006",
pmid = "18003873",
keywords = "Action Potentials, Action Potentials: physiology,
Animals, Artifacts, Computer Simulation, Eye, Eye:
cytology, Hermissenda, Hermissenda: physiology,
Invertebrate, Invertebrate: physiology, Nerve Net,
Nerve Net: physiology, Neurons, Neurons:
physiology, Ocular, Ocular Physiological Phenomena,
Ocular: physiology, Photic Stimulation,
Photoreceptor Cells, Reaction Time, Reaction Time:
physiology, Sensory Thresholds, Sensory Thresholds:
physiology, Synaptic Transmission, Synaptic
Transmission: physiology, Vision",
url = "http://www.sci.utah.edu/publications/But2008b/Butson_JNeurophys2007a.pdf",
}
@Article{SCI:But2008c,
author = "C.R. Butson and C.C. McIntyre",
title = "Current Steering to Control the Volume of Tissue
Activated During Deep Brain Stimulation",
journal = "Brain Stimulation",
volume = "1",
number = "1",
pages = "7--15",
year = "2008",
month = "January",
doi = "10.1016/j.brs.2007.08.004",
pmid = "19142235",
url = "http://www.sci.utah.edu/publications/But2008c/Butson_BrainStim2008.pdf",
}
@Article{SCI:But2011a,
author = "C.R. Butson and S.E. Cooper and J.M. Henderson and
B. Wolgamuth and C.C. McIntyre",
title = "Probabilistic Analysis of Activation Volumes
Generated During Deep Brain Stimulation",
journal = "NeuroImage",
volume = "54",
pages = "2096--2104",
year = "2011",
issn = "1095-9572",
doi = "10.1016/j.neuroimage.2010.10.059",
pmid = "20974269",
url = "http://www.sci.utah.edu/publications/But2011a/Butson_NeuroImage2011.pdf",
}
@Article{SCI:But2011b,
author = "C.R. Butson and I.O. Miller and R.A. Normann and
G.A. Clark",
title = "Selective neural activation in a histologically
derived model of peripheral nerve",
journal = "Journal of Neural Engineering",
volume = "8",
number = "3",
pages = "036009",
year = "2011",
month = "June",
issn = "1741-2552",
doi = "10.1088/1741-2560/8/3/036009",
pmid = "21478574",
url = "http://www.sci.utah.edu/publications/But2011b/Butson_JNE2011.pdf",
}
@Article{SCI:But2012a,
author = "C. Butson and G. Tamm and S. Jain and T. Fogal and
J. Kr{\"u}ger",
title = "Evaluation of Interactive Visualization on Mobile
Computing Platforms for Selection of Deep Brain
Stimulation Parameters",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
pages = "(accepted)",
year = "2012",
issn = "1077-2626",
doi = "10.1109/TVCG.2012.92",
keywords = "scidac, dbs",
url = "http://www.sci.utah.edu/publications/But2012a/Butson_TVCG2012.pdf",
}
@InCollection{SCI:But2012b,
author = "C.R. Butson",
title = "Computational Models of Neuromodulation",
booktitle = "Emerging Horizons in Neuromodulation",
pages = "5--22",
year = "2012",
editor = "Elena Moro and Clement Hamani",
publisher = "Academic Press",
isbn = "978012404706",
url = "http://www.sci.utah.edu/publications/But2012b/Butson_IntRevNeurobio2012.pdf",
}
@Article{SCI:But2013a,
author = "C. Butson and G. Tamm and S. Jain and T. Fogal and
J. Kr{\"u}ger",
title = "Evaluation of Interactive Visualization on Mobile
Computing Platforms for Selection of Deep Brain
Stimulation Parameters",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "19",
number = "1",
pages = "108--117",
year = "2013",
month = "January",
doi = "10.1109/TVCG.2012.92",
pmid = "22450824",
keywords = "Biomedical and Medical Visualization, Mobile and
Ubiquitous Visualization, Computational Model,
Clinical Decision Making, Parkinson’s Disease,
SciDAC, ImageVis3D",
url = "http://www.sci.utah.edu/publications/But2013a/Butson-DBS.pdf",
}
@Article{SCI:But2014a,
author = "M.S. Okun and S.S. Wu and S. Fayad and H. Ward and
D. Bowers and C. Rosado and L. Bowen and C.
Jacobson and C.R. Butson and K.D. Foote",
title = "Acute and Chronic Mood and Apathy Outcomes from a
Randomized Study of Unilateral {STN} and {GPi}
{DBS}",
journal = "PLoS ONE",
volume = "9",
number = "12",
pages = "e114140",
year = "2014",
month = "December",
url = "http://www.sci.utah.edu/publications/But2014a/Okun_PONE2014.pdf",
}
@Article{SCI:But2015a,
author = "C. R. Butson and C. C. McIntyre",
title = "The use of stimulation field models for deep brain
stimulation programming",
journal = "Brain Stimulation",
volume = "8",
number = "5",
pages = "976--978",
year = "2015",
publisher = "Elsevier BV",
month = "September",
doi = "10.1016/j.brs.2015.06.005",
url = "http://www.sci.utah.edu/publications/But2015a/PIIS1935861X15010062.pdf",
}
@Article{SCI:Buz2011a,
author = "G.T. Buzzard and D. Xiu",
title = "Variance-based Global Sensitivity Analysis via
Sparse-grid Interpolation and Cubature",
journal = "Communications in Computational Physics",
volume = "9",
number = "3",
pages = "542--567",
year = "2011",
doi = "10.4208/cicp.230909.160310s",
keywords = "Stochastic collocation, sparse grids, sensitivity
analysis, Smolyak, Sobol",
url = "http://www.sci.utah.edu/publications/buzzard11/Buzzard_CiCP2011.pdf",
}
@TechReport{SCI:Cal2004a,
author = "S.P. Callahan and M. Ikits and J.L.D. Comba and
C.T. Silva",
title = "Hardware-Assisted Visibility Sorting for
Unstructured Volume Rendering",
number = "UUSCI-2004-003",
year = "2004",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
month = "June",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2004-003.pdf",
}
@Article{SCI:Cal2005a,
author = "S.P. Callahan and M. Ikits and J.L.D. Comba and
C.T. Silva",
title = "Hardware-Assisted Visibility Ordering for
Unstructured Volume Rendering",
journal = j-TVCG,
volume = "11",
number = "3",
pages = "285--295",
year = "2005",
publisher = "{IEEE} Educational Activities Department",
issn = "1077-2626",
keywords = "scalar field methods, volume rendering, visibility
ordering, GPU, tetrahedral meshes, unstructured
volume rendering",
url = "http://www.sci.utah.edu/publications/stevec05/HAVS.pdf",
}
@InProceedings{SCI:Cal2005b,
author = "F. Calderero and A. Ghodrati and D.H. Brooks and
G. Tadmor and R.S. MacLeod",
title = "A Method to Reconstruct Activation Wavefronts
Without Isotropy Assumptions Using a Level Sets
Approach",
booktitle = "Functional Imaging and Modeling of the Heart:
Third International Workshop (FIMH 2005)",
pages = "195",
year = "2005",
location = "Barcelona, June 2-4",
keywords = "ncrr",
}
@InProceedings{SCI:Cal2005c,
author = "S.P. Callahan and J.L.D. Comba and P. Shirley and
C.T. Silva",
title = "Interactive Rendering of Large Unstructured Grids
Using Dynamic Level-of-Detail",
booktitle = c-VIS2005,
pages = "26",
year = "2005",
keywords = "interactive rt distributed interactive ray tracing
dirt, interactive volume rendering, multiresolution
meshes, level-of-detail, tetrahedral meshes",
url = "http://www.sci.utah.edu/publications/stevec05/dynamic_lod.pdf",
}
@MastersThesis{SCI:Cal2005d,
author = "S.P. Callahan",
title = "The k-Buffer and its Applications to Volume
Rendering",
year = "2005",
school = "School of Computing, University of Utah",
note = "Masters Thesis",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/stevec05/thesis.pdf",
}
@InProceedings{SCI:Cal2006a,
author = "S.P. Callahan and J. Freire and E. Santos and C.E.
Scheidegger and C.T. Silva and H.T. Vo",
title = "Managing the Evolution of Dataflows with
VisTrails",
booktitle = "Proceedings of The 2006 {IEEE} Workshop on
Workflow and Data Flow for Scientific Applications
(SciFlow 2006)",
year = "2006",
keywords = "vistrails,",
url = "http://www.sci.utah.edu/publications/stevec06/sciflow2006.pdf",
}
@InProceedings{SCI:Cal2006b,
author = "S.P. Callahan and J. Freire and E. Santos and C.
Scheidegger and C.T. Silva and H.T. Vo",
title = "VisTrails: Visualization Meets Data Management",
booktitle = "Proceedings of the 2006 ACM SIGMOD/PODS
Conference",
pages = "745--747",
year = "2006",
keywords = "vistrails, provenance, workflow management",
url = "http://www.sci.utah.edu/publications/stevec06/vt-sigmod.pdf",
}
@TechReport{SCI:Cal2006c,
author = "S.P. Callahan and J. Freire and E. Santos and C.E.
Scheidegger and C.T. Silva and H.T. Vo",
title = "Using Provenance to Streamline Data Exploration
through Visualization",
number = "UUSCI-2006-016",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "VisTrails",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-016.pdf",
}
@TechReport{SCI:Cal2006d,
author = "S.P. Callahan and L. Bavoil and V. Pascucci and
C.T. Silva",
title = "Progressive Volume Rendering of Large Unstructured
Grids",
number = "UUSCI-2006-019",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "volume rendering, rtrt real-time ray tracing,
scientific visualization",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-019.pdf",
}
@Article{SCI:Cal2006e,
author = "S.P. Callahan and L. Bavoil and V. Pascucci and
C.T. Silva",
title = "Progressive Volume Rendering of Large Unstructured
Grids",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "12",
number = "5",
pages = "1307--1314",
year = "2006",
note = "Updated version of UUSCI-2006-019.",
doi = "10.1109/TVCG.2006.171",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/stevec06/pro-havs.pdf",
}
@TechReport{SCI:Cal2007a,
author = "M. Callahan and M.J. Cole and J.F. Shepherd and
J.G. Stinstra and C.R. Johnson",
title = "{BioMesh3D}: A Meshing Pipeline for Biomedical
Models",
number = "UUSCI-2007-009",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ncrr, biomesh3d",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-009.pdf",
}
@Article{SCI:Cal2007b,
author = "M. Callahan and M.J. Cole and J.F. Shepherd and
J.G. Stinstra and C.R. Johnson",
title = "A Meshing Pipeline for Biomedical Computing",
journal = "Engineering with Computers",
pages = "(in press)",
year = "2007",
series = "Special Issue on Computational Bioengineering",
url = "http://www.sci.utah.edu/publications/callahan07/Meshing-Pipeline07.pdf",
}
@Article{SCI:Cal2007c,
author = "S.P. Callahan and L. Bavoil and V. Pascucci and
C.T. Silva",
title = "Progressive Volume Rendering of Large Unstructured
Grids",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "13",
number = "1",
pages = "1307-1314",
year = "2007",
}
@Article{SCI:Cal2008a,
author = "S.P. Callahan and J.H. Callahan and C.E.
Scheidegger and C.T. Silva",
title = "Direct Volume Rendering: A 3D Plotting Technique
for Scientific Data",
journal = "Computing in Science and Engineering",
volume = "10",
number = "1",
pages = "88--92",
year = "2008",
url = "http://www.sci.utah.edu/publications/callahan08/cise08.pdf",
}
@TechReport{SCI:Cal2008b,
author = "S.P. Callahan",
title = "Adaptive Visualization of Dynamic Unstructured
Meshes",
number = "UUSCI-2008-003",
year = "2008",
institution = "University of Utah School of Computing",
type = "SCI Technical Report",
note = "Ph.D. Thesis",
keywords = "meshing, ph.d. thesis",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-003.pdf",
}
@TechReport{SCI:Cal2008c,
author = "S.P. Callahan and C.T. Silva",
title = "Image-Space Acceleration for Direct Volume
Rendering of Unstructured Grids using Joint
Bilateral Upsampling",
number = "UUSCI-2008-002",
year = "2008",
institution = "University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-002.pdf",
}
@InProceedings{SCI:Cal2008d,
author = "S.P. Callahan and J. Freire and C.E. Scheidegger
and C.T. Silva and and H.T. Vo",
title = "Towards a Provenance-Enabling ParaView",
booktitle = "Proceedings of the Second International Provenance
and Annotation Workshop ({IPAW} 2008)",
pages = "120--127",
year = "2008",
keywords = "vistrails, provenance, workflow management",
url = "http://www.sci.utah.edu/publications/callahan08/ipaw08.pdf",
}
@Article{SCI:Cal2009a,
author = "M. Callahan and M.J. Cole and J.F. Shepherd and
J.G. Stinstra and C.R. Johnson",
title = "A Meshing Pipeline for Biomedical Models",
journal = "Engineering with Computers",
volume = "25",
number = "1",
pages = "115-130",
year = "2009",
publisher = "SpringerLink",
doi = "10.1007/s00366-008-0106-1",
url = "http://www.sci.utah.edu/publications/callahan09/scirun_meshing.pdf",
}
@Article{SCI:Can2011a,
author = "C.D. Cantwell and S.J. Sherwin and R.M. Kirby and
P.H.J. Kelly",
title = "From h to p Efficiently: Strategy Selection for
Operator Evaluation on Hexahedral and Tetrahedral
Elements",
journal = "Computers and Fluids",
volume = "43",
number = "1",
pages = "23--28",
year = "2011",
doi = "10.1016/j.compfluid.2010.08.012",
url = "http://www.sci.utah.edu/publications/cantwell11/Cantwell_CF2011.pdf",
}
@Article{SCI:Can2011b,
author = "C.D. Cantwell and S.J. Sherwin and R.M. Kirby and
P.H.J. Kelly",
title = "From h to p Efficiently: Selecting the Optimal
Spectral/hp Discretisation in Three Dimensions",
journal = "Mathematical Modelling of Natural Phenomena",
volume = "6",
number = "3",
pages = "84--96",
year = "2011",
url = "http://www.sci.utah.edu/publications/cantwell11/Cantwell_MMNP2011.pdf",
}
@TechReport{SCI:Car2006a,
author = "C.D. Carbonera and J.F. Shepherd",
title = "On the Existence of a Perfect Matching for
4-regular Graphs derived from Quadrilateral
Meshes",
number = "UUSCI-2006-021",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-021.pdf",
}
@InProceedings{SCI:Car2006b,
author = "C.D. Carbonera and J.F. Shepherd",
title = "A Constructive Approach to Constrained Hexahedral
Mesh Generation",
booktitle = "Proceedings of the 15th International Meshing
Roundtable",
year = "2006",
month = "September",
location = "Birmingham, AL",
keywords = ", meshing, open problem 27",
url = "http://www.sci.utah.edu/publications/carbonera06/carbonera.pdf",
}
@Article{SCI:Car2015a,
author = "H. Carr and Z. Geng and J. Tierny and A.
Chattophadhyay and and A. Knoll",
title = "Fiber Surfaces: Generalizing Isosurfaces to
Bivariate Data",
journal = "Computer Graphics Forum",
volume = "34",
number = "3",
pages = "241-250",
year = "2015",
url = "http://www.sci.utah.edu/publications/Car2015a/carr_eurovis15.pdf",
}
@Article{SCI:Cas2006a,
author = "C.J. Cascio and M. Styner and R.G. Smith and M.D.
Poe and G. Gerig and H.C. Hazlett and M. Jomier and
R. Bammer and J. Piven",
title = "Tractography-Based Segmentation of the Corpus
Callosum Reveals a Reduced Relationship to Cortical
White Matter Volume in Young Children with
Developmental Delay",
journal = "Am J Psychiatry",
volume = "163",
pages = "2157--2163",
year = "2006",
month = "December",
}
@Article{SCI:Cas2007a,
author = "C.J. Cascio and G. Gerig and J. Piven",
title = "Diffusion Tensor Imaging: Application to the Study
of the Developing Brain",
journal = "Journal of the American Academy of Child and
Adolescent Psychiatry JAACAP",
year = "2006",
month = "August",
}
@Article{SCI:Cas2007b,
author = "C.J. Cascio and G. Gerig and J. Piven",
title = "Diffusion Tensor Imaging: Application to the Study
of the Developing Brain",
journal = "J Am Acad Child Adolesc Psychiatry",
volume = "46",
number = "2",
pages = "213--223",
year = "2007",
month = "February",
keywords = "ucnia",
}
@Article{SCI:Cas2012a,
author = "C. Cascio and M.J. Gribbin and S. Gouttard and
R.G. Smith and M. Jomier and S.H. Field and M.
Graves and H.C. Hazlett and K. Muller and G. Gerig
and J. Piven",
title = "Fractional Anisotropy Distributions in 2-6
Year-Old Children with Autism",
journal = "Journal of Intellectual Disability Research
(JIDR)",
pages = "(in print)",
year = "2012",
url = "http://www.sci.utah.edu/publications/cascio12/Cascio_JIDR2012.pdf",
}
@InProceedings{SCI:Cat2003a,
author = "J. Cates and R.T. Whitaker",
title = "Interactive Medical Image Segmentation Using the
Insight Toolkit",
booktitle = c-RSNA2003,
year = "2003",
month = "November",
keywords = "ip image processing signal processing,
segmentation, insight itk",
}
@TechReport{SCI:Cat2004a,
author = "J. Cates and A. Lefohn and R.T. Whitaker",
title = "GIST: an Interactive, GPU-Based Level Set
Segmentation Tool for 3D Medical Images",
number = "UUCS-04-007",
year = "2004",
institution = "University of Utah School of Computing",
keywords = "ip image processing signal processing,
segmentation",
url = "http://www.sci.utah.edu/publications/cates04/Cates_MedIA2004Tech.pdf",
}
@TechReport{SCI:Cat2004b,
author = "J. Cates and R.T. Whitaker and G.M. Jones",
title = "Case Study: An Evaluation of User-Assisted
Hierarchical Watershed Segmentation",
number = "UUCS-04-006",
year = "2004",
institution = "University of Utah School of Computing",
keywords = "ip image processing signal processing,
segmentation, watershed, ncrr",
url = "http://www.sci.utah.edu/publications/cates04/UUCS-04-006.pdf",
}
@Article{SCI:Cat2004c,
author = "J. Cates and A. Lefohn and R.T. Whitaker",
title = "GIST: An Interactive, GPU-Based Level Set
Segmentation Tool for 3D Medical Images",
journal = "Medical Image Analysis",
volume = "8",
number = "3",
pages = "217--231",
year = "2004",
month = "September",
keywords = "ip image processing signal processing,
segmentation, ncrr",
}
@InProceedings{SCI:Cat2006a,
author = "J. Cates and M.D. Meyer and P.T. Fletcher and R.T.
Witaker",
title = "Entropy-Based Particle Systems for Shape
Correspondence",
booktitle = "Workshop on Mathematical Foundations of
Computational Anatomy, MICCAI 2006",
pages = "90--99",
year = "2006",
month = "October",
keywords = "particle systems, , particle systems",
url = "http://www.sci.utah.edu/publications/cates06/Cates-miccai2006.pdf",
}
@InProceedings{SCI:Cat2006b,
author = "J. Cates and D. Weinsten and M. Davis",
title = "The Center for Integrative Biomedical Computing:
Advancing Biomedical Science with Open Source",
booktitle = "Proceedings of the {IEEE} International Symposium
on Biomedical Imaging ({ISBI}) 2006",
year = "2006",
keywords = "ncrr, open source software, biomedical",
url = "http://www.sci.utah.edu/publications/cates06/Cates-isbi2006.pdf",
}
@InProceedings{SCI:Cat2007a,
author = "J. Cates and P.T. Fletcher and M. Styner and M.
Shenton and R.T. Whitaker",
title = "Shape Modeling and Analysis with Entropy-Based
Particle Systems",
booktitle = "Proceedings of Information Processing in Medical
Imaging (IPMI) 2007",
pages = "333--345",
year = "2007",
series = "LNCS 4584",
url = "http://www.sci.utah.edu/publications/cates07/Cates-IPMI2007.pdf",
}
@InProceedings{SCI:Cat2008a,
author = "J. Cates and P.T. Fletcher and Z. Warnock and R.T.
Whitaker",
title = "A Shape Analysis Framework for Small Animal
Phenotyping with Application to Mice with a
Targeted Disruption of Hoxd11",
booktitle = "Proceedings of the 5th IEEE International
Symposium on Biomedical Imaging (ISBI '08)",
pages = "512--516",
year = "2008",
doi = "10.1109/ISBI.2008.4541045",
keywords = "phenotyping, genetic mutation analysis",
url = "http://www.sci.utah.edu/publications/cates98/Cates_ISBI08.pdf",
}
@InProceedings{SCI:Cat2008b,
author = "J. Cates and P.T. Fletcher and M. Styner and H.
Hazlett and R.T. Whitaker",
title = "Particle-Based Shape Analysis of Multi-Object
Complexes",
booktitle = "Proceedings of the 11th International Conference
on Medical Image Computing and Computer Assisted
Intervention (MICCAI '08)",
pages = "477--485",
year = "2008",
series = "Lecture Notes In Computer Science (LCNS)",
isbn = "978-3-540-85987-1",
url = "http://www.sci.utah.edu/publications/cates08/CatesMICCAI08.pdf",
}
@Article{SCI:Cat2017a,
author = "J. Cates and L. Nevell and S. I. Prajapati and L.
D. Nelon and J. Y. Chang and M. E. Randolph and B.
Wood and C. Keller and R. T. Whitaker",
title = "Shape analysis of the basioccipital bone in
Pax7-deficient mice",
journal = "Scientific Reports",
volume = "7",
number = "1",
year = "2017",
publisher = "Springer Nature",
month = "Dec",
doi = "10.1038/s41598-017-18199-9",
url = "http://www.sci.utah.edu/publications/Cat2017a/Cates_et_al-2017-Scientific_Reports.pdf",
}
@InProceedings{SCI:Cha2004a,
author = "E. Chaney and S. Pizer and S. Joshi and R.
Broadhurst and P.T. Fletcher and G. Gash and Q. Han
and J.Y. Jeong and C. Lu and D. Merck and J. Stough
and G. Tracton and M.D.J. Bechtel and J. Rosenman
and Y.Y. Chi and K. Muller",
title = "Automatic Male Pelvis Segmentation from CT Images
via Statistically Trained Multi-Object Deformable
M-rep Models",
booktitle = "Presented at American Society for Therapeutic
Radiology and Oncology (ASTRO)",
year = "2004",
url = "http://www.sci.utah.edu/publications/chaney04/ASTRO04_Chaney.pdf",
}
@Article{SCI:Cha2010a,
author = "A. Chaturvedi and C.R. Butson and S.F. Lempka and
S.E. Cooper and C.C. McIntyre",
title = "Patient-specific models of deep brain stimulation:
influence of field model complexity on neural
activation predictions",
journal = "Brain Stimulation",
volume = "3",
number = "2",
pages = "65--67",
year = "2010",
publisher = "Elsevier Inc.",
month = "April",
issn = "1935-861X",
doi = "10.1016/j.brs.2010.01.003",
pmid = "20607090",
keywords = "Action Potentials, Action Potentials: physiology,
Computer Simulation, Deep Brain Stimulation, Deep
Brain Stimulation: instrumentation, Deep Brain
Stimulation: methods, Humans, Male, Middle Aged,
Models, Neurological, Parkinson Disease, Parkinson
Disease: therapy, Subthalamic Nucleus, Subthalamic
Nucleus: physiology",
url = "http://www.sci.utah.edu/publications/Cha2010a/Chaturvedi_BrainStim2010.pdf",
}
@Article{SCI:Cha2012a,
author = "C.C. Chang and L. Krishnan and S.S. Nunes and K.H.
Church and L.T. Edgar and E.D. Boland and J.A.
Weiss and S.K. Williams and J.B. Hoying",
title = "Determinants of microvascular network topology in
implanted neovasculatures",
journal = "Arteriosclerosis, Thrombosis, and Vascular
Biology",
volume = "32",
number = "1",
pages = "5--14",
year = "2012",
doi = "10.1161/ATVBAHA.111.238725",
url = "http://www.sci.utah.edu/publications/chang12/Chang_atvb_2012.pdf",
}
@Unpublished{SCI:Cha2014a,
author = "B. Chapman and H. Calandra and S. Crivelli and J.
Dongarra and J. Hittinger and C.R. Johnson and S.A.
Lathrop and V. Sarkar and E. Stahlberg and J.S.
Vetter and D. Williams",
title = "ASCAC Workforce Subcommittee Letter",
year = "2014",
month = "July",
note = "Office of Scientific and Technical Information",
howpublished = "DOE ASCAC Committee Report",
doi = "10.2172/1222711",
url = "http://www.sci.utah.edu/publications/Cha2014a/ASCAC_Workforce_Letter_Report2014.pdf",
}
@Article{SCI:Che2002a,
author = "Z. Chen and S. Pizer and E. Chaney and S. Joshi",
title = "Medical Image Synthesis via Monte Carlo
Simulation",
journal = "Medical Image Computing and Computer-Assisted
Intervention (MICCAI)",
pages = "347--354",
year = "2002",
editor = "T Dohi and R Kikinis",
url = "http://www.sci.utah.edu/publications/chen02/MICCAI02-chenzj.pdf",
}
@Article{SCI:Che2004a,
author = "A.B. Cheryauka and J.N. Lee and A.A. Samsonov and
M. Defrise and G.T. Gullberg",
title = "{MRI} Diffusion Tensor Reconstruction with
{PROPELLER} Data Acquisition",
journal = j-JMRI,
volume = "22",
number = "2",
pages = "139--148",
year = "2004",
keywords = "tensor field methods, diffusion tensor imaging, ip
image processing signal processing, bisti,
PROPELLER, Imaging, propeller, imaging, ncrr",
url = "http://www.sci.utah.edu/publications/cheryauka04/propeller.pdf",
}
@Article{SCI:Che2011b,
author = "G. Chen and D. Palke and Z. Lin and H. Yeh and P.
Vincent and R.S. Laramee and E. Zhang",
title = "Asymmetric Tensor Field Visualization for
Surfaces",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "17",
number = "12",
pages = "1979-1988",
year = "2011",
publisher = "IEEE",
month = "Dec",
doi = "10.1109/tvcg.2011.170",
url = "http://www.sci.utah.edu/publications/Che2011b/Chen_HybridTensorVis_Vis2011.pdf",
url = "http://www.sci.utah.edu/publications/Che2011b/Chen_HybridTensorVis_Vis2011.mov",
}
@Article{SCI:Che2011c,
author = "Guoning Chen and Qingqing Deng and Andrzej
Szymczak and Robert S. Laramee and and Eugene
Zhang",
title = "Morse Set Classification and Hierarchical
Refinement using Conley Index",
journal = "IEEE Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "18",
number = "5",
pages = "767--782",
year = "2011",
month = "June",
doi = "10.1109/TVCG.2011.107",
pmid = "21690641 ",
url = "http://www.sci.utah.edu/publications/Che2011c/Chen_fastMorseDecomp2011.pdf",
}
@Article{SCI:Che2012a,
author = "F. Chen and H. Obermaier and H. Hagen and B.
Hamann and J. Tierny and V. Pascucci.",
title = "Topology Analysis of Time-Dependent Multi-Fluid
Data Using the Reeb Graph",
journal = "Computer Aided Geometric Design",
year = "2012",
publisher = "Elsevier",
note = "Published online Apr 24.",
doi = "10.1016/j.cagd.2012.03.019",
url = "http://www.sci.utah.edu/publications/chen12/Chen_CAGD2012.pdf",
}
@Article{SCI:Che2012b,
author = "G. Chen and V. Kwatra and L.-Y. Wei and C.D.
Hansen and E. Zhang",
title = "Design of {2D} Time-Varying Vector Fields",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics {TVCG}",
volume = "18",
number = "10",
pages = "1717--1730",
year = "2012",
doi = "10.1109/TVCG.2011.290",
url = "http://www.sci.utah.edu/publications/chen11/Chen_TVCG2011.pdf",
}
@Unpublished{SCI:Che2013a,
author = "J. Chen and A. Choudhary and S. Feldman and B.
Hendrickson and C.R. Johnson and R. Mount and V.
Sarkar and V. White and D. Williams",
title = "Synergistic Challenges in Data-Intensive Science
and Exascale Computing",
year = "2013",
month = "March",
note = "Summary Report of the Advanced Scientific
Computing Advisory Committee (ASCAC)
Subcommittee",
url = "http://www.sci.utah.edu/publications/Che2013a/ASCAC_Data_Intensive_Computing_report_final.pdf",
}
@Article{SCI:Che2013b,
author = "F. Chen and H. Obermaier and H. Hagen and B.
Hamann and J. Tierny and V. Pascucci",
title = "Topology analysis of time-dependent multi-fluid
data using the Reeb graph",
journal = "Computer Aided Geometric Design",
volume = "30",
number = "6",
pages = "557--566",
year = "2013",
doi = "10.1016/j.cagd.2012.03.019",
keywords = "Multi-phase fluid, Level set, Topology method,
Point-based multi-fluid simulation",
url = "http://www.sci.utah.edu/publications/Che2013b/Chen_CAGD2013.pdf",
}
@Article{SCI:Che2017b,
author = "M. Chen and G. Grinstein and C. R. Johnson and J.
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title = "Pathways for Theoretical Advances in
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year = "2017",
publisher = "IEEE",
month = "July",
url = "http://www.sci.utah.edu/publications/Che2017b/Theoretical-Advances-Visualization-2017.pdf",
}
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author = "T.H.C. Childs and M. Berzins and G.R. Ryder and A.
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title = "Selective Laser Sintering of an Amorphous
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author = "D. Chisnall and M. Chen and C.D. Hansen",
title = "Ray-Driven Dynamic Working Set Rendering for
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pages = "167--179",
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author = "C.-S. Chiang and C. Hoffmann and P. Rosen",
title = "A Generalized Malfatti Problem",
journal = "Computational Geometry: Theory and Applications",
volume = "45",
number = "8",
pages = "425--435",
year = "2012",
keywords = "Malfatti's problem, circle packing, geometric
constraint solving, GPU programming",
url = "http://www.sci.utah.edu/publications/chiang12/Chiang_CGTA2012.pdf",
}
@Article{SCI:Chi2020a,
author = "H. Childs and S. D. Ahern and J. Ahrens and A. C.
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S. Petruzza and N. Podhorszki and D. Pugmire and M.
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Usher and R. Vickery and V. Vishwanath and I. Wald
and R. Wang and G. H. Weber and B. Whitlock and M.
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author = "A.N.M. Imroz Choudhury and K. Potter and S.G.
Parker",
title = "Interactive Visualization for Memory Reference
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journal = "Computer Graphics Forum",
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pages = "815--822",
year = "2008",
month = "May",
url = "http://www.sci.utah.edu/publications/choudhury08/reftrace-vis.eurovis08.pdf",
}
@InProceedings{SCI:Cho2009a,
author = "A.N.M. Imroz Choudhury and S.G. Parker",
title = "Ray Tracing NPR-Style Feature Lines",
booktitle = "Proceedings of the 7th International Symposium on
Non-Photorealistic Animation and Rendering ({NPAR})
2009",
pages = "5--14",
year = "2009",
keywords = "ray-tracing",
url = "http://www.sci.utah.edu/publications/choudhury09/NPR-lines.NPAR09.pdf",
}
@Article{SCI:Cho2010a,
author = "A.N.M. Imroz Choudhury and M.D. Steffen and J.E.
Guilkey and S.G. Parker",
title = "Enhanced Understanding of Particle Simulations
Through Deformation-Based Visualization",
journal = "Computer Modeling in Engineering \& Sciences",
volume = "63",
number = "2",
pages = "117--136",
year = "2010",
keywords = "csafe",
url = "http://www.sci.utah.edu/publications/Cho2010a/Choudhury_particle-deformation.CMES2010.pdf",
}
@InProceedings{SCI:Cho2011a,
author = "A.N.M. Imroz Choudhury and P. Rosen",
title = "Abstract Visualization of Runtime Memory
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booktitle = "6th {IEEE} International Workshop on Visualizing
Software for Understanding and Analysis ({VISSOFT}
2011)",
pages = "22--29",
year = "2011",
url = "http://www.sci.utah.edu/publications/choudhury11/Choudhury.2011.VisSoft.pdf",
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author = "A.N.M. Imroz Choudhury and Bei Wang and P. Rosen
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title = "Topological Analysis and Visualization of Cyclical
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booktitle = "Proceedings of the {IEEE} Pacific Visualization
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pages = "9--16",
year = "2012",
doi = "10.1109/PacificVis.2012.6183557",
keywords = "scidac",
url = "http://www.sci.utah.edu/publications/choudhury12/Choudhury_PacVis2012.pdf",
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author = "G.E. Christensen and R.D. Rabbitt and M.I. Miller
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author = "G.E. Christensen and S.C. Joshi and M. Miller",
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@Article{SCI:Chr1997b,
author = "G.E. Christensen and S.C. Joshi and M.I. Miller",
title = "Volumetric Transformation of Brain Anatomy",
journal = "IEEE Transactions on Medical Imaging",
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author = "C. Christensen and S. Liu and G. Scorzelli and J.
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title = "Embedded Domain-Specific Language and Runtime
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journal = "Symposium on Large Data Analysis and
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author = "{CIBC}",
year = "2015",
note = "Data Sets: {NCRR} Center for Integrative
Biomedical Computing ({CIBC}) data set archive.
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keywords = "datasets, CIBC",
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author = "D. Clark and K. Johnson and C. Butson and C. Lebel
and D. Gobbi and R. Ramasubbu and Z. Kiss",
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author = "CIBC",
year = "2015",
note = "Cleaver: A MultiMaterial Tetrahedral Meshing
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keywords = "Cleaver, CIBC",
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author = "M.J.M. Cluitmans and S. Ghimire and J. Dhamala and
J. Coll-Font and J.D. Tate and S. Giffard-Roisin
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number = "Supplement",
year = "2018",
publisher = "Oxford University Press",
month = "March",
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author = "M. Cluitmans and D. H. Brooks and R. MacLeod and
O. D{\"o}ssel and M. S. Guillem and P. M. van Dam and
J. Svehlikova and B. He and J. Sapp and L. Wang and
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title = "Validation and Opportunities of
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year = "2018",
publisher = "Frontiers Media SA",
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pages = "412--431",
year = "2003",
publisher = "IEEE Computer Society",
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author = "M. Cole and S.G. Parker",
title = "Dynamic Compilation of C++ Template Code",
booktitle = "Scientific Programming",
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year = "2003",
publisher = "IOS Press",
keywords = "ncrr, scirun, problem solving environments",
url = "http://www.sci.utah.edu/publications/mcole01/dyn.pdf",
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Harer and V. Natarajan and V. Pascucci",
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pages = "344--350",
year = "2003",
month = "June",
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author = "K. Cole-McLaughlin and H. Edelsbrunner and J.
Harer and V. Natarajan and V. Pascucci",
title = "Loops in Reeb Graphs of 2-Manifolds",
booktitle = "Proceedings of the 19th ACM Symposium on
Computational Geometry",
pages = "344--350",
year = "2003",
month = "June",
note = "UCRL-JC-151933",
}
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author = "M. Cole and F.B. Sachse and D.M. Weinstein and
S.G. Parker and R.M. Kirby",
title = "A Software Framework for Solving Problems of
Bioelectricity Applying High-Order Finite
Elements",
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year = "2004",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions, finite elements,
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author = "K. Cole-McLaughlin and V. Pascucci",
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year = "2004",
month = "September",
location = "Marbella, Spain",
note = "UCRL-PROC-208680",
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author = "J.L.D. Comba and J.S.B. Mitchell and C.T. Silva",
title = "On the Convexification of Unstructured Grids From
A Scientific Visualization Perspective",
number = "UUSCI-2004-004",
year = "2004",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "unstructured grids, convexification, Delaunay
triangulations, binary space, partitioning trees,
delaunay triangulations",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2004-004.pdf",
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year = "2008",
isbn = "978-1-60558-102-6",
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editor = "V. Alexandrov and J. Dongarra and B. Juliano and
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editor = "M. Bubak et al",
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year = "2006",
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year = "2009",
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year = "2006",
publisher = "ACM Press",
address = "New York, NY, USA",
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title = "Chronic atrial fibrillation causes left
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month = "September",
doi = "10.1152/ajpheart.00440.2013",
pmid = "23812387",
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keywords = "animal models, chronic atrial fibrillation,
fibrosis, heart failure, rapid atrial pacing",
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title = "Workshop on Dynamic Data-Driven Application
Systems",
booktitle = "ICCS 2003",
year = "2003",
month = "June 2-3",
location = "Melbourne, Australia",
keywords = "scirun, pse, problem solving environments, data
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url = "http://www.sci.utah.edu/publications/douglas03/douglas.pdf",
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author = "C.C. Douglas and C.E. Shannon and Y. Efendiev and
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title = "A Note on Dynamic Data Driven Application
Simulation ({DDDAS}) Using Virtual Telemetry",
booktitle = "International Conference on Parallel Algorithms
and Computing Environments",
pages = "pp.193--198",
year = "2003",
keywords = "scirun, pse, problem solving environments, data
driven",
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}
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author = "C.C. Douglas and J.C. Harris and M. Iskandarani
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Lazarov and G. Qin",
title = "Dynamic Contaminant Identification in Water",
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author = "C.C. Douglas and M.J. Cole and P. Dostert and Y.
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title = "Dynamic data-driven application systems for empty
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author = "N.J. Drury and B.J. Ellis and J.A. Weiss and P.J.
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}
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pages = "13--20",
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D.R. Schikore and K. Lin and R.B. Borgens",
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A. C. Dorval and C. R. Butson",
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author = "L.J.K. Durbeck and M. Berzins",
title = "Unstructured Tetrahedral Mesh Quality Analysis
Using an Interactive Haptic and Visual Interface",
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year = "2002",
publisher = "Springer-Verlag",
keywords = "computational pde pdes computational partial
differential equations evaporation, adaptive mesh
generation, evaporation, atmospherics weather
meterology, scientific computing",
url = "http://www.sci.utah.edu/publications/ldurbeck02/ldmb.pdf",
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author = "S. Durrleman and X. Pennec and A. Trouv{\’e} and G.
Gerig and N. Ayache",
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year = "2009",
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author = "S. Durrleman and X. Pennec and A. Trouv{\’e} and N.
Ayache and J. Braga",
title = "Comparison of the endocast growth of chimpanzees
and bonobos via temporal regression and
spatiotemporal registration",
booktitle = "Proceedings of the MICCAI Workshop on
Spatio-Temporal Image Analysis for Longitudinal and
Time-Series Image Data",
pages = "(in press)",
year = "2010",
month = "September",
location = "Beijing, China",
url = "http://www.sci.utah.edu/publications/durrleman10/Durrleman_STIA10.pdf",
}
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author = "S. Durrleman and P. Fillard and X. Pennec and A.
Trouv{\’e} and N. Ayache",
title = "Registration, Atlas Estimation and Variability
Analysis of White Matter Fiber Bundles Modeled as
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year = "2010",
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author = "S. Durrleman and M.W. Prastawa and G. Gerig and S.
Joshi",
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booktitle = "Proceedings of the IPMI 2011 conference",
volume = "6801/2011",
pages = "123--134",
year = "2011",
series = "Springer LNCS",
month = "July",
doi = "10.1007/978-3-642-22092-0_11",
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author = "S. Durrleman and X. Pennec and A. Trouv{\’e} and N.
Ayache and J. Braga",
title = "Comparison of the endocranial ontogenies between
chimpanzees and bonobos via temporal regression and
spatiotemporal registration",
booktitle = "Journal of Human Evolution",
pages = "74--88",
year = "2011",
month = "January",
doi = "10.1016/j.jhevol.2011.10.004",
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}
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author = "S. Durrleman and M.W. Prastawa and S. Joshi and G.
Gerig and A. Trouve",
title = "Topology Preserving Atlas Construction from Shape
Data without Correspondence using Sparse
Parameters",
booktitle = "Proceedings of MICCAI 2012",
pages = "223--230",
year = "2012",
series = "Lecture Notes in Computer Science (LNCS)",
month = "October",
url = "http://www.sci.utah.edu/publications/durrleman12/Durrleman_miccai2012.pdf",
}
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author = "S. Durrleman and S. Allassonniere and S. Joshi",
title = "Sparse Adaptive Parameterization of Variability in
Image Ensembles",
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pages = "1--23",
year = "2012",
url = "http://www.sci.utah.edu/publications/durrleman12/Durrleman_IJCV_2012.pdf",
}
@Article{SCI:Dur2013a,
author = "S. Durrleman and X. Pennec and A. Trouv{\’e} and J.
Braga and G. Gerig and N. Ayache",
title = "Toward a comprehensive framework for the
spatiotemporal statistical analysis of longitudinal
shape data",
journal = "International Journal of Computer Vision (IJCV)",
volume = "103",
number = "1",
pages = "22--59",
year = "2013",
month = "September",
doi = "10.1007/s11263-012-0592-x",
url = "http://www.sci.utah.edu/publications/Dur2013a/Durrleman_IJCV_2012_Longitudinal.pdf",
}
@Article{SCI:Dur2013b,
author = "S. Durrleman and S. Allassonni{\‘e}re and S. Joshi",
title = "Sparse adaptive parameterization of variability in
image ensembles",
journal = "International Journal of Computer Vision
({IJCV})",
volume = "101",
number = "1",
pages = "161--183",
year = "2013",
doi = "10.1007/s11263-012-0556-1",
url = "http://www.sci.utah.edu/publications/Dur2013b/Durrleman_IJCV_2013.pdf",
}
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author = "S. Durrleman and M. Prastawa and N. Charon and
J.R. Korenberg and S. Joshi and G. Gerig and A.
Trouv{\’e}",
title = "Morphometry of anatomical shape complexes with
dense deformations and sparse parameters",
journal = "NeuroImage",
year = "2014",
doi = "10.1016/j.neuroimage.2014.06.043",
keywords = "morphometry, deformation, varifold, anatomy,
shape, statistics",
url = "http://www.sci.utah.edu/publications/Dur2014a/Durrleman_NeuroImage2014.pdf",
}
@Book{SCI:Dur2015a,
author = "S. Durrleman and T.P. Fletcher and G. Gerig and M.
Niethammer and X. Pennec (Eds.)",
title = "Spatio-temporal Image Analysis for Longitudinal
and Time-Series Image Data",
title_url =
"http://www.springer.com/computer/image+processing/book/978-3-642-33554-9",
booktitle = "Proceedings of the Third International Workshop,
STIA 2014",
volume = "8682",
year = "2015",
series = "Image Processing, Computer Vision, Pattern
Recognition, and Graphics",
publisher = "Springer {LNCS}",
publisher_url = "http://www.springer.com/lncs",
isbn = "978-3-319-14905-9",
}
@InProceedings{SCI:Dur98a,
author = "L.J.K Durbeck and N.J. Macias and D.M. Weinstein
C.R. and J.M. Hollerbach",
title = "{SCIR}un/Haptic Display for Flow Fields",
booktitle = "Proceedings of the Third {PHANTOM} Users Group
Workshop",
pages = "71--75",
year = "1998",
editor = "J.K. Salisbury and M.A. Srinivasan",
series = "AI Lab Technical Report No. 1643 and {RLE}
Technical Report No. 624",
month = "Dec",
keywords = "scirun, haptic, visual haptic workbench, vr
virtual reality haptics",
url = "http://www.sci.utah.edu/publications/ldurbeck/pug98.pdf",
url = "http://www.sci.utah.edu/publications/ldurbeck/pug98.ps.gz",
url = "http://www.sci.utah.edu/publications/ldurbeck/pug98.ps",
}
@InProceedings{SCI:Dur99c,
author = "L. Durbeck",
title = "Evaporation: A Technique for Visualizing Mesh
Quality",
booktitle = "8th International Meshing Roundtable",
pages = "259--265",
year = "1999",
organization = "Sandia National Laboratories",
month = "Oct",
keywords = "computational pde pdes computational partial
differential equations evaporation, evaporation,
scirun, atmospherics weather meterology",
url = "http://www.sci.utah.edu/publications/ldurbeck/roundtable.ps.gz",
url = "http://www.sci.utah.edu/publications/ldurbeck/roundtable.ps",
url = "http://www.sci.utah.edu/publications/ldurbeck/roundtable.pdf",
url = "http://www.sci.utah.edu/publications/ldurbeck/evap.zip",
}
@InProceedings{SCI:Ede2003a,
author = "H. Edelsbrunner and J. Harer and V. Natarajan and
V. Pascucci",
title = "Morse Complexes for Piecewise Linear
3-Manifolds",
booktitle = "Proceedings of the 19th ACM Symposium on
Computational Geometry",
pages = "361--370",
year = "2003",
month = "June",
note = "UCRL-PROC-208698",
}
@InProceedings{SCI:Ede2004a,
author = "H. Edelsbrunner and J. Harer and V. Natarajan and
V. Pascucci",
title = "Local and Global Comparison of Continuous
Functions",
booktitle = "Proceedings of the {IEEE} Conference on
Visualization ({VIS}-04)",
pages = "275--280",
year = "2004",
month = "October",
note = "UCRL-PROC-208677",
}
@InProceedings{SCI:Ede2004b,
author = "H. Edelsbrunner and J. Harer and A. Mascarenhas
and V. Pascucci",
title = "Time-Varying Reeb Graphs for Continuous Space-Time
Data",
booktitle = "SCG '04: Proceedings of the Twentieth Annual
Symposium on Computational Geometry",
pages = "366--372",
year = "2004",
publisher = "ACM Press",
location = "Brooklyn, New York, USA",
note = "UCRL-PROC-208697",
isbn = "1-58113-885-7",
}
@InProceedings{SCI:Ede2006a,
author = "H. Edelsbrunner and D. Morozov and V. Pascucci",
title = "Persistence-based Simplification of Real-Valued
Functions on 2-Manifolds",
booktitle = "Proceedings of the 22nd International Annual
Symposium on Computational Geometry",
pages = "212--220",
year = "2006",
note = "To appear",
}
@Article{SCI:Edg2013a,
author = "L.T. Edgar and S.C. Sibole and C.J. Underwood and
J.E. Guilkey and J.A. Weiss",
title = "A computational model of in vitro angiogenesis
based on extracellular matrix fiber orientation",
journal = "Computer Methods in Biomechanical and Biomedical
Engineering",
volume = "16",
number = "7",
pages = "790--801",
year = "2013",
doi = "10.1080/10255842.2012.662678",
url = "http://www.sci.utah.edu/publications/edgar13/Edgar_CMBBE2013.pdf",
}
@Article{SCI:Edg2014a,
author = "L.T. Edgar and C.J. Underwood and J.E. Guilkey and
J.B. Hoying and J.A. Weiss",
title = "Extracellular matrix density regulates the rate of
neovessel growth and branching in sprouting
angiogenesis",
journal = "PLOS one",
volume = "9",
number = "1",
year = "2014",
doi = "10.1371/journal.pone.0085178",
url = "http://www.sci.utah.edu/publications/edgar14/Edgar_PlosOne2014.pdf",
}
@InProceedings{SCI:Edm2011a,
author = "M. Edmunds and T. McLoughlin and R.S. Laramee and
G. Chen and E. Zhang and N. Max",
title = "Automatic Stream Surface Seeding",
booktitle = "EUROGRAPHICS 2011 Short Papers",
pages = "53--56",
year = "2011",
url = "http://www.sci.utah.edu/publications/edmunds11/Edmunds_EG11short2049_AutomaticStreamSurfaceSeeding.pdf",
}
@Article{SCI:Edw2015a,
author = "J. Edwards and S. Kumar and V. Pascucci",
title = "Big data from scientific simulations",
journal = "Big Data and High Performance Computing",
volume = "26",
pages = "32",
year = "2015",
publisher = "IOS Press",
url = "http://www.sci.utah.edu/publications/Edw2015a/BiG_Data_Chapter.pdf",
}
@Article{SCI:Edw2015b,
author = "J. Edwards and E. Daniel and V. Pascucci and C.
Bajaj",
title = "Approximating the Generalized Voronoi Diagram of
Closely Spaced Objects",
journal = "Computer Graphics Forum",
volume = "34",
number = "2",
pages = "299-309",
year = "2015",
publisher = "Wiley-Blackwell",
month = "May",
doi = "10.1111/cgf.12561",
url = "http://www.sci.utah.edu/publications/Edw2015b/edwards2015eg.pdf",
}
@InProceedings{SCI:Eid2006a,
author = "E. Eide and L. Stoller and T. Stack and J. Freire
and J. Lepreau",
title = "Integrated Scientific Workflow Management for the
Emulab Network Testbed",
booktitle = "Proceedings of the 2006 USENIX Annual Technical
Conference",
pages = "33",
year = "2006",
keywords = "provenance, workflows, workflow management,
vistrails",
}
@InProceedings{SCI:Ela2001a,
author = "V. Elangovan and R.T. Whitaker",
title = "From Sinograms to Surfaces: A Direct Approach to
Segmenting Tomographic Data",
booktitle = c-MICCAI2001,
pages = "213--223",
year = "2001",
month = "October",
keywords = "ip image processing signal processing,
segmentation, surface processing, imaging",
url = "http://www.sci.utah.edu/publications/miccai01/sino_surf.pdf",
}
@InProceedings{SCI:Elh2013a,
author = "S. Elhabian and A. Farag and D. Tasman and W.
Aboelmaaty and A. Farman",
title = "Clinical Crowns Shape Reconstruction - An
Image-based Approach",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "93--96",
year = "2013",
doi = "10.1109/ISBI.2013.6556420",
url = "http://www.sci.utah.edu/publications/elhabian13/Elhabian_ISBI2013.pdf",
}
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author = "S. Elhabian and Y. Gur and C. Vachet and J. Piven
and M. Styner and I. Leppert and G.B. Pike and G.
Gerig",
title = "A Preliminary Study on the Effect of Motion
Correction On {HARDI} Reconstruction",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "(accepted)",
year = "2014",
keywords = "Diffusion MRI, HARDI, motion correction,
interpolation",
url = "http://www.sci.utah.edu/publications/elhabian14/ElhabianISBI2014.pdf",
}
@InProceedings{SCI:Elh2014b,
author = "S. Elhabian and Y. Gur and J. Piven and M. Styner
and I. Leppert and G.B. Pike and G. Gerig",
title = "Subject-Motion Correction in {HARDI} Acquisitions:
Choices and Consequences",
title_url =
"http://journal.frontiersin.org/Journal/10.3389/fneur.2014.00240/abstract",
booktitle = "Proceeding of the 2014 Joint Annual Meeting
{ISMRM-ESMRMB}",
pages = "(accepted)",
year = "2014",
doi = "10.3389/fneur.2014.00240 ",
url = "http://www.sci.utah.edu/publications/Elh2014b/ISMRM-DTI_QC_submitted_abstract.pdf",
}
@InProceedings{SCI:Elh2014c,
author = "S. Elhabian and Y. Gur and J. Piven and M. Styner
and I. Leppert and G. Bruce Pike and G. Gerig",
title = "Motion is inevitable: The impact of motion
correction schemes on hardi reconstructions",
booktitle = "Proceedings of the {MICCAI} 2014 Workshop on
Computational Diffusion {MRI}",
year = "2014",
month = "September",
url = "http://www.sci.utah.edu/publications/Elh2014c/Elhabian_CDMRI2014.pdf",
}
@Article{SCI:Elh2014d,
author = "S.Y. Elhabian and Y. Gur and C. Vachet and J.
Piven and M.A. Styner and I.R. Leppert and B. Pike
and G. Gerig",
title = "Subject-Motion Correction in HARDI Acquisitions:
Choices and Consequences",
journal = "Frontiers in Neurology - Brain Imaging Methods",
year = "2014",
doi = "10.3389/fneur.2014.00240 ",
url = "http://www.sci.utah.edu/publications/Elh2014d/Elhabian_FrontNeuro-BIM2014.pdf",
}
@InProceedings{SCI:Elh2016a,
author = "S. Elhabian and C. Vachet and J. Piven and M.
Styner and G. Gerig",
title = "Compressive sensing based Q-space resampling for
handling fast bulk motion in hardi acquisitions",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
pages = "907--910",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493412",
url = "http://www.sci.utah.edu/publications/Elh2016a/ELHABIAN_ISBI_2016_CAMERA_READY.pdf",
}
@InProceedings{SCI:Elh2016b,
author = "S. Elhabian and P. Agrawal and R. Whitaker",
title = "Optimal parameter map estimation for shape
representation: A generative approach",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
pages = "660--663",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493353",
url = "http://www.sci.utah.edu/publications/Elh2016b/07493353.pdf",
}
@Article{SCI:Eli2013a,
author = "J.T. Elison and J.J. Wolff and D.C. Heimer and
S.J. Paterson and H. Gu and M. Styner and G. Gerig
and J. Piven and the IBIS Network",
title = "Frontolimbic neural circuitry at 6 months predicts
individual differences in joint attention at 9
months",
journal = "Developmental Science",
volume = "16",
number = "2",
pages = "186--197",
year = "2013",
publisher = "Wiley-Blackwell",
doi = "10.1111/desc.12015",
pmcid = "PMC3582040",
url = "http://www.sci.utah.edu/publications/elison13/Elison_DevScience2013.pdf",
}
@Article{SCI:Eli2013b,
author = "J.T. Elison and S.J. Paterson and J.J. Wolff and
J.S. Reznick and N.J. Sasson and H. Gu and K.N.
Botteron and S.R. Dager and A.M. Estes and A.C.
Evans and G. Gerig and H.C. Hazlett and R.T.
Schultz and M. Styner and L. Zwaigenbaum and J.
Piven for the IBIS Network",
title = "White Matter Microstructure and Atypical Visual
Orienting in 7 Month-Olds at Risk for Autism",
journal = "American Journal of Psychiatry",
volume = "AJP-12-09-1150.R2",
year = "2013",
month = "March",
doi = "10.1176/appi.ajp.2012.12091150",
pmid = "23511344",
url = "http://www.sci.utah.edu/publications/elison12/Elison_AJP_submission_12112012.pdf",
}
@Article{SCI:Elk2011a,
author = "J.M. Elkins and J.S. Stroud and M.J. Rudert and Y.
Tochigi and D.R. Pedersen and B.J. Ellis and J.J.
Callaghan and J.A. Weiss and T.D. Brown",
title = "{T}he capsule's contribution to total hip
construct stability - a finite element analysis",
journal = "Journal of Orthopedic Research",
volume = "29",
number = "11",
pages = "1642--1648",
year = "2011",
month = "November",
note = "William Harris, MD Award",
doi = "10.1002/jor.21435",
url = "http://www.sci.utah.edu/publications/elkins11/Elkins_JOR2011.pdf",
}
@Article{SCI:Ell2006a,
author = "B.J. Ellis and R.E. Debski and S.M. Moore and P.J.
McMahon and J.A. Weiss",
title = "Methodology and Sensitivity Studies for Finite
Element Modeling of the Inferior Glenohumeral
Ligament Complex",
journal = j-BM,
volume = "40",
number = "3",
pages = "603--612",
year = "2006",
month = "January",
keywords = "finite elements, computational mechanics,
computational biomechanics, multiscale tissue
modeling multiscale tissue simulation, mrl",
url = "http://www.sci.utah.edu/publications/ellis06/ellis_jbiomech_2006.pdf",
}
@Article{SCI:Ell2006b,
author = "B.J. Ellis and T.J. Lujan and M.S. Dalton and J.A.
Weiss",
title = "MCL Insertion Site and Contact Forces in the
ACL-Deficient Knee",
journal = "Journal of Orthopaedic Research",
volume = "24",
number = "4",
pages = "800--810",
year = "2006",
publisher = "Elsevier",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/ellis06/ellis_jor_2006.pdf",
}
@InProceedings{SCI:Ell2008a,
author = "T. Ellkvist and D. Koop and E.W. Anderson and J.
Freire and C.T. Silva",
title = "Using Provenance to Support Real-Time
Collaborative Design of Workflows",
booktitle = "Proceedings of the Second International Provenance
and Annotation Workshop ({IPAW} 2008)",
pages = "266--279",
year = "2008",
keywords = "vistrails, provenance, workflow management,
collaborative workflow design",
url = "http://www.sci.utah.edu/publications/ellkvist08/ipaw2008c.pdf",
}
@InProceedings{SCI:Ell2008b,
author = "T. Ellkvist and D. Koop and J. Freire and C.T.
Silva and L. Stromback",
title = "Using Mediation to Achieve Provenance
Interoperability",
booktitle = "Proceedings of the 2008 Fourth {IEEE}
International Conference on eScience",
pages = "398--399",
year = "2008",
keywords = "vistrails, provenance, workflows, workflow
management",
}
@InProceedings{SCI:Ell2009a,
author = "T. Ellkvist and L. Stromback and L. Lins and J.
Freire",
title = "A First Study on Strategies for Generating
Workflow Snippets",
booktitle = "Proceedings of the ACM SIGMOD Intenational
Workshop on Keyword Search on Structured Data
(KEYS)",
pages = "15--20",
year = "2009",
isbn = "978-1-60558-570-3",
keywords = "data searching",
url = "http://www.sci.utah.edu/publications/ellkvist09/workflowsnippets-keys2009.pdf",
}
@InProceedings{SCI:Ell2009b,
author = "T. Ellkvist and D. Koop and J. Freire and C.T.
Silva and L. Stromback",
title = "Using Mediation to Achieve Provenance
Interoperability",
booktitle = "Proceedings of the {IEEE} International Workshop
on Scientific Workflows, 2009",
pages = "291--298",
year = "2009",
isbn = "978-0-7695-3708-5",
keywords = "workflow management, provenance, vistrails",
url = "http://www.sci.utah.edu/publications/ellkvist09/provinterop-swf2009.pdf",
}
@Unpublished{SCI:Ell2009c,
author = "M. Ellisman and R. Stevens and M. Colvin and T.
Schlick and E. Delong and G. Olsen and J. George
and G. Karniakadis and C.R. Johnson and N.
Sematova",
title = "Scientific Grand Challenges: Opportunities in
biology at the Extreme Scale of Computing",
year = "2009",
month = "August",
note = "DOE Office of Advanced Scientific Computing
Research",
url = "http://www.sci.utah.edu/publications/Ell2009c/Ellisman_BiologyReport2009.pdf",
}
@PhdThesis{SCI:Ell2011a,
author = "B.J. Ellis",
title = "Finite element modeling of knee and shoulder
ligaments",
year = "2011",
school = "Department of Bioengineering, University of
Utah",
note = "Ph.D. Thesis",
url = "http://www.sci.utah.edu/publications/ellis11/BenEllis_Dissertation.pdf",
}
@Article{SCI:Els2010a,
author = "M. El-Sayed and R.G. Steen and M.D. Poe and T.C.
Bethea and G. Gerig and J. Lieberman and L.
Sikich",
title = "Deficits in gray matter volume in psychotic youth
with schizophrenia-spectrum disorders are not
evident in psychotic youth with mood disorders",
journal = "J Psychiatry Neurosci",
year = "2010",
month = "July",
}
@Article{SCI:Els2010b,
author = "M. El-Sayed and R.G. Steen and M.D. Poe and T.C.
Bethea and G. Gerig and J. Lieberman and L.
Sikich",
title = "Brain volumes in psychotic youth with
schizophrenia and mood disorders",
journal = "Journal of Psychiatry and Neuroscience",
volume = "35",
number = "4",
pages = "229--236",
year = "2010",
month = "July",
pmid = "20569649",
url = "http://www.sci.utah.edu/publications/elsayed10/El-Sayed_JPN2010b.pdf",
}
@InProceedings{SCI:Elw2016a,
author = "M. Elwardy and T. Tasdizen and M. Cetin",
title = "Disjunctive Normal Unsupervised LDA for P300-based
Brain-Computer Interfaces",
booktitle = "2016 24th Signal Processing and Communication
Application Conference (SIU)",
year = "2016",
publisher = "IEEE",
month = "May",
doi = "10.1109/siu.2016.7496226",
url = "http://www.sci.utah.edu/publications/Elw2016a/07496226.pdf",
}
@InProceedings{SCI:Erd2015a,
author = "E. Erdil and A.O. Argunsah and T. Tasdizen and D.
Unay and M. Cetin",
title = "A joint classification and segmentation approach
for dendritic spine segmentation in 2-photon
microscopy images",
booktitle = "2015 IEEE 12th International Symposium on
Biomedical Imaging (ISBI)",
year = "2015",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2015.7163992",
url = "http://www.sci.utah.edu/publications/Erd2015a/07163992.pdf",
}
@InProceedings{SCI:Erd2016a,
author = "E. Erdil and M. Cetin and T. Tasdizen",
title = "MCMC Shape Sampling for Image Segmentation with
Nonparametric Shape Priors",
booktitle = "2016 IEEE Conference on Computer Vision and
Pattern Recognition (CVPR)",
year = "2016",
publisher = "IEEE",
month = "June",
doi = "10.1109/cvpr.2016.51",
url = "http://www.sci.utah.edu/publications/Erd2016a/Erdil_MCMC_Shape_Sampling_CVPR_2016_paper.pdf",
}
@InProceedings{SCI:Erd2016b,
author = "E. Erdil and L. Rada and A.O. Argunsah and D. Unay
and T. Tasdizen and M. Cetin",
title = "Nonparametric joint shape and feature priors for
segmentation of dendritic spines",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493279",
url = "http://www.sci.utah.edu/publications/Erd2016b/07493279.pdf",
}
@Article{SCI:Erd2017a,
author = "E. Erdil and M.U. Ghani and L. Rada and A.O.
Argunsah and D. Unay and T. Tasdizen and M.
Cetin",
title = "Nonparametric joint shape and feature priors for
image segmentation",
journal = "IEEE Transactions on Image Processing",
volume = "26",
number = "11",
pages = "5312--5323",
year = "2017",
publisher = "IEEE",
month = "Nov",
doi = "10.1109/tip.2017.2728185",
url = "http://www.sci.utah.edu/publications/Erd2017a/07982806.pdf",
}
@Article{SCI:Erd2018a,
author = "A. Erdemir and P.J. Hunter and G.A. Holzapfel and
L.M. Loew and J. Middleton and C.R. Jacobs and P.
Nithiarasu and R. L{\"o}hner and G. Wei and B.A.
Winkelstein and V.H. Barocas and F. Guilak and J.P.
Ku and J.L. Hicks and S.L. Delp and M.S. Sacks and
J.A. Weiss and G.A. Ateshian and S.A. Maas and A.D.
McCulloch and G.C.Y. Peng",
title = "Perspectives on Sharing Models and Related
Resources in Computational Biomechanics Research",
journal = "Journal of Biomechanical Engineering",
volume = "140",
number = "2",
pages = "024701",
year = "2018",
publisher = "ASME International",
month = "Jan",
doi = "10.1115/1.4038768",
url = "http://www.sci.utah.edu/publications/Erd2018a/BIO-17-1530.pdf",
}
@InProceedings{SCI:Ere2011a,
author = "B. Erem and D.H. Brooks and P.M. van Dam and J.G.
Stinstra and R.S. MacLeod",
title = "Spatiotemporal Estimation of Activation Times of
Fractionated {ECGs} on Complex Heart Surfaces",
booktitle = "Proceedings of the International Coference of the
{IEEE} Engineering in Medicine and Biology Society
({EMBS})",
pages = "5884--5887",
year = "2011",
doi = "10.1109/IEMBS.2011.6091455",
pmid = "22255678",
pmcid = "PMC3345888",
url = "http://www.sci.utah.edu/publications/erem11/Erem_EMBS2011.pdf",
}
@Article{SCI:Ere2013a,
author = "B. Erem and J. Coll-Font and R.M. Orellana and P.
Stovicek and D.H. Brooks and R.S. MacLeod",
title = "Noninvasive reconstruction of potentials on
endocardial surface from body surface potentials
and CT imaging of partial torso",
journal = "Journal of Electrocardiology",
volume = "46",
number = "4",
pages = "e28",
year = "2013",
doi = "10.1016/j.jelectrocard.2013.05.104",
}
@Article{SCI:Ere2013b,
author = "B. Erem and R.M. Orellana and P. Stovicek and D.H.
Brooks and R.S. MacLeod",
title = "Improved averaging of multi-lead ECGs and
electrograms",
journal = "Journal of Electrocardiology",
volume = "46",
number = "4",
pages = "e28",
year = "2013",
publisher = "Elsevier",
month = "July",
doi = "10.1016/j.jelectrocard.2013.05.103",
}
@Article{SCI:Ere2016a,
author = "B. Erem and R.M. Orellana and D.E. Hyde and J.M.
Peters and F.H. Duffy and P. Stovicek and S.K.
Warfield and R.S. MacLeod and G. Tadmor and D.H.
Brooks",
title = "Extensions to a manifold learning framework for
time-series analysis on dynamic manifolds in
bioelectric signals",
journal = "Physical Review E",
volume = "93",
number = "4",
year = "2016",
publisher = "American Physical Society",
month = "apr",
doi = "10.1103/physreve.93.042218",
url = "http://www.sci.utah.edu/publications/Ere2016a/nihms782978.pdf",
}
@Article{SCI:Eti2009a,
author = "T. Etiene and C.E. Scheidegger and L.G. Nonato and
R. Kirby and C.T. Silva",
title = "Verifiable Visualization for Isosurface
Extraction",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics, Proceedings of the 2009 {IEEE}
Visualization Conference",
volume = "15",
number = "6",
pages = "1227--1234",
year = "2009",
month = "Sept/Oct",
url = "http://www.sci.utah.edu/publications/etiene2009/verifiable-vis.pdf",
}
@TechReport{SCI:Eti2010a,
author = "T. Etiene and L.G. Nonato and C.E. Scheidegger and
J. Tierny and T.J. Peters and V. Pascucci and R.M.
Kirby and C.T. Silva",
title = "Topology Verification for Isosurface Extraction",
number = "UUSCI-2010-003",
year = "2010",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2010-003.pdf",
}
@Article{SCI:Eti2011b,
author = "T. Etiene and L.G. Nonato and C. Scheidegger and
J. Tierny and T.J. Peters and V. Pascucci and R.M.
Kirby and C.T. Silva",
title = "Topology Verfication for Isosurface Extraction",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
pages = "(accepted)",
year = "2011",
url = "http://www.sci.utah.edu/publications/etiene11/Etiene_TVCG2011.pdf",
}
@TechReport{SCI:Eti2013a,
author = "T. Etiene and D. Jonsson and T. Ropinski and C.
Scheidegger and J. Comba and L. Gustavo Nonato and
R.M. Kirby and A. Ynnerman and C.T. Silva",
title = "Verifying Volume Rendering Using Discretization
Error Analysis",
number = "UUSCI-2013-001",
year = "2013",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "discretization errors, volume rendering,
verifiable visualization",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2013-001.pdf",
}
@Article{SCI:Eti2014a,
author = "T. Etiene and D. Jonsson and T. Ropinski and C.
Scheidegger and J.L.D. Comba and L. G. Nonato and
R. M. Kirby and A. Ynnerman and and C. T. Silva",
title = "Verifying Volume Rendering Using Discretization
Error Analysis",
journal = "IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER
GRAPHICS",
volume = "20",
number = "1",
pages = "140-154",
year = "2014",
publisher = "IEEE",
month = "January",
url = "http://www.sci.utah.edu/publications/Eti2014a/Kirby-79.pdf",
}
@Book{SCI:Eti2015b,
author = "T. Etiene and R.M. Kirby and C. Silva",
title = "An Introduction to Verification of Visualization
Techniques",
year = "2015",
publisher = "Morgan \& Claypool Publishers",
url = "http://www.sci.utah.edu/publications/Eti2015b/s00679ed1v01y201511cgr022.pdf",
}
@InProceedings{SCI:Fai2003a,
author = "R. Fairlie and C.E. Goodyer and M. Berzins and
L.E. Scales",
title = "Numerical Modelling of Thermal Effects in
Elastohydrodynamic Lubrication Solvers",
booktitle = "Tribological Research and Design for Engineering
Systems, Proceedings of the 29th Leeds-Lyon
Symposium on Tribology",
pages = "675--683",
year = "2003",
editor = "D. Dowson et al.",
publisher = "Elsevier",
keywords = "EHL",
url = "http://www.sci.utah.edu/publications/fairlie03/leedslyon02pap.pdf",
}
@Article{SCI:Fak2013a,
author = "K. Fakhar and E. Hastings and C.R. Butson and K.D.
Foote and P. Zeilman and M.S. Okun",
title = "Management of deep brain stimulator battery
failure: battery estimators, charge density, and
importance of clinical symptoms",
journal = "PloS One",
volume = "8",
number = "3",
pages = "e58665",
year = "2013",
month = "January",
issn = "1932-6203",
doi = "10.1371/journal.pone.0058665",
pmid = "23536810",
url = "http://www.sci.utah.edu/publications/Fak2013a/Fakhar_PlosOne2013.pdf",
}
@InProceedings{SCI:Far2013a,
author = "M. Farzinfar and Y. Li and A.R. Verde and I. Oguz
and G. Gerig and M.A. Styner",
title = "{DTI} Quality Control Assessment via Error
Estimation From Monte Carlo Simulations",
booktitle = "Proceedings of {SPIE} 8669, Medical Imaging 2013:
Image Processing",
volume = "8669",
year = "2013",
doi = "10.1117/12.2006925",
pmid = " 23833547",
pmcid = " PMC3702180",
url = "http://www.sci.utah.edu/publications/Far2013a/Farzinfar_SPIE2013.pdf",
}
@Article{SCI:Far2013b,
author = "M. Farzinfar and I. Oguz and R.G. Smith and A.R.
Verde and C. Dietrich and A. Gupta and M.L. Escolar
and J. Piven and S. Pujol and C. Vachet and S.
Gouttard and G. Gerig and S. Dager and R.C.
McKinstry and S. Paterson and A.C. Evans and M.A.
Styner",
title = "Diffusion imaging quality control via entropy of
principal direction distribution",
title_url =
"http://www.sciencedirect.com/science/article/pii/S1053811913005168",
journal = "NeuroImage",
volume = "82",
pages = "1--12",
year = "2013",
issn = "1053-8119",
doi = "10.1016/j.neuroimage.2013.05.022",
keywords = "Diffusion magnetic resonance imaging, Diffusion
tensor imaging, Quality assessment, Entropy",
url = "http://www.sci.utah.edu/publications/farzinfar13/Farzinfar_NeuroImage2013.pdf",
}
@Article{SCI:Far2013c,
author = "N. Farah and A. Zoubi and S. Matar and L. Golan
and A. Marom and C.R. Butson and I. Brosh and S.
Shoham",
title = "Holographically patterned activation using
photo-absorber induced neural-thermal
stimulation",
journal = "Journal of Neural Engineering",
volume = "10",
number = "5",
pages = "056004",
year = "2013",
month = "October",
issn = "1741-2560",
doi = "10.1088/1741-2560/10/5/056004",
url = "http://www.sci.utah.edu/publications/Far2013c/Farah_JNeuralEng2013.pdf",
}
@InProceedings{SCI:Fau2014a,
author = "A. Faucett and T. Harman and T. Ameel",
title = "Computational Determination of the Modified Vortex
Shedding Frequency for a Rigid, Truncated,
Wall-Mounted Cylinder in Cross Flow",
booktitle = "Volume 10: Micro- and Nano-Systems Engineering and
Packaging",
year = "2014",
publisher = "ASME International Mechanical Engineering Congress
and Exposition (IMECE)",
organization = "International Conference on Computational
Science",
month = "November",
location = "Montreal",
doi = "10.1115/imece2014-39064",
}
@InProceedings{SCI:Fed2008a,
author = "A. Fedorov and E. Billet and M.W. Prastawa and G.
Gerig and A. Radmanesh and S.K. Warfield and R.
Kikinis and N. Chrisochoides",
title = "Evaluation of Brain MRI Alignment with the Robust
Hausdorff Distance Measures",
booktitle = "Lecture Notes in Computer Science",
volume = "5358",
pages = "594--603",
year = "2008",
publisher = "Springer",
doi = "10.1007/978-3-540-89639-5_57",
url = "http://www.sci.utah.edu/publications/fedorov08/Fedorov_LCNS2008a.pdf",
}
@Article{SCI:Fei2017a,
author = "M. Feiszli and A. Narayan",
title = "Numerical Computation of Weil-Peterson Geodesics
in the Universal Teichmueller Space",
journal = "SIAM Journal on Imaging Sciences",
volume = "10",
number = "3",
pages = "1322--1345",
year = "2017",
publisher = "SIAM",
month = "Jan",
doi = "10.1137/15M1043947",
url = "http://www.sci.utah.edu/publications/Fei2017a/1307.2358.pdf",
}
@Article{SCI:Fie2016a,
author = "L.D.J. Fiederer and J. Vorwerk and F. Lucka and M.
Dannhauer and S. Yang and M. D{\"u}mpelmann and A.
Schulze-Bonhage and A. Aertsen and O. Speck and
C.H. Wolters and T. Ball",
title = "The role of blood vessels in high-resolution
volume conductor head modeling of EEG",
journal = "NeuroImage",
volume = "128",
pages = "193--208",
year = "2016",
publisher = "Elsevier",
month = "March",
doi = "10.1016/j.neuroimage.2015.12.041",
url = "http://www.sci.utah.edu/publications/Fie2016a/fiederer_neuroimage_2016.pdf",
}
@Article{SCI:Fif2005b,
author = "P. Fife and T. Wei and J.C. Klewicki and P.A.
McMurtry",
title = "Stress Gradient Balance Layers and Scale
Hierarchies in Wall-Bounded Flows",
journal = "Journal of Fluid Mechanics",
volume = "532",
pages = "165--189",
year = "2005",
month = "June",
doi = "10.1017/S0022112005003988",
url = "http://www.sci.utah.edu/publications/Fif2005b/Fife_JFM2005.pdf",
}
@InCollection{SCI:Fis2011a,
author = "J. Fishbaugh and S. Durrleman and G. Gerig",
title = "Estimation of Smooth Growth Trajectories with
Controlled Acceleration from Time Series Shape
Data",
booktitle = "Lecture Notes in Computer Science",
pages = "401--408",
year = "2011",
series = "LNCS 6892",
publisher = "Springer",
doi = "10.1007/978-3-642-23629-7_49",
keywords = "na-mic",
url = "http://www.sci.utah.edu/publications/Fis2011a/fishbaugh_miccai2011.pdf",
}
@InProceedings{SCI:Fis2012a,
author = "J. Fishbaugh and S. Durrleman and J. Piven and G.
Gerig",
title = "A framework for longitudinal data analysis via
shape regression",
booktitle = "Medical Imaging 2012: Image Processing",
year = "2012",
editor = "David R. Haynor and Sebastien Ourselin",
publisher = "SPIE Intl Soc Optical Eng",
month = "Feb",
doi = "10.1117/12.911721",
url = "http://www.sci.utah.edu/publications/Fis2012a/Fishbaugh_spie2012_final-annot.pdf",
}
@InProceedings{SCI:Fis2012b,
author = "J. Fishbaugh and M.W. Prastawa and S. Durrleman
and G. Gerig",
title = "Analysis of Longitudinal Shape Variability via
Subject Specific Growth Modeling",
booktitle = "Medical Image Computing and Computer-Assisted
Intervention – Proceedings of MICCAI 2012",
volume = "7510",
pages = "731--738",
year = "2012",
series = "Lecture Notes in Computer Science (LNCS)",
month = "October",
doi = "10.1007/978-3-642-33415-3_90",
url = "http://www.sci.utah.edu/publications/fishbaugh12/Fishbaugh_miccai2012.pdf",
}
@InProceedings{SCI:Fis2013a,
author = "J. Fishbaugh and M.W. Prastawa and G. Gerig and S.
Durrleman",
title = "Geodesic Shape Regression in the Framework of
Currents",
booktitle = "Proceedings of the International Conference on
Information Processing in Medical Imaging
({IPMI})",
volume = "23",
pages = "718--729",
year = "2013",
pmid = "24684012",
pmcid = "PMC4127488",
url = "http://www.sci.utah.edu/publications/Fis2013a/Fishbaugh_ipmi2013.pdf",
}
@Article{SCI:Fis2013b,
author = "J. Fishbaugh and M. Prastawa and G. Gerig and S.
Durrleman",
title = "Geodesic image regression with a sparse
parameterization of diffeomorphisms",
booktitle = "Proceedings of the Geometric Science of
Information Conference (GSI)",
journal = "Geometric Science of Information Lecture Notes in
Computer Science ({LNCS})",
volume = "8085",
pages = "95--102",
year = "2013",
url = "http://www.sci.utah.edu/publications/Fis2013b/Fishbaugh_GSI2013.pdf",
}
@InProceedings{SCI:Fis2014a,
author = "J. Fishbaugh and M. Prastawa and G. Gerig and S.
Durrleman",
title = "Geodesic Regression of Image and Shape Data for
Improved Modeling of {4D} Trajectories",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "(accepted)",
year = "2014",
url = "http://www.sci.utah.edu/publications/fishbaugh14/fishbaugh_isbi2014.pdf",
}
@InProceedings{SCI:Fle2002a,
author = "P.T. Fletcher and S.M. Pizer and G. Gash and S.
Joshi",
title = "Deformable {M}-rep segmentation of object
complexes",
booktitle = "Proceedings of the {IEEE} International Symposium
on Biomedical Imaging ({ISBI})",
pages = "26--29",
year = "2002",
url = "http://www.sci.utah.edu/publications/fletcher02/ISBI02-fletcher-defmrep.pdf",
}
@Article{SCI:Fle2003a,
author = "P.T. Fletcher and S. Joshi and C. Lu and S.
Pizer",
title = "Gaussian Distributions on Lie Groups and Their
Application to Statistical Shape Analysis",
journal = "Inf Process Med Imaging",
volume = "18",
pages = "450--462",
year = "2003",
note = "Runner-up for the Francois Erbsmann Prize",
url = "http://www.sci.utah.edu/publications/fletcher03/IPMI03_Fletcher_GausDist.pdf",
}
@InProceedings{SCI:Fle2003b,
author = "P.T. Fletcher and C. Lu and S. Joshi",
title = "Statistics of Shape via Principal Component
Analysis on Lie Groups",
booktitle = "Proceedings of the Conference on Computer Vision
and Pattern Recognition (CVPR)",
pages = "95--101",
year = "2003",
month = "June",
location = "Los Alamitos, CA",
url = "http://www.sci.utah.edu/publications/fletcher03/CVPR03_Fletcher_StatsShape.pdf",
}
@Article{SCI:Fle2003c,
author = "S. Fleishman and M. Alexa and D. Cohen-Or and C.T.
Silva",
title = "Progressive Point Set Surfaces",
journal = "ACM Transactions on Graphics (TOG)",
volume = "22",
number = "4",
pages = "997--1011",
year = "2003",
issn = "0730-0301",
url = "http://www.sci.utah.edu/publications/fleishman03/ppss.pdf",
}
@Article{SCI:Fle2004a,
author = "P.T. Fletcher and C. Lu and S.M. Pizer and S.
Joshi",
title = "Principal Geodesic Analysis for the Study of
Nonlinear Statistics of Shape",
journal = "IEEE Trans Med Imaging",
volume = "23",
number = "8",
pages = "995--1005",
year = "2004",
month = "August",
url = "http://www.sci.utah.edu/publications/fletcher04/TMI04_Fletcher_PGA.pdf",
}
@Article{SCI:Fle2004b,
author = "P.T. Fletcher and S. Joshi",
title = "Principal Geodesic Analysis on Symmetric Spaces:
Statistics of Diffusion Tensors",
journal = "Computer Vision and Mathematical Methods in
Medical and Biomedical Image Analysis",
volume = "3117",
pages = "87--98",
year = "2004",
series = "Springer-Verlag, Lecture Notes In Computer
Science",
doi = "10.1109/TMI.2004.831793",
url = "http://www.sci.utah.edu/publications/fletcher04/CVAMIA04_Fletcher_DTStats.pdf",
}
@PhdThesis{SCI:Fle2004c,
author = "P.T. Fletcher",
title = "Statistical Variability in Nonlinear Spaces:
Application to Shape Analysis and DT-MRI",
year = "2004",
school = "University of North Carolina Department of
Computer Science",
month = "August",
note = "Ph.D. Thesis",
url = "http://www.sci.utah.edu/publications/fletcher04/fletcher_thesis.pdf",
}
@InCollection{SCI:Fle2006a,
author = "P.T. Fletcher and S.M. Pizer and S. Joshi",
title = "Shape Variation of Medial Axis Representations via
Principal Geodesic Analysis on Symmetric Spaces",
booktitle = "Statistics and Analysis of Shapes",
pages = "29--59",
year = "2006",
publisher = "Springer",
doi = "10.1007/0-8176-4481-4_2",
}
@InProceedings{SCI:Fle2006b,
author = "P.T. Fletcher and R.T. Whitaker",
title = "Riemannian Metrics on the Space of Solid Shapes",
booktitle = "MICCAI Workshop on Mathematical Foundations of
Computational Anatomy",
year = "2006",
month = "October",
url = "http://www.sci.utah.edu/publications/fletcher06/FletcherMFCA2006.pdf",
}
@Article{SCI:Fle2007a,
author = "P.T. Fletcher and S. Joshi",
title = "Riemannian Geometry for the Statistical Analysis
of Diffusion Tensor Data",
journal = "Signal Processing",
volume = "87",
number = "2",
pages = "250--262",
year = "2007",
month = "February",
keywords = "diffusion tensor,",
url = "http://www.sci.utah.edu/publications/fletcher07/FletcherTensorStatsSP.pdf",
}
@Article{SCI:Fle2007b,
author = "P.T. Fletcher and R. Tao and W.-K. Jeong and R.T.
Whitaker",
title = "A Volumetric Approach to Quantifying
Region-to-Region White Matter Connectivity in
Diffusion Tensor MRI",
journal = "Information Processing in Medical Imaging",
volume = "4584/2007",
pages = "346--358",
year = "2007",
keywords = "tensor field methods, diffusion tensor imaging,
neuro brain",
}
@InCollection{SCI:Fle2007c,
author = "P.T. Fletcher and S. Powell and N.L. Foster and S.
Joshi",
title = "Quantifying Metabolic Asymmetry Modulo Structure
in Alzheimer's Disease",
booktitle = "Lecture Notes in Computer Science",
pages = "446--457",
year = "2007",
publisher = "Springer",
doi = "10.1007/978-3-540-73273-0_37",
pmid = "17633720",
keywords = "alzheimers",
}
@InProceedings{SCI:Fle2008a,
author = "P.T. Fletcher and S. Venkatasubramanian and S.
Joshi",
title = "Robust Statistics on Riemannian Manifolds via the
Geometric Median",
booktitle = "{IEEE} Conference on Computer Vision and Pattern
Recognition ({CVPR} 2008)",
pages = "1--8",
year = "2008",
doi = "10.1109/CVPR.2008.4587747",
url = "http://www.sci.utah.edu/publications/fletcher08/Fletcher_CVPR2008.pdf",
}
@Article{SCI:Fle2009a,
author = "P.T. Fletcher PT and S. Venkatasubramanian and S.
Joshi",
title = "The geometric median on Riemannian manifolds with
application to robust atlas estimation",
journal = "Neuroimage",
volume = "45",
number = "1",
pages = "S143--S152",
year = "2009",
month = "March",
pmid = "19056498",
url = "http://www.sci.utah.edu/publications/fletcher09/Fletcher_NeuroImage2009.pdf",
}
@InProceedings{SCI:Fle2009b,
author = "P.T. Fletcher and J. Moeller and J.M. Phillips and
S. Venkatasubramanian",
title = "Computing Hulls In Positive Definite Space",
booktitle = "In Proceedings of the 19th Fall Workshop on
Computational Geometry",
year = "2009",
month = "November",
url = "http://www.sci.utah.edu/publications/fletcher09/Fletcher_WorksCompGeo2009.pdf",
}
@Article{SCI:Fle2010a,
author = "P.T. Fletcher and R.T. Whitaker and R. Tao and
M.B. DuBray and A. Froehlich and C. Ravichandran
and A.L. Alexander and E.D. Bigler and N. Lange and
J.E. Lainhart",
title = "Microstructural connectivity of the arcuate
fasciculus in adolescents with high-functioning
autism",
journal = "NeuroImage",
volume = "51",
number = "3",
pages = "1117--1125",
year = "2010",
month = "July",
note = "Epub Feb 2 2010",
pmid = "20132894",
url = "http://www.sci.utah.edu/publications/fletcher10/Fletcher_Neuroimage2010.pdf",
}
@InProceedings{SCI:Fle2011a,
author = "P.T. Fletcher",
title = "Geodesic Regression on Riemannian Manifolds",
booktitle = "Proceedings of the Third MICCIA International
Workshop on Mathematical Foundations of
Computational Anatomy (MFCA)",
pages = "75--86",
year = "2011",
location = "Toronto, Canada",
url = "http://www.sci.utah.edu/publications/fletcher11/Fletcher_MFCA2011.pdf",
}
@Article{SCI:Fle2011b,
author = "P.T. Fletcher and J. Moeller and J. Phillips and
S. Venkatasubramanian",
title = "Horoball hulls and extents in positive definite
space",
journal = "Algorithms and Data Structures",
volume = "6844/2011",
pages = "386--398",
year = "2011",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-22300-6_33",
url = "http://www.sci.utah.edu/publications/fletcher11/Fletcher_ADS2011.pdf",
}
@Misc{SCI:FluoRender,
author = "{SCI} Institute",
year = "2015",
note = "{FluoRender}: An interactive rendering tool for
confocal microscopy data visualization. Scientific
Computing and Imaging Institute ({SCI}) Download
from: http://www.fluorender.org",
keywords = "FluoRender, volume rendering",
}
@InProceedings{SCI:Fog2009b,
author = "T. Fogal and J. Kr{\"u}ger",
title = "Size Matters - Revealing Small Scale Structures in
Large Datasets",
booktitle = "Proceedings of the World Congress on Medical
Physics and Biomedical Engineering, September 7 -
12, 2009, Munich, Germany",
volume = "25/13",
pages = "41--44",
year = "2009",
series = "IFMBE Proceedings",
publisher = "Springer Berlin Heidelberg",
url = "http://www.sci.utah.edu/publications/Fog2009b/Fogal_IFMBE2009b.pdf",
}
@InProceedings{SCI:Fog2010a,
author = "T. Fogal and J. Kr{\"u}ger",
title = "Tuvok, an Architecture for Large Scale Volume
Rendering",
booktitle = "Proceedings of the 15th International Workshop on
Vision, Modeling, and Visualization",
pages = "139--146",
year = "2010",
month = "November",
doi = "10.2312/PE/VMV/VMV10/139-146",
url = "http://www.sci.utah.edu/publications/Fog2010a/Fogal_Tuvok2010.pdf",
}
@InProceedings{SCI:Fog2010b,
author = "T. Fogal and H. Childs and S. Shankar and J.
Kr{\"u}ger and R.D. Bergeron and P. Hatcher",
title = "Large Data Visualization on Distributed Memory
Multi-GPU Clusters",
booktitle = "Proceedings of High Performance Graphics 2010",
pages = "57--66",
year = "2010",
url = "http://www.sci.utah.edu/publications/Fog2010b/Fogal_MultiGPU2010.pdf",
}
@InProceedings{SCI:Fog2011a,
author = "T. Fogal and J. Kr{\"u}ger",
title = "Efficient {I/O} for Parallel Visualization",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization (2011)",
pages = "81--90",
year = "2011",
editor = "T. Kuhlen and R. Pajarola and K. Zhou",
url = "http://www.sci.utah.edu/publications/Fog2011a/Fogal_PracticalIO.pdf",
}
@InProceedings{SCI:Fog2013a,
author = "T. Fogal and A. Schiewe and J. Kr{\"u}ger",
title = "An Analysis of Scalable GPU-Based Ray-Guided
Volume Rendering",
booktitle = "2013 {IEEE} Symposium on Large Data Analysis and
Visualization ({LDAV})",
year = "2013",
url = "http://www.sci.utah.edu/publications/Fog2013a/Fogal_Analysis2013.pdf",
}
@InProceedings{SCI:Fog2014a,
author = "T. Fogal and F. Proch and A. Schiewe and O.
Hasemann and A. Kempf and J. Kr{\"u}ger",
title = "{Free}processing: Transparent in situ
visualization via data interception",
booktitle = "Proceedings of the 14th Eurographics Conference on
Parallel Graphics and Visualization",
year = "2014",
series = "EGPGV",
publisher = "Eurographics Association",
url = "http://www.sci.utah.edu/publications/Fog2014a/Fogal-2014-InSitu.pdf",
}
@InCollection{SCI:Foo2017a,
author = "M. Foote and P. Sabouri and A. Sawant and S.
Joshi",
title = "Rank Constrained Diffeomorphic Density Motion
Estimation for Respiratory Correlated Computed
Tomography",
title_url =
"https://link.springer.com/chapter/10.1007/978-3-319-67675-3_16",
booktitle = "Graphs in Biomedical Image Analysis, Computational
Anatomy and Imaging Genetics",
pages = "177--185",
year = "2017",
publisher = "Springer International Publishing",
doi = "10.1007/978-3-319-67675-3_16",
}
@InProceedings{SCI:Foo2018a,
author = "M.D. Foote and B. Zimmerman and A. Sawant and S.
Joshi",
title = "Real-Time Patient-Specific Lung Radiotherapy
Targeting using Deep Learning",
booktitle = "1st Conference on Medical Imaging with Deep
Learning (MIDL 2018)",
year = "2018",
location = "Amsterdam, The Netherlands",
url = "http://www.sci.utah.edu/publications/Foo2018a/1b1f81764bafb31175a3acf9212b32e2ef140679.pdf",
}
@InProceedings{SCI:For2000a,
author = "A. Forsberg and R.M. Kirby and D.H. Laidlaw and
G.E. Karniadakis and A. van Dam and J. Elion",
title = "Immersive Virtual Reality for Visualizing Flow
Through an Artery",
booktitle = "Proceedings of {IEEE} Visualization 2000",
pages = "457--460",
year = "2000",
month = "October",
location = "Salt Lake City, UT",
}
@Article{SCI:For92a,
author = "D. Forslunk and P. Hinker and C.D. Hansen and
W.St. John and S. Tenbrink and J. Brewton",
title = "High-speed Networks, Visualization and Massive
Parallelism in the Advanced Computing Laboratory",
journal = "Computing Systems in Engineering",
volume = "3",
number = "1-4",
year = "1992",
}
@Article{SCI:Fos2005a,
author = "M. Foskey and B. Davis and L. Goyal and S. Chang
and E. Chaney and N. Strehl and S. Tomei and J.
Rosenman and S. Joshi",
title = "Large Deformation Three-Dimensional Image
Registration in Image-Guided Radiation Therapy",
journal = "Phys Med Biol",
volume = "50",
number = "24",
pages = "5869--5892",
year = "2005",
month = "December 21",
url = "http://www.sci.utah.edu/publications/foskey05/Foskey05_submission.pdf",
}
@Article{SCI:Fos2008a,
author = "N.L. Foster and A.Y. Wang and T. Tasdizen and P.T.
Fletcher and J.M. Hoffman and R.A. Koeppe",
title = "Realizing the Potential of Positron Emission
Tomography with 18F-Fluorodeoxyglucose to Improve
the Treatment of Alzheimer",
journal = "Journal of the Alzheimer",
volume = "4",
number = "1, Suppl. 1",
pages = "S29--36",
year = "2008",
pmid = "18631997",
keywords = "PET, alzheimers",
}
@Article{SCI:Fos2008b,
author = "N. L. Foster and A.Y. Wang and T. Tasdizen and K.
Chen and W. Jagust and R.A. Koeppe and E. Reiman
and M.W. Weiner and S. Minoshima",
title = "Cerebral Hypometabolism Suggesting Frototemporal
Dementia in an Alzheimer’s Disease Clinical
Trial",
journal = "Neurology",
volume = "70",
number = "11",
pages = "A103",
year = "2008",
}
@InProceedings{SCI:Fou2005a,
author = "N. Fout and H. Akiba and K-L. Ma and A.E. Lefohn
and J.M. Kniss",
title = "High-Quality Rendering of Compressed Volume Data
Formats",
booktitle = "Proceedings of The Joint {EUROGRAPHICS-IEEE}
{VGTC} Symposium on Visualization 2005",
year = "2005",
keywords = "scalar field methods, volume rendering",
url = "http://www.sci.utah.edu/publications/fout05/fout_eurovis05.pdf",
}
@Article{SCI:Fow2011a,
author = "C. Fowlkes and K. Eckenrode and M. Bragdon and
M.D. Meyer and Z. Wunderlich and L. Simirenko and
C. Luengo and S. Keranen and C. Henriquez and D.
Knowles and M. Biggin and M. Eisen and A. DePace",
title = "A Conservered Developmental Patterning Network
Produces Quantitatively Different Output in
Multiple Species of Drosophila",
journal = "PLoS Genetics",
volume = "7",
number = "10:e1002346",
pages = "17 pages",
year = "2011",
month = "October",
url = "http://www.sci.utah.edu/publications/fowlkes11/Fowlkes_PLoS2011.pdf",
}
@Article{SCI:Fra1993a,
author = "E.P. France and J.A. Weiss and L.E. Paulos",
title = "Allograft Ligament Reconstruction: Biomechanical
Issues and Testing",
journal = "Sports Medicine and Arthroscopy Review",
volume = "1",
pages = "47--60",
year = "1993",
}
@InProceedings{SCI:Fre2002a,
author = "J. Freire and J. Haritsa and M. Ramanath and P.
Roy and J. Simeon",
title = "StatiX: Making XML Count",
booktitle = "Proceedings of the 2002 ACM SIGMOD International
Conference on Management of Data",
pages = "181--191",
year = "2002",
keywords = "xml",
url = "http://www.sci.utah.edu/publications/freire02/Freire_SIGMOD2002.pdf",
}
@Article{SCI:Fre2003a,
author = "J. Freire and J. Simeon",
title = "Adaptive XML Shredding: Architecture,
Implementation, and Challenges",
journal = "Efficiency and Effectiveness of XML Tools and
Techniques and Data Integration over the Web",
volume = "2590/2008",
pages = "104--116",
year = "2003",
series = "Lecture Notes in Computer Science (LNCS)",
url = "http://www.sci.utah.edu/publications/freire03/Freire_LNCS2003.pdf",
}
@Article{SCI:Fre2004a,
author = "J. Freire and M. Benedikt",
title = "Managing XML Data: An Abridged Overview",
journal = "Computing in Science and Engineering",
volume = "6",
number = "4",
pages = "12--19",
year = "2004",
publisher = "IEEE Computer Society",
issn = "1521-9615",
keywords = "xml",
}
@InProceedings{SCI:Fre2004b,
author = "J. Freire and M. Ramanath and L. Zhang",
title = "A Flexible Infrastructure for Gathering XML
Statistics and Estimating Query Cardinality",
booktitle = "Proceedings of the 20th International Conference
on Data Engineering",
pages = "857",
year = "2004",
isbn = "0-7695-2065-0",
url = "http://www.sci.utah.edu/publications/freire04/Freire_ICDE2004.pdf",
}
@Article{SCI:Fre2006a,
author = "J. Freire and C.T. Silva and S.P. Callahan and E.
Santos and C.E. Scheidegger and H.T. Vo",
title = "Managing Rapidly-Evolving Scientific Workflows",
booktitle = "Proceedings of The 2006 International Provenance
and Annotation Workshop",
journal = "Provenance and Annotation of Data",
pages = "10--18",
year = "2006",
series = "Lecture Notes in Computer Science (LNCS)",
keywords = "scirun, pse pses problem solving envoronment,
vistrails, provenance",
url = "http://www.sci.utah.edu/publications/freire06/ipaw2006.pdf",
}
@InProceedings{SCI:Fre2008a,
author = "J. Freire and C.T. Silva",
title = "Towards Enabling Social Analysis of Scientific
Data",
booktitle = "Proceedings of CHI Social Data Analysis Workshop
2008",
year = "2008",
url = "http://www.sci.utah.edu/publications/Fre2008a/chi2008.pdf",
}
@Article{SCI:Fre2008b,
author = "J. Freire and D. Koop and C.T. Silva",
title = "Provenance for Computational Tasks: A Survey",
journal = "Computing in Science and Engineering",
volume = "10",
number = "3",
pages = "11--21",
year = "2008",
keywords = "vistrails, provenance, workflow management",
url = "http://www.sci.utah.edu/publications/freire08/cise2008a.pdf",
}
@Article{SCI:Fre2009a,
author = "J. Freire",
title = "Provenance Management: Challenges and
Opportunities",
journal = "Datenbanksysteme in Business, Technologie und Web
(BTW)",
pages = "4",
year = "2009",
}
@InProceedings{SCI:Fri2007a,
author = "H. Friedrich and I. Wald and P. Slusallek",
title = "Interactive Iso-Surface Ray Tracing of Massive
Volumetric Data Sets",
booktitle = "Proceedings of the 2007 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "109--116",
year = "2007",
keywords = "volume rendering, parallel visualization,
interactive rt distributed interactive ray tracing
dirt, rtcenter, large dataset visualization",
url = "http://www.sci.utah.edu/publications/friedrich07/async.pdf",
}
@Article{SCI:Fu2011a,
author = "Z. Fu and W.-K. Jeong and Y. Pan and R.M. Kirby
and R.T. Whitaker",
title = "A fast iterative method for solving the Eikonal
equation on triangulated surfaces",
journal = "SIAM Journal of Scientific Computing",
volume = "33",
number = "5",
pages = "2468--2488",
year = "2011",
doi = "10.1137/100788951",
pmcid = "PMC3360588",
url = "http://www.sci.utah.edu/publications/fu11/Fu_SIAM-JSC2011.pdf",
}
@Article{SCI:Fu2013a,
author = "Z. Fu and R.M. Kirby and R.T. Whitaker",
title = "A Fast Iterative Method for Solving the Eikonal
Equation on Tetrahedral Domains",
journal = "{SIAM} Journal on Scientific Computing",
volume = "35",
number = "5",
pages = "C473--C494",
year = "2013",
url = "http://www.sci.utah.edu/publications/Fu2013a/Fu_JSC2013.pdf",
}
@TechReport{SCI:Fu2014a,
author = "Z. Fu and H.K. Dasari and M. Berzins and B.
Thompson",
title = "Parallel Breadth First Search on GPU Clusters",
number = "UUSCI-2014-002",
year = "2014",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "GPU cluster, MPI, BFS, graph, parallel graph
algorithm",
url = "http://www.sci.utah.edu/publications/Fu2014a/UUSCI-2014-002.pdf",
}
@InProceedings{SCI:Fu2014b,
author = "Z. Fu and H.K. Dasari and M. Berzins and B.
Thompson",
title = "Parallel Breadth First Search on {GPU} Clusters",
booktitle = "Proceedings of the {IEEE} {BigData} 2014
Conference",
year = "2014",
month = "October",
location = "Washington DC",
keywords = "GPU cluster, MPI, BFS, graph, parallel graph
algorithm",
url = "http://www.sci.utah.edu/publications/Fu2014b/Fu_BigData2014.pdf",
}
@InProceedings{SCI:Fuc2008a,
author = "M. Fuchs and S. Gerber",
title = "Variational Shape Detection in Microscope Images
Based on Joint Shape and Image Feature
Statistics",
booktitle = "Proceedings of the {IEEE} Computer Society
Workshop on Mathematical Methods in Biomedical
Image Analysis ({MMBIA} 2008)",
pages = "1--8",
year = "2008",
doi = "10.1109/CVPRW.2008.4563012",
url = "http://www.sci.utah.edu/publications/fuchs08/Fuchs_MMBIA08.pdf",
}
@Article{SCI:Fur2017a,
author = "K. Furmanova and S. Gratzl and H. Stitz and T.
Zichner and M. Jaresova and M. Ennemoser and A. Lex
and M. Streit",
title = "Taggle: Scalable Visualization of Tabular Data
through Aggregation",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Fur2017a/1712.05944.pdf",
}
@Misc{SCI:Fusion,
year = "2015",
note = "{FusionView}: Problem Solving Environment for
{MHD} Visualization. Scientific Computing and
Imaging Institute ({SCI}), Download from:
http://www.scirun.org",
keywords = "Fusion, VACET",
}
@Article{SCI:Gal2016a,
author = "C. Gall and S. Schmidt and M.P. Schittkowski and
A. Antal and G. Ambrus and W. Paulus and M.
Dannhauer and R. Michalik and A. Mante and M. Bola
and A. Lux and S. Kropf and S.A. Brandt and B.A.
Sabel",
title = "Alternating Current Stimulation for Vision
Restoration after Optic Nerve Damage: A Randomized
Clinical Trial",
journal = "PLOS ONE",
volume = "11",
number = "6",
pages = "e0156134",
year = "2016",
publisher = "Public Library of Science",
month = "June",
doi = "10.1371/journal.pone.0156134",
url = "http://www.sci.utah.edu/publications/Gal2016a/journal.pone.0156134.PDF",
}
@InProceedings{SCI:Gam2013a,
author = "M. Gamell and I. Rodero and M. Parashar and J.C.
Bennett and H. Kolla and J.H. Chen and P.-T. Bremer
and A. Landge and A. Gyulassy and P. McCormick and
Scott Pakin and Valerio Pascucci and Scott
Klasky",
title = "Exploring Power Behaviors and Trade-offs of
In-situ Data Analytics",
booktitle = "Proceedings of the International Conference for
High Performance Computing, Networking, Storage and
Analysis",
year = "2013",
publisher = "Association for Computing Machinery",
isbn = "978-1-4503-2378-9",
doi = "10.1145/2503210.2503303",
keywords = "SDAV",
url = "http://www.sci.utah.edu/publications/Gam2013a/Gamell_SC2013.pdf",
}
@Article{SCI:Gao2008a,
author = "W. Gao and Y. Chen and G. Gerig and J.K. Smith and
V. Jewells and J.H. Gilmore and W. Lin",
title = "Temporal and Spatial Development of Axonal
Maturation and Myelination of White Matter in the
Developing Brain",
journal = "American Journal of Neuroradiology",
pages = "(published online)",
year = "2008",
month = "Nov 11",
doi = "10.3174/ajnr.A1363",
keywords = "ucnia",
}
@Article{SCI:Gao2009a,
author = "W. Gao and W. Lin and Y. Chen and G. Gerig and
J.K. Smith and V. Jewells and J.H. Gilmore",
title = "Temporal and Spatial Development of Axonal
Maturation and Myelination of White Matter in the
Developing Brain",
journal = "American Journal of Neuroradiology (AJNR)",
volume = "30",
pages = "290--296",
year = "2009",
pmid = "19001533",
url = "http://www.sci.utah.edu/publications/gao09/Gao_AJNR2009.pdf",
}
@InProceedings{SCI:Gao2014a,
author = "Y. Gao and M. Prastawa and M. Styner and J. Piven
and G. Gerig",
title = "A Joint Framework for {4D} Segmentation and
Estimation of Smooth Temporal Appearance Changes",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "(accepted)",
year = "2014",
url = "http://www.sci.utah.edu/publications/gao14/Gao_ISBI2014.pdf",
}
@Article{SCI:Gao2015a,
author = "Y. Gao and L. Zhu and J. Cates and R. S. MacLeod
and S. Bouix and and A. Tannenbaum",
title = "A Kalman Filtering Perspective for Multiatlas
Segmentation",
journal = "SIAM J. Imaging Sciences",
volume = "8",
number = "2",
pages = "1007-1029",
year = "2015",
doi = "10.1137/130933423",
url = "http://www.sci.utah.edu/publications/Gao2015a/gao_siam_imaging2015.pdf",
}
@InProceedings{SCI:Gao2016a,
author = "Y. Gao and M. Zhang and K. Grewen and P. T.
Fletcher and G. Gerig",
title = "Image registration and segmentation in
longitudinal MRI using temporal appearance
modeling",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
pages = "629--632",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493346",
url = "http://www.sci.utah.edu/publications/Gao2016a/ISBI2016_Yang_edited.pdf",
}
@Article{SCI:Gar2001a,
author = "J.C. Gardiner and J.A. Weiss and T.D. Rosenberg",
title = "Strain in the Human Medial Collateral Ligament
During Valgus Loading",
journal = "Clinical Orthopaedics and Related Research",
volume = "391",
pages = "266--274",
year = "2001",
url = "http://www.sci.utah.edu/publications/gardiner01/mclstrain_clinorthop.pdf",
}
@Article{SCI:Gar2001b,
author = "J.C. Gardiner and J.A. Weiss",
title = "Simple Shear Testing of Parallel-Fibered Planar
Soft Tissues",
journal = "Journal of Biomechanical Engineering",
volume = "123",
pages = "1--5",
year = "2001",
url = "http://www.sci.utah.edu/publications/gardiner01/JBMEshear.pdf",
}
@Article{SCI:Gar2003a,
author = "J.C. Gardiner and J.A. Weiss",
title = "Subject-Specific Finite Element Analysis of the
Human Medial Collateral Ligament During Valgus Knee
Loading",
journal = "Journal of Orthopaedic Research",
volume = "21",
pages = "1098--1106",
year = "2003",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
finite elements, forward problems inverse problems
forward simulation inverse solutions, computational
biomechanics, ip image processing signal
processing, segmentation",
url = "http://www.sci.utah.edu/publications/gardiner03/gardiner_jor_2003.pdf",
}
@InProceedings{SCI:Gar2004a,
author = "C. Garth and X. Tricoche and G. Scheuermann",
title = "Tracking of Vector Field Singularities in
Unstructured 3D Time-Dependent Datasets",
booktitle = c-VIS2004,
pages = "329--336",
year = "2004",
keywords = "cfd computational fluid dynamics, vector field
methods, Poincare index, time dependent topology,
poincare index, ncrr",
url = "http://www.sci.utah.edu/publications/garth04/tracking3d.pdf",
}
@InProceedings{SCI:Gar2004b,
author = "C. Garth and X. Tricoche and T. Salzbrunn and T.
Bobach and G. Scheuermann",
title = "Surface Techniques for Vortex Visualization",
booktitle = "Proceedings of Joint Eurographics - {IEEE} {TCVG}
Symposium on Visualization",
pages = "155--164",
year = "2004",
month = "May",
keywords = "cfd computational fluid dynamics, computational
mechanics, fluid structure problems, aerodynamics,
ncrr",
url = "http://www.sci.utah.edu/publications/garth04/vissym04.pdf",
}
@InProceedings{SCI:Gar2007a,
author = "C. Garth and G. Li and X. Tricoche and C.D. Hansen
and H. Hagen",
title = "Visualization of Coherent Structures in Transient
2D Flows",
booktitle = "Proceedings of the 2007 Workshop on Topology-Based
Method in Visualization (TopoInVis)",
year = "2007",
month = "March",
location = "Grimma, Germany",
keywords = "csafe c-safe",
url = "http://www.sci.utah.edu/publications/garth07/topoinvis07.pdf",
}
@InProceedings{SCI:Gar2007b,
author = "C. Garth and F. Gerhardt and X. Tricoche and H.
Hagen",
title = "Efficient Computation and Visualization of
Coherent Structures in Fluid Flow Applications",
booktitle = "Proceeding of {IEEE} Visualization 2007",
pages = "1464--1471",
year = "2007",
keywords = "vacet, cfd computational fluid dynamics,
aerodynamics",
url = "http://www.sci.utah.edu/publications/garth07/garth-vis07.pdf",
}
@InCollection{SCI:Gar2007c,
author = "C. Garth and B. Laramee and X. Tricoche and H.
Hauser and J. Schneider",
title = "Extraction and Visualization of Swirl and Tumble
Motion from Engine Simulation Data",
booktitle = " Topology-based Methods in Visualization",
pages = "121--135",
year = "2007",
series = "Mathematics and Visualization",
publisher = "Springer Berlin Heidelberg",
isbn = "978-3-540-70822-3",
doi = "10.1007/978-3-540-70823-0_9",
url = "http://www.sci.utah.edu/publications/Gar2007c/Garth_TopoInVis2007.pdf",
}
@InProceedings{SCI:Gar2013a,
author = "G. Gardner and A. Morris and K. Higuchi and R.S.
MacLeod and J. Cates",
title = "A Point-Correspondence Approach to Describing the
Distribution of Image Features on Anatomical
Surfaces, with Application to Atrial
Fibrillation",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "226--229",
year = "2013",
doi = "10.1109/ISBI.2013.6556453",
url = "http://www.sci.utah.edu/publications/gardener13/Gardner_ISBI2013.pdf",
}
@InProceedings{SCI:Gen2005a,
author = "S.E. Geneser and S. Choe and R.M. Kirby and R.S.
MacLeod",
title = "Influence of Stochastic Organ Conductivity in 2D
ECG Forward Modeling: A Stochastic Finite Element
Study",
booktitle = c-BEMNFSI2005,
pages = "5528--5531",
year = "2005",
keywords = "forward problems inverse problems forward
simulation inverse solutions, forward simulation,
cardiac heart, ncrr",
url = "http://www.sci.utah.edu/publications/geneser05/Geneser_Stochastic_FE_study.pdf",
}
@Article{SCI:Gen2007a,
author = "S.E. Geneser and R.M. Kirby and D. Xiu and F.B.
Sachse",
title = "Stochastic Markovian Modeling of Electrophysiology
of Ion Channels: Reconstruction of Standard
Deviations in Macroscopic Currents",
journal = "Journal of Theoretical Biology",
volume = "245",
number = "4",
pages = "627--637",
year = "2007",
doi = "10.1016/j.jtbi.2006.10.016",
keywords = "Stochastic Galerkin, Polynomial chaos, Stochastic
processes, Markov modeling, Ion channels",
url = "http://www.sci.utah.edu/publications/geneser07/Kirby-20.pdf",
}
@Article{SCI:Gen2008a,
author = "S.E. Geneser and R.M. Kirby and R.S. MacLeod",
title = "Application of Stochastic Finite Element Methods
to Study the Sensitivity of ECG Forward Modeling to
Organ Conductivity",
journal = "{IEEE} Transations on Biomedical Engineering",
volume = "55",
number = "1",
pages = "31--40",
year = "2008",
month = "January",
url = "http://www.sci.utah.edu/publications/geneser08/geneser08-ieee-bme.pdf",
}
@Article{SCI:Gen2009a,
author = "S.E. Geneser and R.M. Kirby and Brian Wang and B.
Salter and S. Joshi",
title = "Incorporating patient breathing variability into a
stochastic model of dose deposition for
stereotactic body radiation therapy",
journal = "Information Processing in Medical Imaging",
volume = "5636",
pages = "688--700",
year = "2009",
series = "Lecture Notes in Computer Science LNCS",
pmid = "19694304",
url = "http://www.sci.utah.edu/publications/geneser09/Geneser_LNCS2009.pdf",
}
@Article{SCI:Gen2010a,
author = "S.E. Geneser and J.D. Hinkle and R.M. Kirby and
Brian Wang and B. Salter and S. Joshi",
title = "Quantifying Variability in Radiation Dose Due to
Respiratory-Induced Tumor Motion",
journal = "Medical Image Analysis",
volume = "15",
number = "4",
pages = "640--649",
year = "2010",
doi = "10.1016/j.media.2010.07.003",
url = "http://www.sci.utah.edu/publications/geneser10/MEDIA-D-09-00276_abstract.pdf",
}
@Article{SCI:Gen2011a,
author = "S.E. Geneser and J.D. Hinkle and R.M. Kirby and Bo
Wang and B. Salter and S. Joshi",
title = "Quantifying variability in radiation dose due to
respiratory-induced tumor motion",
journal = "Medical Image Analysis",
volume = "15",
number = "4",
pages = "640--649",
year = "2011",
doi = "10.1016/j.media.2010.07.003",
url = "http://www.sci.utah.edu/publications/geneser11/Geneser_MIA2011.pdf",
}
@Article{SCI:Gen2012a,
author = "X. Geng and S. Gouttard and A. Sharma and H. Gu
and M. Styner and W. Lin and G. Gerig and J.H.
Gilmore",
title = "Quantitative Tract-Based White Matter Development
from Birth to Age Two Years",
journal = "NeuroImage",
pages = "1-44",
year = "2012",
month = "March",
doi = "10.1016/j.neuroimage.2012.03.057",
url = "http://www.sci.utah.edu/publications/geng12/Geng_NeuroImage2012.pdf",
}
@Article{SCI:Gen2014a,
author = "M.G. Genton and C.R. Johnson and K. Potter and G.
Stenchikov and Y. Sun",
title = "Surface boxplots",
journal = "Stat Journal",
volume = "3",
number = "1",
pages = "1--11",
year = "2014",
url = "http://www.sci.utah.edu/publications/Gen2014a/Genton_GJPSS2014.pdf",
}
@InProceedings{SCI:Ger2000a,
author = "J.D. de St. Germain and J. McCorquodale and S.G.
Parker and C.R. Johnson",
title = "Uintah: A Massively Parallel Problem Solving
Environment",
booktitle = "Ninth {IEEE} International Symposium on High
Performance and Distributed Computing",
pages = "33--41",
year = "2000",
publisher = "{IEEE}, Piscataway, NJ",
month = "Nov",
keywords = "scirun, uintah, csafe",
url = "http://www.sci.utah.edu/publications/dav00/uintah-hpdc00.pdf",
}
@InProceedings{SCI:Ger2002a,
author = "J.D. de St. Germain and A. Morris and S.G. Parker
and A.D. Malony and S. Shende",
title = "Integrating Performance Analysis in the Uintah
Software Development Cycle",
booktitle = c-ISHPC2002,
pages = "190--206",
year = "2002",
month = "May 15-17",
keywords = "scirun, uintah, csafe, csafe c-safe, problem
solving environments, pse",
url = "http://www.sci.utah.edu/publications/dav02/ishpc2002.pdf",
}
@InProceedings{SCI:Ger2003a,
author = "J.D. de St. Germain and S.G. Parker",
title = "Software Integration in an Academic Environment",
booktitle = "Software Quality Forum (SQF)",
pages = "(published on CD)",
year = "2003",
month = "March",
location = "Arlington, Virginia",
keywords = "SCIRun, scirun, biopse, uintah, scirun fusion,
scirun insight, csafe c-safe, PSE, software
integration, problem solving environments, pse",
}
@Article{SCI:Ger2003b,
author = "J.D. de St. Germain and A. Morris and S.G. Parker
and A.D. Malony and S. Shende",
title = "Performance Analysis Integration in the Uintah
Software Development Cycle",
journal = "International Journal of Parallel Programming",
volume = "31",
number = "1",
pages = "35--53",
year = "2003",
keywords = "uintah",
url = "http://www.sci.utah.edu/publications/Ger2003b/ijpp03.pdf",
}
@InProceedings{SCI:Ger2006a,
author = "G. Gerig and B. Davis and P. Lorenzen and S. Xu
and M. Jomier and J. Piven and S. Joshi",
title = "Computational Anatomy to Assess Longitudinal
Trajectory of Brain Growth",
booktitle = "Proceedings of The Third International Symposium
on 3D Data Processing, Visualization, and
Transmission",
pages = "1041--1047",
year = "2006",
month = "June",
url = "http://www.sci.utah.edu/publications/gerig06/CompAnat-3dpvt-Gerig-final.pdf",
}
@InProceedings{SCI:Ger2006b,
author = "G. Gerig and S. Joshi and P.T. Fletcher and K.
Gorczowski and S. Xu and S.M. Pizer and M.
Styner",
title = "Statistics of Populations of Images and its
Embedded Objects: Driving Applications in
Neuroimaging",
booktitle = "Proceedings of {IEEE} International Symposium on
Biomedical Imaging ({ISBI})",
pages = "1120--1123",
year = "2006",
month = "April",
url = "http://www.sci.utah.edu/publications/gerig06/ISBI06_Gerig.pdf",
}
@InProceedings{SCI:Ger2007a,
author = "S. Gerber and T. Tasdizen and R.T. Whitaker",
title = "Robust Non-linear Dimensionality Reduction using
Successive 1-Dimensional Laplacian Eigenmaps",
booktitle = "Proceedings of the 2007 International Conference
on Machine Learning (ICML)",
pages = "281--288",
year = "2007",
keywords = "crcns",
url = "http://www.sci.utah.edu/publications/gerber07/Gerber_ICML2007.pdf",
}
@InCollection{SCI:Ger2009a,
author = "S. Gerber and T. Tasdizen and S. Joshi and R.T.
Whitaker",
title = "On the Manifold Structure of the Space of Brain
Images",
booktitle = "Medical Image Computing and Computer-Assisted
Intervention (MICCAI 2009)",
pages = "305--312",
year = "2009",
publisher = "Springer",
doi = "10.1007/978-3-642-04268-3_38",
pmid = "20426001",
url = "http://www.sci.utah.edu/publications/Ger2009a/brainmanifold.pdf",
}
@InProceedings{SCI:Ger2009b,
author = "S. Gerber and T. Tasdizen and R.T. Whitaker",
title = "Dimensionality Reduction and Principal Surfaces
via Kernel Map Manifolds",
booktitle = "Proceedings of the 2009 International Conference
on Computer Vison (ICCV 2009)",
pages = "529--536",
year = "2009",
month = "September",
issn = "1550-5499",
doi = "10.1109/ICCV.2009.5459193",
url = "http://www.sci.utah.edu/publications/Ger2009b/kmm_iccv09.pdf",
}
@Article{SCI:Ger2010a,
author = "S. Gerber and T. Tasdizen and P.T. Fletcher and S.
Joshi and R.T. Whitaker and the Alzheimers Disease
Neuroimaging Initiative (ADNI)",
title = "Manifold modeling for brain population analysis",
journal = "Medical Image Analysis",
volume = "14",
number = "5",
pages = "643--653",
year = "2010",
series = "Special Issue on the 12th International Conference
on Medical Image Computing and Computer Assisted
Intervention (MICCAI) 2009",
note = "Awarded MICCAI 2010, Best of the Journal Issue
Award",
issn = "1361-8415",
doi = "10.1016/j.media.2010.05.008",
pmid = "20579930",
keywords = "Neurological image analysis; Population analysis;
Brain MRI; Manifold learning; Computer aided
clinical diagnosis",
url = "http://www.sci.utah.edu/publications/gerber10/Gerber_MICCAI2010.pdf",
}
@Article{SCI:Ger2010b,
author = "S. Gerber and P.-T. Bremer and V. Pascucci and
R.T. Whitaker",
title = "Visual Exploration of High Dimensional Scalar
Functions",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "16",
number = "6",
pages = "1271--1280",
year = "2010",
series = "IEEE Transactions on Visualization and Computer
Graphics",
publisher = "IEEE",
month = "Nov",
doi = "10.1109/TVCG.2010.213",
pmid = "20975167",
pmcid = "PMC3099238",
url = "http://www.sci.utah.edu/publications/Ger2010b/Gerber_hdviz2010.pdf",
}
@Article{SCI:Ger2011c,
author = "G. Gerig and I. Oguz and S. Gouttard and J. Lee
and H. An and W. Lin and M. McMurray and K. Grewen
and J. Johns and M.A. Styner",
title = "Synergy of image analysis for animal and human
neuroimaging supports translational research on
drug abuse",
journal = "Frontiers in Child and Neurodevelopmental
Psychiatry",
volume = "2",
pages = "9 pages",
year = "2011",
editor = "Linda Mayes",
issn = "1664-0640",
doi = "10.3389/fpsyt.2011.00053",
url = "http://www.sci.utah.edu/publications/gerig11/Gerig_FCNP2011.pdf",
}
@Article{SCI:Ger2011d,
author = "G. Gerig and J.H. Gilmore and W. Lin",
title = "Brain Maturation of Newborns and Infants",
journal = "Encyclopedia on Early Childhood Development
(online): Brain Development in Children - According
to Experts",
journal_url =
"http://www.child-encyclopedia.com/en-ca/child-brain/according-to-experts.html",
pages = "1--6",
year = "2011",
publisher = "Centre of Excellence for Early Childhood
Development and Strategic Knowledge Cluster on
Early Child Development",
location = "Montreal, Quebec",
url = "http://www.sci.utah.edu/publications/gerig11/Gerig-Gilmore-LinANGxp1.pdf",
}
@Article{SCI:Ger2012a,
author = "S. Gerber and K. Potter",
title = "Data Analysis with the Morse-Smale Complex: The
msr Package for R",
journal = "Journal of Statistical Software",
volume = "50",
number = "2",
year = "2012",
url = "http://www.sci.utah.edu/publications/gerber11/Gerber_JSS2011.pdf",
}
@Article{SCI:Ger2013a,
author = "S. Gerber and O. Reubel and P.-T. Bremer and V.
Pascucci and R.T. Whitaker",
title = "Morse-Smale Regression",
journal = "Journal of Computational and Graphical
Statistics",
volume = "22",
number = "1",
pages = "193--214",
year = "2013",
doi = "10.1080/10618600.2012.657132",
url = "http://www.sci.utah.edu/publications/gerber12/Gerber_msregression2012.pdf",
}
@Article{SCI:Ges2012a,
author = "P.H. Gesteland and Y. Livnat and N. Galli and M.H.
Samore and A.V. Gundlapalli",
title = "The {EpiCanvas} infectious disease weather map: an
interactive visual exploration of temporal and
spatial correlations",
journal = "J. Amer. Med. Inform. Assoc.",
volume = "19",
pages = "954--959",
year = "2012",
note = "Awarded 1st place for Outstanding Research Article
at ISDS 2012 and the Homer R. Warner Award at the
AMIA Annual Symposium 2012",
doi = "10.1136/amiajnl-2011-000486",
url = "http://www.sci.utah.edu/publications/gesteland12/Gesteland_EpiCanvas2012.pdf",
}
@InProceedings{SCI:Gey2011a,
author = "T. Geymayer and A. Lex and M. Streit and D.
Schmalstieg",
title = "Visualizing the Effects of Logically Combined
Filters",
booktitle = "Proceedings of the Conference on Information
Visualisation (IV '11)",
pages = "47--52",
year = "2011",
publisher = "IEEE",
url = "http://www.sci.utah.edu/publications/Gey2011a/2011_iv_filter-pipeline.pdf",
}
@InProceedings{SCI:Gey2014a,
author = "T. Geymayer and M. Steinberger and A. Lex and M.
Streit and and D. Schmalstieg",
title = "Show me the Invisible: Visualizing Hidden
Content",
booktitle = "Proceedings of the ACM SIGCHI Conference on Human
Factors in Computing Systems (CHI '14)",
pages = "3705--3714",
year = "2014",
series = "CHI '14",
publisher = "ACM",
isbn = "978-1-4503-2473-1",
doi = "10.1145/2556288.2557032",
url = "http://www.sci.utah.edu/publications/Gey2014a/2014_chi_hidden-content.pdf",
}
@InProceedings{SCI:Gha2015a,
author = "M.U. Ghani and S.D. Kanik and A.O. Argunsah and T.
Tasdizen and D. Unay and M. Cetin",
title = "Dendritic spine shape classification from
two-photon microscopy images",
booktitle = "2015 23nd Signal Processing and Communications
Applications Conference (SIU)",
year = "2015",
publisher = "IEEE",
month = "May",
doi = "10.1109/siu.2015.7129985",
url = "http://www.sci.utah.edu/publications/Gha2015a/07129985.pdf",
}
@InCollection{SCI:Gha2016a,
author = "M.U. Ghani and E. Erdil and S.D. Kanik and A.O.
Argunsah and A. Hobbiss and I. Israely and D. Unay
and T. Tasdizen and M. Cetin",
title = "Dendritic Spine Shape Analysis: A Clustering
Perspective",
booktitle = "Lecture Notes in Computer Science",
pages = "256--273",
year = "2016",
publisher = "Springer International Publishing",
doi = "10.1007/978-3-319-46604-0_19",
url = "http://www.sci.utah.edu/publications/Gha2016a/1607.05523.pdf",
}
@InProceedings{SCI:Gha2016b,
author = "M.U. Ghani and A.O. Argunsah and I. Israely and D.
Unay and T. Tasdizen and M. Cetin",
title = "On comparison of manifold learning techniques for
dendritic spine classification",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493278",
url = "http://www.sci.utah.edu/publications/Gha2016b/07493278.pdf",
}
@InProceedings{SCI:Gha2016c,
author = "M.U. Ghani and F. Mesadi and S..D Kanik and A.O.
Argunsah and I. Israely and D. Unay and T. Tasdizen
and M. Cetin",
title = "Dendritic spine shape analysis using disjunctive
normal shape models",
booktitle = "2016 IEEE 13th International Symposium on
Biomedical Imaging (ISBI)",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493280",
url = "http://www.sci.utah.edu/publications/Gha2016c/07493280.pdf",
}
@Article{SCI:Gha2017a,
author = "E. Ghafoori and E.G. Kholmovski and S. Thomas and
J. Silvernagel and N. Angel and N. Hu and D.J.
Dosdall and R.s. MacLeod and R. Ranjan",
title = "Characterization of Gadolinium Contrast
Enhancement of Radiofrequency Ablation Lesions in
Predicting Edema and Chronic Lesion Size",
journal = "Circulation: Arrhythmia and Electrophysiology",
volume = "10",
number = "11",
pages = "e005599",
year = "2017",
publisher = "Ovid Technologies (Wolters Kluwer Health)",
month = "Oct",
doi = "10.1161/circep.117.005599",
url = "http://www.sci.utah.edu/publications/Gha2017a/e005599.full.pdf",
}
@InProceedings{SCI:Gha93a,
author = "P.B. Gharpure and C.R. Johnson",
title = "A 3D Cellular Automata Model of the Heart",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
15th Annual International Conference",
pages = "752--753",
year = "1993",
publisher = "{IEEE} Press",
keywords = "scalar field methods, cardiac heart",
}
@TechReport{SCI:Gha95,
author = "P. Gharpure and C.R. Johnson",
title = "A Cellular Automaton Model of Electrical
Activation in Canine Ventricles: A Validation
Study",
number = "UUSCI-1995-002",
year = "1995",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-1995-002.pdf",
}
@Article{SCI:Ghi2017a,
author = "S. Ghimire and J. Dhamala and J. Coll-Font and J.
D. Tate and M. S. Guillem and D. H. Brooks and R.
S. MacLeod and L. Wang",
title = "Overcoming Barriers to Quantification and
Comparison of Electrocardiographic Imaging Methods:
A Community-Based Approach",
journal = "Computing in Cardiology",
volume = "44",
year = "2017",
url = "http://www.sci.utah.edu/publications/Ghi2017a/370-289.pdf",
}
@Article{SCI:Gho2000a,
author = "S. Ghorai and A.S. Tomlin and M. Berzins",
title = "Resolution of pollutant concentrations in the
boundary layer using a fully 3-D adaptive gridding
technique",
journal = "Atmospheric Environment",
volume = "34",
number = "18",
pages = "2851-2863",
year = "2000",
url = "http://www.sci.utah.edu/publications/ghorai00/atm2000paper.pdf",
}
@InProceedings{SCI:Gho2004a,
author = "A. Ghodrati and D.H. Brooks and R.S. MacLeod",
title = "On Selecting and Using Reduced Sets of Leads for
Electrocardiographic Imaging Using
Reconstruction-Quality Criteria",
booktitle = "Proceedings of The SIAM Conference on Imaging
Science 2004",
year = "2004",
month = "May",
location = "Salt Lake City, UT",
note = "abstract.",
keywords = "ncrr",
}
@InProceedings{SCI:Gho2004b,
author = "A. Ghodrati and F. Calderero and D.H. Brooks and
G. Tadmor and R.S. MacLeod",
title = "A Level Sets Algorithm for the Inverse Problem of
Electrocardiography",
booktitle = "Proceedings of the Asilomar Conf. on Sig. and
Sys.",
volume = "2",
pages = "1590--1594",
year = "2004",
month = "November",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr",
}
@Article{SCI:Gho2005a,
author = "A. Ghodrati and D.H. Brooks and G. Tadmor and B.B.
Punske and R.S. MacLeod",
title = "Wavefront-based Inverse Electrocardiography using
an Evolving Curve State Vector and Phenomenological
Propagation and Potential Models",
journal = "IJBEM",
volume = "7",
number = "2",
pages = "210--213",
year = "2005",
keywords = "cardiac heart, ncrr, cibc",
}
@Article{SCI:Gho2006a,
author = "A. Ghodrati and D.H. Brooks and G. Tadmor and R.S.
MacLeod",
title = "Wavefront-based Models for Inverse
Electrocardiography",
journal = j-BME,
volume = "53",
number = "9",
pages = "1821--1831",
year = "2006",
doi = "10.1109/TBME.2006.878117",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr, cibc simulation
math modeling",
url = "http://www.sci.utah.edu/publications/ghodrati06/Ghodrati_TBE2006.pdf",
}
@Article{SCI:Gho2006b,
author = "A. Ghodrati and D.H. Brooks and G. Tadmor and R.S.
MacLeod",
title = "Lead Selection for Inverse Electrocardiography",
journal = j-BME,
pages = "in press",
year = "2006",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr",
}
@InProceedings{SCI:Gho2006c,
author = "A. Ghodrati and A. Keely and G. Tadmor and R.S.
MacLeod and D.H. Brooks",
title = "A Wavefront-Based Constraint for Potential Surface
Solutions in Inverse Electrocardiography",
booktitle = "2006 International Conference of the {IEEE}
Engineering in Medicine and Biology Society",
year = "2006",
publisher = "IEEE",
address = "New York, NY, USA",
month = "August",
doi = "10.1109/IEMBS.2006.260373",
keywords = "forward problems inverse problems forward
simulation inverse solutions, simulation math
modeling, bioelectric fields, ncrr, cibc",
url = "http://www.sci.utah.edu/publications/Gho2006c/Ghodrati_EMBS2006.pdf",
}
@Conference{SCI:Gho2006d,
author = "A. Ghodrati and D.H Brooks and G. Tadmor and R.S.
MacLeod",
title = "A Threshold-Based Method for Inverse Solutions to
Reconstruct Complex Obstacles, with Application to
the Inverse Problem of Electrocardiography",
booktitle = "SIAM Conference on Imaging Science",
year = "2006",
address = "Minneapolis, MN, USA",
month = "May",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr, simulation math
modeling, bioelectric fields",
}
@Article{SCI:Gho2007a,
author = "A. Ghodrati and D.H. Brooks and R.S. MacLeod",
title = "Methods of Solving Reduced Lead Systems for
Inverse Electrocardiography",
journal = "{IEEE} Trans Biomed Eng",
volume = "54",
number = "2",
pages = "339--343",
year = "2007",
month = "February",
pmid = "17278592",
keywords = "ncrr, cibc",
url = "http://www.sci.utah.edu/publications/ghodrati07/Ghodrati_TBE2007.pdf",
}
@Article{SCI:Gil2006a,
author = "J.H. Gilmore and W. Lin and G. Gerig",
title = "IMAGES IN NEUROSCIENCE: Fetal and Neonatal Brain
Development",
journal = "Am J Psychiatry",
volume = "163",
pages = "2046",
year = "2006",
month = "December",
}
@Article{SCI:Gil2007a,
author = "J.H. Gilmore and W. Lin and I. Corouge and Y.S.
Vetsa and J.K. Smith and C. Kang and H. Gu and R.M.
Hamer and J.A. Lieberman and G. Gerig",
title = "Early Postnatal Development of Corpus Callosum and
Corticospinal White Matter Assessed with
Quantitative Tractography",
journal = "American Journal of Neuroradiology",
volume = "28",
number = "9",
pages = "1789--1795",
year = "2007",
month = "October",
url = "http://www.sci.utah.edu/publications/gilmore07/Gilmore_AJNR_Oct2007.pdf",
}
@Article{SCI:Gil2007b,
author = "J.H. Gilmore and W. Lin and M.W. Prastawa and C.B.
Looney and Y.S.K. Vetsa and R.C. Knickmeyer and
D.D. Evans and J.K. Smith and R.M. Hamer and J.A.
Lieberman and G. Gerig",
title = "Regional Gray Matter Growth, Sexual Dimorphism,
and Cerebral Asymmetry in the Neonatal Brain",
journal = "Journal of Neuroscience",
volume = "27",
number = "6",
pages = "1255--1260",
year = "2007",
url = "http://www.sci.utah.edu/publications/gilmore07/JN-12-1-06.pdf",
}
@InProceedings{SCI:Gil2007c,
author = "J.H. Gilmore and L. Smith and C. Kang and R. Hamer
and H. Wolfe and B. Hertzberg and J.K. Smith and N.
Chescheir and W. Lin and G. Gerig",
title = "Neonatal Brain Structure in Children with Prenatal
Isolated Mild Ventriculomegaly",
booktitle = "Proceedings American Conference of
Neuropharmacology (ACNP) 2007",
year = "2007",
location = "Boca Raton, FL",
note = "abstract.",
}
@Article{SCI:Gil2007d,
author = "J.H. Gilmore and W. Lin and M.W. Prastawa and C.B.
Looney and Y.S.K. Vetsa and R.C. Knickmeyer and
D.D. Evans and J.K. Smith and R.M. Hamer and J.A.
Lieberman and G. Gerig",
title = "Regional Gray Matter Growth, Sexual Dimorphism,
and Cerebral Asymmetry in the Neonatal Brain",
journal = "Journal of Neuroscience",
volume = "27",
number = "6",
pages = "1255--1260",
year = "2007",
keywords = "ucnia",
}
@Article{SCI:Gil2008a,
author = "J.H. Gilmore and L. Smith and H. Wolfe and B.
Hertzberg and J.K. Smith and N. Chescheir and D.
Evans and C. Kang and R.M. Hamer and W. Lin and G.
Gerig",
title = "Prenatal Mild Ventriculomegaly Predicts Abnormal
Development of the Neonatal Brain",
journal = "Biological Psychiatry",
volume = "64",
number = "12",
pages = "1069-1076",
year = "2008",
month = "Dec",
pmid = "18835482",
keywords = "brain development, ventriculomegaly, ucnia",
url = "http://www.sci.utah.edu/publications/gilmore08/Prenatal_Ventriculomegaly.pdf",
}
@Article{SCI:Gil2010a,
author = "J.H. Gilmore and C. Kang and D.D. Evans and H.M.
Wolfe and M.D. Smith and J.A. Lieberman and W. Lin
and R.M. Hamer and M. Styner and G. Gerig",
title = "Prenatal and Neonatal Brain Structure and White
Matter Maturation in Children at High Risk for
Schizophrenia",
journal = "American Journal of Psychiatry",
volume = "167",
number = "9",
pages = "1083--1091",
year = "2010",
month = "September",
note = "Epub 2010 Jun 1",
pmid = "20516153",
url = "http://www.sci.utah.edu/publications/gilmore10/Gilmore_AJP2010.pdf",
}
@Article{SCI:Gil2010b,
author = "J.H. Gilmore and J.E. Schmitt and R.C. Knickmeyer
and J.K. Smith and W. Lin and M. Styner and G.
Gerig and M.C. Neale",
title = "Genetic and environmental contributions to
neonatal brain structure: A twin study",
journal = "Human Brain Mapping",
volume = "31",
number = "8",
pages = "1174--1182",
year = "2010",
note = "ePub 8 Jan 2010",
pmid = "20063301",
url = "http://www.sci.utah.edu/publications/gilmore10/Gilmore_HBM2010.pdf",
}
@Article{SCI:Gil2013a,
author = "J.M. Gililland and L.A. Anderson and H.B.
Henninger and E.N. Kubiak and C.L. Peters",
title = "Biomechanical analysis of acetabular revision
constructs: is pelvic discontinuity best treated
with bicolumnar or traditional unicolumnar
fixation?",
journal = "Journal of Arthoplasty",
volume = "28",
number = "1",
pages = "178--186",
year = "2013",
doi = "10.1016/j.arth.2012.04.031",
url = "http://www.sci.utah.edu/publications/gililland13/Gililland_JArthroplasty2013.pdf",
}
@Article{SCI:Gil2015a,
author = "K. Gillette and J.D. Tate and B. Kindall and P.
Van Dam and E. Kholmovski and R.S. MacLeod",
title = "Generation of Combined-Modality Tetrahedral
Meshes",
journal = "Computing in Cardiology",
year = "2015",
url = "http://www.sci.utah.edu/publications/Gil2015a/gillette-comp-in-cardio15-2.pdf",
}
@InProceedings{SCI:Gil2017a,
author = "T. Gilray and S. Kumar",
title = "Toward parallel CFA with datalog, MPI, and CUDA",
booktitle = "Scheme and Functional Programming Workshop",
year = "2017",
url = "http://www.sci.utah.edu/publications/Gil2017a/Scheme.pdf",
}
@TechReport{SCI:Git94a,
author = "C.S. Gitlin and C.R. Johnson",
title = "Techniques for Visualizing 3D Unstructured
Meshes",
number = "UUCS-94-018",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "computational pde pdes computational partial
differential equations evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/gitlin94/gitlin95_2.ps",
url = "http://www.sci.utah.edu/publications/gitlin94/gitlin95_2.ps.Z",
}
@InProceedings{SCI:Git96,
author = "C.S. Gitlin and C.R. Johnson",
title = "MeshView: A tool for exploring 3D unstructured
tetrahedral meshes",
booktitle = "5th International Meshing Roundtable",
pages = "333--345",
year = "1996",
keywords = "computational pde pdes computational partial
differential equations evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/gitlin96/mesh96.ps.Z",
}
@InCollection{SCI:Goo2000a,
author = "C.E. Goodyer and R. Fairlie and M. Berzins and
L.E. Scales",
title = "An In-depth Investigation of the Multigrid
Approach to Steady and Transient EHL Problems",
booktitle = "Thinning Films and Tribological
InterfacesProceedings of the 26th Leeds-Lyon
Symposium on Tribology",
volume = "38",
pages = "95--102",
year = "2000",
editor = "D. Dowson, M. Priest, C.M. Taylor, P. Ehret,
T.H.C. Childs, G. Dalmaz, A.A. Lubrecht, Y.
Berthier, L. Flamand and J.-M. Georges",
series = "Tribology Series",
publisher = "Elsevier",
issn = "0167-8922",
url = "http://www.sci.utah.edu/publications/Goo2000a/paper-goodyer.pdf",
}
@InProceedings{SCI:Goo2000b,
author = "C.E. Goodyera and R. Fairliea and M. Berzinsa and
L.E. Scales",
title = "An in-depth investigation of the multigrid
approach to steady and transient EHL problems",
title_url =
"https://www.scopus.com/record/display.uri?view=basic\&eid=2-s2.0-0034350987\&origin=resultslist#http://",
booktitle = " 26th Leeds-Lyon Symposium on Tribology",
volume = "38",
pages = "95-102",
year = "2000",
publisher = "Elsevier",
}
@InProceedings{SCI:Goo2001a,
author = "C.E. Goodyer and R. Fairlie and M. Berzins and
L.E. Scales",
title = "Adaptive Techniques for Elastohydrodynamic
Lubrication Solvers",
booktitle = "Tribology Research: From Model Experiment to
Industrial Problem, Proceedings of the 27th
Leeds-Lyon Symposium on Tribology",
year = "2001",
editor = "G. Dalmaz et al.",
publisher = "Elsevier",
keywords = "EHL, , ehl",
url = "http://www.sci.utah.edu/publications/goodyer01/LeedsLyon2000.pdf",
}
@InProceedings{SCI:Goo2001b,
author = "C.E. Goodyer and R. Fairlie and M. Berzins and
L.E. Scales",
title = "Adaptive Mesh Methods for Elastohydrodynamic
Lubrication",
booktitle = "ECCOMAS CFD 2001: Computational Fluid Dynamics
Conference Proceedings",
year = "2001",
publisher = "Institute of Mathematics and its Applications",
isbn = "0-905-091-12-4",
keywords = "EHL",
url = "http://www.sci.utah.edu/publications/goodyer01/ECCOMAS_Goodyer01.pdf",
}
@PhdThesis{SCI:Goo2001c,
author = "C.E. Goodyer",
title = "Adaptive Numerical Methods for Elastohydrodynamic
Lubrication",
year = "2001",
school = "School of Computing, University of Leeds",
month = "May",
note = "Advisor: Martin Berzins",
url = "http://www.sci.utah.edu/publications/Goo2001c/Goodyer_PhDThesis2001.pdf",
}
@InProceedings{SCI:Goo2002a,
author = "C.E. Goodyer and M. Berzins",
title = "Eclipse and Ellipse: {PSE}s for {EHL} Solutions
using {IRIS} Explorer and {SCIR}un",
booktitle = c-ICCS2002,
volume = "2329",
pages = "523--532",
year = "2002",
editor = "P.M.A. Sloot and C.J.K. Tan and J.J. Dongarra and
A.G. Hoekstra",
publisher = "Springer Berlin",
location = "Amsterdam, The Netherlands",
url = "http://www.sci.utah.edu/publications/goodyer02/2002EclipseEllipse.pdf",
}
@InProceedings{SCI:Goo2002b,
author = "C.E. Goodyer and J. Wood and M. Berzins",
title = "A Parallel Grid Based {PSE} for {EHL} Problems",
booktitle = c-PARA2002,
volume = "2367",
pages = "521--530",
year = "2002",
editor = "J. Fagerholm and J. Haatja and J. Jarvinen and M.
Lyly and P. Raback and V. Savolainen",
publisher = "Springer Lecture Notes in Computer Science",
location = "Espoo, Finland",
keywords = "pse grid computing",
url = "http://www.sci.utah.edu/publications/goodyer02/CEGJWMB02.pdf",
}
@InProceedings{SCI:Goo2003a,
author = "C.E. Goodyer and M. Berzins and P.K. Jimack and
L.E. Scales",
title = "Grid-Based Numerical Optimisation in a Problem
Solving Environment",
booktitle = "Proceedings of Second {UK} {E}-Science All-Hands
Meeting",
pages = "854--861",
year = "2003",
editor = "S.J. Cox",
location = "Nottingham, {UK}",
isbn = "1-904425-11-9",
keywords = "computational pde pdes computational partial
differential equations evaporation, pse grid
computing, scientific computing, numerics",
url = "http://www.sci.utah.edu/publications/goodyer03/GBJS03.pdf",
}
@InProceedings{SCI:Goo2004a,
author = "C.E. Goodyer and R. Fairlie and D.E. Hart and M.
Berzins and L.E. Scales",
title = "Calculation of Friction in Steady-State and
Transient EHL Simulations Transient Processes in
Tribology",
booktitle = "Transient Processes in Tribology: Proceeding of
the 31st Leeds-Lyon Symposium on Tribology",
pages = "579--590",
year = "2004",
editor = "A.A. Lubrecht and G. Dalmaz",
publisher = "Elsevier",
keywords = "computational mechanics, EHL, ehl",
url = "http://www.sci.utah.edu/publications/goodyer04/GoodyerFairlieHartBerzinsScales04.pdf",
}
@TechReport{SCI:Goo2005a,
author = "C.E. Goodyer and M. Berzins",
title = "Parallelisation and Scalability Issues in a
Multilevel EHL Solver",
number = "2005.05",
year = "2005",
institution = "School of Computing, University of Leeds",
type = "Report",
url = "http://www.sci.utah.edu/publications/goodyer05/2005_05.pdf",
}
@Article{SCI:Goo2006b,
author = "C.E. Goodyer and M. Berzins and P.K. Jimack and
L.E. Scales",
title = "A {G}rid-enabled Problem Solving Environment for
Parallel Computational Engineering Design",
journal = "Advances in Engineering Software",
volume = "37",
number = "7",
pages = "439--449",
year = "2006",
url = "http://www.sci.utah.edu/publications/goodyer06/GBJS05.pdf",
}
@InCollection{SCI:Goo2006c,
author = "C.E. Goodyer and M. Berzins",
title = "Solving Computationally Intensive Engineering
Problems on the {G}rid using {P}roblem {S}olving
{E}nvironments",
booktitle = "Grid Computing: Software Environments and Tools",
pages = "284--301",
year = "2006",
editor = "J.C. Cunha and O.F. Rana",
publisher = "Springer Verlag",
url = "http://www.sci.utah.edu/publications/goodyer06/CEGMBchapter12.pdf",
}
@Article{SCI:Goo2006d,
author = "C.E. Goodyer and M. Berzins",
title = "Adaptive Timestepping for Elastohydrodynamic
Lubrication Solvers",
journal = "SIAM Journal on Scientific Computing",
volume = "28",
number = "2",
pages = "626-650",
year = "2006",
publisher = "SIAM",
doi = "10.1137/050622092",
keywords = "EHL, elastohydrodynamic lubrication, method of
lines, differential-algebraic equations, variable
timestepping, error balancing",
url = "http://www.sci.utah.edu/publications/goodyer06/GoodyerSIAM2006.pdf",
}
@InProceedings{SCI:Goo2007a,
author = "C. Goodlett and P.T. Fletcher and W. Lin and G.
Gerig",
title = "Quantification of Measurement Error in DTI:
Theoretical Predictions and Validation",
booktitle = "Proceedings of The 10th International Conference
on Medical Image Computing and Computer Assisted
Intervention (MICCAI 2007)",
volume = "4792",
pages = "10--17",
year = "2007",
series = "Lecture Notes in Computer Science",
month = "November",
pmid = "18051038",
keywords = "tensor field methods, diffusion tensor imaging",
}
@Article{SCI:Goo2007b,
author = "C.E. Goodyer and M. Berzins",
title = "Parallelisation and Scalability Issues of a
Multilevel EHL Solver",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "19",
number = "4",
pages = "369--396",
year = "2007",
url = "http://www.sci.utah.edu/publications/goodyer07/Goodyer_EHLsolver.pdf",
}
@InProceedings{SCI:Goo2007c,
author = "C.B. Goodlett and P.T. Fletcher and W. Lin and G.
Gerig",
title = "Noise-Induced Bias in Low-Direction Diffusion
Tensor {MRI}: Replication of Monte-Carlo Simulation
with In-Vivo Scans",
booktitle = "Proceedings of {ISMRM} 2007",
year = "2007",
}
@InCollection{SCI:Goo2008a,
author = "C. Goodlett and P.T. Fletcher and J. Gilmore and
G. Gerig",
title = "Group Statistics of DTI Fiber Bundles Using
Spatial Functions of Tensor Measures",
booktitle = "Medical Image Computing and Computer-Assisted
Intervention (MICCAI 2008)",
pages = "1068--1075",
year = "2008",
publisher = "Springer Verlag",
pmid = "18979851",
keywords = "ucnia",
url = "http://www.sci.utah.edu/publications/Goo2008a/tractstats.pdf",
}
@InProceedings{SCI:Goo2008c,
author = "C.E. Goodyer and J. Wood and M. Berzins",
title = "Mathematical modeling of chemical diffusion
through skin using Grid-based {PSEs}",
booktitle = "Modeling, Simulation and Optimization of Complex
Processes: Proceedings of the Third International
Conference on High Performance Scientific
Computing",
pages = "249--258",
year = "2008",
editor = "H.G. Bock and E. Kostina and H.X. Phu and R.
Rannacher",
publisher = "Springer",
url = "http://www.sci.utah.edu/publications/goodyer08/Goodyer_SkinDiffusion2008.pdf",
}
@Article{SCI:Goo2009a,
author = "C. Goodlett and P.T. Fletcher and J.H. Gilmore and
G. Gerig",
title = "Group analysis of DTI fiber tract statistics with
application to neurodevelopment",
journal = "Neuroimage",
volume = "45",
number = "1 (suppl 1)",
pages = "S133--S142",
year = "2009",
pmid = "19059345",
url = "http://www.sci.utah.edu/publications/goodlett09/Goodlett_NeuroImage2009.pdf",
}
@Article{SCI:Goo2009b,
author = "C. Goodlett and P.T. Fletcher and J.H. Gilmore and
G. Gerig",
title = "Group Analysis of DTI Fiber Tract Statistics with
Application to Neurodevelopment",
journal = "NeuroImage",
volume = "45",
pages = "S133--S142",
year = "2009",
month = "December",
doi = "10.1016/j.neuroimage.2008.10.060",
pmid = "19059345",
pmcid = "PMC2727755",
url = "http://www.sci.utah.edu/publications/Goo2009b/DTI_population.pdf",
}
@Article{SCI:Goo2015a,
author = "B. D. Goodwin and C. R. Butson",
title = "Subject-Specific Multiscale Modeling to
Investigate Effects of Transcranial Magnetic
Stimulation",
journal = "Neuromodulation: Technology at the Neural
Interface",
volume = "18",
number = "8",
pages = "694--704",
year = "2015",
publisher = "Wiley-Blackwell",
month = "May",
doi = "10.1111/ner.12296",
url = "http://www.sci.utah.edu/publications/Goo2015a/Goodwin_et_al-2015-Neuromodulation__Technology_at_the_Neural_Interface.pdf",
}
@Article{SCI:Goo2017a,
author = "W. W. Good and B. Erem and J. Coll-Font and D. H.
Brooks and R. S. MacLeod",
title = "Detecting Ischemic Stress to the Myocardium Using
Laplacian Eigenmaps and Changes to Conduction
Velocity",
journal = "Computing in Cardiology",
volume = "44",
year = "2017",
publisher = "IEEE",
url = "http://www.sci.utah.edu/publications/Goo2017a/269-417.pdf",
}
@Article{SCI:Gop2011a,
author = "G. Gopalakrishnan and R.M. Kirby and S. Siegel and
R. Thakur and W. Gropp and E. Lusk and B.R. de
Supinski and M. Schultz and G. Bronevetsky",
title = "Formal Analysis of {MPI-Based} Parallel Programs:
Present and Future",
journal = "Communications of the {ACM}",
pages = "(accepted)",
year = "2011",
url = "http://www.sci.utah.edu/publications/gopalakrishnan11/Gopalakrishnan_ACM2011.pdf",
}
@InProceedings{SCI:Gor2007a,
author = "K. Gorczowski and M. Styner and J.Y. Jeong and
J.S. Marron and J. Piven and H.C. Hazlett and S.M.
Pizer and G. Gerig",
title = "Statistical Shape Analysis of Multi-Object
Complexes",
booktitle = "Proceedings of the 2007 {IEEE} Conference on
Computer Vision and Pattern Recognition",
pages = "1--8",
year = "2007",
url = "http://www.sci.utah.edu/publications/gorczowski07/Gorczowski_CVPR2007a.pdf",
}
@InProceedings{SCI:Gor2007b,
author = "K. Gorczowski and M. Stynera and J.Y. Jeonga and
J.S. Marron and J. Piven and H.C. Hazlett and S.M.
Pizer and G. Gerig",
title = "Discrimination Analysis using Multi-Object
Statistics of Shape and Pose",
booktitle = "Proceedings of the 2007 SPIE Conference",
volume = "6512",
year = "2007",
month = "January",
}
@Article{SCI:Gor2010a,
author = "K. Gorczowski and M. Styner and J.Y. Jeong and
J.S. Marron and J. Piven and H.C. Hazlett and S.M.
Pizer and G. Gerig",
title = "Multi-object analysis of volume, pose, and shape
using statistical discrimination",
journal = "IEEE Trans Pattern Anal Mach Intell.",
volume = "32",
number = "4",
pages = "652--661",
year = "2010",
month = "April",
doi = "10.1109/TPAMI.2009.92",
pmid = "20224121",
url = "http://www.sci.utah.edu/publications/gorczowski10/Gorczowski_PAMI2010.pdf",
}
@InProceedings{SCI:Got2001,
author = "A. Gothandaraman and R.T. Whitaker and J.
Gregor",
title = "Total Variation For The Removal of Blocking
Effects in {DCT} based Encoding",
booktitle = c-ICIP,
pages = "455--458",
year = "2001",
month = "October",
keywords = "ip image processing signal processing, imaging",
}
@Article{SCI:Got2008a,
author = "D. Gottlieb and D. Xiu",
title = "Galerkin Method for Wave Equations with Uncertain
Coefficients",
journal = "Communications in Computational Physics",
volume = "3",
number = "2",
pages = "505--518",
year = "2008",
keywords = "Generalized polynomial chaos, stochastic PDE,
Galerkin method, hyperbolic equation, uncertainty
quantification",
url = "http://www.sci.utah.edu/publications/gottlieb08/GottliebXiu_CiCP2008.pdf",
}
@InProceedings{SCI:Gou2007a,
author = "S. Gouttard and M. Styner and S. Joshi and R.G.
Smith and H.C. Hazlett and G. Gerig",
title = "Subcortical Structure Segmentation Using
Probabilistic Atlas Priors",
booktitle = "Medical Imaging 2007: Image Processing",
volume = "6512",
number = "65122J",
year = "2007",
editor = "J.P. W. Pluim and J.M. Reinhardt",
publisher = "SPIE Intl Soc Optical Eng",
month = "March",
note = "Presented at Worshop - 3D Segmentation in the
Clinic: a Grand Challenge",
keywords = "neuro brain, brain atlasing",
url = "http://www.sci.utah.edu/publications/Gou2007a/MICCAI07_SegmentationWorkshop.pdf",
}
@InProceedings{SCI:Gou2008a,
author = "S. Gouttard and M. Styner and M.W. Prastawa and J.
Piven and G. Gerig",
title = "Assessment of Reliability of Multi-site
Neuroimaging via Traveling Phantom Study",
booktitle = "Proceedings of Medical Image Computing and
Computer Assisted Intervention 2008, Lecture Notes
in Computer Science LNCS",
volume = "5242",
pages = "263--270",
year = "2008",
month = "September",
keywords = "ucnia",
url = "http://www.sci.utah.edu/publications/gouttard08/Gouttard-MICCAI08.pdf",
}
@Article{SCI:Gou2009a,
author = "S. Gouttard and M.W. Prastawa and E. Bullitt and
W. Lin and C. Goodlett and G. Gerig",
title = "Constrained Data Decomposition and Regression for
Analyzing Healthy Aging from Fiber Tract Diffusion
Properties",
journal = "Medical Image Computing and Computer-Assisted
Intervention – MICCAI 2009",
volume = "5761",
pages = "321--328",
year = "2009",
series = "Lecture Notes in Computer Science LNCS",
pmid = "20426003",
url = "http://www.sci.utah.edu/publications/gouttard09/Gouttard_MICCAI2009.pdf",
}
@InProceedings{SCI:Gou2012a,
author = "S. Gouttard and C.B. Goodlett and M. Kubicki and
G. Gerig",
title = "Measures for Validation of DTI Tractography",
booktitle = "Medical Imaging 2012: Image Processing",
year = "2012",
editor = "David R. Haynor and Sebastien Ourselin",
publisher = "SPIE Intl Soc Optical Eng",
month = "Feb",
doi = "10.1117/12.911546",
url = "http://www.sci.utah.edu/publications/Gou2012a/Gouttarad_dti_validation_spie2012-final-annot.pdf",
}
@InProceedings{SCI:Gra2005a,
author = "L. Grady and T. Tasdizen",
title = "A Geometric Multigrid Approach to Solving the 2D
Inhomogeneous Laplace Equation with Internal
Dirichlet Boundary Conditions",
booktitle = c-ICIP,
volume = "2",
pages = "642--645",
year = "2005",
month = "September",
keywords = "ip image processing signal processing",
}
@Article{SCI:Gra2010a,
author = "M. Grabherr and P. Russell and M.D. Meyer and E.
Mauceli and J. Alf{\"o}ldi and F. Di Palma and K.
Lindblad-Toh",
title = "Genome-wide synteny through highly sensitive
sequence alignment: Satsuma",
journal = "Bioinformatics",
volume = "26",
number = "9",
pages = "1145--1151",
year = "2010",
url = "http://www.sci.utah.edu/publications/grabherr10/Grabherr_Satsuma2010.pdf",
}
@Article{SCI:Gra2013a,
author = "S. Gratzl and A. Lex and N. Gehlenborg and H.
Pfister and and M. Streit",
title = "LineUp: Visual Analysis of Multi-Attribute
Rankings",
journal = "IEEE Transactions on Visualization and Computer
Graphics (InfoVis '13)",
volume = "19",
number = "12",
pages = "2277--2286",
year = "2013",
issn = "1077-2626",
doi = "10.1109/TVCG.2013.173",
url = "http://www.sci.utah.edu/publications/Gra2013a/2013_infovis_lineup.pdf",
}
@Article{SCI:Gra2014a,
author = "S. Gratzl and N. Gehlenborg and A. Lex and H.
Pfister and M. Streit",
title = "Domino: Extracting, Comparing, and Manipulating
Subsets across Multiple Tabular Datasets",
journal = "IEEE Transactions on Visualization and Computer
Graphics (InfoVis '14)",
volume = "20",
number = "12",
pages = "2023--2032",
year = "2014",
issn = "1077-2626",
doi = "10.1109/TVCG.2014.2346260",
url = "http://www.sci.utah.edu/publications/Gra2014a/2014_infovis_domino.pdf",
}
@Article{SCI:Gra2016a,
author = "Samuel Gratzl and Alexander Lex and Nils
Gehlenborg and Nicola Cosgrove and Marc Streit ",
title = "From Visual Exploration to Storytelling and Back
Again",
journal = "Computer Graphics Forum",
volume = "35",
number = "3",
pages = "491--500",
year = "2016",
month = "jun",
issn = "1467-8659",
doi = "10.1111/cgf.12925",
url = "http://www.sci.utah.edu/publications/Gra2016a/2016_eurovis_clue.pdf",
}
@Article{SCI:Gre2002a,
author = "J. Gregor and R.T. Whitaker",
title = "Indoor Scene Reconstruction for Sets of Noisy
Range Images",
journal = "Graphical Models",
volume = "63",
number = "5",
pages = "304--332",
year = "2002",
month = "September",
keywords = "ip image processing signal processing, surface
processing, imaging",
}
@Article{SCI:Gre2002b,
author = "J. Gregor and S.S. Gleason and M.J. Paulus and J.
Cates",
title = "Fast Feldkamp Reconstruction Based on Focus of
Attention and Distributed Computing",
journal = j-IJIST,
volume = "12",
number = "6",
pages = "229--234",
year = "2002",
}
@InProceedings{SCI:Gre2002c,
author = "B. Gregoski and M. Duchaineau and P. Lindstrom and
V. Pascucci and K. Joy",
title = "Interactive View-Dependent Rendering of Large
Isosurfaces",
booktitle = "Proceedings of IEEE Conference on Visualization
({VIS}-02)",
pages = "475--482",
year = "2002",
month = "October",
location = "Boston, MA",
note = "UCRL-JC-146819",
}
@Article{SCI:Gre2014a,
author = "K. Grewen and M. Burchinal and C. Vachet and S.
Gouttard and J.H. Gilmore and W. Lin and J. Johns
and M. Elam and G. Gerig",
title = "Prenatal cocaine effects on brain structure in
early infancy",
journal = "NeuroImage",
volume = "101",
pages = "114--123",
year = "2014",
month = "November",
doi = "10.1016/j.neuroimage.2014.06.070",
url = "http://www.sci.utah.edu/publications/Gre2014a/2014-Prenatal-cocaine-effects-on-brain-structure-in-early-infancy.pdf",
}
@TechReport{SCI:Gri2003a,
author = "C.P. Gribble and S.G. Parker",
title = "A Survey of the Itanium Architecture from a
Programmer's Perspective",
number = "UUSCI-2003-003",
year = "2003",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
month = "August",
keywords = "survey, Itanium cluster, hardware",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2003-003.pdf",
}
@TechReport{SCI:Gri2004a,
author = "C. Gribble and S.G. Parker and C.D. Hansen",
title = "Interactive Volume Rendering of Large Datasets
Using the Silicon Graphics Onyx4 Visualization
System",
number = "UUCS-04-003",
year = "2004",
institution = "University of Utah School of Computing",
month = "January 27th",
keywords = "volume rendering, parallel visualization, rhesus,
fire pool, csafe c-safe",
}
@TechReport{SCI:Gri2006a,
author = "C. Gribble and T. Ize and A. Kensler and I. Wald
and S.G. Parker",
title = "A Coherent Grid Traversal Approach to Visualizing
Particle-based Simulation Data",
number = "UUSCI-2006-024",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "rtrt real-time ray tracing, interactive rt
distributed interactive ray tracing dirt, grid
traversal, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-024.pdf",
}
@InProceedings{SCI:Gri2006b,
author = "C.P. Gribble and A.J. Stephens and J.E. Guilkey
and S.G. Parker",
title = "Visualizing Particle-Based Simulation Datasets on
the Desktop",
booktitle = "Proceedings of the British HCI 2006 Workshop on
Combining Visualization and Interaction to
Facilitate Scientific Exploration and Discovery",
year = "2006",
keywords = "mpm material point method, rtrt real-time ray
tracing, csafe c-safe",
url = "http://www.sci.utah.edu/publications/Gri2006b/gpup-hci06.pdf",
}
@InProceedings{SCI:Gri2006c,
author = "C.P. Gribble and S.G. Parker",
title = "Enhancing Interactive Particle Visualization with
Advanced Shading Models",
booktitle = "Proceedings of the {ACM} Siggraph Third Symposium
on Applied Perception in Graphics and
Visualization",
pages = "111--118",
year = "2006",
keywords = "mpm material point method, rtrt real-time ray
tracing, csafe c-safe, rtcenter",
url = "http://www.sci.utah.edu/publications/Gri2006c/plt-apgv06.pdf",
}
@InProceedings{SCI:Gri2007a,
author = "C.P. Gribble and S.G. Parker",
title = "Interactive Visualization with Advanced Shading
Models using Lazy Evaluation",
booktitle = "Proceedings of the 2007 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "37--44",
year = "2007",
keywords = "interactive rt distributed interactive ray tracing
dirt, rtcenter",
}
@Article{SCI:Gri2007b,
author = "C.P. Gribble and C. Brownlee and S.G. Parker",
title = "Practical Global Illumination for Interactive
Particle Visualization",
journal = "Computers and Graphics",
volume = "32",
number = "1",
pages = "14--24",
year = "2007",
month = "February",
}
@Article{SCI:Gri2008a,
author = "C. Gribble and C. Brownlee and S.G. Parker",
title = "Practical Global Illumination for Interactive
Particle Visualization",
journal = "Computers and Graphics",
volume = "32",
number = "1",
pages = "14--24",
year = "2008",
month = "February",
doi = "10.1016/j.cag.2007.11.001",
keywords = "Interactive particle visualization, Global
illumination, Ray tracing",
url = "http://www.sci.utah.edu/publications/Gri2008a/Gribble_CG2008.pdf",
}
@MastersThesis{SCI:Gri2014a,
author = "C.E. Gritton",
title = "Ringing Instabilities in Particle Methods",
year = "2014",
school = "School of Computing, University of Utah",
month = "August",
note = "M.S. in Computational Engineering and Science,
advisor Martin Berzins",
url = "http://www.sci.utah.edu/publications/Gri2014a/CGritton_MSThesis2014.pdf",
}
@InProceedings{SCI:Gri2015a,
author = "C. Gritton and M. Berzins and R. M. Kirby",
title = "Improving Accuracy In Particle Methods Using Null
Spaces and Filters",
booktitle = "Proceedings of the IV International Conference on
Particle-Based Methods - Fundamentals and
Applications",
booktitle_url =
"http://congress.cimne.com/particles2015/frontal/doc/E-book_PARTICLES_2015.pdf",
pages = "202-213",
year = "2015",
editor = "E. Onate and M. Bischoff and D.R.J. Owen and P.
Wriggers and T. Zohdi",
publisher = "CIMNE",
month = "September",
location = "Barcelona, Spain",
isbn = "978-84-944244-7-2",
url = "http://www.sci.utah.edu/publications/Gri2015a/paperforP15-2.pdf",
}
@Article{SCI:Gri2016a,
author = "C. Gritton and M. Berzins",
title = "Improving accuracy in the MPM method using a null
space filter",
journal = "Computational Particle Mechanics",
pages = "1--12",
year = "2016",
issn = "2196-4386",
doi = "10.1007/s40571-016-0134-3",
url = "http://www.sci.utah.edu/publications/Gri2016a/mpmpaper.pdf",
}
@Article{SCI:Gri2017b,
author = "C. Gritton and J. Guilkey and J. Hooper and D.
Bedrov and R. M. Kirby and M. Berzins",
title = "Using the material point method to model
chemical/mechanical coupling in the deformation of
a silicon anode",
journal = "Modelling and Simulation in Materials Science and
Engineering",
volume = "25",
number = "4",
pages = "045005",
year = "2017",
url = "http://www.sci.utah.edu/publications/Gri2017b/mpm_nanopillar.pdf",
}
@InProceedings{SCI:Gro2013a,
author = "A. Grosset and M. Schott and G.-P. Bonneau and
C.D. Hansen",
title = "Evaluation of Depth of Field for Depth Perception
in {DVR}",
booktitle = "Proceedings of the 2013 {IEEE} Pacific
Visualization Symposium ({PacificVis})",
pages = "81--88",
year = "2013",
url = "http://www.sci.utah.edu/publications/grosset13/Grosset_PacVis2013.pdf",
}
@InProceedings{SCI:Gro2015a,
author = "A. V. P. Grosset and M. Prasad and C. Christensen
and A. Knoll and C. Hansen",
title = "TOD-Tree: Task-Overlapped Direct send Tree Image
Compositing for Hybrid MPI Parallelism",
booktitle = "Eurographics Symposium on Parallel Graphics and
Visualization (2015)",
year = "2015",
editor = "C. Dachsbacher, P. Navrátil",
url = "http://www.sci.utah.edu/publications/Gro2015a/grosset_epvg2015.pdf",
}
@InProceedings{SCI:Gro2016a,
author = "A.V. P. Grosset and A. Knoll and C.D. Hansen",
title = "Dynamically Scheduled Region-Based Image
Compositing",
booktitle = "Eurographics Symposium on Parallel Graphics and
Visualization",
year = "2016",
month = "June",
url = "http://www.sci.utah.edu/publications/Gro2016a/paper_egpgv_16.pdf",
}
@Article{SCI:Gro2016b,
author = "A. V. P. Grosset and M. Prasad and C. Christensen
and A. Knoll and C. Hansen",
title = "TOD-Tree: Task-Overlapped Direct send Tree Image
Compositing for Hybrid MPI Parallelism and GPUs",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
pages = "1--1",
year = "2016",
publisher = "IEEE",
doi = "10.1109/tvcg.2016.2542069",
url = "http://www.sci.utah.edu/publications/Gro2016b/07433468.pdf",
}
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author = "J. Grueninger and H. Hoffman and U. Kloos and J.
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title = "Multi-Resolution-Display System for Virtual
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booktitle = "Proceedings of the 14th International Conference
on Human-Computer Interaction, HCI International",
volume = "6779/2011",
pages = "180--189",
year = "2011",
series = "Lecture Notes in Computer Science",
doi = "10.1007/978-3-642-21716-6_19",
url = "http://www.sci.utah.edu/publications/Gru2011a/Gruninger_HCI2011.pdf",
}
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author = "R. Grupen and C.D. Hansen and T. Henderson",
title = "Apparent Symmetries in Range Data",
journal = "Pattern Recognition Letters",
volume = "7",
pages = "107--111",
year = "1988",
month = "February",
}
@InProceedings{SCI:Gue1999a,
author = "C. Guerra and V. Pascucci",
title = "On Matching Sets of {3D} Segments",
booktitle = "Proceedings of SPIE Vision Geometry VIII",
pages = "157-167",
year = "1999",
address = "Denver, USA",
}
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author = "C. Guerra and V. Pascucci",
title = "{3D} Segment Matching Using the Hausdorff
Distance",
booktitle = "Proceedings of the {IEEE} Conference on Image
Processing and its Applications, IPA99",
pages = "18--22",
year = "1999",
}
@InProceedings{SCI:Gue1999c,
author = "C. Guerra and V. Pascucci",
title = "Segment Matching for Protein Secondary Structure
Comparison",
booktitle = "Proceedings of the Third International Conference
on Computational Molecular Biology, {RECOMB}'99",
pages = "30",
year = "1999",
organization = "ACM",
address = "Lyon, France",
}
@Article{SCI:Gue2001a,
author = "C. Guerra and V. Pascucci",
title = "Finding Line Segments with Tabu Search",
journal = "{IEICE} Transactions on Information \& Systems",
volume = "E84-D",
number = "12",
pages = "1739-1744",
year = "2001",
month = "December",
}
@Article{SCI:Gue2004a,
author = "C. Guerra and V. Pascucci",
title = "Line-Based Object Recognition Using Hausdorff
Distance: From Range Images to Molecular Secondary
Structure",
journal = "Image and Vision Computing",
volume = "23",
number = "4",
pages = "405-415",
year = "2005",
month = "April",
note = "UCRL-JRNL-208551",
}
@Article{SCI:Gui2003a,
author = "J.E. Guilkey and J.A. Weiss",
title = "Implicit Time Integration with the Material Point
Method",
journal = "International Journal for Numerical Methods in
Engineering",
volume = "57",
pages = "1323--1338",
year = "2003",
url = "http://www.sci.utah.edu/publications/guilkey03/impmpm_FINAL.pdf",
}
@InProceedings{SCI:Gui2004a,
author = "J.E. Guilkey and Y. Zhang and J.B. Hoying and J.A.
Weiss",
title = "Mechanical Simulation of Multicellular Structures
with the Material Point Method",
booktitle = "Proc 6th International Symposium on Computer
Methods in Biomechanics and Biomedical
Engineering",
year = "2004",
month = "March",
location = "Madrid, Spain",
note = "Winner of the Taylor and Francis Prize for
Outstanding Innovation in Computer Methods in
Biomechanics and Biomedical Engineering",
keywords = "computational mechanics, computational
biomechanics, mpm material point method",
url = "http://www.sci.utah.edu/publications/guilkey04/guilkey_cmbbe_2004.pdf",
}
@Article{SCI:Gui2005a,
author = "J.E. Guilkey and J.B. Hoying JB and J.A. Weiss",
title = "Computational modeling of multicellular constructs
with the Material Point Method",
journal = "Journal of Biomechanics",
pages = "(published online)",
year = "2005",
month = "June",
keywords = "computational mechanics, mpm material point
method, computational biomechanics, angiogenesis",
url = "http://www.sci.utah.edu/publications/guilkey05/Journal_Biomech2005.pdf",
}
@Article{SCI:Gui2006a,
author = "J.E. Guilkey and J.B. Hoying and J.A. Weiss",
title = "Computational Modeling of Multicellular Constructs
with the Material Point Method",
journal = "Journal of Biomechanics",
volume = "39",
number = "11",
pages = "2074--2086",
year = "2006",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/guilkey06/guilkey_j_biomech_2006.pdf",
}
@TechReport{SCI:Gui2009a,
author = "J. Guilkey and T. Harman and J. Luitjens and J.
Schmidt and J. Thornock and J.D. de St. Germain and
S. Shankar and J. Peterson and C. Brownlee",
title = "Uintah User Guide Version 1.1",
number = "UUSCI-2009-007",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "csafe, c-safe, uintah, scirun, fire simulation",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2009-007.pdf",
}
@Article{SCI:Gul2005a,
author = "D. Gullmar and J.R. Reichenbach and A. Anwander
and T. Knosche and C.H. Wolters and M. Eiselt and
J. Haueisen",
title = "Influence of Anisotropic Conductivity of the White
Matter Tissue on EEG Source Reconstruction - An FEM
Simulation Study",
journal = j-IJBEM,
volume = "7",
number = "1",
pages = "108--110",
year = "2005",
keywords = "forward problems inverse problems forward
simulation inverse solutions, inverse eeg, focusing
inversion, forward simulation, neuro brain, ncrr,
simulation math modeling, bioelectric fields",
url = "http://www.sci.utah.edu/publications/gullmar05/Gullmar_IJBEM.pdf",
}
@Article{SCI:Gul2016a,
author = "S. Guler and M. Dannhauer and B. Erem and R.S.
Macleod and D. Tucker and S. Turovets and P. Luu
and D. Erdogmus and D. Brooks",
title = "Optimization of focality and direction in dense
electrode array transcranial direct
currentstimulation (tDCS)",
journal = "Journal of Neural Engineering",
volume = "13",
number = "3",
pages = "036020",
year = "2016",
publisher = "IOP Publishing",
month = "May",
doi = "10.1088/1741-2560/13/3/036020",
url = "http://www.sci.utah.edu/publications/Gul2016a/Guler2016JNE.pdf",
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A. Gkogkidis and R. Macleod and T. Ball and J. G.
Ojemann and D. H. Brooks",
title = "Computationally optimized ECoG stimulation with
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year = "2018",
publisher = "Elsevier BV",
month = "June",
doi = "10.1016/j.neuroimage.2018.01.088",
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}
@InProceedings{SCI:Gum2001a,
author = "S. Gumhold and X. Wang and R.S. MacLeod",
title = "Feature Extraction from Point Clouds",
booktitle = "Proceedings, 10th International Meshing Round
Table",
pages = "293--305",
year = "2001",
publisher = "Sandia National Laboratories",
keywords = "ncrr, computational pde pdes computational partial
differential equations evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/gumhold01/sr0006.pdf",
}
@Article{SCI:Gun2015a,
author = "A. Gunduz and H. Morita and P. J. Rossi and W. L.
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S. Stanslaski and G. K. Steinke and P. Stypulkowski
and A. I. Tr{\"o}ster and L. Verhagen and H. Walker
and M. S. Okun",
title = "Proceedings of the Second Annual Deep Brain
Stimulation Think Tank: What's in the Pipeline",
journal = "International Journal of Neuroscience",
volume = "125",
number = "7",
pages = "475-485",
year = "2015",
publisher = "Taylor \& Francis",
doi = "10.3109/00207454.2014.999268",
pmid = "25526555",
url = "http://www.sci.utah.edu/publications/Gun2015a/Proceedings of the Second Annual Deep Brain Stimulation Think Tank What s in the Pipeline.pdf",
}
@InProceedings{SCI:Guo2005a,
author = "H. Guo and A. Rangarajan and S. Joshi",
title = "3-D Diffeomorphic Shape Registration on
Hippocampal Data Sets",
booktitle = "Med Image Comput Comput Assist Interv Int Conf Med
Image Comput Comput Assist Interv",
volume = "8 (Pt. 2)",
pages = "984--991",
year = "2005",
}
@Article{SCI:Guo2010a,
author = "X. Guo and J. Li and D. Xiu and A. Alexeenko",
title = "Uncertainty Quantification Models for Microscale
Squeeze-Film Damping",
journal = "International Journal for Numerical Methods in
Engineering",
volume = "84",
number = "10",
pages = "1257--1272",
year = "2010",
doi = "10.1002/nme.2952",
keywords = "uncertainty quantification, squeeze-film damping,
gPC expansion, rarefied flow",
url = "http://www.sci.utah.edu/publications/guo10/Guo_IJNME2010.pdf",
}
@Article{SCI:Guo2017a,
author = "L. Guo and A. Narayan and T. Zhou and Y. Chen",
title = "Stochastic Collocation Methods via L1 Minimization
Using Randomized Quadratures",
journal = "SIAM Journal on Scientific Computing",
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number = "1",
pages = "A333--A359",
year = "2017",
month = "Jan",
issn = "1064-8275",
doi = "10.1137/16M1059680",
url = "http://www.sci.utah.edu/publications/Guo2017a/1602.00995.pdf",
}
@Article{SCI:Guo2018a,
author = "L. Guo and A. Narayan and T. Zhou",
title = "A gradient enhanced ℓ1-minimization for sparse
approximation of polynomial chaos expansions",
journal = "Journal of Computational Physics",
volume = "367",
pages = "49--64",
year = "2018",
publisher = "Elsevier BV",
month = "Aug",
url = "http://www.sci.utah.edu/publications/Guo2018a/1-s2.0-S0021999118302420-main.pdf",
}
@Article{SCI:Guo2018b,
author = "L. Guo and A. Narayan and L. Yan and T. Zhou",
title = "Weighted approximate fekete points: sampling for
least-squares polynomial approximation",
journal = "SIAM Journal on Scientific Computing",
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number = "1",
pages = "A366--A387",
year = "2018",
publisher = "SIAM",
month = "Jan",
doi = "10.1137/17m1140960",
url = "http://www.sci.utah.edu/publications/Guo2018b/17m1140960.pdf",
}
@Article{SCI:Gup2012a,
author = "A. Gupta and M. Escolar and C. Dietrich and J.
Gilmore and G. Gerig and M. Styne",
title = "{3D} Tensor Normalization for Improved Accuracy in
{DTI} Registration Methods",
booktitle = " Biomedical Image Registration Lecture Notes in
Computer Science ({LNCS})",
journal = " Biomedical Image Registration Lecture Notes in
Computer Science ({LNCS})",
volume = "7359",
pages = "170--179",
year = "2012",
doi = "10.1007/978-3-642-31340-0_18",
url = "http://www.sci.utah.edu/publications/Gup2012a/Gupta_3DNorm_WBIR2012.pdf",
}
@InProceedings{SCI:Gur2012a,
author = "Y. Gur and F. Jiao and S.X. Zhu and C.R.
Johnson",
title = "White matter structure assessment from reduced
{HARDI} data using low-rank polynomial
approximations",
booktitle = "Proceedings of {MICCAI} 2012 Workshop on
Computational Diffusion {MRI} ({CDMRI12})",
pages = "186-197",
year = "2012",
series = "Lecture Notes in Computer Science ({LNCS})",
month = "October",
location = "Nice, France",
url = "http://www.sci.utah.edu/publications/gur12/Gur_CDMRI2012.pdf",
}
@InProceedings{SCI:Gur2014a,
author = "Y. Gur and C.R. Johnson",
title = "Generalized {HARDI} Invariants by Method of Tensor
Contraction",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "718--721",
year = "2014",
month = "April",
keywords = "Diffusion MRI, HARDI, invariants",
url = "http://www.sci.utah.edu/publications/Gur2014a/Gur_ISBI2014.pdf",
}
@InProceedings{SCI:Gyu2005a,
author = "A. Gyulassy and V. Natarajan and V. Pascucci and
P.-T. Bremer and B. Hamann",
title = "Topology-based Simplification for Feature
Extraction from 3D Scalar Fields",
booktitle = "Proceedings of the {IEEE} Conference on
Visualization ({VIS}-05)",
pages = "275--280",
year = "2005",
month = "October",
}
@Article{SCI:Gyu2006a,
author = "A. Gyulassy and V. Natarajan and V. Pascucci and
P.-T. Bremer and B. Hamann",
title = "A Topological Approach to Simplification of
Three-Dimensional Scalar Functions",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "12",
number = "4",
pages = "474--484",
year = "2006",
month = "August",
}
@Article{SCI:Gyu2007a,
author = "A. Gyulassy and V. Natarajan and B. Hamann and V.
Pascucci",
title = "Efficient Computation of Morse-Smale Complexes for
Three-dimensional Scalar Functions",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
year = "2007",
note = "(presented at IEEE VIS 2007)",
}
@Article{SCI:Gyu2007b,
author = "A. Gyulassy and V. Natarajan and B. Hamann and M.
Duchaineau and V. Pascucci and E. Bringa and A.
Higginbotham",
title = "Topologically Clean Distance Fields",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
year = "2007",
note = "(presented at IEEE VIS 2007)",
}
@InProceedings{SCI:Gyu2011a,
author = "Attila Gyulassy and J.A. Levine and V. Pascucci",
title = "Visualization of Discrete Gradient Construction
(Multimedia submission)",
booktitle = "Proceedings of the 27th Symposium on Computational
Geometry",
pages = "289--290",
year = "2011",
publisher = "ACM",
month = "June",
location = "Paris, France",
doi = "10.1145/1998196.1998241",
url = "http://www.sci.utah.edu/publications/gyulassy11/Gyulassy_SymCompGeo2011.pdf",
}
@InProceedings{SCI:Gyu2012a,
author = "A. Gyulassy and V. Pascucci and T. Peterka and R.
Ross",
title = "The Parallel Computation of Morse-Smale
Complexes",
booktitle = "Proceedings of the Parallel and Distributed
Processing Symposium ({IPDPS})",
pages = "484--495",
year = "2012",
doi = "10.1109/IPDPS.2012.52",
url = "http://www.sci.utah.edu/publications/gyulassy12/Gyulassy_IPDPS2012.pdf",
}
@Article{SCI:Gyu2012b,
author = "A. Gyulassy and P.-T. Bremer and V. Pascucci",
title = "Computing Morse-Smale Complexes with Accurate
Geometry",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "18",
number = "12",
pages = "2014--2022",
year = "2012",
doi = "10.1109/TVCG.2011.272",
url = "http://www.sci.utah.edu/publications/gyulassy12/Gyulassy_TVCG2012.pdf",
}
@Article{SCI:Gyu2012c,
author = "A. Gyulassy and N. Kotava and M. Kim and C. Hansen
and H. Hagen and and V. Pascucci",
title = "Direct Feature Visualization Using Morse-Smale
Complexes",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "18",
number = "9",
pages = "1549--1562",
year = "2012",
month = "September",
doi = "10.1109/TVCG.2011.272",
url = "http://www.sci.utah.edu/publications/gyulassy12/Gyulassy_TVCG2012b.pdf",
}
@Conference{SCI:Gyu2015a,
author = "A. Gyulassy and A. Knoll and K. C. Lau and Bei
Wang and P. T. Bremer and M. E. Papka and L. A.
Curtiss and V. Pascucci",
title = "Morse-Smale Analysis of Ion Diffusion for DFT
Battery Materials Simulations",
title_url =
"http://www.sci.utah.edu/~beiwang/publications/Nanosphere_TopoInVis_BeiWang_2015.pdf",
booktitle = "Topology-Based Methods in Visualization
(TopoInVis)",
year = "2015",
}
@InProceedings{SCI:Gyu2015b,
author = "A. Gyulassy and A. Knoll and K. C. Lau and Bei
Wang and PT. Bremer and M.l E. Papka and L. A.
Curtiss and V. Pascucci",
title = "Interstitial and Interlayer Ion Diffusion Geometry
Extraction in Graphitic Nanosphere Battery
Materials",
booktitle = "Proceedings IEEE Visualization Conference",
year = "2015",
url = "http://www.sci.utah.edu/publications/Gyu2015b/Nanosphere_Vis_BeiWang_2015.pdf",
}
@Article{SCI:Gyu2019a,
author = "A. Gyulassy and P.-T. Bremer and V. Pascucci",
title = "Shared-Memory Parallel Computation of Morse-Smale
Complexes with Improved Accuracy",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "25",
number = "1",
pages = "1183--1192",
year = "2019",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/tvcg.2018.2864848",
url = "http://www.sci.utah.edu/publications/Gyu2019a/08440034.pdf",
}
@InProceedings{SCI:Ha2009a,
author = "L.K. Ha and J. Kr{\"u}ger and T. Fletcher and S.
Joshi and C.T. Silva",
title = "Fast Parallel Unbiased Diffeomorphic Atlas
Construction on Multi-Graphics Processing Units",
booktitle = "Proceedings of the Eurographics Symposium on
Parallel Graphics and Visualization 2009",
year = "2009",
doi = "0.2312/EGPGV/EGPGV09/041-048",
url = "http://www.sci.utah.edu/publications/Ha2009a/Ha_egpgv2009.pdf",
}
@Article{SCI:Ha2009b,
author = "L.K. Ha and J. Kr{\"u}ger and C.T. Silva",
title = "Fast 4-way parallel radix sorting on GPUs",
journal = "Computer Graphic Forum",
year = "2009",
url = "http://www.sci.utah.edu/publications/Ha2009b/Ha_CGF2009.pdf",
}
@Article{SCI:Ha2010a,
author = "L. Ha and M.W. Prastawa and G. Gerig and J.H.
Gilmore and C.T. Silva and S. Joshi",
title = "Image Registration Driven by Combined
Probabilistic and Geometric Descriptors",
journal = "Med Image Comput Comput Assist Interv.",
volume = "13",
number = "2",
pages = "602--609",
year = "2010",
pmid = "20879365",
url = "http://www.sci.utah.edu/publications/ha10/Ha_ImageReg2010.pdf",
}
@InProceedings{SCI:Ha2010b,
author = "L.K. Ha and J. Kr{\"u}ger and S. Joshi and C.T.
Silva",
title = "Multi-scale Unbiased Diffeomorphic Atlas
Construction on Multi-GPUs",
booktitle = "GPU Computing Gems",
volume = "1",
year = "2010",
url = "http://www.sci.utah.edu/publications/Ha2010b/Ha_MultiDiff_GPUGems2010.pdf",
}
@InProceedings{SCI:Ha2010c,
author = "L.K. Ha and M.W. Prastawa and G. Gerig and J.H.
Gilmore and C.T. Silva and S. Joshi",
title = "Image Registration Driven by Combined
Probabilistic and Geometric Descriptors",
booktitle = "Proceedings of Medical Image Computing and
Computer-Assisted Intervention – MICCAI 2010",
volume = "6362/2010",
pages = "602--609",
year = "2010",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-15745-5_74",
keywords = "netl",
url = "http://www.sci.utah.edu/publications/ha10/Ha_LNCS2010.pdf",
}
@InProceedings{SCI:Ha2011a,
author = "L.K. Ha and J. Kr{\"u}ger and J. Comba and S. Joshi
and C.T. Silva",
title = "Optimal Multi-Image Processing Streaming Framework
on Parallel Heterogeneous Systems",
booktitle = "Proceedings of Eurographics Symposium on Parallel
Graphics and Visualization 2011",
pages = "1--10",
year = "2011",
note = "Awarded Best Paper!",
doi = "10.2312/EGPGV/EGPGV11/001-010",
url = "http://www.sci.utah.edu/publications/Ha2011a/Ha_MIP-egpgv2011.pdf",
}
@Article{SCI:Ha2011b,
author = "L.K. Ha and M.W. Prastawa and G. Gerig and J.H.
Gilmore and C.T. Silva",
title = "Efficient Probabilistic and Geometric Anatomical
Mapping Using Particle Mesh Approximation on
GPUs",
journal = "International Journal of Biomedical Imaging,
Special Issue in Parallel Computation in Medical
Imaging Applications",
volume = "2011",
pages = "16 pages",
year = "2011",
note = "Article ID 572187",
doi = "10.1155/2011/572187",
url = "http://www.sci.utah.edu/publications/ha11/Ha_IJBI2011.pdf",
}
@InBook{SCI:Ha2011c,
author = "L.K. Ha and J. Kr{\"u}ger and S. Joshi and C.T.
Silva",
title = "Multi-scale Unbiased Diffeomorphic Atlas
Construction on Multi-GPUs",
volume = "1",
pages = "42",
year = "2011",
chapter = "10",
publisher = "Morgan Kaufmann",
url = "http://www.sci.utah.edu/publications/Ha2011c/Ha_GPUCG2011.pdf",
}
@Article{SCI:Ha2012a,
author = "L.K. Ha and J. Kr{\"u}ger and J.L.D. Comba and C.T.
Silva and S. Joshi",
title = "ISP: An Optimal Out-of-Core Image-Set Processing
Streaming Architecture for Parallel Heterogeneous
Systems",
journal = "IEEE Transactions on Visualization and Computer
Graphics (TVCG)",
volume = "18",
number = "6",
pages = "838--851",
year = "2012",
doi = "10.1109/TVCG.2012.32",
url = "http://www.sci.utah.edu/publications/Ha2012a/Ha_TVCG2012.pdf",
}
@Article{SCI:Ha2012b,
author = "L.K. Ha and J. Kr{\"u}ger and J.L.D. Comba and C.T.
Silva and S. Joshi",
title = "{ISP}: An Optimal Out-of-Core Image-Set Processing
Streaming Architecture for Parallel Heterogeneous
Systems",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "18",
number = "5",
pages = "838--851",
year = "2012",
doi = "10.1109/TVCG.2012.32",
}
@TechReport{SCI:Ha2013a,
author = "L.K. Ha and J. King and Z. Fu and R.M. Kirby",
title = "A High-Performance Multi-Element Processing
Framework on GPUs",
number = "UUSCI-2013-005",
year = "2013",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2013-005.pdf",
}
@InProceedings{SCI:Haj2018a,
author = "M. Hajij and B. Wang and C. Scheidegger and P.
Rosen",
title = "Visual Detection of Structural Changes in
Time-Varying Graphs Using Persistent Homology",
booktitle = "2018 IEEE Pacific Visualization Symposium
(PacificVis)",
year = "2018",
publisher = "IEEE",
month = "April",
doi = "10.1109/pacificvis.2018.00024",
url = "http://www.sci.utah.edu/publications/Haj2018a/08365984.pdf",
}
@Article{SCI:Haj2018c,
author = "M. Hajij and B. Wang and P. Rosen",
title = "MOG: Mapper on Graphs for Relationship Preserving
Clustering",
journal = "CoRR",
year = "2018",
url = "http://www.sci.utah.edu/publications/Haj2018c/1804.11242.pdf",
}
@InProceedings{SCI:Hal1995a,
author = "J.W. Haller and M.I. Miller and G.E. Christensen
and S. Joshi and M. Gado and J. Csernansky and M.W.
Vannier",
title = "A Comparison of Automated and Manual Segmentation
of Hippocampus MR Images",
booktitle = "Proceedings of SPIE Medical Imaging",
pages = "206--215",
year = "1995",
month = "March",
}
@InProceedings{SCI:Hal1995b,
author = "J.W. Haller and G.E. Christensen and S. Joshi and
M.I. Miller and M.W. Vannier",
title = "Digital Atlas-Based Segmentation of the
Hippocampus",
booktitle = "Computer Assisted Radiology: Proceedings of the
International Symposium on Computer and
Communications Systems for Image Guided Diagnosis
and Therapy",
pages = "152--157",
year = "1995",
editor = "C.C. Jaffe and H.U. Lemke and K. Inamura and M.W.
Vannier",
month = "June",
}
@Article{SCI:Hal1996a,
author = "J.W. Haller and G.E. Christensen and S.C. Joshi
and J.W. Newcomer and M.I. Miller and J.G.
Csernansky and M. Vannier",
title = "Hippocampal MR Imaging Morphometry by Means of
General Pattern Matching",
journal = "Radiology",
volume = "199",
number = "3",
pages = "787--791",
year = "1996",
month = "June",
}
@Article{SCI:Hal1997a,
author = "J.W. Haller and A. Banerjee and G.E. Christensen
and M. Gado and S. Joshi and M.I. Miller and Y.
Sheline and M.W. Vannier and J. Csernansky",
title = "Three-Dimensional Hippocampal {MR} Morphometry
with High-Dimensional Transformation of a
Neuroanatomic Atlas",
journal = "Radiology",
volume = "202",
number = "2",
pages = "504--510",
year = "1997",
month = "February",
}
@Article{SCI:Hal2012a,
author = "J.P. Halloran and S. Sibole and C.C. Van Donkelaar
and M.C. Van Turnhout and O.W. Oomens and J.A.
Weiss and F. Guilak and A. Erdemir",
title = "Multiscale mechanics of articular cartilage:
potentials and challenges of coupling
musculoskeletal, joint, and microscale
computational models",
journal = "Annals of Biomedical Engineering",
volume = "40",
number = "11",
pages = "2456--2474",
year = "2012",
pmid = "10.1007/s10439-012-0598-0",
}
@Article{SCI:Hal2013a,
author = "M. Hall and R.M. Kirby and F. Li and M.D. Meyer
and V. Pascucci and J.M. Phillips and R. Ricci and
J. Van der Merwe and S. Venkatasubramanian",
title = "Rethinking Abstractions for Big Data: Why, Where,
How, and What",
journal = "Cornell University Library",
year = "2013",
url = "http://www.sci.utah.edu/publications/Hal2013a/Hall_1306.3295v1.pdf",
}
@InProceedings{SCI:Hal2013b,
author = "M. Hall and J.C. Beckvermit and C.A. Wight and T.
Harman and M. Berzins",
title = "The influence of an applied heat flux on the
violence of reaction of an explosive device",
booktitle = "Proceedings of the Conference on Extreme Science
and Engineering Discovery Environment: Gateway to
Discovery",
pages = "11:1--11:8",
year = "2013",
series = "{XSEDE '13}",
location = "San Diego, California",
isbn = "978-1-4503-2170-9",
doi = "10.1145/2484762.2484786",
keywords = "DDT, cook-off, deflagration, detonation, violence
of reaction, c-safe",
url = "http://www.sci.utah.edu/publications/Hal2013b/Hall_XSEDE2013.pdf",
}
@TechReport{SCI:Ham2005a,
author = "C.W. Hamman and R.M. Kirby and M. Berzins",
title = "Parallelization and Scalability of a Spectral
Element Solver",
number = "UUSCI-2005-011",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "parallel processing, scaling, spectral element
solver",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-011.pdf",
}
@InProceedings{SCI:Ham2006b,
author = "C.W. Hamman and R.M. Kirby and J.C. Klewicki",
title = "On the Lamb Vector Divergence as a Momentum Field
Diagnostic Employed in Turbulent Channel Flow",
booktitle = "Proceedings of the 59th Annual Meeting of the
American Physical Society, Division of Fluid
Dynamics",
year = "2006",
month = "November",
location = "Tampa Bay, Fl",
}
@Article{SCI:Ham2007a,
author = "C.W. Hamman and R.M. Kirby and M. Berzins",
title = "Parallelization and Scalability of a Spectral
Element Channel Flow Solver for Incompressible
Navier-Stokes Equations",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "14",
number = "10",
pages = "1403--1422",
year = "2007",
keywords = "parallel processing, scaling, spectral element
solver, , parallel processing",
url = "http://www.sci.utah.edu/publications/hamman07/hammankirbyberzins07.pdf",
}
@Article{SCI:Ham2007b,
author = "C.R. Hamman and R.M. Kirby and M. Berzins",
title = "Parallel Direct Simulation of Incompressible
Navier Stokes Equations",
journal = "Concurrency and Computation",
volume = "19",
number = "10",
pages = "1403-1427",
year = "2007",
keywords = "cfd computational fluid dynamics, fluid structure
problems, parallel visualization",
url = "http://www.sci.utah.edu/publications/hamman07/Kirby-21.pdf",
}
@Article{SCI:Ham2008a,
author = "C.W. Hamman and J.C. Klewicki and R.M. Kirby",
title = "On the Lamb Vector Divergence in Navier-Stokes
Flows",
journal = "Journal of Fluid Mechanics",
volume = "610",
pages = "261--284",
year = "2008",
keywords = "navier-stokes, flow visualization, computational
fluid dynamics, cfd",
}
@InProceedings{SCI:Ham2013a,
author = "D.K. Hammond and Y. Gur and C.R. Johnson",
title = "Graph Diffusion Distance: A Difference Measure for
Weighted Graphs Based on the Graph Laplacian
Exponential Kernel",
booktitle = "Proceedings of the {IEEE} global conference on
information and signal processing
({GlobalSIP'13})",
pages = "419--422",
year = "2013",
location = "Austin, Texas",
doi = "10.1109/GlobalSIP.2013.6736904",
url = "http://www.sci.utah.edu/publications/hammond13/Hammond_GlobalSIP2013.pdf",
}
@Article{SCI:Ham2014a,
author = "C. Hamani and B.O. Amorim and A.L. Wheeler and M.
Diwan and K. Driesslein and L. Covolan and C.R.
Butson and J.N. Nobrega",
title = "Deep brain stimulation in rats: Different targets
induce similar antidepressant-like effects but
influence different circuits",
journal = "Neurobiology of Disease",
volume = "71",
pages = "205--214",
year = "2014",
publisher = "Elsevier Inc.",
month = "August",
issn = "1095-953X",
doi = "10.1016/j.nbd.2014.08.007",
pmid = "25131446",
keywords = "Anterior capsule, Connectivity, Deep brain
stimulation, Depression, Nucleus accumbens,
Prefrontal cortex",
url = "http://www.sci.utah.edu/publications/Ham2014a/Hamani_NeurobioDisease2014.pdf",
}
@Article{SCI:Ham2018a,
author = "J. Hampton and HR. Fairbanks and A. Narayan and A.
Doostan",
title = "Practical error bounds for a non-intrusive
bi-fidelity approach to parametric/stochastic model
reduction",
journal = "Journal of Computational Physics",
volume = "368",
pages = "315--332",
year = "2018",
publisher = "Elsevier BV",
month = "September",
doi = "10.1016/j.jcp.2018.04.015",
url = "http://www.sci.utah.edu/publications/Ham2018a/1-s2.0-S0021999118302298-main.pdf",
}
@Article{SCI:Han2002a,
author = "K.A. Hansen and J.A. Weiss and J.K. Barton",
title = "Recruitment of Tendon Crimp with Applied Tensile
Strain",
journal = "Journal of Biomechanical Engineering",
volume = "124",
pages = "72--77",
year = "2002",
url = "http://www.sci.utah.edu/publications/hansen02/octjbme.pdf",
}
@Article{SCI:Han2003a,
author = "C.D. Hansen and C.R. Johnson",
title = "Graphics Applications for Grid Computing",
journal = j-CGA,
pages = "20--21",
year = "2003",
month = "March/April",
keywords = "collaborative remote visualization, parallel
visualization",
url = "http://www.sci.utah.edu/publications/hansen03/Graphics-Applications-Grid03.pdf",
}
@InProceedings{SCI:Han2004a,
author = "Q. Han and C. Lu and G. Liu and S.M. Pizer and S.
Joshi and A. Thall",
title = "Representing Multi-Figure Anatomical Objects",
booktitle = "Proceedings of the International Symposium on
Biomedical Imaging (ISBI)",
pages = "1251--1254",
year = "2004",
location = "Piscataway, NJ",
url = "http://www.sci.utah.edu/publications/han04/ISBI04-Han_multi-fig.pdf",
}
@Book{SCI:Han2005a,
author = "C.D. Hansen and C.R. Johnson",
title = "The Visualization Handbook",
year = "2005",
publisher = "Elsevier",
isbn = "0-12-387582-X",
keywords = "forward problems inverse problems forward
simulation inverse solutions, inverse eeg, inverse
meg, forward simulation, cfd computational fluid
dynamics, computational mechanics, computational
pde pdes computational partial differential
equations, pse grid computing, scalar field
methods, isosurface extraction, volume rendering,
transfer functions, rtrt real-time ray tracing,
vector field methods, visual haptic workbench,
tensor field methods, vr virtual reality haptics,
remote visualization, remote isosurface
visualization, parallel visualization, ip image
processing signal processing, surface processing,
scirun, biopse, ncrr",
}
@InCollection{SCI:Han2005b,
author = "Q. Han and S.M. Pizer and D. Merck and S. Joshi
and J.-Y. Jeong",
title = "Multi-figure Anatomical Objects for Shape
Statistics",
booktitle = "Lecture Notes in Computer Science",
pages = "701-712",
year = "2005",
editor = "G. Christensen and M. Sonka",
publisher = "Springer",
doi = "10.1007/11505730_58",
url = "http://www.sci.utah.edu/publications/Han2005b/IPMI05_Han.pdf",
}
@InCollection{SCI:Han2009a,
author = "C.D. Hansen and C.R. Johnson and V. Pascucci and
C.T. Silva",
title = "Visualization for Data-Intensive Science",
booktitle = "The Fourth Paradigm: Data-Intensive Science",
pages = "153--164",
year = "2009",
editor = "S. Tansley and T. Hey and K. Tolle",
publisher = "Microsoft Research",
url = "http://www.sci.utah.edu/publications/hansen09/Vis-Book-Chapter-Aug09.pdf",
}
@Article{SCI:Han2012a,
author = "B.J. Hansen and M.D. Harris and L.A. Anderson and
C.L. Peters and J.A. Weiss and A.E. Anderson",
title = "Correlation between radiographic measures of
acetabular morphology with 3D femoral head coverage
in patients with acetabular retroversion",
journal = "Acta Orthopaedica",
volume = "83",
number = "3",
pages = "233--239",
year = "2012",
doi = "10.3109/17453674.2012.684138",
url = "http://www.sci.utah.edu/publications/hansen12/Hansen_ao_2012.pdf",
}
@Book{SCI:Han2014a,
author = "C.D. Hansen and M. Chen and C.R. Johnson and A.E.
Kaufman and H. Hagen (Eds.)",
title = "Scientific Visualization: Uncertainty, Multifield,
Biomedical, and Scalable Visualization",
title_url =
"http://www.springer.com/mathematics/computational+science+engineering/book/978-1-4471-6496-8",
year = "2014",
series = "Mathematics and Visualization",
publisher = "Springer",
isbn = "978-1-4471-6496-8",
}
@Article{SCI:Han2019a,
author = "M. Han and I. Wald and W. Usher and Q. Wu and F.
Wang and V. Pascicci and C. D. Hansen and C. R.
Johnson",
title = "Ray Tracing Generalized Tube Primitives: Method
and Applications",
journal = "Computer Graphics Forum",
volume = "38",
number = "3",
year = "2019",
publisher = "John Wiley \& Sons Ltd.",
url = "http://www.sci.utah.edu/publications/Han2019a/tubes-final.pdf",
}
@Article{SCI:Han2019b,
author = "A. B. Hanson and R. N. Lee and C. Vachet and I. J.
Schwerdt and T. Tasdizen and L. W. McDonald IV",
title = "Quantifying Impurity Effects on the Surface
Morphology of α-U3O8",
title_url =
"https://pubs.acs.org/doi/10.1021/acs.analchem.9b02013",
journal = "Analytical Chemistry",
year = "2019",
doi = "doi:10.1021/acs.analchem.9b02013",
}
@InProceedings{SCI:Han87a,
author = "C.D. Hansen and T. Henderson",
title = "{CAGD}-Based Computer Vision",
booktitle = "{IEEE} Computer Vision Workshop",
pages = "100--106",
year = "1987",
month = "December",
location = "Miami Beach, Florida",
}
@InProceedings{SCI:Han88a,
author = "C.D. Hansen and T. Henderson",
title = "Automatic Generation of Recognition Strategies",
booktitle = "International Conference on Computer Vision",
pages = "275--279",
year = "1988",
month = "December",
location = "Tampa, Florida",
}
@InProceedings{SCI:Han88b,
author = "C.D. Hansen and N. Ayache and F. Lustman",
title = "Towards Real-time Trinocular Stereo",
booktitle = "International Conference on Computer Vision",
pages = "129--133",
year = "1988",
month = "December",
location = "Tampa, Florida",
}
@InProceedings{SCI:Han88c,
author = "C.D. Hansen and N. Ayache and Francis Lustman",
title = "Efficient Depth Estimation using Trinocular
Stereo",
booktitle = "{SPIE} Conference on Intelligent Robots",
year = "1988",
month = "November",
location = "Cambridge, Massachusetts",
note = "Refereed abstract.",
}
@Article{SCI:Han89a,
author = "C.D. Hansen and T. Henderson",
title = "{CAGD}-Based Computer Vision",
journal = "{IEEE} Pattern Recognition and Machine
Intelligence",
volume = "11",
number = "10",
pages = "1181--1193",
year = "1989",
month = "November",
}
@InProceedings{SCI:Han90a,
author = "C.D. Hansen",
title = "High-level Tools for Scientific Visualization",
booktitle = "Computer Use By Engineers (CUBE) Symposium",
year = "1990",
month = "November",
location = "Sante Fe, NM.",
note = "Refereed abstract.",
}
@InProceedings{SCI:Han91a,
author = "C.D. Hansen and S. Tenbrink",
title = "The Impact of Gigabit Networking on Imaging",
booktitle = "Digital Imaging",
pages = "191--194",
year = "1991",
month = "April",
location = "Anaheim, Ca.",
}
@InProceedings{SCI:Han92a,
author = "C.D. Hansen and P. Hinker",
title = "Massively Parallel Isosurface Extraction",
booktitle = "Visualization 1992",
pages = "77--83",
year = "1992",
month = "October",
location = "Boston, Ma.",
}
@Article{SCI:Han92b,
author = "C.D. Hansen and D. Butler",
title = "Visualization '91 Workshop Report: Scientific
Visualization Environments",
journal = "Computer Graphics Quarterly",
volume = "26",
number = "3",
pages = "213--216",
year = "1992",
month = "August",
}
@Article{SCI:Han93a,
author = "C.D. Hansen and S. Tenbrink",
title = "The Impact of Gigabit Network Research on
Scientific Visualization",
journal = "The Visual Computer",
volume = "9",
number = "6",
pages = "318--323",
year = "1993",
}
@InProceedings{SCI:Han93b,
author = "C.D. Hansen and M. Krogh",
title = "Visualization on Massively Parallel Computers
using {CM}/{AVS}",
booktitle = "AVS Users Conference",
pages = "129--137",
year = "1993",
month = "May",
location = "Orlando, Fl.",
}
@Article{SCI:Han94a,
author = "C.D. Hansen T.Crockett and S. Whitman",
title = "Parallel Rendering",
journal = "{IEEE} Parallel and Distributed Technology",
volume = "2",
number = "2",
pages = "7",
year = "1994",
month = "Summer",
note = "Guest editors' introduction",
keywords = "parallel visualization",
}
@InProceedings{SCI:Han95a,
author = "C.D. Hansen and G.C. de Verdiere and M. Krogh and
J. Painter and R. Troutman",
title = "Binary-Swap Volumetric Rendering on the T3D",
booktitle = "Cray Users Group Conference",
pages = "61--69",
year = "1995",
month = "March",
location = "Denver, Co.",
keywords = "volume rendering",
}
@InProceedings{SCI:Han95b,
author = "C.D. Hansen and M. Krogh and W. White",
title = "Massively Parallel Visualization: Parallel
Rendering",
booktitle = "{SIAM} Parallel Computation Conference",
pages = "790--795",
year = "1995",
month = "February",
location = "San Francisco, Ca.",
}
@InProceedings{SCI:Han97a,
author = "C.D. Hansen and M. Krogh and J. Painter",
title = "Parallel Rendering Techniques for Massively
Parallel Visualization",
booktitle = "International Symposium on Parallel
Algorithms/Architecture Synthesis",
pages = "276--281",
year = "1997",
month = "March",
location = "Aizu-Wakamatsu, Japan",
}
@Article{SCI:Han98a,
author = "C.D. Hansen",
title = "{EUROGRAPHICS} '97 Conference Report",
journal = "Computer Graphics Quarterly",
volume = "32",
number = "1",
pages = "39",
year = "1998",
month = "February",
}
@Article{SCI:Han98b,
author = "C.D. Hansen",
title = "{EUROGRAPHICS} '97: Budapest, Hungary, September
4-8, 1997: Meeting Report",
journal = "Computer Graphics Forum",
volume = "16",
number = "5",
pages = "323--324",
year = "1998",
month = "February",
}
@InProceedings{SCI:Han99a,
author = "C.D. Hansen and T. Udeshi and S.G. Parker and P.
Shirley",
title = "Parallel Methods for Isosurface Visualization",
booktitle = "Ninth {SIAM} Conference on Parallel Processing for
Scientific Computing",
year = "1999",
note = "extended abstract",
keywords = "isosurface extraction, parallel visualization",
url = "http://www.sci.utah.edu/publications/siam99/siam99a.ps.gz",
url = "http://www.sci.utah.edu/publications/siam99/siam99a.ps",
}
@Article{SCI:Hao2011b,
author = "X. Hao and R.T. Whitaker and P.T. Fletcher",
title = "Adaptive Riemannian Metrics for Improved Geodesic
Tracking of White Matter",
journal = "Information Processing in Medical Imaging
(IPMI)",
volume = "6801/2011",
pages = "13--24",
year = "2011",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-22092-0_2",
keywords = "namic",
url = "http://www.sci.utah.edu/publications/hao11/Hao_IPMI2011.pdf",
}
@InProceedings{SCI:Hao2013a,
author = "X. Hao and P.T. Fletcher",
title = "Joint Fractional Segmentation and Multi-Tensor
Estimation in Diffusion MRI",
booktitle = "Proceedings of the International Conference on
Information Processing in Medical Imaging
({IPMI})",
pages = "(accepted)",
year = "2013",
series = "Lecture Notes in Computer Science ({LNCS})",
url = "http://www.sci.utah.edu/publications/hao13/Hao_IPMI2013a.pdf",
}
@Article{SCI:Hao2014a,
author = "X. Hao and K. Zygmunt and R.T. Whitaker and P.T.
Fletcher",
title = "Improved Segmentation of White Matter Tracts with
Adaptive Riemannian Metrics",
journal = "Medical Image Analysis",
volume = "18",
number = "1",
pages = "161--175",
year = "2014",
month = "Jan",
doi = "10.1016/j.media.2013.10.007",
pmid = "24211814",
keywords = "Conformal factor, Diffusion tensor imaging,
Front-propagation, Geodesic, Riemannian manifold",
url = "http://www.sci.utah.edu/publications/hao14/Hao_MIA2014.pdf",
}
@Article{SCI:Har1998a,
author = "G. Hart and A. Tomlin and J. Smith and M.
Berzins",
title = "Multi-scale Atmospheric Dispersion Modelling by
the Use of Adaptive Grid Techniques",
journal = "Environmental Monitoring and Assessment",
volume = "52",
pages = "225--228",
year = "1998",
url = "http://www.sci.utah.edu/publications/Har1998a/HartTomlinBerzins.pdf",
}
@Article{SCI:Har2005a,
author = "D.E. Hart and C.E. Goodyer and M. Berzins and P.K.
Jimack and L.E. Scales",
title = "Adjoint Error Estimation for EHL-Like Models",
journal = j-IJNMF,
volume = "47",
number = "10-11",
pages = "1069--1075",
year = "2005",
keywords = "EHL, computational mechanics, ehl",
url = "http://www.sci.utah.edu/publications/hart05/HGBJS04.pdf",
}
@InCollection{SCI:Har2006a,
author = "D. Hart and C.E. Goodyer and M. Berzins and P.K.
Jimack and L. Scales",
title = "Adjoint Error Estimation and Spatial Adaptivity
for EHL-Like Models",
booktitle = "IUTAM Symposium on Elastohydrodynamics and
Micro-elastohydrodynamics",
pages = "47--58",
year = "2006",
publisher = "Springer",
doi = "10.1007/1-4020-4533-6_3",
keywords = "computational mechanics, error estimation,
discrete adjoint, EHL, friction calculation, mesh
adaptation, ehl",
url = "http://www.sci.utah.edu/publications/Har2006a/HGBJS06.pdf",
}
@PhdThesis{SCI:Har2008a,
author = "D.E. Hart",
title = "Adjoint Error Estimation for Elastohydrodynamic
Lubrication",
year = "2008",
school = "School of Computing, University of Leeds",
month = "January",
note = "Advisor: Martin Berzins",
url = "http://www.sci.utah.edu/publications/Har2008a/Hart_PhDThesis2008.pdf",
}
@Article{SCI:Har2011a,
author = "D.E. Hart and M. Berzins and C.E. Goodyer and P.K.
Jimack",
title = "Using Adjoint Error Estimation Techniques for
Elastohydrodynamic Lubrication Line Contact
Problems",
journal = "International Journal for Numerical Methods in
Fluids",
volume = "67",
pages = "1559--1570",
year = "2011",
note = "Published online 29 October",
keywords = "EHL",
url = "http://www.sci.utah.edu/publications/hart11/Hart_HBGJ10.pdf",
}
@InProceedings{SCI:Har2012a,
author = "M.D. Harris and M. Datar and E. Jurrus and C.L.
Peters and R.T. Whitaker and A.E. Anderson",
title = "Statistical Shape Modeling of CAM-type
Femoroacetabular Impingement",
booktitle = "Proceedings of the International Symposium on
Computer Methods in Biomechanics and Biomedical
Engineering ({CMBBE} 2012)",
year = "2012",
url = "http://www.sci.utah.edu/publications/harris12/Harris_CMBBE2012.pdf",
}
@Article{SCI:Har2012b,
author = "M.D. Harris and A.E. Anderson and C.R. Henak and
B.J. Ellis and C.L. Peters and J.A. Weiss",
title = "Finite element prediction of cartilage contact
stresses in normal human hips",
journal = "Journal of Orthopaedic Research",
volume = "30",
number = "7",
pages = "1133--1139",
year = "2012",
doi = "10.1002/jor.22040",
keywords = "hip, finite element, biomechanics, cartilage
contact stresses, cartilage pressure",
url = "http://www.sci.utah.edu/publications/harris12/Harris_jor_2012.pdf",
}
@Article{SCI:Har2013a,
author = "M.D. Harris and S.P. Reese and C.L. Peters and
J.A. Weiss and A.E. Anderson",
title = "Three-dimensional Quantification of Femoral Head
Shape in Controls and Patients with Cam-type
Femoroacetabular Impingement",
journal = "Annals of Biomedical Engineering",
volume = "41",
number = "6",
pages = "1162--1171",
year = "2013",
doi = "10.1007/s10439-013-0762-1",
url = "http://www.sci.utah.edu/publications/harris13/Harris_ABE2013.pdf",
}
@Article{SCI:Har2013b,
author = "M.D. Harris and M. Datar and R.T. Whitaker and
E.R. Jurrus and C.L. Peters and A.E. Anderson",
title = "Statistical Shape Modeling of Cam Femoroacetabular
Impingement",
journal = "Journal of Orthopaedic Research",
volume = "31",
number = "10",
pages = "1620--1626",
year = "2013",
doi = "10.1002/jor.22389",
url = "http://www.sci.utah.edu/publications/harris13/Harris_JOR2013.pdf",
}
@PhdThesis{SCI:Har2013c,
author = "M.D. Harris",
title = "The geometry and biomechanics of normal and
pathomorphologic human hips",
year = "2013",
school = "Department of Bioengineering, University of
Utah",
note = "Ph.D. Thesis",
url = "http://www.sci.utah.edu/publications/harris13/MHarris_phd_dissertation_062013.pdf",
}
@InProceedings{SCI:Haw2005a,
author = "P. Hawkes and G. Kindlmann and D. Weinstein and
G.M. Jones and C. Keller",
title = "Practical Vessel Imaging by Computed Tomography in
Live Transgenic Mouse Models for Human Tumors",
booktitle = "Proceedings of 2005 SMI Conference, 4th Annual
Meeting of the Society for Molecular Imaging",
year = "2005",
location = "Cologne, Germany",
}
@Article{SCI:Haz2006a,
author = "H.C. Hazlett and M.D. Poe and G. Gerig and R.G.
Smith and J. Piven",
title = "Cortical Gray and White Brain Tissue Volume in
Adolescents and Adults with Autism",
journal = "Biological Psychiatry",
volume = "59",
number = "1",
pages = "1--96",
year = "2006",
month = "January",
}
@Article{SCI:Haz2009a,
author = "H.C. Hazlett and M.D. Poe and A.A. Lightbody and
G. Gerig and J.R. MacFall and A.K. Ross and J.
Provenzale and A. Martin and A.L. Reiss and J.
Piven",
title = "Teasing apart the heterogeneity of autism: Same
behavior, different brains in toddlers with fragile
X syndrome and autism",
journal = "Journal of Neurodevelopmental Disorders",
volume = "1",
number = "1",
pages = "81--90",
year = "2009",
pmid = "20700390",
url = "http://www.sci.utah.edu/publications/hazlett09/Hazlett_NeurodevelopDisord2009.pdf",
}
@Article{SCI:Haz2011a,
author = "H.C. Hazlett and M. Poe and G. Gerig and M. Styner
and C. Chappell and R.G. Smith and C. Vachet and J.
Piven",
title = "Early Brain Overgrowth in Autism Associated with
an Increase in Cortical Surface Area Before Age
2",
journal = "Arch of Gen Psych",
volume = "68",
number = "5",
pages = "467--476",
year = "2011",
doi = "10.1001/archgenpsychiatry.2011.39",
url = "http://www.sci.utah.edu/publications/hazlett11/Hazlett_AGP2011.pdf",
}
@Article{SCI:Haz2012a,
author = "H.C. Hazlett and H. Gu and R.C. McKinstry and
D.W.W. Shaw and K.N. Botteron and S. Dager and M.
Styner and C. Vachet and G. Gerig and S. Paterson
and R.T. Schultz and A.M. Estes and A.C. Evans and
J. Piven",
title = "Brain Volume Findings in Six Month Old Infants at
High Familial Risk for Autism",
journal = "American Journal of Psychiatry ({AJP})",
pages = "(in print)",
year = "2012",
url = "http://www.sci.utah.edu/publications/hazlett12/Hazlett_AJP2012.pdf",
}
@Article{SCI:He2018a,
author = "Y. He and M. Razi and C. Forestiere and L. Dal
Negro and R.M. Kirby",
title = "Uncertainty quantification guided robust design
for nanoparticles' morphology",
journal = "Computer Methods in Applied Mechanics and
Engineering",
pages = "578--593",
year = "2018",
publisher = "Elsevier BV",
month = "July",
doi = "10.1016/j.cma.2018.03.027",
url = "http://www.sci.utah.edu/publications/He2018a/1-s2.0-S0045782518301518-main.pdf",
}
@Article{SCI:Hef2019a,
author = "S. T. Heffernan and N. Ly and B. J. Mower and C.
Vachet and I. J. Schwerdt and T. Tasdizen and L. W.
McDonald IV",
title = "Identifying surface morphological characteristics
to differentiate between mixtures of U3O8
synthesized from ammonium diuranate and uranyl
peroxide",
title_url =
"https://www.degruyter.com/view/j/ract.ahead-of-print/ract-2019-3140/ract-2019-3140.xml",
journal = "Radiochimica Acta",
year = "2019",
}
@InCollection{SCI:Hen2004a,
author = "C.S. Henriquez and J.V. Tranquillo and D.M.
Weinstein and E.W. Hsu and C.R. Johnson",
title = "Three-dimensional Propagation in Mathematic
Models: Integrative Model of the Mouse Heart",
booktitle = "Cardiac Electrophysiology: From Cell to Bedside",
pages = "273--281",
year = "2004",
editor = "D.P. Zipes and J. Jalife",
chapter = "30",
publisher = "Saunders",
edition = "4th edition",
keywords = "forward problems inverse problems forward
simulation inverse solutions, forward simulation,
cardiac heart, ncrr",
url = "http://www.sci.utah.edu/publications/henriquez04/CardiacElectrophysiologyChapter.pdf",
}
@Article{SCI:Hen2007a,
author = "H.B. Henninger and C.J. Underwood and S.A. Maas
and R.T. Whitaker and J.A. Weiss",
title = "Spatial Distribution and Orientation of Dermatan
Sulfate in Human Medial Collateral Ligament",
journal = "Journal of Structural Biology",
volume = "158",
number = "1",
pages = "33--45",
year = "2007",
month = "April",
doi = "10.1016/j.jsb.2006.10.008",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/Hen2007a/henninger_j_struct_biol_2007.pdf",
}
@Article{SCI:Hen2009a,
author = "H.B. Henninger and S.A. Maas and J.H. Shepherd and
S. Joshi and J.A. Weiss",
title = "Transversely Isotropic Distribution of Sulfated
Glycosaminoglycans in Human Medial Collateral
Ligament: A Quantitative Analysis",
journal = "Journal of Structural Biology",
volume = "165",
pages = "176-183",
year = "2009",
pmid = "19126431",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/henninger09/henninger_jsb_2009.pdf",
}
@Article{SCI:Hen2009c,
author = "H.B. Henninger and S.P. Reese and A.E. Anderson
and J.A. Weiss",
title = "Validation of computational models in
biomechanics",
journal = "Proceedings of the Institution of Mechanical
Engineers, Part H: Journal of Engineering in
Medicine",
volume = "224",
number = "7",
pages = "801--812",
year = "2009",
publisher = "SAGE Publications",
url = "http://www.sci.utah.edu/publications/Hen2009c/henninger_pime_j_eng_med_2010_validation.pdf",
}
@Article{SCI:Hen2010a,
author = "H.B. Henninger and C.J. Underwood and G.A.
Ateshian and J.A. Weiss",
title = "Effect of sulfated glycosaminoglycan digestion on
the transverse permeability of medial collateral
ligament.",
journal = "Journal of Biomechanics",
volume = "43",
pages = "2567--2573",
year = "2010",
url = "http://www.sci.utah.edu/publications/henninger10/henninger_j_biomech_2010.pdf",
}
@Article{SCI:Hen2011a,
author = "C.R. Henak and B.J. Ellis and M.D. Harris and A.E.
Anderson and C.L. Peters and J.A. Weiss",
title = "{R}ole of the acetabular labrum in load support
across the hip joint",
journal = "Journal of Biomechanics",
volume = "44",
number = "12",
pages = "2201-2206",
year = "2011",
url = "http://www.sci.utah.edu/publications/henak11/Henak_JBM2011.pdf",
}
@Article{SCI:Hen2012a,
author = "H.B. Henninger and Barg A and A.E. Anderson and
K.N. Bachus and R.Z. Tashjian and R.T. Burks",
title = "Effect of deltoid tension and humeral version in
reverse total shoulder arthroplasty: a
biomechanical study",
journal = "Journal of Shoulder and Elbow Surgery",
volume = "21",
number = "4",
pages = "483–-490",
year = "2012",
doi = "10.1016/j.jse.2011.01.040",
keywords = "Shoulder, reverse arthroplasty, deltoid tension,
humeral version, biomechanical simulator",
url = "http://www.sci.utah.edu/publications/henninger12/Henninger_jses_2012a.pdf",
}
@Article{SCI:Hen2012b,
author = "H.B. Henninger and A. Barg and A.E. Anderson and
K.N. Bachus and R.T. Burks and R.Z. Tashjian",
title = "Effect of lateral offset center of rotation in
reverse total shoulder arthroplasty: a
biomechanical study",
journal = "Journal of Shoulder and Elbow Surgery",
volume = "21",
number = "9",
pages = "1128--1135",
year = "2012",
doi = "10.1016/j.jse.2011.07.034",
keywords = "Shoulder simulator, reverse arthroplasty, lateral
offset, center of rotation",
url = "http://www.sci.utah.edu/publications/henninger12/Henninger_jses_2012b.pdf",
}
@Article{SCI:Hen2013a,
author = "C.R. Henak and A.E. Anderson and J.A. Weiss",
title = "Subject-specific analysis of joint contact
mechanics: application to the study of
osteoarthritis and surgical planning",
journal = "Journal of Biomechanical Engineering",
volume = "135",
number = "2",
year = "2013",
doi = "10.1115/1.4023386",
pmid = "23445048",
}
@Article{SCI:Hen2013b,
author = "H.B. Henninger and C.J. Underwood and S.J. Romney
and G.L. Davis and J.A. Weiss",
title = "Effect of Elastin Digestion on the Quasi-Static
Tensile Response of Medial Collateral Ligament",
journal = "Journal of Orthopaedic Research",
pages = "(published online)",
year = "2013",
doi = "10.1002/jor.22352",
url = "http://www.sci.utah.edu/publications/henninger13/Henninger_JOR2013.pdf",
}
@Article{SCI:Hen2013c,
author = "C.R. Henak and Carruth E and A.E. Anderson and
M.D. Harris and B.J. Ellis and C.L. Peters and J.A.
Weiss",
title = "Finite element predictions of cartilage contact
mechanics in hips with retroverted acetabula",
journal = "Osteoarthritis and Cartilage",
volume = "21",
pages = "1522-1529",
year = "2013",
doi = "10.1016/j.joca.2013.06.008",
url = "http://www.sci.utah.edu/publications/henak13/Henak_OaC2013.pdf",
}
@Article{SCI:Hen2013d,
author = "C.R. Henak and A.K. Kapron and B.J. Ellis and S.A.
Maas and A.E. Anderson and J.A. Weiss",
title = "Specimen-specific predictions of contact stress
under physiological loading in the human hip:
validation and sensitivity studies",
journal = "Biomechanics and Modeling in Mechanobiology",
pages = "1-14",
year = "2013",
doi = "10.1007/s10237-013-0504-1",
}
@PhdThesis{SCI:Hen2013e,
author = "C.R. Henak",
title = "Cartilage and labrum mechanics in the normal and
pathomorphologic human hip",
year = "2013",
school = "Department of Bioengineering, University of
Utah",
note = "Ph.D. Thesis",
url = "http://www.sci.utah.edu/publications/henak13/CorinneHenak_dissertation.pdf",
}
@InProceedings{SCI:Hen83a,
author = "T.C. Henderson and C.D. Hansen and E. Shilcrat and
W.S. Fai",
title = "Logical Sensor Specification",
booktitle = "{SPIE} Conference on Intelligent Robots",
pages = "578--583",
year = "1983",
month = "November",
location = "Cambridge, Massachusetts",
note = "refereed abstract.",
}
@Article{SCI:Hen84a,
author = "T.C. Henderson and W.S. Fai and C.D. Hansen",
title = "{MKS}: A Multi-sensor Kernel System",
journal = "{IEEE} Transactions on Systems, Man and
Cybernetics",
volume = "{SMC}-14",
number = "5",
pages = "784--791",
year = "1984",
month = "September/October",
}
@InProceedings{SCI:Hen84b,
author = "T.C. Henderson and C.D. Hansen and B. Bhanu",
title = "{ASP}: An Algorithm and Sensor Performance
Evaluation System",
booktitle = "{PECORA} {IX} Conference on Spatial Information
Technologies for Remote Sensing Today and
Tomorrow",
pages = "201-207",
year = "1984",
month = "October",
location = "Sioux Falls, S.D.",
}
@InProceedings{SCI:Hen84c,
author = "T.C. Henderson and E. Shilcrat and C.D. Hansen",
title = "A Fault Tolerant Sensor Scheme",
booktitle = "International Conference on Pattern Recognition",
pages = "663--665",
year = "1984",
month = "August",
location = "Montreal, Canada",
}
@InProceedings{SCI:Hen84d,
author = "T.C. Henderson and B. Bhanu and C.D. Hansen",
title = "Distributed Control in the Multi-sensor Kernel
System",
booktitle = "{SPIE} Conference on Intelligent Robots",
pages = "253--255",
year = "1984",
month = "November",
location = "Cambridge, Massachusetts",
note = "refereed abstract.",
}
@Article{SCI:Hen85a,
author = "T.C. Henderson and C.D. Hansen and W.S. Fai",
title = "Organizing Spatial Data for Robotics Systems",
journal = "Computers in Industry",
volume = "6",
number = "5",
pages = "331--344",
year = "1985",
month = "October",
}
@InProceedings{SCI:Hen85b,
author = "T.C. Henderson and C.D. Hansen and B. Bhanu",
title = "A Framework for Distributed Sensing and Control",
booktitle = "International Joint Conference on Artificial
Intelligence",
pages = "1106--1109",
year = "1985",
month = "August",
location = "Los Angeles, Ca.",
}
@InProceedings{SCI:Hen85c,
author = "T.C. Henderson and C.D. Hansen",
title = "A Kernel for Multi-sensor Robotics Systems",
booktitle = "Proceedings of the {CAD}/{CAM}, Robotics, and
Automation Institute and Conference",
pages = "217--222",
year = "1985",
month = "February",
location = "Tucson, Arizona",
}
@InProceedings{SCI:Hen85d,
author = "T.C. Henderson and C.D. Hansen and B. Bhanu",
title = "The Synthesis of Logical Sensor Specifications",
booktitle = "{SPIE} Conference on Intelligent Robots",
year = "1985",
month = "September",
location = "Cambridge, Massachusetts",
note = "refereed abstract.",
}
@Article{SCI:Hen86a,
author = "T. Henderson and C.D. Hansen and B. Bhanu",
title = "The Specification of Distributed Sensing and
Control",
journal = "Journal of Robotic Systems",
volume = "2",
number = "4",
pages = "387--396",
year = "1986",
}
@InProceedings{SCI:Hen86b,
author = "T.C. Henderson and C.D. Hansen and A. Samal and
C.C. Ho and B. Bhanu",
title = "{CAGD} Based 3-D Visual Recognition",
booktitle = "International Conference on Pattern Recognition",
pages = "230--232",
year = "1986",
month = "October",
location = "Paris, France",
}
@InCollection{SCI:Hen87a,
author = "T. Henderson and C.D. Hansen and Bir Bhanu",
title = "Intrinsic Characteristics as the Interface between
{CAD} and Machine Vision Systems",
booktitle = "Pattern Recognition Theory and Applications",
pages = "461--470",
year = "1987",
editor = "P. Devijver and J. Kittler",
series = "NATO-ASI Series",
publisher = "Springer-Verlag",
}
@InProceedings{SCI:Hen87b,
author = "T.C. Henderson and C.D. Hansen and A. Samal and
C.C. Ho and B. Bhanu",
title = "{CAD}-Based Robotics",
booktitle = "{IEEE} Conference on Robotics and Automation",
pages = "631--635",
year = "1987",
month = "May",
location = "Raleigh, NC.",
}
@Article{SCI:Hen88a,
author = "T.C. Henderson and A. Mitiche and E. Weitz and
C.D. Hansen",
title = "Multisensor Knowledge Systems: Interpreting 3-D
structure",
journal = "International Journal of Robotics Research,
Special Issue on Multisensor Integration",
volume = "7",
number = "6",
pages = "114--137",
year = "1988",
month = "December",
}
@InProceedings{SCI:Hen88b,
author = "T. Henderson and C.D. Hansen",
title = "{CAD}-Based Computer Vision",
booktitle = "{SPIE} Conference",
year = "1988",
month = "April",
location = "Orlando, Florida",
}
@InProceedings{SCI:Hen89a,
author = "T. Henderson and C.D. Hansen and R. Grupen",
title = "{CAD}-Based 3-D Object Recognition",
booktitle = "{IEEE} Systems, Man and Cybernetics Conference",
pages = "168--172",
year = "1989",
month = "November",
location = "Boston, Ma.",
}
@Article{SCI:Hen94a,
author = "C.S. Henriquez and C.R. Johnson and K.A. Henneberg
and L.J. Leon and A.E. Pollard.",
title = "Large Scale Biomedical Modeling and Simulation:
From Concepts to Results",
journal = "Frontiers in Biomedical Computing",
year = "1994",
editor = "N. Thakor",
publisher = "{IEEE} Press",
address = "Philadelphia",
keywords = ", scientific computing, scientific
visualization",
}
@TechReport{SCI:Hen95a,
author = "C.S. Henriquez and C.R. Johnson and K.A. Henneberg
L.J. and A.E. Pollard",
title = "Large Scale Biomedical Modeling and Simulation:
From Concepts to Results",
number = "UUSCI-1995-001",
year = "1995",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
finite elements, computational pde pdes
computational partial differential equations
evaporation, cardiac heart, scientific computing,
scientific visualization",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-1995-001.pdf",
}
@InProceedings{SCI:Her2003a,
author = "W. Herrera-Jimenez and W. Correa and C.T. Silva
and A. Baptista",
title = "Visualizing Spatial and Temporal Variability in
Coastal Observatories",
booktitle = "Proceedings of the 14th {IEEE} Visualization 2003
({VIS}'03)",
pages = "75",
year = "2003",
isbn = "0-7695-2030-8",
url = "http://www.sci.utah.edu/publications/herrera-jimenez03/vis2003.pdf",
}
@InProceedings{SCI:Her2013a,
author = "H. Hernandez and J. Knezevic and T. Fogal and T.
Sherman and T. Jevremovic",
title = "Visual numerical steering in {3D AGENT} code
system for advanced nuclear reactor modeling and
design",
booktitle = "Annals of Nuclear Energy",
volume = "55",
pages = "248--257",
year = "2013",
keywords = "Numerical steering, AGENT code, Deterministic
neutron transport codes, Method of Characteristics,
R-functions, Numerical visualizations",
url = "http://www.sci.utah.edu/publications/Her2013a/Hernandez_ANE2013.pdf",
}
@Article{SCI:Hes2008a,
author = "J.S. Hesthaven and R.M. Kirby",
title = "Filtering in Legendre Spectral Methods",
journal = "Mathematics of Computation",
volume = "77",
number = "263",
pages = "1425--1452",
year = "2008",
url = "http://www.sci.utah.edu/publications/hesthaven08/Hesthaven_FiltLegendreSpecMeth.pdf",
}
@Unpublished{SCI:Hig2001a,
author = "G. Higgins and B. Athey and J. Bassingthwaighte
and J. Burgess and H. Champion and K. Cleary and P.
Dev and J. Duncan and M. Hopmeier and D. Jenkins
and C.R. Johnson and H. Kelly and R. Leitch and W.
Lorensen and D. Metaxas and V. Spitzer and N.
Vaidehi and K. Vosburgh and R. Winslow",
title = "Modeling and Simulation in Medicine: Towards an
Integrated Framework",
journal = "Computer Aided Surgery",
volume = "6",
number = "1",
year = "2001",
note = "Final report of the meeting of the same title held
July 20-21, 2000, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland,
USA.",
doi = "10.1002/igs.1008",
}
@Article{SCI:Hig2013a,
author = "K. Higuchi and M. Akkaya and M. Koopmann and J.J.
Blauer and N.S. Burgon and K. Damal and R. Ranjan
and E. Kholmovski and R.S. Macleod and N.F.
Marrouche.",
title = "The Effect of Fat Pad Modification during Ablation
of Atrial Fibrillation: Late Gadolinium Enhancement
MRI Analysis",
journal = "Pacing and Clinical Electrophysiology ({PACE})",
volume = "36",
number = "4",
pages = "467--476",
year = "2013",
month = "April",
doi = "10.1111/pace.12084",
pmid = "23356963",
pmcid = "PMC3651513",
keywords = "ganglionated plexi, fat pad, atrial fibrillation,
catheter ablation, {LGE-MRI}",
url = "http://www.sci.utah.edu/publications/higuchi13/Higuchi_PACE2013.pdf",
}
@TechReport{SCI:Hij2008a,
author = "Y. Hijazi and A. Knoll and M. Schott and A.
Kensler and C.D. Hansen and H. Hagen",
title = "CSG Operations of Arbitrary Primitives with
Interval Arithmetic and Real-Time Ray Tracing",
number = "UUSCI-2008-008",
year = "2008",
institution = "University of Utah School of Computing",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-008.pdf",
}
@InProceedings{SCI:Hij2010a,
author = "Y. Hijazi and A. Knoll and M. Schott and A.
Kensler and C.D. Hansen and H. Hagen",
title = "CSG Operations of Arbitary Primitives with
Interval Arithmetic and Real-Time Ray Casting",
booktitle = "Scientific Visualization: Advanced Concepts",
journal = "DROPS - Dagstuhl Research Online Publication
Server",
pages = "78-89",
year = "2010",
editor = "Hans Hagen",
publisher = "Schloss Dagstuhl - Leibniz-Zentrum fuer
Informatik",
keywords = "Implicit Surface, Constructive Solid Geometry,
Interval Arithmetic, Ray Casting, Data processing
Computer science",
url = "http://www.sci.utah.edu/publications/Hij2010a/Hijazi_CSG-Operations2010.pdf",
}
@Article{SCI:Hin2009a,
author = "J. Hinkle and P.T. Fletcher and Brian Wang and B.
Salter and S. Joshi",
title = "4D MAP image reconstruction incorporating organ
motion",
journal = "Information Processing in Medical Imaging",
volume = "5636",
pages = "676--687",
year = "2009",
series = "Lecture Notes in Computer Science LNCS",
pmid = "19694303",
url = "http://www.sci.utah.edu/publications/hinkle09/Hinkle_LCNS2009.pdf",
}
@Article{SCI:Hin2012a,
author = "J. Hinkle and P. Muralidharan and P.T. Fletcher
and S. Joshi",
title = "Polynomial Regression on Riemannian Manifolds",
journal = "arXiv",
volume = "1201.2395",
year = "2012",
url = "http://www.sci.utah.edu/publications/hinkle12/Hinkle_arXiv2012.pdf",
}
@InProceedings{SCI:Hin2013a,
author = "J. Hinkle and S. Joshi",
title = "{PDiff:} Irrotational Diffeomorphisms for
Computational Anatomy",
booktitle = "Proceedings of the International Conference on
Information Processing in Medical Imaging
({IPMI})",
pages = "(accepted)",
year = "2013",
series = "Lecture Notes in Computer Science ({LNCS})",
keywords = "image registration, computational anatomy,
irrotational, Helmholtz-Hodge decomposition, polar
factorization",
url = "http://www.sci.utah.edu/publications/hinkle13/Hinkle_IPMI2013.pdf",
}
@Article{SCI:Hin2014a,
author = " J. Hinkle and P.T. Fletcher and S. Joshi ",
title = "Intrinsic Polynomials for Regression on Riemannian
Manifolds",
journal = "Journal of Mathematical Imaging and Vision",
pages = "1-21",
year = "2014",
url = "http://www.sci.utah.edu/publications/Hin2014a/Hinkle_JMIV2014.pdf",
}
@InProceedings{SCI:Hin93a,
author = "P. Hinker and C.D. Hansen",
title = "Geometric Optimization",
booktitle = "Visualization 1993",
pages = "189--195",
year = "1993",
month = "October",
location = "San Jose, Ca.",
}
@Article{SCI:Hoa2019a,
author = "D. Hoang and P. Klacansky and H. Bhatia and P.-T.
Bremer and P. Lindstrom and V. Pascucci",
title = "A Study of the Trade-off Between Reducing
Precision and Reducing Resolution for Data Analysis
and Visualization",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "25",
number = "1",
pages = "1193--1203",
year = "2019",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/tvcg.2018.2864853",
url = "http://www.sci.utah.edu/publications/Hoa2019a/08440822.pdf",
}
@InProceedings{SCI:Hod1995a,
author = "D.C. Hodgson and P.K. Jimack and P. Selwood and M.
Berzins",
title = "Scalable, Parallel Generation of Partitioned
Unstructured Meshes",
booktitle = "Parallel {C.F.D.} -- Implementations and Results
using Parallel Computers",
pages = "665-672",
year = "1995",
editor = "A. Ecer and J. Periaux and N. Satufoka and S.
Taylor",
month = "June",
location = "Parallel {CFD} Conference 1995, pasadena,
California",
isbn = "0-444 823220",
url = "http://www.sci.utah.edu/publications/hodgson95/scalable-parallel-generation.pdf",
}
@Article{SCI:Hog1999a,
author = "R.E. Hogan and K.E. Mark and L. Wang and S.C.
Joshi and M.I. Miller and R.D. Bucholz",
title = "MR Imaging Deformation-Based Segmentation of the
Hippocampus in Patients with Mesial Temporal
Sclerosis and Temporal Lobe Epilepsy",
journal = "Epilepsia",
volume = "40",
number = "7",
year = "1999",
}
@Article{SCI:Hog2000a,
author = "R.E. Hogan and K.E. Mark and L. Wang and S. Joshi
and M.I. Miller and R. Bucholz",
title = "Mesial Temporal Sclerosis and Temporal Lobe
Epilepsy: MR Imaging Deformation-Based Segmentation
of the Hippocampus in Five Patients",
journal = "Radiology",
volume = "216",
number = "1",
pages = "291--297",
year = "2000",
month = "July",
}
@Article{SCI:Hog2000b,
author = "R.E. Hogan and K.E. Mark and I. Choudhuri and L.
Wang and S. Joshi and M.I. Miller and R. Bucholz",
title = "Magnetic Resonance Imaging Deformation-Based
Segmentation of the Hippocampus in Patients with
Mesial Temporal Sclerosis and Temporal Lobe
Epilepsy",
journal = "J Digit Imaging",
volume = "13",
number = "2 (Suppl. 1)",
pages = "217--218",
year = "2000",
month = "May",
}
@Article{SCI:Hog2000c,
author = "R.E. Hogan and R.D. Bucholz and I. Choudhuri and
K.E. Mark and C.S. Butler and S. Joshi",
title = "Shape-analysis of hippocampal surface structure in
patients with unilateral mesial temporal
sclerosis",
journal = "Journal of Digital Imaging",
volume = "13",
number = "2",
pages = "39--42",
year = "2000",
}
@Article{SCI:Hog2003a,
author = "R.E. Hogan and R.D. Bucholz and S. Joshi",
title = "Hippocampal Deformation-Based Shape Analysis in
Epilepsy and Unilateral Mesial Temporal
Sclerosis",
journal = "Epilepsia",
volume = "44",
number = "6",
pages = "800--806",
year = "2003",
month = "June",
}
@InProceedings{SCI:Hog2011a,
author = "L. Hogrebe and A. Paiva and E. Jurrus and C.
Christensen and M. Bridge and J.R. Korenberg and T.
Tasdizen",
title = "Trace Driven Registration of Neuron Confocal
Microscopy Stacks",
booktitle = "{IEEE} International Symposium on Biomedical
Imaging ({ISBI})",
pages = "1345--1348",
year = "2011",
doi = "10.1109/ISBI.2011.5872649",
url = "http://www.sci.utah.edu/publications/hogrebe11/Hogrebe_ISBI2011.pdf",
}
@Article{SCI:Hog2012a,
author = "L. Hogrebe and A.R.C. Paiva and E. Jurrus and C.
Christensen and M. Bridge and L. Dai and R.L.
Pfeiffer and P.R. Hof and B. Roysam and J.R.
Korenberg and T. Tasdizen",
title = "Serial section registration of axonal confocal
microscopy datasets for long-range neural circuit
reconstruction",
journal = "Journal of Neuroscience Methods",
volume = "207",
number = "2",
pages = "200--210",
year = "2012",
doi = "10.1016/j.jneumeth.2012.03.002",
url = "http://www.sci.utah.edu/publications/hogrebe12/Hogrebe_JNM2012.pdf",
}
@InProceedings{SCI:Hol2012a,
author = "C. Holzh{\"u}ter and A. Lex and D. Schmalstieg and H.
Schulz and H. Schumann and M. Streit",
title = "Visualizing Uncertainty in Biological Expression
Data",
booktitle = "Proceedings of the SPIE Conference on
Visualization and Data Analysis (VDA '12)",
volume = "8294",
pages = "82940O-82940O-11",
year = "2012",
doi = "10.1117/12.908516",
url = "http://www.sci.utah.edu/publications/Hol2012a/2012_vda_uncertainty.pdf",
}
@InProceedings{SCI:Hol2013a,
author = "T. H{\"o}llt and A. Magdy and G. Chen and G.
Gopalakrishnan and I. Hoteit and C.D. Hansen and M.
Hadwiger",
title = "Visual Analysis of Uncertainties in Ocean
Forecasts for Planning and Operation of Off-Shore
Structures",
booktitle = "Proceedings of 2013 {IEEE} Pacific Visualization
Symposium ({PacificVis})",
pages = "185--192",
year = "2013",
note = "Received Honerable Mention",
keywords = "Uncertainty, Ensemble Simulation, Risk Estimate",
url = "http://www.sci.utah.edu/publications/hollt13/Hollt_PacVis2013.pdf",
}
@Article{SCI:Hol2014a,
author = "T. Hollt and A. Magdy and P. Zhan and G. Chen and
G. Gopalakrishnan and I. Hoteit and C.D. Hansen and
M. Hadwiger",
title = "Ovis: A Framework for Visual Analysis of Ocean
Forecast Ensembles",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "PP",
number = "99",
pages = "1",
year = "2014",
doi = "10.1109/TVCG.2014.2307892",
keywords = "Ensemble Visualization, Ocean Visualization, Ocean
Forecast, Risk Estimation",
url = "http://www.sci.utah.edu/publications/Hol2014a/Hollt_Ovis2014.pdf",
}
@InCollection{SCI:Hol2015a,
author = "J. K. Holmen and A. Humphrey and M. Berzins",
title = "Exploring Use of the Reserved Core",
booktitle = "High Performance Parallelism Pearls",
pages = "229-242",
year = "2015",
editor = "J. Reinders and J. Jeffers",
publisher = "Elsevier",
doi = "10.1016/b978-0-12-803819-2.00010-0",
url = "http://www.sci.utah.edu/publications/Hol2015a/exploring-use-of-the-reserved-core-2.pdf",
}
@Article{SCI:Hol2016a,
author = "B. Hollister and G. Duffley and C. Butson and and
C.R. Johnson",
title = "Visualization for Understanding Uncertainty in
Activation Volumes for Deep Brain Stimulation",
journal = "Eurographics Conference on Visualization",
year = "2016",
editor = "K.L. Ma G. Santucci, and J. van Wijk",
url = "http://www.sci.utah.edu/publications/Hol2016a/final-eurovis16-rev2.pdf",
}
@InProceedings{SCI:Hol2017b,
author = "J. K. Holmen and A. Humphrey and D. Sutherland and
M. Berzins",
title = "Improving Uintah's Scalability Through the Use of
Portable Kokkos-Based Data Parallel Tasks",
booktitle = "Proceedings of the Practice and Experience in
Advanced Research Computing 2017 on Sustainability,
Success and Impact",
number = "27",
pages = "27:1--27:8",
year = "2017",
series = "PEARC17",
isbn = "978-1-4503-5272-7",
doi = "10.1145/3093338.3093388",
url = "http://www.sci.utah.edu/publications/Hol2017b/pearc17.pdf",
}
@TechReport{SCI:Hol2019a,
author = "J. K. Holmen and B. Peterson and A. Humphrey and
D. Sunderland and O. H. Diaz-Ibarra and J. N.
Thornock and M. Berzins",
title = "Portably Improving Uintah's Readiness for Exascale
Systems Through the Use of Kokkos",
year = "2019",
institution = "SCI Institute",
url = "http://www.sci.utah.edu/publications/Hol2019a/UUSCI-2019-001.pdf",
}
@InProceedings{SCI:Hol2019b,
author = "J. K. Holmen and B. Peterson and M. Berzins",
title = "An Approach for Indirectly Adopting a Performance
Portability Layer in Large Legacy Codes",
booktitle = "2nd International Workshop on Performance,
Portability, and Productivity in HPC (P3HPC)",
year = "2019",
organization = "In conjunction with SC19",
url = "http://www.sci.utah.edu/publications/Hol2019b/Holmenws_p3hpc115s2-file1-2.pdf",
}
@InProceedings{SCI:Hon2012a,
author = "Y. Hong and S. Joshi and M. Sanchez and M. Styner
and M. Niethammer",
title = "Metamorphic Geodesic Regression",
booktitle = "Proceedings of Medical Image Computing and
Computer-Assisted Intervention (MICCAI) 2012",
pages = "197--205",
year = "2012",
url = "http://www.sci.utah.edu/publications/hong12/Hong_MICCAI2012.pdf",
}
@Article{SCI:Hop2004a,
author = "B. Hopenfeld and J.G. Stinstra and R.S. MacLeod",
title = "Mechanism for {ST} Depression Associated with
Contiguous Subendocardial Ischemia",
journal = j-JCE,
volume = "15",
number = "10",
pages = "1200--1206",
year = "2004",
keywords = "cardiac heart, ncrr",
url = "http://www.sci.utah.edu/publications/hopenfeld04/ischemiarev.pdf",
}
@Article{SCI:Hop2005a,
author = "B. Hopenfeld and J.G. Stinstra and R.S. MacLeod",
title = "The Effect of Conductivity on {ST}-Segment
Epicardial Potentials Arising from Subendocardial
Ischemia",
journal = j-ABE,
volume = "33",
number = "6",
pages = "751--763",
year = "2005",
keywords = "cardiac heart, ncrr",
url = "http://www.sci.utah.edu/publications/hopenfeld05/condsensrev.pdf",
}
@InProceedings{SCI:How2008a,
author = "B. Howe and P. Lawson and R. Bellinger and J.
Freire and E. Anderson and E. Santos and C.E.
Scheidegger and A. Baptista and C.T. Silva",
title = "End-to-End eScience: Integrating Workflow, Query,
Visualization, and Provenance at an Ocean
Observatory",
booktitle = "Proceedings of the 2008 Fourth {IEEE}
International Conference on eScience",
pages = "127--134",
year = "2008",
keywords = "vistrails, provenance, workflows, workflow
management",
url = "http://www.sci.utah.edu/publications/howe08/vistrails-escience2008.pdf",
}
@Article{SCI:Hoy2014a,
author = "J.B. Hoying and U. Utzinger and J.A. Weiss",
title = "Formation of microvascular networks: role of
stromal interactions directing angiogenic growth",
journal = "Microcirculation",
volume = "21",
number = "4",
pages = "278--289",
year = "2014",
month = "May",
doi = "10.1111/micc.12115",
pmid = "24447042",
pmcid = "PMC4032604",
keywords = "angiogenesis, matrix, neovessel, remodeling,
stroma",
url = "http://www.sci.utah.edu/publications/Hoy2014a/Hoying_MicroCirc2014.pdf",
}
@Article{SCI:Hua2007a,
author = "X. Huang and Y.Z. Lee and M. McKeown and G. Gerig
and H. Gu and W. Lin and M.M. Lewis and S. Ford and
A.I. Troster and D.R. Weinberger and Styner",
title = "Asymmetrical ventricular enlargement in
Parkinson's Disease",
journal = "Movement Disorders",
volume = "22",
number = "11",
pages = "1657--1660",
year = "2007",
month = "August 15",
keywords = "cardiac, heart, parkinsons disease",
url = "http://www.sci.utah.edu/publications/huang07/Huang_MovDisord_Aug2007.pdf",
}
@InProceedings{SCI:Hua2012a,
author = "J. Huang and W. Pei and C. Wen and G. Chen and W.
Chen and H. Bao",
title = "Output-Coherent Image-Space {LIC} for Surface Flow
Visualization",
booktitle = "Proceedings of the {IEEE} Pacific Visualization
Symposium 2012",
pages = "137--144",
year = "2012",
location = "Korea",
url = "http://www.sci.utah.edu/publications/huang12/Huang_ConsistentLIC_PacificVis2012.pdf",
}
@Article{SCI:Hua2012b,
author = "A.H. Huang and B.M. Baker and G.A. Ateshian and
R.L. Mauch",
title = "Sliding Contact Loading Enhances The Tensile
Properties Of Mesenchymal Stem Cell-Seeded
Hydrogels",
journal = "European Cells and Materials",
volume = "24",
pages = "29--45",
year = "2012",
pmid = "22791371",
url = "http://www.sci.utah.edu/publications/huang12/Huang_ECM2012.pdf",
}
@InCollection{SCI:Hub2003a,
author = "M.E. Hubbard and M. Berzins",
title = "A Positivity Preserving Finite Element Method for
Hyperbolic Partial Differential Equations",
booktitle = "Computational Fluid Dynamics 2002",
pages = "205--210",
year = "2003",
editor = "S. Armfield and P. Morgan and K. Srinivas",
publisher = "Springer-Verlag",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational pde pdes computational partial
differential equations",
url = "http://www.sci.utah.edu/publications/hubbard03/Hubbard_ICCFD2003.pdf",
}
@TechReport{SCI:Hum2012a,
author = "A. Humphrey and Q. Meng and M. Berzins and T.
Harman",
title = "Radiation Modeling Using the Uintah Heterogeneous
CPU/GPU Runtime System",
number = "UUSCI-2012-003",
year = "2012",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "csafe, uintah",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2012-003.pdf",
}
@InProceedings{SCI:Hum2012b,
author = "A. Humphrey and Q. Meng and M. Berzins and T.
Harman",
title = "Radiation Modeling Using the Uintah Heterogeneous
CPU/GPU Runtime System",
booktitle = "Proceedings of the first conference of the Extreme
Science and Engineering Discovery Environment
(XSEDE'12)",
year = "2012",
publisher = "Association for Computing Machinery",
doi = "10.1145/2335755.2335791",
keywords = "Uintah, hybrid parallelism, scalability, parallel,
adaptive, GPU, heterogeneous systems, Keeneland,
TitanDev",
url = "http://www.sci.utah.edu/publications/Hum2012b/Humphrey_uintah_xsede12_gpu.pdf",
}
@Article{SCI:Hum2014a,
author = "A. Humphrey and Q. Meng and M. Berzins and D.
Caminha B.de Oliveira and Z. Rakamaric and G.
Gopalakrishnan",
title = "Systematic Debugging Methods for Large-Scale {HPC}
Computational Frameworks",
journal = "Computing in Science Engineering",
volume = "16",
number = "3",
pages = "48--56",
year = "2014",
month = "May",
issn = "1521-9615",
doi = "10.1109/MCSE.2014.11",
keywords = "Computational Modeling and Frameworks, Parallel
Programming, Reliability, Debugging Aids",
url = "http://www.sci.utah.edu/publications/Hum2014a/Humphrey_CISE_Uintah_May_June_2014.pdf",
}
@InCollection{SCI:Hum2015a,
author = "A. Humphrey and T. Harman and M. Berzins and P.
Smith",
title = "A Scalable Algorithm for Radiative Heat Transfer
Using Reverse Monte Carlo Ray Tracing",
title_url = "http://dx.doi.org/10.1007/978-3-319-20119-1_16",
booktitle = "High Performance Computing",
volume = "9137",
pages = "212-230",
year = "2015",
editor = "Kunkel, Julian M. and Ludwig, Thomas",
series = "Lecture Notes in Computer Science",
publisher = "Springer International Publishing",
isbn = "978-3-319-20118-4",
doi = "10.1007/978-3-319-20119-1_16",
keywords = "Uintah; Radiation modeling; Parallel; Scalability;
Adaptive mesh refinement; Simulation science;
Titan",
url = "http://www.sci.utah.edu/publications/Hum2015a/humphrey_isc2015.pdf",
}
@InProceedings{SCI:Hum2016a,
author = "A. Humphrey and D. Sunderland and T. Harman and M.
Berzins",
title = "Radiative Heat Transfer Calculation on 16384 GPUs
Using a Reverse Monte Carlo Ray Tracing Approach
with Adaptive Mesh Refinement",
booktitle = "2016 IEEE International Parallel and Distributed
Processing Symposium Workshops (IPDPSW)",
pages = "1222-1231",
year = "2016",
month = "May",
doi = "10.1109/IPDPSW.2016.93",
url = "http://www.sci.utah.edu/publications/Hum2016a/ipdps-pdsec16.pdf",
}
@PhdThesis{SCI:Hum2019a,
author = "Alan Humphrey",
title = "Scalable Asynchronous Many-Task Runtime Solutions
to Globally Coupled Problems",
year = "2019",
school = "School of Computing, University of Utah",
url = "http://www.sci.utah.edu/publications/Hum2019a/AlanHumphrey_phd_thesis_FINAL_2019.pdf",
}
@InProceedings{SCI:Hum2019b,
author = "A. Humphrey and M. Berzins",
title = "An Evaluation of An Asynchronous Task Based
Dataflow Approach For Uintah",
booktitle = "2019 IEEE 43rd Annual Computer Software and
Applications Conference (COMPSAC)",
volume = "2",
pages = "652-657",
year = "2019",
month = "July",
issn = "0730-3157",
doi = "10.1109/COMPSAC.2019.10282",
url = "http://www.sci.utah.edu/publications/Hum2019b/dfm19_humphrey_berzins.pdf",
}
@InProceedings{SCI:Hwa2003a,
author = "D. Hwang and O. Portniaguine and S. Nagarajan and
C.R. Johnson and K. Sekihara",
title = "Minimum Support {MEG} (Magnetoencephalography)
Imaging: Study on Effects of Noise, Discretization,
Depth, and Separation of Multiple Sources",
booktitle = "World Congress on Medical Physics and Biomedical
Engineering",
year = "2003",
month = "August",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements, MEG,
scientific computing, , meg",
}
@InProceedings{SCI:Hwa2003b,
author = "D. Hwang and S. Nagarajan and O. Portniaguine and
K. Sekihara",
title = "Multiresolution {MEG} (Magnetoencephalography)
Imaging By Adaptive Beamformer Scanning",
booktitle = "25th Annual International Conference of the {IEEE}
Engineering In Medicine And Biology Society",
volume = "1",
pages = "955--958",
year = "2003",
month = "September",
doi = "10.1109/IEMBS.2003.1279925",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements, ip
image processing signal processing, MEG, scientific
computing, Beamformer, meg, beamformer",
}
@Book{SCI:Iba2003a,
author = "L. Ibanez and W. Schroeder and L. Ng and J.
Cates",
title = "The ITK Software Guide",
year = "2003",
publisher = "Kitware, Inc.",
isbn = "1-930934-10-6",
keywords = "ip image processing signal processing,
segmentation, insight itk",
url = "http://www.sci.utah.edu/publications/ibanez03/ItkSoftwareGuide.pdf",
}
@InProceedings{SCI:Iki2001,
author = "M. Ikits and J.D. Brederson and C.D. Hansen and
J.M. Hollerbach",
title = "An Improved Calibration Framework for
Electromagnetic Tracking Devices",
booktitle = c-VR2001,
pages = "63--70",
year = "2001",
address = "Yokohama, Japan,",
month = "Mar",
keywords = "vr virtual reality haptics, uve, scientific
visualization, haptics",
url = "http://www.sci.utah.edu/publications/ikits01/vr01.pdf",
}
@InProceedings{SCI:Iki2001b,
author = "M. Ikits and J.D. Brederson and C.D. Hansen and
J.M. Hollerbach",
title = "Calibration of 6DOF Electromagnetic Tracking
Devices",
booktitle = "{IEEE} VR2001",
pages = "63--70",
year = "2001",
location = "Japan",
keywords = "vr virtual reality haptics, uve",
url = "http://www.sci.utah.edu/publications/ikits01/Ikits_VR2001.pdf",
}
@InProceedings{SCI:Iki2003a,
author = "M. Ikits and C.D. Hansen and C.R. Johnson",
title = "A Comprehensive Calibration and Registration
Procedure for the Visual Haptic Workbench",
booktitle = "Proceedings of the Ninth Eurographics Workshop on
Virtual Environments",
pages = "247--254",
year = "2003",
address = "Zurich, Switzerland,",
month = "May",
keywords = "vr virtual reality haptics, uve, Visualization,
haptics, callibration, visualization",
url = "http://www.sci.utah.edu/publications/ikits03/Ikits_EGVE_03.pdf",
}
@InProceedings{SCI:Iki2003b,
author = "M. Ikits and J.D. Brederson and C.D. Hansen and
C.R. Johnson",
title = "A Constraint-Based Technique for Haptic Volume
Exploration",
booktitle = "Proceedings {IEEE} Visualization 2003",
pages = "263--269",
year = "2003",
month = "October",
location = "Seattle, WA",
keywords = "tensor field methods, diffusion tensor imaging, vr
virtual reality haptics, uve, scientific
visualization, haptics",
}
@InCollection{SCI:Iki2004a,
author = "M. Ikits and J.M. Kniss and A.E. Lefohn and C.D.
Hansen",
title = "Volume Rendering Techniques",
booktitle = "{GPU} Gems: Programming Techniques, Tipsand Tricks
for Real-Time Graphics",
pages = "667--692",
year = "2004",
editor = "Randima Fernando",
publisher = "Addison Wesley",
keywords = "scalar field methods, volume rendering",
}
@InCollection{SCI:Iki2005a,
author = "M. Ikits and J.D. Brederson",
title = "The Visual Haptic Workbench",
booktitle = "The Visualization Handbook",
pages = "431--447",
year = "2005",
editor = "C.D. Hansen and C.R. Johnson",
publisher = "Elsevier",
isbn = "0-12-387582-X",
keywords = "vr virtual reality haptics, uve",
url = "http://www.sci.utah.edu/publications/ikits05/ch22_ikits.pdf",
}
@PhdThesis{SCI:Iki2007a,
author = "M. Ikits",
title = "Interactive Exploration of Volumetric Data Sets
With a Combined Visual and Haptic Interface",
year = "2007",
school = "University of Utah School of Computing",
note = "Ph.D. Thesis",
keywords = "visual haptic workbench, vr virtual reality
haptics, Ph.D. Thesis, ph.d. thesis",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-005.pdf",
}
@Misc{SCI:ImageVis3D,
author = "{CIBC}",
year = "2015",
note = "{ImageVis3D}: An interactive visualization
software system for large-scale volume data.
Scientific Computing and Imaging Institute ({SCI}),
Download from: http://www.imagevis3d.org",
keywords = "ImageVis3D, CIBC",
}
@InProceedings{SCI:Ion2005a,
author = "I. Ionescu and J. Guilkey and M. Berzins and R.M.
Kirby and J.A. Weiss",
title = "Computational Simulation of Penetrating Trauma in
Biological Soft Tissues Using the Material Point
Method",
booktitle = "Proceedings, Medicine Meets Virtual Reality",
volume = "13",
pages = "213--218",
year = "2005",
editor = "James D Westwood et al.",
publisher = "IOS Press",
isbn = "1-58603-498-7",
keywords = "computational mechanics, computational
biomechanics, mpm material point method",
url = "http://www.sci.utah.edu/publications/ionescu05/ionescu_mmvr_2005.pdf",
}
@Article{SCI:Ion2006a,
author = "I. Ionescu and J.E. Guilkey and M. Berzins and
R.M. Kirby and J.A. Weiss",
title = "Simulation of Soft Tissue Failure Using the
Material Point Method",
journal = "Journal of Biomechanical Engineering",
volume = "128",
number = "6",
pages = "917--924",
year = "2006",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/ionescu06/ionescu_jbme_2006.pdf",
}
@Article{SCI:Iri2011a,
author = "A. Irimia and M.C. Chambers and J.R. Alger and M.
Filippou and M.W. Prastawa and Bo Wang and D. Hovda
and G. Gerig and A.W. Toga and R. Kikinis and P.M.
Vespa and J.D. Van Horn",
title = "Comparison of acute and chronic traumatic brain
injury using semi-automatic multimodal segmentation
of MR volumes",
journal = "Journal of Neurotrauma",
volume = "28",
number = "11",
pages = "2287--2306",
year = "2011",
month = "November",
doi = "10.1089/neu.2011.1920",
pmid = "21787171",
keywords = "namic",
url = "http://www.sci.utah.edu/publications/irimia11/Irimia_JNeuro2011.pdf",
}
@Article{SCI:Iri2012a,
author = "A. Irimia and M.C. Chambers and C.M. Torgerson and
M. Filippou and D.A. Hovda and J.R. Alger and G.
Gerig and A.W. Toga and P.M. Vespa and R. Kikinis
and J.D. Van Horn",
title = "Patient-tailored connectomics visualization for
the assessment of white matter atrophy in traumatic
brain injury",
title_url =
"http://www.frontiersin.org/neurotrauma/10.3389/fneur.2012.00010/abstract",
journal = "Frontiers in Neurotrauma",
year = "2012",
note =
"http://www.frontiersin.org/neurotrauma/10.3389/fneur.2012.00010/abstract",
doi = "10.3389/fneur.2012.00010",
url = "http://www.sci.utah.edu/publications/irimia12/Irimia_FNeuro2012.pdf",
}
@Article{SCI:Iri2012b,
author = "A. Irimia and Bo Wang and S.R. Aylward and M.W.
Prastawa and D.F. Pace and G. Gerig and D.A. Hovda
and R.Kikinis and P.M. Vespa and J.D. Van Horn",
title = "Neuroimaging of Structural Pathology and
Connectomics in Traumatic Brain Injury: Toward
Personalized Outcome Prediction",
journal = "NeuroImage: Clinical",
volume = "1",
number = "1",
pages = "1--17",
year = "2012",
publisher = "Elsvier",
doi = "10.1016/j.nicl.2012.08.002",
url = "http://www.sci.utah.edu/publications/irimia12/Irimia_NeuroImage2012.pdf",
}
@Article{SCI:Isa2009a,
author = "B.M. Isaacson and J.G. Stinstra and R.S. MacLeod
and J.B. Webster and J.P. Beck and R.D. Bloebaum",
title = "Bioelectric Analyses of an Osseointegrated
Intelligent Implant Design System for Amputees",
title_url = "http://www.jove.com/index/Details.stp?ID=1237",
journal = "JoVE",
volume = "29",
year = "2009",
url = "http://www.sci.utah.edu/publications/isaacson09/JoVE_Protocol_1237.pdf",
}
@Article{SCI:Isa2010a,
author = "B.M. Isaacson and J.G. Stinstra and R.S. MacLeod
and P.F. Pasquina and R.D. Bloebaum",
title = "Developing a Quantitative Measurement System for
Assessing Heterotopic Ossification and Monitoring
the Bioelectric Metrics from Electrically Induced
Osseointegration in the Residual Limb of Service
Members",
journal = "Annals of Biomedical Engineering",
volume = "38",
number = "9",
pages = "2968-–2978",
year = "2010",
pmid = "20458630",
keywords = "cibc",
url = "http://www.sci.utah.edu/publications/isaacson10/Isaacson_ABE2010a.pdf",
}
@Article{SCI:Isa2011a,
author = "B.M. Isaacson and J.G. Stinstra and R.D. Bloebaum
and COL P.F. Pasquina and R.S. MacLeod",
title = "Establishing Multiscale Models for Simulating
Whole Limb Estimates of Electric Fields for
Osseointegrated Implants",
journal = "IEEE Transactions on Biomedical Engineering",
volume = "58",
number = "10",
pages = "2991--2994",
year = "2011",
doi = "10.1109/TBME.2011.2160722",
pmid = "21712151",
pmcid = "PMC3179554",
url = "http://www.sci.utah.edu/publications/isaacson11/Isaacson_TBE2011.pdf",
}
@Article{SCI:Isa2011b,
author = "S.A. Isaacson and R.M. Kirby",
title = "Numerical Solution of Linear Volterra Integral
Equations of the Second Kind with Sharp
Gradients",
journal = "Journal of Computational and Applied
Mathematics",
volume = "235",
number = "14",
pages = "4283--4301",
year = "2011",
url = "http://www.sci.utah.edu/publications/isaacson11/Isaacson_JCAM2011.pdf",
}
@TechReport{SCI:Itk2000,
author = "M. Ikits",
title = "Coregistration of Pose Measurement Devices Using
Nonlinear Least Squares Parameter Estimation",
number = "UUCS-00-018",
year = "2000",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "vr virtual reality haptics, scientific
visualization, haptics",
url = "http://www.sci.utah.edu/publications/ikits00/UUCS-00-018.ps",
url = "http://www.sci.utah.edu/publications/ikits00/UUCS-00-018.ps.gz",
url = "http://www.sci.utah.edu/publications/ikits00/UUCS-00-018.pdf",
}
@InProceedings{SCI:Iye2010b,
author = "S.K. Iyer and E. DiBella and T. Tasdizen",
title = "Edge enhanced spatio-temporal constrained
reconstruction of undersampled dynamic contrast
enhanced radial {MRI}",
booktitle = "{IEEE} International Symposium on Biomedical
Imaging ({ISBI}): From Nano to Macro",
pages = "704--707",
year = "2010",
doi = "10.1109/ISBI.2010.5490077",
url = "http://www.sci.utah.edu/publications/iyer10/Iyer_ISBI2010.pdf",
}
@Article{SCI:Iye2012a,
author = "S.K. Iyer and T. Tasdizen and E.V.R. DiBella",
title = "Edge Enhanced Spatio-Temporal Constrained
Reconstruction of Undersampled Dynamic Contrast
Enhanced Radial MRI",
journal = "Magnetic Resonance Imaging",
volume = "30",
number = "5",
pages = "610--619",
year = "2012",
keywords = "MRI, Reconstruction, Edge enhanced, Compressed
sensing, Regularization, Cardiac perfusion",
url = "http://www.sci.utah.edu/publications/iyer12/Iyer_MRI2012.pdf",
}
@Article{SCI:Iye2016a,
author = "S.K. Iyer and T. Tasdizen and D. Likhite and
E.V.R. DiBella",
title = "Split Bregman multicoil accelerated reconstruction
technique: A new framework for rapid reconstruction
of cardiac perfusion MRI",
journal = "Medical Physics",
volume = "43",
number = "4",
pages = "1969--1981",
year = "2016",
publisher = "Wiley-Blackwell",
month = "March",
doi = "10.1118/1.4943643",
url = "http://www.sci.utah.edu/publications/Iye2016a/Iyer_et_al-2016-Medical_Physics.pdf",
}
@Article{SCI:Iye2016b,
author = "S.K. Iyer and T. Tasdizen and N. Burgon and E.
Kholmovski and N. Marrouche and G. Adluru and
E.V.R. DiBella",
title = "Compressed sending for rapid late gadolinium
enhanced imaging of the left atrium: A preliminary
study, Magnetic Resonance Imaging",
journal = "Magnetic Resonance Imaging",
volume = "34",
number = "7",
pages = "846--854",
year = "2016",
publisher = "Elsevier BV",
month = "September",
doi = "10.1016/j.mri.2016.03.002",
url = "http://www.sci.utah.edu/publications/Iye2016b/1-s2.0-S0730725X16000242-main.pdf",
}
@TechReport{SCI:Ize2006a,
author = "T. Ize and I. Wald and C. Robertson and S.G.
Parker",
title = "An Evaluation of Parallel Grid Construction for
Ray Tracing Dynamic Scenes",
number = "UUSCI-2006-025",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "interactive rt distributed interactive ray tracing
dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-025.pdf",
}
@InProceedings{SCI:Ize2006b,
author = "T. Ize and I. Wald and C. Robertson and S.G.
Parker",
title = "An Evaluation of Parallel Grid Construction for
Ray Tracing Dynamic Scenes",
booktitle = "Proceedings of the 2006 {IEEE} Symposium on
Interactive Ray Tracing",
volume = "1",
pages = "47--55",
year = "2006",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt",
url = "http://www.sci.utah.edu/publications/thiago06/parallelBuild.pdf",
}
@TechReport{SCI:Ize2006c,
author = "T. Ize and I. Wald and S.G. Parker",
title = "Asynchronous BVH Construction for Ray Tracing
Dynamic Scenes",
year = "2006",
institution = "SCI Institute",
note = "UUSCI-2006-034",
keywords = "rtrt real-time ray tracing, rtcenter",
url = "http://www.sci.utah.edu/publications/Ize2006c/UUSCI-2006-034.pdf",
}
@InProceedings{SCI:Ize2007a,
author = "T. Ize and I. Wald and S.G. Parker",
title = "Asynchronous BVH Construction for Ray Tracing
Dynamic Scenes on Parallel Multi-Core
Architectures",
booktitle = "Proceedings of the 2007 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "101--108",
year = "2007",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/ize07/async.pdf",
}
@InProceedings{SCI:Ize2007b,
author = "T. Ize and P. Shirley and S.G. Parker",
title = "Grid Creation Strategies for Efficient Ray
Tracing",
booktitle = "Proceedings of the 2007 {IEEE}/Eurographics
Symposium on Interactive Ray Tracing",
pages = "27--32",
year = "2007",
keywords = "rtrt real-time ray tracing, parallel
visualization, interactive rt distributed
interactive ray tracing dirt, rtcenter",
url = "http://www.sci.utah.edu/publications/ize07/rgrid.pdf",
}
@InProceedings{SCI:Ize2008a,
author = "T. Ize and I. Wald and S.G. Parker",
title = "Ray Tracing with the {BSP} Tree",
booktitle = "Proceedings of the {IEEE} Symposium on Interactive
Ray Tracing, 2008",
pages = "159--166",
year = "2008",
doi = "10.1109/RT.2008.4634637",
keywords = "rt, ray tracing, bsp tree",
url = "http://www.sci.utah.edu/publications/ize08/BSP_RT08.pdf",
}
@Article{SCI:Ize2011a,
author = "T. Ize and C.D. Hansen",
title = "RTSAH Traversal Order for Occlusion Rays",
journal = "Computer Graphics Forum",
volume = "30",
number = "2",
pages = "297--305",
year = "2011",
publisher = "Wiley-Blackwell",
month = "April",
doi = "10.1111/j.1467-8659.2011.01861.x",
url = "http://www.sci.utah.edu/publications/Ize2011a/Ize_rtsah2011.pdf",
}
@InProceedings{SCI:Ize2011b,
author = "T. Ize and C. Brownlee and C.D. Hansen",
title = "Real-Time Ray Tracer for Visualizing Massive
Models on a Cluster",
booktitle = "Proceedings of the 2011 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "61--69",
year = "2011",
url = "http://www.sci.utah.edu/publications/ize11/Ize_EGPGV2011.pdf",
}
@TechReport{SCI:Jad2010a,
author = "S. Jadhav and H. Bhatia and P.-T. Bremer and J.A.
Levine and L.G. Nonato and V. Pascucci",
title = "Consistent Approximation of Local Flow Behavior
for 2D Vector Fields using Edge Maps",
number = "UUSCI-2010-004",
year = "2010",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2010-004.pdf",
}
@InCollection{SCI:Jad2011a,
author = "S. Jadhav and H. Bhatia and P.-T. Bremer and J.A.
Levine and L.G. Nonato and V. Pascucci",
title = "Consistent Approximation of Local Flow Behavior
for 2D Vector Fields",
booktitle = "Mathematics and Visualization",
pages = "141--159",
year = "2011",
publisher = "Springer",
month = "Nov",
doi = "10.1007/978-3-642-23175-9 10",
url = "http://www.sci.utah.edu/publications/Jad2011a/Jadhav_Topo2012_Local2DFlow.pdf",
}
@Article{SCI:Jak2010a,
author = "J. Jakeman and M. Eldred and D. Xiu",
title = "Numerical Approach for Quantification of Epistemic
Uncertainty",
journal = "Journal of Computational Physics",
volume = "229",
number = "12",
pages = "4648--4663",
year = "2010",
doi = "10.1016/j.jcp.2010.03.003",
keywords = "Uncertainty quantification, Epistemic uncertainty,
Generalized polynomial chaos, Stochastic
collocation, Encapsulation problem",
url = "http://www.sci.utah.edu/publications/jakeman10/Jakeman_JCP2010.pdf",
}
@Article{SCI:Jak2011a,
author = "J. Jakeman and R. Archibald and D. Xiu",
title = "Characterization of Discontinuities in
High-dimensional Stochastic Problmes on Adaptive
Sparse Grids",
journal = "Journal of Computational Physics",
volume = "230",
number = "10",
pages = "3977--3997",
year = "2011",
doi = "10.1016/j.jcp.2011.02.022",
keywords = "Adaptive sparse grids, Stochastic partial
differential equations, Multivariate discontinuity
detection, Generalized polynomial chaos method,
High-dimensional approximation",
url = "http://www.sci.utah.edu/publications/jakeman11/Jakeman_JCP2011.pdf",
}
@Article{SCI:Jak2017a,
author = "J. Jakeman and A. Narayan and T. Zhou",
title = "A Generalized Sampling and Preconditioning Scheme
for Sparse Approximation of Polynomial Chaos
Expansions",
journal = "SIAM Journal on Scientific Computing",
volume = "39",
number = "3",
pages = "A1114--A1144",
year = "2017",
publisher = "SIAM",
month = "Jan",
issn = "1064-8275",
doi = "10.1137/16M1063885",
url = "http://www.sci.utah.edu/publications/Jak2017a/1602.06879.pdf",
}
@Article{SCI:Jal2018a,
author = "A. Jallepalli and J. Docampo-Sánchez and J.K.
Ryan and R. Haimes and R.M. Kirby",
title = "On the treatment of field quantities and elemental
continuity in fem solutions",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "24",
number = "1",
pages = "903--912",
year = "2018",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/tvcg.2017.2744058",
url = "http://www.sci.utah.edu/publications/Jal2018a/08017592.pdf",
}
@Article{SCI:Jan2018a,
author = "A. Janson and C. Butson",
title = "Targeting Neuronal Fiber Tracts for Deep Brain
Stimulation Therapy Using Interactive,
Patient-Specific Models",
title_url =
"https://www.jove.com/video/57292/targeting-neuronal-fiber-tracts-for-deep-brain-stimulation-therapy",
journal = "Journal of Visualized Experiments",
number = "138",
year = "2018",
publisher = "MyJove Corporation",
month = "Aug",
doi = "10.3791/57292",
url = "http://www.sci.utah.edu/publications/Jan2018a/jove_janson.pdf",
}
@Article{SCI:Jan2020a,
author = "A. P. Janson and D. N. Anderson and C. R.
Butson",
title = "Activation robustness with directional leads and
multi-lead configurations in deep brain
stimulation",
journal = "Journal of Neural Engineering",
volume = "17",
number = "2",
pages = "026012",
year = "2020",
publisher = "IOP Publishing",
month = "March",
doi = "10.1088/1741-2552/ab7b1d",
url = "http://www.sci.utah.edu/publications/Jan2020a/Janson_2020_J._Neural_Eng._17_026012.pdf",
}
@InProceedings{SCI:Jav2018a,
author = "M. Javanmardi and T. Tasdizen",
title = "Domain adaptation for biomedical image
segmentation using adversarial training",
booktitle = "2018 IEEE 15th International Symposium on
Biomedical Imaging (ISBI 2018)",
pages = "554-558",
year = "2018",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2018.8363637",
url = "http://www.sci.utah.edu/publications/Jav2018a/08363637.pdf",
}
@Article{SCI:Jeo2003a,
author = "J. Jeon and A.E. Lefohn and G. A. Voth",
title = "An Improved Polarflex Water Model",
journal = "The Journal of Chemical Physics",
volume = "118",
number = "16",
pages = "7504--7518",
year = "2003",
keywords = "cfd computational fluid dynamics, scientific
computing",
url = "http://www.sci.utah.edu/publications/jeon03/prePrintPF2.pdf",
}
@InProceedings{SCI:Jeo2004a,
author = "Won-Ki Jeong and Tolga Tasdizen and Ross
Whitaker",
title = "Anisotropic Diffusion of Height Field Data using
Multigrid Solver on {GPU}",
booktitle = "Proceedings {ACM} Workshop on General Purpose
Computing on Graphics Processors, 2004",
year = "2004",
keywords = "ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/wkjeong04/gp04_final.pdf",
}
@InProceedings{SCI:Jeo2006a,
author = "W-K. Jeong and R.T. Whitaker and M. Dobin",
title = "Interactive 3D Seismic Fault Detection on the
Graphics Hardware",
booktitle = "Proceedings of International Workshop on Volume
Graphics",
journal = "Proceedings of the 2006 International Workshop on
Volume Graphics",
pages = "111--118",
year = "2006",
keywords = "geophysics geology, fault detection, seismology",
url = "http://www.sci.utah.edu/publications/Jeo2006a/vg06-jeong.pdf",
}
@Article{SCI:Jeo2007a,
author = "W.-K. Jeong and P.T. Fletcher and R. Tao and R.T.
Whitaker",
title = "Interactive Visualization of Volumetric White
Matter Connectivity in {DT-MRI} Using a
Parallel-Hardware Hamilton-Jacobi Solver",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "13",
number = "6",
pages = "1480--1487",
year = "2007",
pmid = "17968100",
keywords = "volume rendering, diffusion tensor imaging,
parallel visualization",
url = "http://www.sci.utah.edu/publications/jeong07/Jeong_vis07.pdf",
}
@Article{SCI:Jeo2008a,
author = "W.-K. Jeong and R.T. Whitaker",
title = "A Fast Iterative Method for Eikonal Equations",
journal = "SIAM Journal on Scientific Computing",
volume = "30",
number = "5",
pages = "2512-2534",
year = "2008",
doi = "10.1137/060670298",
url = "http://www.sci.utah.edu/publications/jeong08/Jeong_SIAM2008.pdf",
}
@Article{SCI:Jeo2009a,
author = "W.-K. Jeong and J. Beyer and M. Hadwiger and A.
Vazquez and H. Pfister and R.T. Whitaker",
title = "Scalable and Interactive Segmentation and
Visualization of Neural Processes in {EM}
Datasets",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics, Proceedings of the 2009 {IEEE}
Visualization Conference",
volume = "15",
number = "6",
pages = "1505--1514",
year = "2009",
month = "Sept/Oct",
url = "http://www.sci.utah.edu/publications/jeong09/Jeong_TVCG2009.pdf",
}
@InProceedings{SCI:Jia2010a,
author = "F. Jiao and J.M. Phillips and J.G. Stinstra and J.
Kueger and R. Varma and E. Hsu and J. Korenberg and
C.R. Johnson",
title = "Metrics for Uncertainty Analysis and Visualization
of Diffusion Tensor Images",
booktitle = "Proceedings of the 5th international conference on
Medical imaging and augmented reality (MIAR)",
pages = "179--190",
year = "2010",
publisher = "Springer-Verlag",
address = "Berlin, Heidelberg",
month = "September",
location = "Beijing, China",
url = "http://www.sci.utah.edu/publications/jiao10/Jiao_fiber-uncertainty.pdf",
}
@InProceedings{SCI:Jia2011b,
author = "F. Jiao and Y. Gur and C.R. Johnson and S.
Joshi",
title = "Detection of crossing white matter fibers with
high-order tensors and rank-k decompositions",
booktitle = "Proceedings of the International Conference on
Information Processing in Medical Imaging (IPMI
2011)",
volume = "6801",
pages = "538--549",
year = "2011",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-22092-0_44",
pmcid = "PMC3327305",
url = "http://www.sci.utah.edu/publications/jiao11/Jiao_IPMI2011_Tensor_Decompositions.pdf",
}
@InProceedings{SCI:Jia2013a,
author = "F. Jiao and J.M. Phillips and Y. Gur and C.R.
Johnson",
title = "Uncertainty Visualization in HARDI based on
Ensembles of ODFs",
booktitle = "Proceedings of 2013 {IEEE} Pacific Visualization
Symposium",
pages = "193--200",
year = "2013",
pmid = "24466504",
pmcid = "PMC3898522",
url = "http://www.sci.utah.edu/publications/Jia2013a/Jiao_PacVis2013.pdf",
}
@Article{SCI:Jia2017b,
author = "J. Jiang and Y. Chen and A. Narayan",
title = "Offline-Enhanced Reduced Basis Method Through
Adaptive Construction of the Surrogate Training
Set",
journal = "Journal of Scientific Computing",
volume = "73",
number = "2-3",
pages = "853--875",
year = "2017",
publisher = "Springer Nature",
month = "September",
doi = "10.1007/s10915-017-0551-3",
url = "http://www.sci.utah.edu/publications/Jia2017b/s10915-017-0551-3.pdf",
}
@Article{SCI:Jim2002a,
author = "P.K. Jimack and R. Mahmood and M.A. Walkley and M.
Berzins",
title = "A Multilevel Approach for Obtaining Locally
Optimal Finite Element Meshes",
journal = j-AES,
volume = "33",
pages = "403--415",
year = "2002",
keywords = "finite elements",
url = "http://www.sci.utah.edu/publications/jimack02/JMWB00.pdf",
}
@Article{SCI:Jim2010a,
author = "P.K. Jimack and R.M. Kirby",
title = "Towards the Development on an h-p-Refinement
Strategy Based Upon Error Estimate Sensitivity",
journal = "Computers and Fluids",
volume = "46",
number = "1",
pages = "277--281",
year = "2010",
doi = "10.1016/j.compfluid.2010.08.003",
url = "http://www.sci.utah.edu/publications/jimack10/ICFDpaperJimackKirbyRevised_abstract.pdf",
}
@Article{SCI:Jim2011a,
author = "P.K. Jimack and R.M. Kirby",
title = "Towards the Development on an h-p-Refinement
Strategy Based Upon Error Estimate Sensitivity",
journal = "Computers and Fluids",
volume = "46",
number = "1",
pages = "277--281",
year = "2011",
url = "http://www.sci.utah.edu/publications/jimack11/Jimack_CF2011.pdf",
}
@Article{SCI:Joh1992e,
author = "C.R. Johnson and R.S. MacLeod and P.R. Ershler",
title = "A Computer Model for the Study of Electrical
Current Flow in the Human Thorax",
journal = "Computers in Biology and Medicine",
volume = "22",
number = "5",
pages = "305--323",
year = "1992",
publisher = "Elsevier BV",
keywords = "scalar field methods, vector field methods, tensor
field methods, cardiac heart, scientific
visualization",
url = "http://www.sci.utah.edu/publications/Joh1992e/Computer-Model-Thorax-1992.pdf",
}
@InProceedings{SCI:Joh2000b,
author = "C.R. Johnson and S.G. Parker and D. Weinstein",
title = "Large-Scale Computational Science Applications
Using the {SCIR}un Problem Solving Environment",
booktitle = c-ISC2000,
year = "2000",
keywords = "ncrr, scirun, scientific computing, scientific
visualization",
url = "http://www.sci.utah.edu/publications/crj00/super00_final.pdf",
}
@Article{SCI:Joh2001a,
author = "C.R. Johnson and D. Brederson and C.D. Hansen and
M. Ikits and G. Kindlmann and Y. Livnat and S.G.
Parker and D.M. Weinstein and R.T. Whitaker",
title = "Computational Field Visualization",
journal = "Computer Graphics",
volume = "35",
number = "4",
pages = "5--9",
year = "2001",
keywords = "ncrr",
url = "http://www.sci.utah.edu/publications/crj01/crj_CFV2001.pdf",
}
@InCollection{SCI:Joh2001b,
author = "C.R. Johnson and Y. Livnat and L. Zhukov and D.
Hart and G. Kindlmann",
title = "Computational Field Visualization",
booktitle = "Mathematics Unlimited -- 2001 and Beyond",
volume = "2",
pages = "605--630",
year = "2001",
editor = "B. Engquist and W. Schmid",
publisher = "Springer-Verlag",
keywords = "cfd computational fluid dynamics, computational
pde pdes computational partial differential
equations evaporation, scalar field methods, vector
field methods, tensor field methods, scirun,
biopse, uintah, scirun fusion, scientific
visualization, scientific computing, pse, problem
solving environment",
url = "http://www.sci.utah.edu/publications/math2000/paper_final.pdf",
url = "http://www.sci.utah.edu/publications/math2000/paper_final.ps",
url = "http://www.sci.utah.edu/publications/math2000/paper_final.ps.gz",
}
@InCollection{SCI:Joh2001c,
author = "C.R. Johnson and M. Mohr and U. Ruede and A.
Samsonov and K. Zyp",
title = "Multilevel Methods for Inverse Bioelelectric Field
Problems",
booktitle = "Lecture Notes in Computational Science and
Engineering - Multiscale and Multiresolution
Methods: Theory and Applications",
volume = "20",
pages = "331--346",
year = "2001",
editor = "T.J. Barth and T.F. Chan and R. Haimes",
publisher = "Springer-Verlag Publishing",
address = "Heidelberg",
month = "October",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions finite elements,
scirun, biopse, scientific computing",
url = "http://www.sci.utah.edu/publications/yosemite/paper_final.ps",
}
@InCollection{SCI:Joh2001d,
author = "C.R. Johnson",
title = "Adaptive Finite Element and Local Regularization
Methods for the Inverse {ECG} Problem",
booktitle = "Inverse Problems in Electrocardiology",
volume = "5",
pages = "51--88",
year = "2001",
editor = "Peter Johnston",
series = "Advances in Computational Biomedicine",
publisher = "{WIT} Press",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions finite elements,
inverse eeg, scirun, biopse, cardiac heart,
scientific computing",
url = "http://www.sci.utah.edu/publications/crj01/inverse_ecg99.ps.gz",
url = "http://www.sci.utah.edu/publications/crj01/inverse_ecg99.ps",
}
@Article{SCI:Joh2001e,
author = "C.R. Johnson",
title = "Computational Bioimaging for Medical Diagnosis and
Treatment",
journal = "Communications of the {ACM}",
volume = "44",
number = "3",
pages = "74--76",
year = "2001",
month = "March",
keywords = "pse pses problem solving envoronment, bioelectric
fields",
url = "http://www.sci.utah.edu/publications/crj01/Johnson-ACM-2001.pdf",
}
@Article{SCI:Joh2002a,
author = "C.R. Johnson and S.G. Parker and D. Weinstein and
S. Heffernan",
title = "Component-Based Problem Solving Environments for
Large-Scale Scientific Computing",
journal = j-CCPE,
volume = "14",
pages = "1337--1349",
year = "2002",
keywords = "ncrr, SCIRun, scirun",
url = "http://www.sci.utah.edu/publications/crj02/grids01.pdf",
}
@Article{SCI:Joh2003a,
author = "C.R. Johnson and A.R. Sanderson",
title = "A Next Step: Visualizing Errors and Uncertainty",
journal = "{IEEE} Computer Graphics and Applications",
volume = "23",
number = "5",
pages = "6--10",
year = "2003",
month = "September/October",
keywords = "cfd computational fluid dynamics, scientific
computing, error visualization",
url = "http://www.sci.utah.edu/publications/crj03/g5visv-lo.pdf",
}
@Article{SCI:Joh2004a,
author = "C.R. Johnson",
title = "Top Scientific Visualization Research Problems",
journal = "{IEEE} Computer Graphics and Applications:
Visualization Viewpoints",
volume = "24",
number = "4",
pages = "13--17",
year = "2004",
month = "July/August",
keywords = "ncrr",
url = "http://www.sci.utah.edu/publications/crj04/Vis_Viewpoints04.pdf",
}
@Article{SCI:Joh2004b,
author = "C.R. Johnson and R.S. MacLeod and S.G. Parker and
D.M. Weinstein",
title = "Biomedical Computing and Visualization Software
Environments",
journal = j-ACM-COM,
volume = "47",
number = "11",
pages = "64--71",
year = "2004",
keywords = "forward problems inverse problems forward
simulation inverse solutions, inverse eeg, inverse
meg, forward simulation, scalar field methods,
scirun, biopse, uintah, ncrr, scirun 2, biotensor,
biofem, visualization",
url = "http://www.sci.utah.edu/publications/crj04/ACM-Nov04.pdf",
}
@InProceedings{SCI:Joh2006a,
author = "C.R. Johnson and D.M. Weinstein",
title = "Biomedical Computing and Visualization",
booktitle = "Proceedings of the Twenty-Ninth Australasian
Computer Science Conference (ACSC2006): Conferences
in Research and Practice in Information Technology
(CRPIT)",
volume = "48",
pages = "3-10",
year = "2006",
editor = "Vladimir Estivill-Castro and Gill Dobbie",
location = "Hobart, Australia",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr, scientific
visualization",
url = "http://www.sci.utah.edu/publications/crj06/Chris-Johnson-Keynote-Paper05.pdf",
}
@Unpublished{SCI:Joh2006b,
author = "C.R. Johnson and R. Moorhead and T. Munzner and H.
Pfister and P. Rheingans and T. S. Yoo",
title = "N{IH}-{NSF} {V}isualization {R}esearch
{C}hallenges {R}eport",
year = "2006",
publisher = "IEEE Press",
note = "http://tab.computer.org/vgtc/vrc/index.html",
isbn = "0-7695-2733-7",
keywords = "scalar field methods, volume rendering, vector
field methods, tensor field methods, remote
visualization, parallel visualization, popular",
url = "http://www.sci.utah.edu/publications/crj06/NIH-NSF-VRC-Report-Final.pdf",
}
@Article{SCI:Joh2006c,
author = "J.T. Johnson III and M.S. Hansen and I. Wu and
L.J. Healy and C.R. Johnson and G.M. Jones and M.R.
Capecchi and C. Keller",
title = "Virtual Histology of Transgenic Mouse Embryos for
High-Throughput Phenotyping",
journal = "PLoS Genetics",
volume = "2",
number = "1",
pages = "471--477",
year = "2006",
month = "April",
keywords = "genetic mutation, phenotyping, histology",
url = "http://www.sci.utah.edu/publications/johnson06/johnson_PLOSgen2006.pdf",
}
@InCollection{SCI:Joh2006d,
author = "C.R. Johnson",
title = "Computational Methods and Software for Bioelectric
Field Problems",
booktitle = "Biomedical Engineering Handbook, 2nd Edition",
volume = "1",
pages = "1--23",
year = "2006",
editor = "J.D. Bronzino",
chapter = "23",
publisher = "CRC Press, Boca Raton",
keywords = "ncrr, pse pses problem solving envoronment,
bioelectric fields",
}
@InProceedings{SCI:Joh2006e,
author = "C.R. Johnson and S.G. Parker",
title = "Problem Solving Environments for DDDAS",
booktitle = "Proceedings of the Ninth Copper Mountain
Conference on Iterative Methods",
year = "2006",
month = "April",
location = "Copper Mountain, CO",
note = "Minisymposium: Actually Doing Dynamic Data-driven
Application Simulations",
}
@InProceedings{SCI:Joh2006f,
author = "J.T. Johnson III and M.S. Hansen and I.Q Wu and
L.J. Healy and C.R. Johnson and G.M. Jones and M.R.
Capecchi and C.Keller",
title = "Virtual Histology of Transgenic Mouse Embryos for
High-Throughput Phenotyping",
booktitle = "Proceedings of the Teratology 46th Annual
Meeting",
year = "2006",
location = "Tucson, AZ",
keywords = "genetic mutation, phenotyping, histology",
}
@Unpublished{SCI:Joh2006g,
author = "C.R. Johnson and R. Moorhead and T. Munzner and H.
Pfister and P. Rheingans and T.S. Yoo and (Eds.)",
title = "NIH/NSF Visualization Research Challenges
Report",
title_url =
"http://vgtc.org/about-us/national-initiative/nihnsf-visualization-research-challenges-report",
year = "2006",
note = "IEEE Press",
isbn = "0-7695-2733-7",
}
@Unpublished{SCI:Joh2007a,
author = "C.R. Johnson and R. Ross and S. Ahern and J.
Ahrens and W. Bethel and K.L. Ma and M. Papka and
J. van Rosendale and H.W. Shen and J. Thomas",
title = "{DOE} Visualization and Knowledge Discovery",
year = "2007",
month = "October",
note = "Report from the {DOE/ASCR Workshop on Visual
Analysis and Data Exploration at Extreme Scale}",
url = "http://www.sci.utah.edu/publications/Joh2007a/DOE-Visualization-Report-2007.pdf",
}
@InCollection{SCI:Joh2008a,
author = "C.R. Johnson and X. Tricoche",
title = "Biomedical Visualization",
booktitle = "Advances in Biomedical Engineering",
pages = "209--272",
year = "2008",
editor = "Pascal Verdonck",
chapter = "6",
publisher = "Elsvier Science",
keywords = "computational biomechanics, bioengineering,
biomedicine, forward problems inverse problems
forward simulation inverse solutions, pse grid
computing, volume rendering, transfer functions,
diffusion tensor imaging, map3d, scirun, biopse,
visible human, ncrr, cvrti, scientific
visualization, bioelectric fields",
url = "http://www.sci.utah.edu/publications/crj08/Johnson_Biomedvis2008.pdf",
}
@Article{SCI:Joh2012a,
author = "C.R. Johnson",
title = "Biomedical Visual Computing: Case Studies and
Challenges",
journal = "{IEEE} Computing in Science and Engineering",
volume = "14",
number = "1",
pages = "12--21",
year = "2012",
pmid = "22545005",
pmcid = "PMC3336198",
keywords = "kaust",
url = "http://www.sci.utah.edu/publications/johnson12/Johnson_Biomedical-Vis2012.pdf",
}
@Article{SCI:Joh2013a,
author = "C.R. Johnson and A. Pang (Eds.)",
title = "International Journal for Uncertainty
Quantification",
title_url =
"http://www.dl.begellhouse.com/journals/52034eb04b657aea,3b447596502fa0fe.html",
subtitle = "Special Issue on Working with Uncertainty:
Representation, Quantification, Propagation,
Visualization, and Communication of Uncertainty",
journal = "Int. J. Uncertainty Quantification",
volume = "3",
number = "2",
pages = "vii--viii",
year = "2013",
publisher = "Begell House, Inc.",
issn = "2152-5080",
doi = "10.1615/Int.J.UncertaintyQuantification.v3.i2",
}
@Article{SCI:Joh2013b,
author = "C.R. Johnson and A. Pang (Eds.)",
title = "International Journal for Uncertainty
Quantification",
title_url =
"http://www.dl.begellhouse.com/journals/52034eb04b657aea,2c3d9a3c1f471d44.html",
subtitle = "Special Issue on Working with Uncertainty:
Representation, Quantification, Propagation,
Visualization, and Communication of Uncertainty",
journal = "Int. J. Uncertainty Quantification",
volume = "3",
number = "3",
year = "2013",
publisher = "Begell House, Inc.",
issn = "2152-5080",
doi = "10.1615/Int.J.UncertaintyQuantification.v3.i3",
}
@InCollection{SCI:Joh2015a,
author = "C.R. Johnson and K. Potter",
title = "Visualization",
booktitle = "The Princeton Companion to Applied Mathematics",
booktitle_url =
"http://press.princeton.edu/titles/10592.html",
pages = "843-846",
year = "2015",
editor = "Nicholas J. Higham",
publisher = "Princeton University Press",
month = "September",
isbn = "9780691150390",
}
@InCollection{SCI:Joh2015b,
author = "H. De Sterck and C.R. Johnson",
title = "Data Science: What Is It and How Is It Taught?",
title_url =
"https://sinews2.siam.org/DetailsPage/tabid/607/ArticleID/565/Data-Science.aspx",
booktitle = "SIAM News",
year = "2015",
publisher = "SIAM",
month = "July",
url = "http://www.sci.utah.edu/publications/Joh2015b/Data-Science-SIAM_News-July-2015.pdf",
}
@InBook{SCI:Joh2015c,
author = "C.R. Johnson",
title = "Computational Methods and Software for Bioelectric
Field Problems",
booktitle = "Biomedical Engineering Handbook",
volume = "1",
pages = "1--28",
year = "2015",
editor = "J.D. Bronzino and D.R. Peterson",
chapter = "43",
publisher = "CRC Press",
edition = "4",
url = "http://www.sci.utah.edu/publications/Joh2015c/Computational Methods and Software for Bioelectric Field Problems.pdf",
}
@InCollection{SCI:Joh2015d,
author = "C.R. Johnson",
title = "Visualization",
booktitle = "Encyclopedia of Applied and Computational
Mathematics",
booktitle_url =
"http://www.springer.com/us/book/9783540705284#aboutBook",
pages = "1537-1546",
year = "2015",
editor = "Bj{\"o}rn Engquist",
publisher = "Springer",
isbn = "978-3-540-70528-4",
doi = "10.1007/978-3-540-70529-1_368",
url = "http://www.sci.utah.edu/publications/Joh2015d/Visualization.pdf",
}
@Article{SCI:Joh2019a,
author = "K. A. Johnson and P. T. Fletcher and D. Servello
and A. Bona and M. Porta and J. L. Ostrem and E.
Bardinet and M. Welter and A. M. Lozano and J. C.
Baldermann and J. Kuhn and D. Huys and T. Foltynie
and M. Hariz and E. M. Joyce and L. Zrinzo and Z.
Kefalopoulou and J. Zhang and F. Meng and C. Zhang
and Z. Ling and X. Xu and X. Yu and A. YJM Smeets
and L. Ackermans and V. Visser-Vandewalle and A. Y.
Mogilner and M. H. Pourfar and L. Almeida and A.
Gunduz and W. Hu and K. D. Foote and M. S. Okun and
C. R. Butson",
title = "Image-based analysis and long-term clinical
outcomes of deep brain stimulation for Tourette
syndrome: a multisite study",
journal = "Journal of Neurology, Neurosurgery \& Psychiatry",
year = "2019",
publisher = "BMJ Publishing Group",
doi = "10.1136/jnnp-2019-320379",
url = "http://www.sci.utah.edu/publications/Joh2019a/jnnp-2019-320379.full.pdf",
}
@Article{SCI:Joh2020a,
author = "C. R. Johnson and T. Kapur and W. Schroeder and
and T. Yoo",
title = "Remembering Bill Lorensen: The Man, the Myth, and
Marching Cubes",
journal = "IEEE Computer Graphics and Applications",
volume = "40",
number = "2",
pages = "112-118",
year = "2020",
month = "March",
doi = "10.1109/MCG.2020.2971168",
url = "http://www.sci.utah.edu/publications/Joh2020a/IEEE Xplore Full-Text.pdf",
}
@Article{SCI:Joh2020b,
author = "K. A. Johnson and G. Duffley and D. Nesterovich
Anderson and J. L. Ostrem and M. Welter and J. C.
Baldermann and J. Kuhn and D. Huys and V.
Visser-Vandewalle and T. Foltynie and L. Zrinzo and
M. Hariz and A. F. G. Leentjens and A. Y. Mogilner
and M. H. Pourfar and L. Almeida and A. Gunduz and
K. D. Foote and M. S. Okun and C. R. Butson",
title = "Structural connectivity predicts clinical outcomes
of deep brain stimulation for Tourette syndrome",
journal = "Brain",
year = "2020",
month = "July",
issn = "0006-8950",
doi = "10.1093/brain/awaa188",
url = "http://www.sci.utah.edu/publications/Joh2020b/awaa188.pdf",
}
@InCollection{SCI:Joh90a,
author = "C.R. Johnson and A.E. Pollard",
title = "Electrical Activation of the Heart: Computational
Studies of the Forward and Inverse Problems in
Electrocardiography",
booktitle = "Computer Assisted Analysis and Modeling",
pages = "583--628",
year = "1990",
publisher = "MIT Press",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
}
@InProceedings{SCI:Joh91a,
author = "C.R. Johnson and R.S. MacLeod",
title = "Computer Models for Calculating Transthoracic
Current Flow",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
13th Annual International Conference",
pages = "768--769",
year = "1991",
publisher = "{IEEE} Press",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scalar field methods, vector field methods, cardiac
heart",
}
@Article{SCI:Joh92b,
author = "C.R. Johnson and R.S. MacLeod and M.A. Matheson",
title = "Computer Simulations Reveal Complexity of
Electrical Activity in the Human Thorax",
journal = "Computers in Physics",
volume = "6",
pages = "230--237",
year = "1992",
month = "May/June",
keywords = "scalar field methods, vector field methods, tensor
field methods, cardiac heart",
}
@InProceedings{SCI:Joh92d,
author = "C.R. Johnson and R.S. MacLeod and A. Dutson",
title = "Effects of Anistropy and Inhomogeneity on
Electrocardiographic Fields: A Finite Element
Study",
booktitle = "Engineering in Medicine and Biology Society 14th
Annual International Conference",
pages = "2009--2010",
year = "1992",
publisher = "{IEEE} Press",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
finite elements, cardiac heart",
}
@InCollection{SCI:Joh92e,
author = "C.R. Johnson and R.S. MacLeod",
title = "Computational Studies of Forward and Inverse
Problems in Electrocardiology",
booktitle = "Biomedical Modeling and Simulation",
pages = "283--290",
year = "1992",
editor = "J. Eisenfeld and D.S. Levine and M. Witten",
publisher = "Elsevier Science Publishers",
address = "Elsevier, Amsterdam",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
}
@InCollection{SCI:Joh92f,
author = "C.R. Johnson and R.S. MacLeod",
title = "Nonuniform Spatial Mesh Adaption Using a
Posteriori Error Estimate: Applications to Forward
and Inverse Problems",
booktitle = "Adaptive Methods for Partial Differential
Equations",
volume = "14",
pages = "311--326",
year = "1992",
editor = "J.E. Flaherty and M.S. Shephard",
publisher = "Elsevier",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
computational pde pdes computational partial
differential equations evaporation, adaptive mesh
generation, cardiac heart",
url = "http://www.sci.utah.edu/publications/crj92/mesh_adapt2.ps",
url = "http://www.sci.utah.edu/publications/crj92/mesh_adapt2.ps.Z",
}
@InCollection{SCI:Joh93a,
author = "C.R. Johnson and R.S. MacLeod",
title = "Inverse Solutions for Electric and Potential Field
Imaging",
booktitle = "Physiological Imaging, Spectroscopy,
andEarlyDetection Diagnostic Methods",
volume = "1887",
pages = "130--139",
year = "1993",
editor = "R.L. Barbour and M.J. Carvlin",
publisher = "{SPIE}",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scientific visualization",
}
@Article{SCI:Joh93b,
author = "C.R. Johnson and R.S. MacLeod and M.A. Matheson",
title = "Computational Medicine: Bioelectric Field
Problems",
journal = "{IEEE} Computer",
volume = "26",
number = "26",
pages = "59--67",
year = "1993",
month = "Oct",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scalar field methods, vector field methods",
}
@InProceedings{SCI:Joh93c,
author = "C.R. Johnson and R.S. MacLeod",
title = "High Performance Computing in Medicine: Direct and
Inverse Problems in Cardiology",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
15th Annual International Conference",
pages = "582--583",
year = "1993",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart, scientific computing",
}
@Article{SCI:Joh93d,
author = "C.R. Johnson and R.S. MacLeod and M.A. Matheson
and C. Zimmerman",
title = "The Body Electric",
journal = "Discover Magazine",
pages = "72--77",
year = "1993",
month = "February",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scalar field methods, vector field methods",
}
@InProceedings{SCI:Joh94a,
author = "C.R. Johnson and S.G. Parker",
title = "A Computational Steering Model Applied to Problems
in Medicine",
booktitle = "Supercomputing 94",
pages = "540--549",
year = "1994",
publisher = "{IEEE} Press",
keywords = "scirun, pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/crj94/sc94_9.ps",
url = "http://www.sci.utah.edu/publications/crj94/sc94_9.ps.Z",
}
@Article{SCI:Joh94e,
author = "C.R. Johnson and P. Alfeld",
title = "Computational Engineering and Science at the
University of Utah",
journal = "{IEEE} Computational Science and Engineering",
pages = "7--9",
year = "1994",
keywords = ", scientific computing, scientific visualization,
problem solving environments, pse",
}
@InProceedings{SCI:Joh95a,
author = "C.R. Johnson and R.S. MacLeod and J.A. Schmidt",
title = "Software Tools for Modeling, Computation, and
Visualization in Medicine",
booktitle = "CompMed 94 Proceedings",
year = "1995",
publisher = "World Scientific",
keywords = "pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/crj95/compmed.ps",
url = "http://www.sci.utah.edu/publications/crj95/compmed.ps.Z",
}
@InProceedings{SCI:Joh95b,
author = "C.R. Johnson and S.G. Parker",
title = "Applications in Computational Medicine using
{SCIR}un: A Computational Steering Programming
Environment",
booktitle = "Supercomputer `95",
pages = "2--19",
year = "1995",
editor = "H.W. Meuer",
publisher = "Springer-Verlag",
keywords = "scirun, forward problems inverse problems forward
simulation inverse solutions finite elements,
computational pde pdes computational partial
differential equations evaporation, scientific
computing, pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/super95/super95_6.ps",
url = "http://www.sci.utah.edu/publications/super95/super95_6.ps.Z",
}
@InCollection{SCI:Joh95c,
author = "C.R. Johnson",
title = "Direct and Inverse Bioelectric Field Problems",
booktitle = "Computational Science Education Project",
year = "1995",
editor = "E. Oliver and M. Strayer and V. Meiser and D.
Zachmann and R. Giles",
publisher = "DOE",
address = "Washington, D.C.",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
scientific visualization, bioelectric fields,
scientific computing",
}
@InCollection{SCI:Joh95d,
author = "C.R. Johnson",
title = "Numerical Methods for Bioelectric Field
Problems",
booktitle = "The Biomedical Engineering Handbook",
pages = "161--188",
year = "1995",
editor = "J.D. Bronzino",
publisher = "CRC Press",
address = "Boca Ratan",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
computational pde pdes computational partial
differential equations evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/crj95/bioeng_1.ps",
url = "http://www.sci.utah.edu/publications/crj95/bioeng_1.ps.Z",
}
@Article{SCI:Joh96b,
author = "C.R. Johnson and D.M. Beazley and Y. Livnat and
S.G. Parker and J.A. Schmidt and H.W. Shen and D.M.
Weinstein",
title = "Applications of Large-Scale Computing and
Scientific Visualization in Medicine",
journal = "International Journal on Supercomputer
Applications and High Performance Computing",
year = "1996",
keywords = "scientific computing, scientific visualization",
url = "http://www.sci.utah.edu/publications/crj96/ijsa.ps",
}
@InCollection{SCI:Joh96e,
author = "C.R. Johnson and R.S. MacLeod",
title = "Local regularization and adaptive methods for the
inverse Laplace problem",
booktitle = "Biomedical and Life Physics",
pages = "224--234",
year = "1996",
editor = "D.N. Ghista",
publisher = "Vieweg-Verlag",
address = "Braunschweig",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements, ncrr,
scientific computing",
url = "http://www.sci.utah.edu/publications/crj96/gauss94_2.ps",
url = "http://www.sci.utah.edu/publications/crj96/gauss94_2.ps.Z",
}
@TechReport{SCI:Joh97a,
author = "C.R. Johnson and D.M. Beazley and Y. Livnat and
S.G. Parker and J.A. Schmidt and H.W. Shen and D.M.
Weinstein",
title = "Applications of Large-Scale Computing and
Scientific Visualization in Medicine",
number = "UUSCI-1997-001",
year = "1997",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scirun, scientific visualization, scientific
computing, pse, imaging",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-1997-001.pdf",
}
@Article{SCI:Joh97d,
author = "C.R. Johnson",
title = "Computational and Numerical Methods for
Bioelectric Field Problems",
journal = "Critical Reviews in BioMedical Engineering",
volume = "25",
number = "1",
pages = "1--81",
year = "1997",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
vector field methods, tensor field methods",
url = "http://www.sci.utah.edu/publications/crj97/Crit-Rev-BE-Johnson97.pdf",
}
@Article{SCI:Joh98a,
author = "C.R. Johnson and R.S. MacLeod",
title = "Adaptive local regularization methods for the
inverse {ECG} problem",
journal = "Progress in Biophysics and Biochemistry",
volume = "69",
number = "2/3",
pages = "405",
year = "1998",
month = "Dec",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scirun, inverse ecg, ncrr",
url = "http://www.sci.utah.edu/publications/crj98/biophys97.pdf",
}
@Article{SCI:Joh98b,
author = "C.R. Johnson",
title = "Computer Visualization in Medicine",
journal = "National Forum",
volume = "Fall",
pages = "17--21",
year = "1998",
keywords = ", scientific computing, scientific visualization,
pse, problem solving environments, haptics",
url = "http://www.sci.utah.edu/publications/crj98/icfd98.ps.Z",
url = "http://www.sci.utah.edu/publications/crj98/icfd98.ps",
}
@InProceedings{SCI:Joh98c,
author = "C.R. Johnson and M. Berzins and L. Zhukov and R.
Coffey",
title = "{SCIR}un: Applications to Atmospheric Diffusion
Using Unstructured Meshes",
booktitle = "Numerical Methods for Fluid Dynamics {VI}",
pages = "111--122",
year = "1998",
editor = "M.J. Baines",
publisher = "Oxford University Press",
keywords = "scirun, computational pde pdes computational
partial differential equations evaporation,
adaptive mesh generation, evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/crj98/icfd98.ps.Z",
url = "http://www.sci.utah.edu/publications/crj98/icfd98.ps",
url = "http://www.sci.utah.edu/publications/crj98/icfd98.pdf",
}
@InProceedings{SCI:Joh99b,
author = "C.R. Johnson and S.G. Parker",
title = "The {SCIR}un Parallel Scientific Computing Problem
Solving Environment",
booktitle = "Ninth {SIAM} Conference on Parallel Processing for
Scientific Computing",
year = "1999",
keywords = "scirun, problem solving environments, pse",
url = "http://www.sci.utah.edu/publications/siam99/siam99b.ps.gz",
url = "http://www.sci.utah.edu/publications/siam99/siam99b.ps",
}
@Article{SCI:Joh99c,
author = "C.R. Johnson and S.G. Parker and C.D. Hansen and
G.L. Kindlmann and Y. Livnat",
title = "Interactive Simulation and Visualization",
journal = "{IEEE} Computer",
volume = "32",
number = "12",
pages = "59--65",
year = "1999",
month = "Dec",
keywords = "ncrr, scalar field methods, volume rendering,
transfer functions, scirun, biopse, uintah",
url = "http://www.sci.utah.edu/publications/ieee_computer99/ieee_computer99.ps.gz",
url = "http://www.sci.utah.edu/publications/ieee_computer99/ieee_computer99.pdf",
}
@Conference{SCI:Jol2006a,
author = "M. Jolley and J. Triedman and C.-F. Westin and
D.M. Weinstein and R.S. MacLeod and D.H. Brooks",
title = "Image Based Modeling of Defibrillation in
Children",
booktitle = "Proceedings of the 26th Annual International
Conference of the {IEEE} {EMBS}",
year = "2006",
address = "New York, NY, USA",
month = "August",
keywords = "ncrr",
}
@Article{SCI:Jol2007a,
author = "M. Jolley and J.G. Stinstra and D.M. Weinstein and
S. Pieper and R.S.J. Estepar and G. Kindlmann and
R.S. MacLeod and D.H. Brooks and J.K. Triedman",
title = "Open-Source Environment for Interactive Finite
Element Modeling of Optimal ICD Electrode
Placement",
journal = "Functional Imaging and Modeling of the Heart",
volume = "4466/2007",
pages = "373--382",
year = "2007",
series = "Lecture Notes in Computer Science (LCNS)",
isbn = "978-3-540-72906-8",
url = "http://www.sci.utah.edu/publications/jolley07/jolleyFIMH07.pdf",
}
@Article{SCI:Jol2008a,
author = "M. Jolley and J.G. Stinstra and S. Pieper and R.S.
MacLeod and D.H. Brooks and F. Cecchin and J.K.
Triedman",
title = "A Computer Modeling Tool for Comparing Novel ICD
Electrode Orientations in Children and Adults",
journal = "Heart Rhythm",
volume = "5",
number = "4",
pages = "565--572",
year = "2008",
month = "April",
pmid = "18362024",
keywords = "ncrr, cibc, bioelectric field modeling",
url = "http://www.sci.utah.edu/publications/jolley08/Jolley_HeartRhythm2008.pdf",
}
@Article{SCI:Jol2010a,
author = "M. Jolley and J. Stinstra and J. Tate and S.
Pieper and R.S. Macleod and L. Chu and P. Wang and
J.K. Triedman",
title = "Finite element modeling of subcutaneous
implantable defibrillator electrodes in an adult
torso",
journal = "Heart Rhythm",
volume = "7",
number = "5",
pages = "692--698",
year = "2010",
month = "May",
doi = "10.1016/j.hrthm.2010.01.030",
pmid = "20230927",
pmcid = "PMC3103844",
url = "http://www.sci.utah.edu/publications/Jol2010a/Jolley_HeartRhythm2010.pdf",
}
@InProceedings{SCI:Jon2007a,
author = "B.W. Jones and R.E. Marc and C.B. Watt and K.
Kinardi and D. DeMill and J.H. Yang and T. Tasdizen
and P. Koshevoy and E. Jurrus and R.T. Whitaker",
title = "Structure and Function of Microneuromas in Retinal
Remodeling",
booktitle = "The Association for Research in Vision and
Ophthalmology (ARVO) Conference",
year = "2007",
note = "(abstract)",
keywords = "crcns",
url = "http://www.sci.utah.edu/publications/jones07/ARVO2007_BWJones_poster_FINAL 2_small.pdf",
}
@Article{SCI:Jon2007b,
author = "C. Jones and K.-L. Ma and A.R. Sanderson and L.
Myers",
title = "Visual Interrogation of Gyrokinetic Particle
Simulations",
journal = "Journal of Physics",
volume = "78",
pages = "012033 (6pp)",
year = "2007",
series = "Conference Series",
keywords = "fusion tokamak, particle physics",
url = "http://www.sci.utah.edu/publications/jones07/Jones_JPhys2007.pdf",
}
@InProceedings{SCI:Jon2013a,
author = "C. Jones and T. Liu and M. Ellisman and T.
Tasdizen",
title = "Semi-Automatic Neuron Segmentation in Electron
Microscopy Images Via Sparse Labeling",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "1304--1307",
year = "2013",
month = "April",
doi = "10.1109/ISBI.2013.6556771",
url = "http://www.sci.utah.edu/publications/jones13/Jones_ISBI2013a.pdf",
}
@InProceedings{SCI:Jon2013b,
author = "C. Jones and M. Seyedhosseini and M. Ellisman and
T. Tasdizen",
title = "Neuron Segmentation in Electron Microscopy Images
Using Partial Differential Equations",
booktitle = "Proceedings of 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "1457--1460",
year = "2013",
month = "April",
doi = "10.1109/ISBI.2013.6556809",
url = "http://www.sci.utah.edu/publications/jones13/Jones_ISBI2013b.pdf",
}
@Article{SCI:Jon2013c,
author = "K.B. Jones and M. Datar and S. Ravichandran and H.
Jin and E. Jurrus and R.T. Whitaker and M.R.
Capecchi",
title = "Toward an Understanding of the Short Bone
Phenotype Associated with Multiple
Osteochondromas",
journal = "Journal of Orthopaedic Research",
volume = "31",
number = "4",
pages = "651--657",
year = "2013",
doi = "10.1002/jor.22280",
pmid = "23192691",
pmcid = "PMC3683979",
url = "http://www.sci.utah.edu/publications/jones13/Jones_JOR2013.pdf",
}
@Article{SCI:Jon2015a,
author = "C. Jones and T. Liu and N.W. Cohan and M. Ellisman
and T. Tasdizen",
title = "Efficient semi-automatic 3D segmentation for
neuron tracing in electron microscopy images",
journal = "Journal of Neuroscience Methods",
volume = "246",
pages = "13--21",
year = "2015",
publisher = "Elsevier BV",
month = "May",
doi = "10.1016/j.jneumeth.2015.03.005",
url = "http://www.sci.utah.edu/publications/Jon2015a/1-s2.0-S0165027015000874-main.pdf",
}
@Article{SCI:Joo2014a,
author = "Y. Joon Ahn and C. Hoffmann and P. Rosen",
title = "Geometric constraints on quadratic B{\’e}zier curves
using minimal length and energy",
journal = "Journal of Computational and Applied
Mathematics",
volume = "255",
pages = "887--897",
year = "2014",
url = "http://www.sci.utah.edu/publications/joon14/Ahn.2014.JCAM.pdf",
}
@Article{SCI:Jos1993a,
author = "S. Joshi and M. Miller",
title = "Maximum a Posteriori Estimation with Good's
Roughness for Three-Dimensional Optical-Sectioning
Microscopy",
journal = "J Opt Soc Am A",
volume = "10",
number = "5",
pages = "1078--1085",
year = "1993",
month = "May",
}
@InProceedings{SCI:Jos1995a,
author = "S.C. Joshi and M.I. Miller and G.E. Christensen
and A. Banerjee and T.A. Coogan and U. Grenander",
title = "Hierarchical brain mapping via a generalized
Dirichlet solution for mapping brain manifolds",
booktitle = "Proc. of the SPIE International Symposium on
Optical Science, Engineering, and
Instrumentation",
pages = "278--289",
year = "1995",
month = "August",
}
@InProceedings{SCI:Jos1995b,
author = "S.C. Joshi and J. Wang and M.I. Miller and D.V.
Essen and U. Grenander",
title = "On the Differential Geometry of the Cortical
Surface",
booktitle = "Proceedings of SPIE 1995 International Symposium:
Vision Geometry IV",
pages = "304--311",
year = "1995",
month = "August",
location = "San Diego, CA",
}
@Article{SCI:Jos1997a,
author = "S.C. Joshi and M.I. Miller and U. Grenander",
title = "On the Geometry and Shape of Brain
Sub-Manifolds",
journal = "International Journal of Pattern Recognition and
Artificial Intelligence, special issue on Magnetic
Resonance Imaging",
volume = "11",
number = "8",
pages = "1317--1343",
year = "1997",
}
@InProceedings{SCI:Jos1997b,
author = "S. Joshi and A. Banerjee and G.E. Christensan and
J.G. Csernansky and J.W. Haller and M.I. Miller and
L. Wang",
title = "Gaussian Random Fields on Sub-Manifolds for
Characterizing Brain Surfaces",
booktitle = "Proceedings of the International Conference on
Image Processing in Medical Imaging (IPMI)",
year = "1997",
}
@Article{SCI:Jos1999a,
author = "M. Joshi and J. Cui and K. Doolittle and S. Joshi
and D.C. Van Essen and L. Wang and M. Miller",
title = "Brain Segmentation and the Generation of Cortical
Surfaces",
journal = "Neuroimage",
volume = "9",
number = "5",
pages = "461--476",
year = "1999",
month = "May",
}
@Article{SCI:Jos2001a,
author = "S. Joshi and S. Pizer and P.T. Fletcher and A.
Thall and G. Tracton",
title = "Multi-scale 3-D Deformable Model Segmentation
Based on Medial Description",
journal = "Information Processing in Medical Imaging
(IPMI)",
pages = "64--77",
year = "2001",
editor = "MF Insana and RM Leahy",
month = "June",
url = "http://www.sci.utah.edu/publications/joshi01/IPMI01-Joshi-defm.pdf",
}
@Article{SCI:Jos2001b,
author = "S. Joshi and M.I. Miller",
title = "Landmark Matching Via Large Deformation
Diffeomorphisms",
journal = "IEEE Transactions on Image Processing",
volume = "9",
number = "8",
pages = "1357--1370",
year = "2000",
month = "August",
}
@Article{SCI:Jos2002a,
author = "S. Joshi and S. Pizer and P.T. Fletcher and P.
Yushkevich and A. Thall and J. Marron",
title = "Multiscale Deformable Model Segmentation and
Statistical Shape Analysis Using Medial
Descriptions",
journal = "IEEE Trans Med Imaging",
volume = "21",
number = "5",
pages = "538--550",
year = "2002",
month = "May",
url = "http://www.sci.utah.edu/publications/joshi02/TMI02-Joshi-mreps.pdf",
}
@Article{SCI:Jos2003a,
author = "S. Joshi and P. Lorenzen and G. Gerig and E.
Bullitt",
title = "Structural and Radiometric Asymmetry in Brain
Images",
journal = "Med Image Anal",
volume = "7",
number = "2",
pages = "155--170",
year = "2003",
month = "June",
url = "http://www.sci.utah.edu/publications/joshi03/MEDIA03-Joshi-brain.pdf",
}
@Article{SCI:Jos2004a,
author = "S. Joshi and B. Davis and M Jomier and G. Gerig",
title = "Unbiased Diffeomorphic Atlas Construction for
Computational Anatomy",
journal = "Neuroimage",
volume = "23 Suppl. 1",
pages = "S151--S160",
year = "2004",
url = "http://www.sci.utah.edu/publications/joshi04/NeuroImage04-Joshi.pdf",
}
@InProceedings{SCI:Jur2006a,
author = "E. Jurrus and T. Tasdizen and P. Koshevoy and P.T.
Fletcher and M. Hardy and C-B. Chien and W. Denk
and R.T. Whitaker",
title = "Axon Tracking in Serial Block-Face Scanning
Electron Microscopy",
booktitle = "Workshop on Microscopic Image Analysis with
Applications in Biology, MICCAI",
year = "2006",
month = "October",
keywords = "ip gp image processing goemetry processing,
crcns",
}
@InProceedings{SCI:Jur2008b,
author = "E. Jurrus and R.T. Whitaker and B. Jones and R.
Marc and T. Tasdizen",
title = "An Optimal-Path Approach for Neural Circuit
Reconstruction",
booktitle = "Proceedings of the 5th {IEEE} International
Symposium on Biomedical Imaging: From Nano to
Macro",
pages = "1609--1612",
year = "2008",
pmid = "19172170",
keywords = "crcns, retinal reconstruction, blindness",
url = "http://www.sci.utah.edu/publications/jurrus08/ieeeisbi2008_jurrus.pdf",
}
@Article{SCI:Jur2009a,
author = "E. Jurrus and M. Hardy and T. Tasdizen and P.T.
Fletcher and P. Koshevoy and C.-B. Chien and W.
Denk and R.T. Whitaker",
title = "Axon Tracking in Serial Block-Face Scanning
Electron Microscopy",
journal = "Medical Image Analysis (MEDIA)",
volume = "13",
number = "1",
pages = "180--188",
year = "2009",
publisher = "Elsevier",
month = "February",
pmid = "18617436",
keywords = "CRCNS, neuron tracking",
}
@TechReport{SCI:Jur2009b,
author = "E. Jurrus and A.R.C. Paiva and S. Watanabe and
R.T. Whitaker and E.M. Jorgensen and T. Tasdizen",
title = "Serial Neural Network Classifier for Membrane
Detection using a Filter Bank.",
number = "UUSCI-2009-006",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/jurrus09/UUSCI-2009-006.pdf",
}
@InProceedings{SCI:Jur2009c,
author = "E. Jurrus and A.R.C. Paiva and S. Watanabe and R.
Whitaker and E.M. Jorgensen and T. Tasdizen",
title = "Serial Neural Network Classifier for Membrane
Detection using a Filter Bank",
booktitle = "Proc. Workshop on Microscopic Image Analysis with
Applications in Biology",
year = "2009",
location = "Bethesda, MD, USA",
url = "http://www.sci.utah.edu/publications/jurrus09/Jurrus_2009e.pdf",
}
@Article{SCI:Jur2010a,
author = "E. Jurrus and A.R.C. Paiva and S. Watanabe and
J.R. Anderson and B.W. Jones and R.T. Whitaker and
E.M. Jorgensen and R.E. Marc and T. Tasdizen",
title = "Detection of Neuron Membranes in Electron
Microscopy Images Using a Serial Neural Network
Architecture",
title_url =
"http://www.sciencedirect.com/science/article/B6W6Y-50BB5M8-1/2/9991cfd9d938393ae5775578a69c03e6",
journal = "Medical Image Analysis",
volume = "14",
number = "6",
pages = "770--783",
year = "2010",
doi = "10.1016/j.media.2010.06.002",
pmid = "20598935",
url = "http://www.sci.utah.edu/publications/jurrus10/Jurrus_MIA2010.pdf",
}
@InProceedings{SCI:Jur2011a,
author = "E. Jurrus and S. Watanabe and R. Guily and A.R.C.
Paiva and M.H. Ellisman and E.M. Jorgensen and T.
Tasdizen",
title = "Semi-automated Neuron Boundary Detection and Slice
Traversal Algorithm for Segmentation of Neurons
from Electron Microscopy Images",
booktitle = "Microscopic Image Analysis with Applications in
Biology (MIAAB) Workshop",
year = "2011",
url = "http://www.sci.utah.edu/publications/jurrus11/Jurrus_MIAAB2011.pdf",
}
@Article{SCI:Jur2012a,
author = "E. Jurrus and S. Watanabe and R.J. Giuly and
A.R.C. Paiva and M.H. Ellisman and E.M. Jorgensen
and T. Tasdizen",
title = "Semi-Automated Neuron Boundary Detection and
Nonbranching Process Segmentation in Electron
Microscopy Images",
journal = "Neuroinformatics",
pages = "(published online)",
year = "2012",
url = "http://www.sci.utah.edu/publications/jurrus12/Jurrus_Neuroinformatics2012.pdf",
}
@Article{SCI:Kad2004a,
author = "A. Kadlag and A.V. Wanjari and J. Freire and J.
Haritsa",
title = "Supporting Exploratory Queries in Databases",
journal = "Database Systems for Advanced Applications",
volume = "2973/2004",
pages = "25-26",
year = "2004",
series = "Lecture Notes in Computer Science (LNCS)",
keywords = "database queries",
url = "http://www.sci.utah.edu/publications/kadlag04/Kadlag_LNCS2004.pdf",
}
@Article{SCI:Kap2012a,
author = "T. Kapur and S. Pieper and R.T. Whitaker and S.
Aylward and M. Jakab and W. Schroeder and R.
Kikinis",
title = "The National Alliance for Medical Image Computing,
a roadmap initiative to build a free and open
source software infrastructure for translational
research in medical image analysis",
booktitle = "Journal of the American Medical Informatics
Association",
journal = "Journal of the American Medical Informatics
Association",
volume = "19",
number = "2",
pages = "176--180",
year = "2012",
doi = "10.1136/amiajnl-2011-000493",
url = "http://www.sci.utah.edu/publications/kapur12/Kapur_JAMIA2012l.pdf",
}
@Article{SCI:Kap2018a,
author = "A.L. Kapron and S.K. Aoki and J.A. Weiss and A.J.
Krych and T.G. Maak",
title = "Isolated focal cartilage and labral defects in
patients with femoroacetabular impingement syndrome
may represent new, unique injury patterns",
title_url =
"https://link.springer.com/article/10.1007%2Fs00167-018-4861-2",
journal = "Knee Surgery, Sports Traumatology, Arthroscopy",
year = "2018",
publisher = "Springer Nature",
month = "Feb",
doi = "10.1007/s00167-018-4861-2",
}
@InProceedings{SCI:Kar1999a,
author = "G.-S. Karamanos and C. Evangelinos and R.C. Boes
and R.M. Kirby and G.E. Karniadakis",
title = "Direct Numerical Simulation of Turbulence with a
PC/Linux Cluster: Fact or Fiction?",
booktitle = "Proceedings of SuperComputing 1999",
year = "1999",
month = "November",
location = "Portland, OR",
}
@Article{SCI:Kar2013a,
author = "R. Karim and R.J. Housden and M. Balasubramaniam
and Z. Chen and D. Perry and A. Uddin and Y.
Al-Beyatti and E. Palkhi and P. Acheampong and S.
Obom and A. Hennemuth and Y. Lu and W. Bai and W.
Shi and Y. Gao and H.-O. Peitgen and P. Radau and
R. Razavi and A. Tannenbaum and D. Rueckert and J.
Cates and T. Schaeffter and D. Peters and R.S.
MacLeod and K. Rhode",
title = "Evaluation of Current Algorithms for Segmentation
of Scar Tissue from Late Gadolinium Enhancement
Cardiovascular Magnetic Resonance of the Left
Atrium: An Open-Access Grand Challenge",
journal = "Journal of Cardiovascular Magnetic Resonance",
volume = "15",
number = "105",
year = "2013",
doi = "10.1186/1532-429X-15-105",
keywords = "Late gadolinium enhancement, Cardiovascular
magnetic resonance, Atrial fibrillation,
Segmentation, Algorithm benchmarking",
url = "http://www.sci.utah.edu/publications/karim13/Karim_JCMR2013.pdf",
}
@Article{SCI:Kas2008a,
author = "R. Kashani and M. Hub and J.M. Balter and M.L.
Kessler and L. Dong and L. Zhang and L. Xing and Y.
Xie and D. Hawkes and J.A. Schnabel and J.
McClelland and S. Joshi and Q. Chen and W. Lu",
title = "Objective assessment of deformable image
registration in radiotherapy: a multi-institution
study",
journal = "Medical Physics",
volume = "35",
number = "12",
pages = "5944--5953",
year = "2008",
pmid = "19175149",
url = "http://www.sci.utah.edu/publications/kashani08/Kashani_MedPhys2008.pdf",
}
@Article{SCI:Kea2005a,
author = "P.J. Keall and S. Joshi and S.S. Vedam and J.V.
Siebers and V.R. Kini and R. Mohan",
title = "Four-Dimensional Radiotherapy Planning for
DMLC-Based Respiratory Motion Tracking",
journal = "Med Phys",
volume = "32",
number = "4",
pages = "942--951",
year = "2005",
month = "April",
}
@Article{SCI:Kel2011a,
author = "Y. Keller and Y. Gur",
title = "A Diffusion Approach to Network Localization",
journal = "{IEEE} Transactions on Signal Processing",
volume = "59",
number = "6",
pages = "2642--2654",
year = "2011",
doi = "10.1109/TSP.2011.2122261",
url = "http://www.sci.utah.edu/publications/keller11/sensor_ localization_one_column_sub.pdf",
}
@TechReport{SCI:Ken2008a,
author = "A. Kensler and A. Knoll and P. Shirley",
title = "Better Gradient Noise",
number = "UUSCI-2008-001",
year = "2008",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ray tracing RT",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-001.pdf",
}
@InProceedings{SCI:Ken2008b,
author = "A. Kensler",
title = "Tree Rotations for Improving Bounding Volume
Heirarchies",
booktitle = "Proceedings of the 2008 {IEEE} Symposium on
Interactive Ray Tracing",
pages = "73--76",
year = "2008",
}
@Article{SCI:Ker2017a,
author = "M. Kern and A. Lex and N. Gehlenborg and C. R.
Johnson",
title = "Interactive Visual Exploration And Refinement Of
Cluster Assignments",
journal = "BMC Bioinformatics",
year = "2017",
publisher = "Cold Spring Harbor Laboratory",
month = "April",
doi = "10.1101/123844",
url = "http://www.sci.utah.edu/publications/Ker2017a/document-kern.pdf",
}
@Article{SCI:Kes2018a,
author = "V. Keshavarzzadeh and R.M. Kirby and A. Narayan",
title = "Numerical integration in multiple dimensions with
designed quadrature",
journal = "CoRR",
year = "2018",
url = "http://www.sci.utah.edu/publications/Kes2018a/1804.06501.pdf",
}
@Unpublished{SCI:Key2011a,
author = "D. Keyes and V. Taylor and T. Hey and S. Feldman
and G. Allen and P. Colella and P. Cummings and F.
Darema and J. Dongarra and T. Dunning and M.
Ellisman and I. Foster and W. Gropp and C.R.
Johnson and C. Kamath and R. Madduri and M.
Mascagni and S.G. Parker and P. Raghavan and A.
Trefethen and S. Valcourt and A. Patra and F.
Choudhury and C. Cooper and P. McCartney and M.
Parashar and T. Russell and B. Schneider and J.
Schopf and N. Sharp",
title = "Advisory Committee for CyberInfrastructure Task
Force on Software for Science and Engineering",
year = "2011",
note = "NSF Report",
url = "http://www.sci.utah.edu/publications/Key2011a/TaskForceReport_Software.pdf",
}
@InProceedings{SCI:Kho2002a,
author = "E.G. Kholmovski and A.A. Samsonov and D.L.
Parker",
title = "{POCSENSE}: POCS-based method for reconstruction
from sensitivity-encoded data",
booktitle = c-ISMRM2002,
pages = "194",
year = "2002",
location = "Honolulu",
keywords = "NCRR, ip image processing signal processing, ncrr,
imaging, bisti",
url = "http://www.sci.utah.edu/publications/samsonov02/ismrm02_abs4.pdf",
}
@Article{SCI:Kho2002b,
author = "E.G. Kholmovski and A.A. Samsonov and D.L.
Parker",
title = "Motion Artifact Reduction Technique for Dual
Contrast FSE Imaging",
journal = "Magnetic Resonance Imaging",
volume = "20",
number = "6",
pages = "455--462",
year = "2002",
keywords = "NCRR, ip image processing signal processing, ncrr,
imaging",
url = "http://www.sci.utah.edu/publications/samsonov02/mri02_motion.pdf",
}
@InProceedings{SCI:Kho2005a,
author = "E.G. Kh{\"o}lmovski and E.V.R. DiBella and A.A.
Samsonov",
title = "Accurate Assessment of the Arterial Input Function
using {MRI} with Radial Sampling",
booktitle = c-SCMR2005,
volume = "7",
pages = "292--294",
year = "2005",
keywords = "cardiac heart, ncrr, Cardiad perfusion MRI,
Arterial Input Function, cardiad perfusion mri,
arterial input function, bisti",
}
@Article{SCI:Kho2005b,
author = "E.G. Kh{\"o}lmovski and D.L. Parker",
title = "Application of Phase Consistency to Improve Time
Efficiency and Image Quality in Dual Echo Black
Blood Carotid Angiography",
journal = "Magn Reson Imaging",
volume = "23",
number = "6",
pages = "711--722",
year = "2005",
url = "http://www.sci.utah.edu/publications/kholmovski05/MagResImaging2005.pdf",
}
@InProceedings{SCI:Kho2005c,
author = "E.G. Kh{\"o}lmovski and E.V.R. DiBella and A.A.
Samsonov",
title = "Perfusion {MRI} with Radial Sampling: Arterial
Input Function and Tissue Enhancement Curve
Assessment",
booktitle = "Proc. Intl. Soc. Mag. Reson.",
pages = "252",
year = "2005",
note = "Abstract",
url = "http://www.sci.utah.edu/publications/kholmovski05/Kholmovski_ISMR2005.pdf",
}
@InProceedings{SCI:Kho2005d,
author = "E.G. Kh{\"o}lmovski and A.A. Samsonov",
title = "{GARSE}: Generalized Autocalibrating
Reconstruction for Sensitivity Encoded MRI",
booktitle = "Proc. Intl. Soc. Mag. Reson.",
pages = "2672",
year = "2005",
note = "Abstract",
url = "http://www.sci.utah.edu/publications/kholmovski05/Kholmovski_ISMR2005b.pdf",
}
@InProceedings{SCI:Kim2011a,
author = "S.H. Kim and V. Fonov and J. Piven and J. Gilmore
and C. Vachet and G. Gerig and D.L. Collins and M.
Styner",
title = "Spatial Intensity Prior Correction for Tissue
Segmentation in the Developing human Brain",
booktitle = "Proceedings of {IEEE} {ISBI} 2011",
pages = "2049--2052",
year = "2011",
doi = "10.1109/ISBI.2011.5872815",
url = "http://www.sci.utah.edu/publications/kim11/Kim_ISBI2011.pdf",
}
@InProceedings{SCI:Kim2012a,
author = "M. Kim and G. Chen and C.D. Hansen",
title = "Dynamic particle system for mesh extraction on the
GPU",
booktitle = "Proceedings of the 5th Annual Workshop on General
Purpose Processing with Graphics Processing
Units",
pages = "38--46",
year = "2012",
series = "GPGPU-5",
publisher = "ACM",
address = "New York, NY, USA",
location = "London, England",
isbn = "978-1-4503-1233-2",
doi = "10.1145/2159430.215943",
keywords = "CUDA, GPGPU, particle systems, volumetric data
mesh extraction",
url = "http://www.sci.utah.edu/publications/kim12/Kim_GPGPU5_2012.pdf",
}
@Article{SCI:Kim2013a,
author = "S.H. Kim and V. Fonov and C. Dietrich and C.
Vachet and H.C. Hazlett and R.G. Smith and M.
Graves and J. Piven and J.H. Gilmore and D.L.
Collins and G. Gerig and M. Styner and The IBIS
network",
title = "Adaptive prior probability and spatial temporal
intensity change estimation for segmentation of the
one-year-old human brain",
journal = "Journal of Neuroscience Methods",
volume = "212",
number = "1",
pages = "43--55",
year = "2013",
month = "January",
note = "Published online Sept. 29",
doi = "10.1016/j.jneumeth.2012.09.01",
pmcid = "PMC3513941",
url = "http://www.sci.utah.edu/publications/kim12/Kim_JofNeuroscienceMethods2012.pdf",
}
@Article{SCI:Kim2015a,
author = "M. Kim and C.D. Hansen",
title = "Surface Flow Visualization using the Closest Point
Embedding",
journal = "2015 IEEE Pacific Visualization Symposium",
year = "2015",
month = "April",
keywords = "vector field, flow visualization",
url = "http://www.sci.utah.edu/publications/Kim2015a/Kim_PacVis2015.pdf",
}
@InProceedings{SCI:Kim2015b,
author = "M. Kim and C.D. Hansen",
title = "{GPU} Surface Extraction with the Closest Point
Embedding",
booktitle = "Proceedings of IS\\&T/SPIE Visualization and Data
Analysis, 2015",
year = "2015",
month = "February",
keywords = "scalar field methods, GPGPU, curvature based,
scientific visualization",
url = "http://www.sci.utah.edu/publications/Kim2015b/Kim_SPIEVDA2015.pdf",
}
@Article{SCI:Kim2016a,
author = "S. Kim and I.Lyu and V. Fonov and C. Vachet and H.
Hazlett and R. Smith and J. Piven and S. Dager and
R. Mckinstry and J. Pruett and A. Evans and D.
Collins and K. Botteron and R. Schultz and G. Gerig
and M. Styner",
title = "Development of Cortical Shape in the Human Brain
from 6 to 24 Months of Age via a Novel Measure of
Shape Complexity",
journal = "NeuroImage",
volume = "135",
pages = "163--176",
year = "2016",
publisher = "Elsevier",
month = "July",
doi = "10.1016/j.neuroimage.2016.04.053",
url = "http://www.sci.utah.edu/publications/Kim2016a/kim-neuroimage-2016.pdf",
}
@Article{SCI:Kin2000,
author = "G.L. Kindlmann and D.M. Weinstein and D. Hart",
title = "Strategies for Direct Volume Rendering of
Diffusion Tensor Fields",
journal = j-TVCG,
volume = "6",
number = "2",
pages = "124--138",
year = "2000",
month = "April-June",
keywords = "tensor field methods, diffusion tensor imaging,
biopse, ncrr, scientific visualization",
url = "http://www.sci.utah.edu/publications/gk_tvcg00/strategies-tensor.pdf",
}
@InProceedings{SCI:Kin2003b,
author = "G. Kindlmann and R.T. Whitaker and T. Tasdizen and
T. M{\"o}ller",
title = "Curvature-Based Transfer Functions for Direct
Volume Rendering: Methods and Applications",
booktitle = "Proceedings Visualization 2003",
pages = "67",
year = "2003",
month = "October",
keywords = "scalar field methods, transfer functions,
curvature based, scientific visualization",
url = "http://www.sci.utah.edu/publications/gk03/vis03kindlmann.pdf",
}
@InProceedings{SCI:Kin2004a,
author = "G Kindlmann",
title = "Superquadric Tensor Glyphs",
booktitle = c-VISSYM2004,
pages = "147--154",
year = "2004",
month = "May",
keywords = "tensor field methods, diffusion tensor imaging,
biopse, ncrr",
url = "http://www.sci.utah.edu/publications/gk04/vissym04kindlmann.pdf",
}
@InProceedings{SCI:Kin2004b,
author = "G.L. Kindlmann and D.M. Weinstein and A.D. Lee and
A.W. Toga and P.M. Thompson",
title = "Visualization of Anatomic Covariance Tensor
Fields",
booktitle = "Proceedings of the {IEEE} Engineering in Medicine
and Biology Society 26th Annual International
Conference",
year = "2004",
keywords = "ncrr, biopse",
url = "http://www.sci.utah.edu/publications/gk04/embs04.pdf",
}
@InProceedings{SCI:Kin2004c,
author = "G. Kindlmann and A. L. Alexander and M. Lazar and
J. Lee and T. Tasdizen and R.T. Whitaker",
title = "An Algorithm for Moment-Based Global Registration
of Echo Planar Diffusion-Weighted Images",
booktitle = "Proceedings of 12th Annual ISMRM",
pages = "2200",
year = "2004",
}
@TechReport{SCI:Kin2004d,
author = "G. Kindlmann",
title = "Visualization and Analysis of Diffusion Tensor
Fields",
number = "UUCS-04-014",
year = "2004",
institution = "School of Computing, University of Utah",
type = "Technical Report",
note = "PhD Thesis",
keywords = "diffusion tensor imaging",
url = "http://www.sci.utah.edu/publications/gk04/UUCS-04-014.pdf",
}
@Article{SCI:Kin2005a,
author = "G.L. Kindlmann and D.M. Weinstein and G.M. Jones
and C.R. Johnson and M.R. Capecchi and C. Keller",
title = "Practical Vessel Imaging by Computed Tomography in
Live Transgenic Mouse Models for Human Tumors",
journal = "Journal of Molecular Imaging",
volume = "4",
number = "4",
pages = "417--424",
year = "2005",
keywords = "ncrr, ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/gk05/Kindlmann_et-al_JMI_2005.pdf",
}
@InProceedings{SCI:Kin2006a,
author = "G. Kindlmann and X. Tricoche and C.-F. Westin",
title = "Anisotropy Creases Delineate White Matter
Structure in Diffusion Tensor {MRI}",
booktitle = "Proceedings of the Ninth International Conference
on Medical Image Computing and Computer-Assisted
Intervention (MICCAI'06)",
pages = "126--133",
year = "2006",
series = "Springer Lecture Notes in Computer Science 4190",
month = "October",
location = "Copenhagen, Denmark",
keywords = "diffusion tensor imaging, ncrr",
url = "http://www.sci.utah.edu/publications/gk06/kindlmannMICCAI06.pdf",
}
@Article{SCI:Kin2007a,
author = "G. Kindlmann and D.B. Ennis and R.T. Whitaker and
C.-F. Westin",
title = "Diffusion Tensor Analysis With Invariant Gradients
and Rotation Tangents",
journal = "{IEEE} Transactions on Medical Imaging",
volume = "26",
number = "11",
pages = "1483--1499",
year = "2007",
keywords = "DTI, diffusion tensor imaging",
url = "http://www.sci.utah.edu/publications/kindlmann07/Kindlmann_TMI2007.pdf",
}
@Article{SCI:Kin2012a,
author = "J. King and H. Mirzaee and J.K. Ryan and R.M.
Kirby",
title = "Smoothness-Increasing Accuracy-Conserving (SIAC)
Filtering for discontinuous Galerkin Solutions:
Improved Errors Versus Higher-Order Accuracy",
journal = "Journal of Scientific Computing",
volume = "53",
pages = "129--149",
year = "2012",
doi = "10.1007/s10915-012-9593-8",
url = "http://www.sci.utah.edu/publications/king12/King_JSC2012.pdf",
}
@InProceedings{SCI:Kin98a,
author = "G. Kindlmann and J. Durkin",
title = "Semi-Automatic Generation of Transfer Functions
for Direct Volume Rendering",
booktitle = "{IEEE} Symposium on Volume Visualization",
pages = "79--86",
year = "1998",
publisher = "{IEEE} Press",
month = "Oct",
keywords = "scalar field methods, volume rendering, transfer
functions, scientific visualization",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-paper.ps.gz",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-paper.ps",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-paper.pdf",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-plate.ps.gz",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-plate.ps",
url = "http://www.sci.utah.edu/publications/gk98/vv98glk-plate.pdf",
}
@InProceedings{SCI:Kin99,
author = "G.L. Kindlmann and D.M. Weinstein",
title = "Hue-Balls and Lit-Tensors for Direct Volume
Rendering of Diffusion Tensor Fields",
booktitle = "Proceedings of the {IEEE} Visualization 99",
pages = "183--189",
year = "1999",
keywords = "scalar field methods, volume rendering, transfer
functions, tensor field methods, diffusion tensor
imaging, scientific visualization",
url = "http://www.sci.utah.edu/publications/gk99/vis99_hueballs-paper.ps.gz",
url = "http://www.sci.utah.edu/publications/gk99/vis99_hueballs-paper.ps",
url = "http://www.sci.utah.edu/publications/gk99/vis99_hueballs-paper.pdf",
}
@Article{SCI:Kir1999a,
author = "R.M. Kirby and T.C. Warburton and I. Lomtev and
G.E. Karniadakis",
title = "A Discontinuous Galerkin Spectral/hp Method on
Hybrid Grids",
journal = "Journal of Applied Numerical Mathematics",
volume = "33",
pages = "393--405",
year = "1999",
}
@InProceedings{SCI:Kir1999b,
author = "R.M. Kirby and H. Marmanis and D.H. Laidlaw",
title = "Visualizing Multivalued Data from 2D
Incompressible Flows Using Concepts from
Painting",
booktitle = "Proceedings of IEEE Visualization 1999",
pages = "333--340",
year = "1999",
month = "October",
location = "San Francisco, CA",
}
@InCollection{SCI:Kir2001a,
author = "R.M. Kirby and G.E. Karniadakis and O. Mikulchenko
and K. Mayaram",
title = "Integrated Simulation for MEMS: Coupling
Flow-Structure-Thermal-Electrical Domains",
booktitle = "The MEMS Handbook",
year = "2001",
editor = "M. Gad-el-Hak",
publisher = "Informa UK Limited",
}
@InCollection{SCI:Kir2001b,
author = "R.M. Kirby and G.E. Karniadakis",
title = "Under-Resolution and Diagnostics in Spectral
Simulations of Complex-Geometry Flows",
booktitle = "Turbulent Flow Computation",
pages = "1--42",
year = "2001",
editor = "D. Drikakis and B. Geurts",
publisher = "Springer",
}
@Article{SCI:Kir2001c,
author = "R.M. Kirby and G.E. Karniadakis and O. Mikulchenko
and K. Mayaram",
title = "An Integrated Simulator for Coupled Domain
Problems in MEMS",
journal = "Journal of Microelectromechanical Systems",
volume = "10",
number = "3",
pages = "379--399",
year = "2001",
}
@Article{SCI:Kir2002a,
author = "R.M. Kirby and G.E. Karniadakis",
title = "Coarse Resolution Turbulence Simulations With
Spectral Vanishing Viscosity - Large-Eddy
Simulations (SVV-LES)",
journal = j-JFE,
volume = "124",
number = "4",
pages = "886-891",
year = "2002",
keywords = "cfd computational fluid dynamics, computational
pde pdes computational partial differential
equations evaporation, scientific computing",
}
@Article{SCI:Kir2002b,
author = "R.M. Kirby and G.E. Karniadakis",
title = "Coarse Resolution Turbulence Simulations With
Spectral Vanishing Viscosity - Large-Eddy
Simulations (SVV-LES)",
journal = "Journal of Fluids Engineering",
volume = "124",
number = "4",
pages = "886--891",
year = "2002",
}
@Article{SCI:Kir2003a,
author = "R.M. Kirby and G.E. Karniadakis",
title = "De-Aliasing on Non-Uniform Grids: Algorithms and
Applications",
journal = "J. Comp. Phys.",
volume = "191",
number = "1",
pages = "267--282",
year = "2003",
month = "October",
keywords = "cfd computational fluid dynamics, dealiasing
de-aliasing aliasing non-uniform grids, scientific
computing",
}
@Book{SCI:Kir2003b,
author = "G.E. Karniadakis and R.M. Kirby",
title = "Parallel Scientific Computing in C++ and MPI: A
Seamless Approach to Parallel Algorithms and their
Implementation",
pages = "628 pages",
year = "2003",
publisher = "Cambridge University Press",
month = "June",
isbn = "0521520800",
keywords = "parallel visualization, parallel computing,
programing",
}
@Article{SCI:Kir2003c,
author = "R.M. Kirby and G.E. Karniadakis",
title = "De-Aliasing on Non-Uniform Grids: Algorithms and
Applications",
journal = "Journal of Computational Physics",
volume = "191",
pages = "249--264",
year = "2003",
url = "http://www.sci.utah.edu/publications/kirby03/Kirby-5.pdf",
}
@Article{SCI:Kir2004a,
author = "R.M. Kirby and Z. Yosibash",
title = "Solution of Von-Karman Dynamic Non-linear Plate
Equations Using a Pseudo-spectral Method",
journal = j-CMAME,
volume = "193",
number = "6-8",
pages = "575-599",
year = "2004",
keywords = "fluid structure problems, computational mechanics,
Scientific computing, scientific computing",
url = "http://www.sci.utah.edu/publications/kirby04/Kirby-6.pdf",
}
@InCollection{SCI:Kir2004b,
author = "R.M. Kirby and G.E. Karniadakis",
title = "Spectral Element and hp Methods",
booktitle = "Encyclopedia of Computational Mechanics",
volume = "3",
pages = "61--88",
year = "2004",
editor = "E. Stein and R. de Borst and T.J.R. Hughes",
chapter = "3",
publisher = "John Wiley and Sons, NY",
}
@Article{SCI:Kir2004d,
author = "R.M. Kirby and Z. Yosibash",
title = "Solution of von-Karman Dynamic Non-Linear Plate
Equations Using a Pseudo-Spectral Method",
journal = "Computer Methods in Applied Mechanics and
Engineering",
volume = "193",
number = "6-8",
pages = "575--599",
year = "2004",
url = "http://www.sci.utah.edu/publications/kirby04/Kirby-6.pdf",
}
@InCollection{SCI:Kir2005a,
author = "R.M. Kirby and D.F. Keefe and D.H. Laidlaw",
title = "Painting and Visualization",
booktitle = "The Visualization Handbook",
pages = "873--891",
year = "2005",
editor = "C.D. Hansen and C.R. Johnson",
publisher = "Elsevier",
isbn = "0-12-387582-X",
url = "http://www.sci.utah.edu/publications/kirby05/ch45_kirby.pdf",
}
@Article{SCI:Kir2005b,
author = "R.M. Kirby and G.E. Karniadakis",
title = "Selecting the Numerical Flux in Discontinuous
Galerkin Methods for Diffusion Problems",
journal = "Journal of Scientific Computing",
volume = "22/23",
pages = "385--411",
year = "2005",
url = "http://www.sci.utah.edu/publications/kirby05/Kirby-11.pdf",
}
@Article{SCI:Kir2006a,
author = "N.D. Kirkpatrick and J.B. Hoying and S.K. Botting
and J.A. Weiss and U. Utzinger",
title = "In Vitro Model for Endogenous Optical Signatures
of Collagen",
journal = "Journal of Biomedical Optics",
volume = "11",
number = "5",
year = "2006",
month = "September/October",
keywords = "angiogenesis, computational biomechanics,
multiscale tissue modeling multiscale tissue
simulation",
url = "http://www.sci.utah.edu/publications/kirkpatrick06/kirkpatrick_j_biomed_optics_2006.pdf",
}
@InProceedings{SCI:Kir2006b,
author = "R.M. Kirby and C.R. Johnson and M. Berzins",
title = "Involving Undergraduates in Computational Science
and Engineering Research: Successes and
Challenges",
booktitle = "Proceedings of Computational Science - ICCS 2006:
6th International Conference",
volume = "3992",
year = "2006",
series = "Lecture Notes in Computer Science",
month = "May 28-31",
location = "Reading, UK",
url = "http://www.sci.utah.edu/publications/kirby06/iccs06hpc.pdf",
}
@Article{SCI:Kir2006c,
author = "R.M. Kirby and S.J. Sherwin",
title = "Stabilisation of Spectral/hp Element Methods
Through Spectral Vanishing Viscosity: Application
to Fluid Mechanics Modelling",
journal = "Computer Methods in Applied Mechanics and
Engineering",
volume = "195",
pages = "3128--3144",
year = "2006",
url = "http://www.sci.utah.edu/publications/kirby06/Kirby-12.pdf",
}
@Article{SCI:Kir2006d,
author = "R.M. Kirby and S.J. Sherwin",
title = "Aliasing Errors Due to Quadratic Non-Linearities
On Triangular Spectral/hp Element
Discretisations",
journal = "Journal of Engineering Mathematics",
volume = "56",
number = "3",
pages = "273--288",
year = "2006",
}
@Article{SCI:Kir2006e,
author = "R.M. Kirby and Z. Yosibash and G.E. Karniadakis",
title = "Towards Stable Coupling Methods for High-Order
Discretizations of Fluid-Structure Interaction:
Algorithms and Observations",
journal = "Journal of Computational Physics",
volume = "223",
number = "2",
pages = "489--518",
year = "2006",
}
@Article{SCI:Kir2006f,
author = "R.M. Kirby and S.J. Sherwin",
title = "Aliasing Errors Due to Quadratic Non-Linearities
On Triangular Spectral/hp Element
Discretisations",
journal = "Journal of Engineering Mathematics",
volume = "56",
pages = "273--288",
year = "2006",
url = "http://www.sci.utah.edu/publications/kirby06/Kirby-16.pdf",
}
@Article{SCI:Kir2007a,
author = "R.M. Kirby and Z. Yosibash and G.E. Karniadakis",
title = "Towards Stable Coupling Methods for High-Order
Discretizations of Fluid-Structure Interaction:
Algorithms and Observations",
journal = "Journal of Computational Physics",
volume = "223",
number = "2",
pages = "489--518",
year = "2007",
keywords = "computational mechanics, fluid structure
problems",
url = "http://www.sci.utah.edu/publications/kirby07/Kirby-19.pdf",
}
@Article{SCI:Kir2008a,
author = "R.M. Kirby and C.T. Silva",
title = "The Need For Verifiable Visualization",
journal = "IEEE Computer Graphics and Applications",
volume = "28",
number = "5",
pages = "78--83",
year = "2008",
doi = "10.1109/MCG.2008.103",
url = "http://www.sci.utah.edu/publications/Kir2008a/Kirby_VisViewpoints2008.pdf",
}
@Article{SCI:Kir2011a,
author = "R.M. Kirby and B. Cockburn and S.J. Sherwin",
title = "To {CG} or to {HDG:} A Comparative Study",
journal = "Journal of Scientific Computing",
year = "2011",
note = "published online",
doi = "10.1007/s10915-011-9501-7",
url = "http://www.sci.utah.edu/publications/kirby11/Kirby_JSC2011.pdf",
}
@Article{SCI:Kir2013a,
author = "R.M. Kirby and M.D. Meyer",
title = "Visualization Collaborations: What Works and
Why",
journal = "{IEEE} Computer Graphics and Applications:
Visualization Viewpoints",
volume = "33",
number = "6",
pages = "82--88",
year = "2013",
url = "http://www.sci.utah.edu/publications/Kir2013a/Kirby_VisViewpoints2013.pdf",
}
@Book{SCI:Kir2015c,
author = "R.M. Kirby and M. Berzins and J.S. Hesthaven
(Editors)",
title = "Spectral and High Order Methods for Partial
Differential Equations",
title_url = "http://www.springer.com/us/book/9783319197999",
subtitle = "Selected Papers from the ICOSAHOM'14 Conference,
June 23-27, 2014, Salt Lake City, UT, USA.",
booktitle = "Lecture Notes in Computational Science and
Engineering",
year = "2015",
publisher = "Springer",
}
@InProceedings{SCI:Kla2008a,
author = "S. Klasky and M. Vouk and M. Parashar and A. Khan
and N. Podhorszki and R. Barreto and D. Silver and
S.G. Parker",
title = "Collaborative Visualization Spaces for Petascale
Simulations",
booktitle = "Proceedings of 2008 International Symposium on
Collaborative Technologies and Systems ({CTS}
2008)",
pages = "203--211",
year = "2008",
doi = "10.1109/CTS.2008.4543933",
keywords = "collaborative visualization, large scale
simulation",
}
@InProceedings{SCI:Kle95a,
author = "R.N. Klepfer and C.R. Johnson and R.S. MacLeod",
title = "The Effects of Inhomogeneities and Anisotropies on
Electrocardiographic Fields: A Three-Dimensional
Finite Element Study",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
17th Annual International Conference",
pages = "233--234",
year = "1995",
publisher = "{IEEE} Press",
url = "http://www.sci.utah.edu/publications/klepfer95/embs95_rnk5.ps",
url = "http://www.sci.utah.edu/publications/klepfer95/embs95_rnk5.ps.Z",
}
@Article{SCI:Kle96,
author = "R.N. Klepfer and C.R. Johnson and R.S. MacLeod",
title = "The effects of inhomogeneities and anisotropies on
electrocardiographic fields: A three-dimensional
finite element study",
journal = "{IEEE} Trans. on Biomedical Engineering",
year = "1996",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
finite elements, ncrr, scientific computing",
url = "http://www.sci.utah.edu/publications/klepfer96/ieee_bme96.ps",
url = "http://www.sci.utah.edu/publications/klepfer96/ieee_bme96.ps.Z",
}
@Article{SCI:Kle97a,
author = "R.N. Klepfer and C.R. Johnson and R.S. MacLeod",
title = "The Effects of Inhomogeneities and Anisotropies on
Electrocardiographic Fields: A Three-Dimensional
Finite Element Study",
journal = "{IEEE} Transactions on Biomedical Engineering",
volume = "44",
number = "8",
pages = "706--719",
year = "1997",
month = "August",
url = "http://www.sci.utah.edu/publications/ieee_trans_8-97/FEStudy.ps.gz",
url = "http://www.sci.utah.edu/publications/ieee_trans_8-97/ieee_trans_8-97.html",
}
@InProceedings{SCI:Kne2012a,
author = "J. Knezevic and R.-P. Mundani and E. Rank and A.
Khan and C.R. Johnson",
title = "Extending the SCIRun Problem Solving Environment
to Large-Scale Applications",
booktitle = "Proceedings of Applied Computing 2012",
pages = "171--178",
year = "2012",
organization = "IADIS",
month = "October",
keywords = "scirun",
url = "http://www.sci.utah.edu/publications/knezevic12/Knezevic_Applied_Computing2012.pdf",
}
@InProceedings{SCI:Kni2001a,
author = "J.M. Kniss and G. Kindlmann and C.D. Hansen",
title = "Interactive Volume Rendering Using
Multi-Dimensional Transfer Functions and Direct
Manipulation Widgets",
booktitle = c-VIS2001,
pages = "255--262",
year = "2001",
month = "October",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, scientific visualization",
url = "http://www.sci.utah.edu/publications/jmk01/simian-paper.pdf",
}
@Article{SCI:Kni2001b,
author = "J.M. Kniss and P. McCormick and A. McPherson and
J. Ahrens and J. Painter and A. Keahey and C.D.
Hansen",
title = "Interactive Texture-based Volume Rendering for
Large Datasets",
journal = j-CGA,
volume = "21",
number = "4",
pages = "52--61",
year = "2001",
month = "July/August",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, scientific visualization",
url = "http://www.sci.utah.edu/publications/jmk01/TRex_CGA.pdf",
}
@Article{SCI:Kni2001c,
author = "J.M. Kniss and P. McCormick and A. McPherson and
J. Ahrens and J. Painter and A. Keahey and C.D.
Hansen",
title = "T-Rex, Texture-based Volume Rendering for
Extremely Large Datasets",
journal = j-CGA,
volume = "21",
number = "4",
pages = "52--61",
year = "2001",
keywords = "T-Rex, scalar field methods, volume rendering,
t-rex",
url = "http://www.sci.utah.edu/publications/jmk01/Kniss_TRex2001.pdf",
}
@Article{SCI:Kni2002a,
author = "J.M. Kniss and G. Kindlmann and C.D. Hansen",
title = "Multidimensional Transfer Functions for
Interactive Volume Rendering",
journal = j-TVCG,
volume = "8",
number = "3",
pages = "270--285",
year = "2002",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, scientific visualization",
url = "http://www.sci.utah.edu/publications/jmk02/kniss_tvcg02-small.pdf",
}
@InProceedings{SCI:Kni2002b,
author = "J.M. Kniss and C.D. Hansen and M. Grenier and T.
Robinson",
title = "Volume Rendering Multivariate Data to Visualize
Meteorological Simulations: A Case Study",
booktitle = c-VISSYM2002,
year = "2002",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, atmospherics weather meterology,
scientific visualization",
url = "http://www.sci.utah.edu/publications/jmk02/jmk_vissym02.pdf",
}
@InProceedings{SCI:Kni2002c,
author = "J.M. Kniss and S. Premoze and C.D. Hansen and D.
Ebert",
title = "Interactive Translucent Volume Rendering and
Procedural Modeling",
booktitle = c-VIS2002,
year = "2002",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, scientific visualization",
url = "http://www.sci.utah.edu/publications/jmk02/kniss_volumeshading02.pdf",
}
@Article{SCI:Kni2003a,
author = "J.M. Kniss and S. Premoze and C.D. Hansen and P.
Shirley and A. McPherson",
title = "A Model for Volume Lighting and Modeling",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "9",
number = "2",
year = "2003",
month = "April - June",
url = "http://www.sci.utah.edu/publications/jmk03/kniss_tvcg03_volshade.pdf",
}
@InProceedings{SCI:Kni2003b,
author = "J.M. Kniss and S. Premoze and M. Ikits and A.E.
Lefohn and C.D. Hansen and E. Praun",
title = "Gaussian Transfer Functions for Multi-Field Volume
Visualization",
booktitle = "{IEEE} Visualization 2003",
pages = "497--504",
year = "2003",
month = "October",
location = "Seattle, Wa.",
keywords = "scalar field methods, volume rendering, transfer
functions, simian, scientific visualization,
gaussian",
url = "http://www.sci.utah.edu/publications/jmk03/vis03_kniss.pdf",
}
@TechReport{SCI:Kni2003c,
author = "J.M. Kniss and S. Premoze and M. Ikits and A.E.
Lefohn and C.D. Hansen",
title = "Closed Form Solution to the Volume Rendering
Integral with Gaussian Transfer Functions",
number = "UUCS-03-013",
year = "2003",
institution = "University of Utah School of Computing",
type = "Technical Report",
keywords = "scalar field methods, volume rendering, transfer
functions, Level-set methods, level-set methods",
url = "http://www.sci.utah.edu/publications/jmk03/UUCS-03-013.pdf",
}
@InProceedings{SCI:Kni2004a,
author = "J.M. Kniss and J.P. Schulze and U. W{\"o}ssner and
P. Winkler and U. Lang and C.D. Hansen",
title = "Medical Applications of Multi-field Volume
Rendering and VR Techniques",
booktitle = c-VISSYM2004,
pages = "249--254",
year = "2004",
keywords = "volume rendering, ncrr",
url = "http://www.sci.utah.edu/publications/jmk04/kniss04MAMF.pdf",
}
@InCollection{SCI:Kni2005a,
author = "J.M. Kniss and G. Kindlmann and C.D. Hansen",
title = "Multidimentional Transfer Functions for Volume
Rendering",
booktitle = "The Visualization Handbook",
pages = "189--210",
year = "2005",
editor = "C.D. Hansen and C.R. Johnson",
publisher = "Elsevier",
isbn = "0-12-387582-X",
keywords = "ncrr, volume rendering, transfer functions",
url = "http://www.sci.utah.edu/publications/jmk05/ch09_kniss.pdf",
}
@InProceedings{SCI:Kni2005b,
author = "J.M. Kniss and R. Van Uitert and A.J. Stephens and
G. Li and T. Tasdizen",
title = "Statistically Quantitative Volume Visualization",
booktitle = "{IEEE} Visualization 2005",
year = "2005",
keywords = "volume rendering, transfer functions",
url = "http://www.sci.utah.edu/publications/jmk05/vis05_jmk.pdf",
}
@InCollection{SCI:Kni2005c,
author = "J.M. Kniss and A.E. Lefohn and N. Fout",
title = "Deferred Filtering: Rendering from Difficult Data
Formats",
booktitle = "GPU Gems II: Programming Techniques for
High-Performance Graphics and General-Purpose
Computation",
pages = "669--677",
year = "2005",
editor = "M. Pharr and R. Fernando",
chapter = "41",
publisher = "Addison Wesley",
}
@InProceedings{SCI:Kni2005d,
author = "J.M. Kniss and A.E. Lefohn and R. Strzodka and S.
Sengupta and J.D. Owens",
title = "Octree Textures on Graphics Hardware",
booktitle = "Proceedings of the ACM SIGGRAPH 2005 Conference on
Abstracts and Applications",
year = "2005",
url = "http://www.sci.utah.edu/publications/jmk05/OctreeTexturesonGraphicsHardware.pdf",
}
@Article{SCI:Kni2007a,
author = "J.M. Kniss and W. Hunt and K. Potter and P. Sen",
title = "{IStar:} A Raster Representation for Scalable
Image and Volume Data",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "13",
number = "6",
pages = "1424--1431",
year = "2007",
month = "Nov",
doi = "10.1109/TVCG.2007.70572",
url = "http://www.sci.utah.edu/publications/Kni2007a/Kniss_TVCG2007.pdf",
}
@Article{SCI:Kni2008a,
author = "R.C. Knickmeyer and S. Gouttard and C. Kang and D.
Evans and K. Wilber and K.J. Smith and R.M. Hamer
and W. Lin and G. Gerig and J.H. Gilmore",
title = "A Structural MRI Study of Human Brain Development
from Birth to Two Years",
journal = "The Journal of Neuroscience",
volume = "28",
number = "47",
pages = "12176--12182",
year = "2008",
month = "Nov",
pmid = "19020011",
url = "http://www.sci.utah.edu/publications/knickmeyer08/Knickmeyer_Neurosci2008.pdf",
}
@Article{SCI:Kni2011a,
author = "R.C. Knickmeyer and C. Kang and S. Woolson and
K.J. Smith and R.M. Hamer and W. Lin and G. Gerig
and M. Styner and J.H. Gilmore",
title = "Twin-Singleton Differences in Neonatal Brain
Structure",
journal = "Twin Research and Human Genetics",
volume = "14",
number = "3",
pages = "268--276",
year = "2011",
issn = "1832-4274",
doi = "10.1375/twin.14.3.268",
url = "http://www.sci.utah.edu/publications/knickmeyer11/Knickmeyer_nihms309699.pdf",
}
@TechReport{SCI:Kno2006a,
author = "A. Knoll and I. Wald and S.G. Parker and C.D.
Hansen",
title = "Interactive Isosurface Ray Tracing of Large Octree
Volumes",
number = "UUSCI-2006-026",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "interactive rt distributed interactive ray
tracing, octree, rtcenter",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-026.pdf",
}
@TechReport{SCI:Kno2007a,
author = "A. Knoll and C.D. Hansen and I. Wald",
title = "Coherent Multiresolution Isosurface Ray Tracing",
number = "UUSCI-2007-001",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "vacet",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-001.pdf",
}
@TechReport{SCI:Kno2007b,
author = "A. Knoll and Y. Hijazi and C.D. Hansen and I. Wald
and H. Hagen",
title = "Interactive Ray Tracing of Arbitrary Implicit
Functions",
number = "UUSCI-2007-002",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "interactive rt distributed interactive ray tracing
dirt, vacet",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-002.pdf",
}
@InProceedings{SCI:Kno2007c,
author = "A. Knoll and Y. Hijazi and C.D. Hansen and I. Wald
and H. Hagen",
title = "Interactive Ray Tracing of Arbitrary Implicits
with {SIMD} Interval Arithmetic",
booktitle = "Proceedings of 2nd {IEEE/EG} Symposium on
Interactive Ray Tracing 2007",
pages = "11--18",
year = "2007",
location = "Ulm, Germany",
keywords = "parallel visualization, interactive ray tracing",
url = "http://www.sci.utah.edu/publications/knoll07/rtia-rt07.pdf",
}
@TechReport{SCI:Kno2007d,
author = "A. Knoll and Y. Hijazi and A. Kensler and M.
Schott and C.D. Hansen and H. Hagen",
title = "Fast and Robust Ray Tracing of General Implicits
on the GPU",
number = "UUSCI-2007-014",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ray tracing, GPU",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-014.pdf",
}
@Article{SCI:Kno2009a,
author = "A. Knoll and I. Wald and C.D. Hansen",
title = "Coherent Multiresolution Isosurface Ray Tracing",
journal = "The Visual Computer",
volume = "25",
number = "3",
pages = "209--225",
year = "2009",
url = "http://www.sci.utah.edu/publications/knoll08/cohoctiso.pdf",
}
@Article{SCI:Kno2009b,
author = "A. Knoll and Y. Hijazi and C.D. Hansen and I. Wald
and H. Hagen",
title = "Fast Ray Tracing of Arbitrary Implicit Surfaces
with Interval and Affine Arithmetic",
journal = "Computer Graphics Forum",
volume = "28",
number = "1",
pages = "26--40",
year = "2009",
keywords = "rt, irt, interactive ray-tracing",
url = "http://www.sci.utah.edu/publications/knoll09/CGF-implicits-2009.pdf",
}
@Article{SCI:Kno2009c,
author = "A. Knoll and Y. Hijazi and R. Westerteiger and M.
Schott and C.D. Hansen and H. Hagen",
title = "Volume Ray Casting with Peak Finding and
Differential Sampling",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics, Proceedings of the 2009 {IEEE}
Visualization Conference",
volume = "15",
number = "6",
pages = "1571--1578",
year = "2009",
month = "Sept/Oct",
url = "http://www.sci.utah.edu/publications/knoll09/Knoll_avrc2009.pdf",
}
@Article{SCI:Kno2009d,
author = "A. Knoll and Y. Hijazi and R. Westerteiger and M.
Schott and C.D. Hansen and Hans Hagen",
title = "Volume Ray Casting with Peak Finding and
Differential Sampling",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "15",
number = "6",
pages = "1571-1578",
year = "2009",
url = "http://www.sci.utah.edu/publications/knoll09/Knoll_TVCG2009.pdf",
}
@InProceedings{SCI:Kno2011a,
author = "A. Knoll and S. Thelen and I. Wald and C.D. Hansen
and H. Hagen and M.E. Papka",
title = "Full-Resolution Interactive {CPU} Volume Rendering
with Coherent {BVH} Traversal",
booktitle = "Proceedings of {IEEE} Pacific Visualization
2011",
pages = "3--10",
year = "2011",
url = "http://www.sci.utah.edu/publications/knoll11/PacificVis2011.pdf",
}
@InProceedings{SCI:Kno2013a,
author = "A. Knoll and I. Wald and P. Navratil and M. E
Papka and and K. P Gaither",
title = "Ray Tracing and Volume Rendering Large Molecular
Data on Multi-core and Many-core Architectures.",
booktitle = "Proc. 8th International Workshop on Ultrascale
Visualization at SC13 (Ultravis), 2013",
year = "2013",
url = "http://www.sci.utah.edu/publications/Kno2013a/bnsview.pdf",
}
@Article{SCI:Kno2014a,
author = "A. Knoll and I. Wald and P. Navratil and A. Bowen
and K. Reda and M. E. Papka and K. Gaither",
title = "RBF Volume Ray Casting on Multicore and Manycore
CPUs",
journal = "Computer Graphics Forum",
volume = "33",
number = "3",
pages = "71--80",
year = "2014",
editor = "H. Carr and P. Rheingans and H. Schumann",
publisher = "Wiley-Blackwell",
month = "June",
doi = "10.1111/cgf.12363",
url = "http://www.sci.utah.edu/publications/Kno2014a/bnsview-sph.pdf",
}
@Article{SCI:Knu2018a,
author = "K Knudson and B Wang",
title = "Discrete Stratified Morse Theory: A User's
Guide",
journal = "CoRR",
year = "2018",
url = "http://www.sci.utah.edu/publications/Knu2018a/1801.03183.pdf",
}
@Article{SCI:Kol2012a,
author = "S. Kole and N.P. Singh and R. King",
title = "Whole Brain Fractal Analysis of the Cerebral
Cortex across the Adult Lifespan",
journal = "Neurology",
volume = "78",
pages = "P03.104",
year = "2012",
series = "Meeting Abstracts I",
}
@Article{SCI:Koo2008a,
author = "D. Koop and C.E. Scheidegger and S.P. Callahan and
J. Freire and C.T. Silva",
title = "VisComplete: Automating Suggestions for
Visualization Systems",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics (Proceedings of {IEEE} Visualization
2008)",
volume = "14",
number = "6",
pages = "1691--1698",
year = "2008",
url = "http://www.sci.utah.edu/publications/koop08/vis2008a.pdf",
}
@Article{SCI:Kop2011a,
author = "B.H. Kopell and J. Halverson and C.R. Butson and
M. Dickinson and J. Bobholz and H. Harsch and C.
Rainey and D. Kondziolka and R. Howland and E.
Eskandar and K.C. Evans and D.D. Dougherty",
title = "Epidural cortical stimulation of the left
dorsolateral prefrontal cortex for refractory major
depressive disorder",
journal = "Neurosurgery",
volume = "69",
number = "5",
pages = "1015--1029",
year = "2011",
month = "November",
issn = "1524-4040",
doi = "10.1227/NEU.0b013e318229cfcd",
url = "http://www.sci.utah.edu/publications/Kop2011a/Kopell_Neurosurgery2011.pdf",
}
@InProceedings{SCI:Kop2012a,
author = "D. Kopta and T. Ize and J. Spjut and E. Brunvand
and A. Davis and A. Kensler",
title = "Fast, Effective {BVH} Updates for Animated
Scenes",
booktitle = "Proceedings of the Symposium on Interactive {3D}
Graphics and Games ({I3D} '12)",
pages = "197--204",
year = "2012",
doi = "10.1145/2159616.2159649",
url = "http://www.sci.utah.edu/publications/Kop2012a/Kopta_I3D2012.pdf",
}
@TechReport{SCI:Kos2006a,
author = "P.A. Koshevoy and T. Tasdizen and R.T. Whitaker",
title = "Implementation of an Automatic Slice-to-Slice
Registration Tool",
number = "UUSCI-2006-018",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing, warping,
deformable image registration, TEM, SIFT, crcns,
tem, sift",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-018.pdf",
}
@TechReport{SCI:Kos2006b,
author = "P.A. Koshevoy and T. Tasdizen and R.T. Whitaker",
title = "Implementation of an Automatic Image Registration
Tool",
number = "UUSCI-2006-020",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing, warping,
deformable image registration, tem, sift, crcns",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-020.pdf",
}
@InProceedings{SCI:Kos2006c,
author = "P. Koshevoy and T. Tasdizen and R.T. Whitaker and
B. Jones and R. Marc",
title = "Assembly of Large Three-Dimensional Volumes from
Serial-Section Transmission Electron Microscopy",
booktitle = "Proceedings of 2006 MICCAI Workshop on Microscopic
Image Analysis with Applications in Biology",
year = "2006",
month = "October",
keywords = "ip image processing signal processing, warping,
deformable image registration, crcns",
url = "http://www.sci.utah.edu/publications/koshevoy06/paper9tasdizen.pdf",
}
@TechReport{SCI:Kos2007a,
author = "P.A. Koshevoy and T. Tasdizen and R.T. Whitaker",
title = "Automatic Assembly of TEM Mosaics and Mosaic
Stacks Using Phase Correlation",
number = "UUSCI-2007-004",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing, warping,
deformable image registration, ip gp image
processing goemetry processing, crcns",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-004.pdf",
}
@InProceedings{SCI:Kre1997a,
author = "M. van Kreveld and R. van Oostrum and C. Bajaj and
V. Pascucci and D.R. Schikore",
title = "Contour Trees and Small Seed Sets for Isosurface
Traversal",
booktitle = "Proceedings of the 13th International Annual
Symposium on Computational Geometry ({SCG}-97)",
pages = "212--220",
year = "1997",
publisher = "ACM Press",
address = "New York",
month = "June",
isbn = "0-89791-878-9",
}
@Article{SCI:Kri2004a,
author = "L. Krishnan and J.A. Weiss and M.D. Wessman MD and
J.B. Hoying",
title = "Design and Application of a Test System for
Viscoelastic Characterization of Collagen Gels",
journal = j-TE,
volume = "10",
number = "(1-2)",
pages = "241--252",
year = "2004",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational mechanics, computational
biomechanics, angiogenesis",
url = "http://www.sci.utah.edu/publications/krishnan04/krishnan_tissue_eng_2004.pdf",
}
@Article{SCI:Kri2008a,
author = "L. Krishnan and C.J. Underwood and S.A. Maas and
B.J. Ellis and T.C. Kode and J.B. Hoying and J.A.
Weiss",
title = "Effect of Mechanical Boundary Conditions on
Orientation of Angiogenic Microvessels",
journal = "Cardiovascular Research",
volume = "78",
number = "2",
pages = "324--332",
year = "2008",
keywords = "mrl, angiogenesis, bioengineering",
url = "http://www.sci.utah.edu/publications/krishnan08/krishnan_cardio_res_2008.pdf",
}
@Article{SCI:Kri2008b,
author = "L. Krishnan and J.B. Hoying and H. Ngyuen and H.
Song and J.A. Weiss",
title = "Interaction of Angiogenic Microvessels with the
Extracellular Matrix",
journal = "American Journal of Physiology: Heart and
Circulation Physiology",
volume = "293",
number = "6",
pages = "H3650--H36588",
year = "2007",
}
@Article{SCI:Kro97a,
author = "M. Krogh and J. Painter and C.D. Hansen",
title = "Parallel Sphere Rendering",
journal = "Parallel Computing",
volume = "23",
number = "7",
pages = "961--974",
year = "1997",
}
@Article{SCI:Kru2008a,
author = "J. Kr{\"u}ger",
title = "A GPU Framework for Interactive Simulation and
Rendering of Fluid Effects",
journal = "IT - Information Technology",
volume = "4",
pages = "265--268",
year = "2008",
keywords = "fluid dynamics, cfd",
url = "http://www.sci.utah.edu/publications/Kru2008a/GPU_framework.pdf",
}
@InProceedings{SCI:Kru2008b,
author = "J. Kr{\"u}ger and K. Potter and R.S. MacLeod and C.R.
Johnson",
title = "Unified Volume Format: A General System For
Efficient Handling Of Large Volumetric Datasets",
booktitle = "Proceedings of IADIS Computer Graphics and
Visualization 2008 (CGV 2008)",
pages = "19--26",
year = "2008",
pmid = "20953270",
url = "http://www.sci.utah.edu/publications/Kru2008b/UnifiedVolumeFormat.pdf",
}
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author = "J. Kr{\"u}ger and T. Fogal",
title = "Focus and Context - Visualization without the
Complexity",
booktitle = "Proceedings of the World Congress on Medical
Physics and Biomedical Engineering, September 7 -
12, 2009, Munich, Germany",
volume = "25/13",
pages = "44--48",
year = "2009",
series = "IFMBE Proceedings",
publisher = "Springer Berlin Heidelberg",
url = "http://www.sci.utah.edu/publications/Kru2009a/Fogal_IFMBE2009a.pdf",
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author = "J. Kr{\"u}ger",
title = "A New Sampling Scheme for Slice Based Volume
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booktitle = "Proceedings of {IEEE/EG} International Symposium
on Volume Graphics (2010)",
pages = "1--4",
year = "2010",
doi = "10.2312/VG/VG10/001-004",
url = "http://www.sci.utah.edu/publications/Kru2010a/Krueger_vg2010.pdf",
}
@Article{SCI:Kub2008a,
author = "M. Kubicki and M. Styner and S. Bouix and G. Gerig
and D. Markant and K. Smith and R. Kikinis and R.W.
McCarley and M.E. Shenton",
title = "Reduced Interhemispheric Connectivity in
Schizophrenia- Tractography Based Segmentation of
the Corpus Callosum",
journal = "Schizophrenia Research",
volume = "106",
number = "2-3",
pages = "125--131",
year = "2008",
month = "December",
}
@Article{SCI:Kuh2018b,
author = "L. Kuhnel and T. Fletcher and S. Joshi and S.
Sommer",
title = "Latent Space Non-Linear Statistics",
journal = "CoRR",
year = "2018",
url = "http://www.sci.utah.edu/publications/Kuh2018b/1805.07632.pdf",
}
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author = "G. Kumfert and D.E. Bernholdt and T.G.W. Epperly
and J.A. Kohl and L.C. McInnes and S.G. Parker and
J. Ray",
title = "How the Common Component Architecture Advances
Computational Science",
journal = "J. Phys.: Conf. Ser.",
volume = "46",
pages = "479--493",
year = "2006",
keywords = "ncrr, Common Component Architecture, CCA",
url = "http://www.sci.utah.edu/publications/kumfert06/jpconf6_46_066.pdf",
}
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author = "S. Kumar and V. Vishwanath and P. Carns and V.
Pascucci and R. Latham and T. Peterka and M. Papka
and R. Ross",
title = "Towards Efficient Access of Multi-dimensional,
Multi-resolution Scientific Data",
booktitle = "Proceedings of the 5th Petascale Data Storage
Workshop, Supercomputing 2010",
pages = "(in press)",
year = "2010",
url = "http://www.sci.utah.edu/publications/kumar10/pdsw10-paper21.pdf",
}
@InProceedings{SCI:Kum2011a,
author = "S. Kumar and V. Vishwanath and P. Carns and B.
Summa and G. Scorzelli and V. Pascucci and R. Ross
and J. Chen and H. Kolla and R. Grout",
title = "{PIDX}: Efficient Parallel {I/O} for
Multi-resolution Multi-dimensional Scientific
Datasets",
booktitle = "Proceedings of The {IEEE} International Conference
on Cluster Computing",
pages = "103--111",
year = "2011",
month = "September",
url = "http://www.sci.utah.edu/publications/kumar11/Kumar_ICCC2011.pdf",
}
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author = "S. Kumar and V. Vishwanath and P. Carns and J.A.
Levine and R. Latham and G. Scorzelli and H. Kolla
and R. Grout and R. Ross and M.E. Papka and J. Chen
and V. Pascucci",
title = "Efficient data restructuring and aggregation for
{I/O} acceleration in {PIDX}",
booktitle = "Proceedings of the International Conference on
High Performance Computing, Networking, Storage and
Analysis",
pages = "50:1--50:11",
year = "2012",
publisher = "IEEE Computer Society Press",
isbn = "978-1-4673-0804-5",
url = "http://www.sci.utah.edu/publications/kumar12/Kumar_PIDX_SC2012.pdf",
}
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author = "S. Kumar and A. Saha and V. Vishwanath and P.
Carns and J.A. Schmidt and G. Scorzelli and H.
Kolla and R. Grout and R. Latham and R. Ross and
M.E. Papka and J. Chen and V. Pascucci",
title = "Characterization and modeling of {PIDX} parallel
{I/O} for performance optimization",
booktitle = "Proceedings of {SC13}: International Conference
for High Performance Computing, Networking, Storage
and Analysis",
pages = "67",
year = "2013",
keywords = "I/O, Network Characterization, Performance
Modeling",
url = "http://www.sci.utah.edu/publications/Kum2013a/Kumar_SC2013.pdf",
}
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author = "S. Kumar and C. Christensen and P.-T. Bremer and
E. Brugger and V. Pascucci and J. Schmidt and M.
Berzins and H. Kolla and J. Chen and V. Vishwanath
and P. Carns and R. Grout",
title = "Fast Multi-Resolution Reads of Massive Simulation
Datasets",
booktitle = "Proceedings of the International Supercomputing
Conference {ISC'14}",
year = "2014",
month = "June",
location = "Leipzig, Germany",
url = "http://www.sci.utah.edu/publications/Kum2014a/KumarISC2014.pdf",
}
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author = "S. Kumar and J. Edwards and P.-T. Bremer and A.
Knoll and C. Christensen and V. Vishwanath and P.
Carns and J.A. Schmidt and V. Pascucci",
title = "Efficient I/O and storage of adaptive-resolution
data",
booktitle = "Proceedings of the International Conference for
High Performance Computing, Networking, Storage and
Analysis",
pages = "413--423",
year = "2014",
publisher = "IEEE Press",
doi = "10.1109/SC.2014.39",
url = "http://www.sci.utah.edu/publications/Kum2014b/Kumar_EfficientIO2014.pdf",
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author = "S. Kumar and D. Hoang and S. Petruzza and J.
Edwards and V. Pascucci",
title = "Reducing Network Congestion and Synchronization
Overhead During Aggregation of Hierarchical Data",
booktitle = "2017 IEEE 24th International Conference on High
Performance Computing (HiPC)",
pages = "223-232",
year = "2017",
month = "Dec",
doi = "10.1109/HiPC.2017.00034",
url = "http://www.sci.utah.edu/publications/Kum2017a/HiPC_2017_IEEE.pdf",
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author = "S. Kumar and D. Hoang and S. Petruzza and J.
Edwards and V. Pascucci",
title = "Reducing network congestion and synchronization
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title_url =
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booktitle = "2017 IEEE 24th International Conference on High
Performance Computing (HiPC)",
year = "2017",
publisher = "IEEE",
month = "Dec",
doi = "10.1109/hipc.2017.00034",
url = "http://www.sci.utah.edu/publications/Kum2017b/08287753.pdf",
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author = "S. Kumar and A. Humphrey and W. Usher and S.
Petruzza and B. Peterson and J. A. Schmidt and D.
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and V. Pascucci and and M. Berzins",
title = "Scalable Data Management of the Uintah Simulation
Framework for Next-Generation Engineering Problems
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booktitle = "Supercomputing Frontiers",
pages = "219--240",
year = "2018",
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doi = "10.1007/978-3-319-69953-0_13",
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author = "B. Kundu and A. A. Brock and D. J. Englot and C.
R. Butson and J. D. Rolston",
title = "Deep brain stimulation for the treatment of
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number = "2",
pages = "E14",
year = "2018",
publisher = "Journal of Neurosurgery Publishing Group
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month = "Aug",
doi = "10.3171/2018.5.focus18168",
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title = "A systematic exploration of parameters affecting
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pages = "1232-1244",
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title = "Left atrial strain and strain rate in patients
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volume = "3",
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pages = "231--239",
year = "2010",
pmid = "20133512",
keywords = "cvrti",
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title = "Echocardiographic left atrial reverse remodeling
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year = "2010",
doi = "10.1016/j.ahj.2010.07.003",
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booktitle = "Proceedings from the {EUROTRAC-2} Symposium
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year = "2002",
editor = "Garmisch-Partenkirchenand P.M. Midgley and M.
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keywords = "atmospherics, ozone, environment, pollution",
url = "http://www.sci.utah.edu/publications/lagzi02/Lagzi_Eurotrac2_2002.pdf",
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title = "Modeling Photochemical Air Pollution in Hungary
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booktitle = "Air Pollution modeling and Simulation - Proc.2nd
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pages = "264--273",
year = "2002",
month = "april",
isbn = "3540425152, 9783540425151",
keywords = "atmospherics, pollution, environment, adaptive
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High Performance Computing, Networking, Storage and
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pages = "1020--1031",
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publisher = "IEEE Press",
address = "Piscataway, NJ, USA",
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doi = "10.1109/SC.2014.88",
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author = "A.E. Lefohn and R.T. Whitaker",
title = "A {GPU}-Based, Three-Dimensional Level Set Solver
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number = "UUCS-02-017",
year = "2002",
institution = "University of Utah School of Computing",
type = "Technical Report",
keywords = "ip image processing signal processing,
segmentation, imaging, level set, level-set
methods, level-sets",
url = "http://www.sci.utah.edu/publications/lefohn02/UUCS-02-017.pdf",
}
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author = "A.E. Lefohn and J.M. Kniss and C.D. Hansen and
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title = "Interactive Deformation and Visualization of Level
Set Surfaces Using Graphics Hardware",
booktitle = "{IEEE} Visualization 2003",
pages = "75--82",
year = "2003",
month = "October",
location = "Seattle, Wa.",
keywords = "ip image processing signal processing,
segmentation, imaging, level-set methods,
level-sets",
url = "http://www.sci.utah.edu/publications/lefohn03/visLevelSetPaper.pdf",
}
@TechReport{SCI:Lef2003b,
author = "A.E. Lefohn and J. Cates and R.T. Whitaker",
title = "Interactive, {GPU}-Based Level Sets for 3D Brain
Tumor Segmentation",
number = "UUCS-03-004",
year = "2003",
institution = "University of Utah School of Computing",
type = "Technical Report",
keywords = "ip image processing signal processing,
segmentation, imaging, level-set methods,
level-sets",
url = "http://www.sci.utah.edu/publications/lefohn03/UUCS-03-004.pdf",
}
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author = "A.E. Lefohn and R.T. Caruso and E. Reinhard and B.
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year = "2003",
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url = "http://www.sci.utah.edu/publications/lefohn03/irisSynthesis.pdf",
}
@TechReport{SCI:Lef2003e,
author = "A.E. Lefohn and J.M. Kniss and C.D. Hansen and
R.T. Whitaker",
title = "Interactive Deformation and Visualization of Level
Set Surfaces Using Graphics Hardware",
number = "UUCS-03-005",
year = "2003",
institution = "University of Utah School of Computing",
type = "Technical Report",
keywords = "ip image processing signal processing,
segmentation, imaging, level-set methods,
level-sets",
url = "http://www.sci.utah.edu/publications/lefohn03/UUCS-03-005.pdf",
}
@Article{SCI:Lef2003f,
author = "A.E. Lefohn and J. Cates and R.T. Whitaker",
title = "Interactive, {GPU}-Based Level Sets for 3D
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journal = "Medical Image Computing and Computer Assisted
Intervention ({MICCAI})",
pages = "564--572",
year = "2003",
keywords = "ip image processing signal processing,
segmentation, insight itk, imaging, level-set
methods, level-sets",
url = "http://www.sci.utah.edu/publications/lefohn03/gpuTumorSeg.pdf",
}
@Article{SCI:Lef2004a,
author = "A.E. Lefohn and J.M. Kniss and C.D. Hansen and
R.T. Whitaker",
title = "A Streaming Narrow-Band Algorithm: Interactive
Deformation and Visualization of Level Sets",
journal = j-TVCG,
pages = "422--433",
year = "2004",
keywords = "scalar field methods, volume rendering, ip image
processing signal processing, segmentation, surface
processing, Imaging, modeling, GPU, level-set
methods, imaging, deformable models, gpu, level-set
methods level-sets, streaming computation, virtual
memory, ncrr",
url = "http://www.sci.utah.edu/publications/lefohn04/lefohn_tvcg03.pdf",
}
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author = "A.E. Lefohn and J.M. Kniss and J. Owens",
title = "Implementing Efficient Parallel Data Structures on
GPUs",
booktitle = "GPU Gems II: Programming Techniques for
High-Performance Graphics and General-Purpose
Computation",
pages = "521--545",
year = "2005",
editor = "M. Pharr and R. Fernando",
chapter = "33",
publisher = "Addison Wesley",
}
@InProceedings{SCI:Lef2005b,
author = "A.E. Lefohn and S. Sengupta and J.M. Kniss and R.
Strzodka and J.D. Owens",
title = "Dynamic Adaptive Shadow Maps on Graphics
Hardware",
booktitle = "Proceedings of the ACM SIGGRAPH 2005 Conference on
Abstracts and Applications",
year = "2005",
url = "http://www.sci.utah.edu/publications/lefohn05/DynamicAdaptiveShadowMapsonGraphicsHardware.pdf",
}
@Article{SCI:Lef2006a,
author = "A. Lefohn and J.M. Kniss and R. Strzodka and S.
Sengupta and J. Owens",
title = "Glift: Generic, Efficient Random-Access GPU Data
Structures",
journal = j-ACM-CG,
volume = "25",
number = "1",
pages = "1--37",
year = "2006",
month = "January",
keywords = ", adaptive shadow maps, data structures, graphics
hardware, GPU, GPGPU, multiresolution, octree
textures, parallel computation",
url = "http://www.sci.utah.edu/publications/lefohn06/tog-05-0077.pdf",
}
@Article{SCI:Leg2001a,
author = "I. Lagzi and A.S. Tomlin and T.Turanyi and
L.Haszpra and M.Berzins",
title = "The Simulation of Photochemical Smog Episodes in
Hungary and Central Europe Using Adaptive Gridding
Models",
journal = "Lecture Notes in Computer Science (LCNS),
Computational Science - ICCS 2001",
volume = "2074/2001",
pages = "67--76",
year = "2001",
publisher = "Springer Berlin / Heidelberg",
isbn = "978-3-540-42233-4",
keywords = "atmospherics, pollution, environment, adaptive
grid modeling",
url = "http://www.sci.utah.edu/publications/lagzi01/lagzi_lncs_2001.pdf",
}
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author = "Z. Lei and T. Tasdizen and D.B. Cooper",
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booktitle = "Sixth International Conference on Computer
Vision",
year = "1997",
publisher = "Narosa Publishing House",
doi = "10.1109/iccv.1998.710813",
url = "http://www.sci.utah.edu/publications/Lei1997a/Lei_ICCV97.pdf",
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author = "Z. Leng and J.R. Korenberg and B. Roysam and T.
Tasdizen",
title = "A rapid {2-D} centerline extraction method based
on tensor voting",
booktitle = "2011 {IEEE} International Symposium on Biomedical
Imaging: From Nano to Macro",
pages = "1000--1003",
year = "2011",
doi = "10.1109/ISBI.2011.5872570",
url = "http://www.sci.utah.edu/publications/leng11/Leng_ISBI2011.pdf",
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author = "C.H. Leung and M. Berzins",
title = "A Computational Model for Organism Growth based on
Surface Mesh Generation",
journal = "Journal of Computational Physics",
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pages = "75--99",
year = "2003",
url = "http://www.sci.utah.edu/publications/leung03/JCPmgen.pdf",
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K.R. Smith and A.M. Hammoud and J.M. Henderson and
S. Joshi and K.E. Mark and C.D. Sturm and L.L.
McDurmont Jr and R. Bucholz",
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pages = "231--237",
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author = "J.A. Levine and D.J. Swenson and Z. Fu and R.S.
MacLeod and R.T. Whitaker",
title = "A Comparison of Delaunay Based Meshing Algorithms
for Electrophysiological Cardiac Simulations",
journal = "Virtual Physiological Human",
pages = "181--183",
year = "2010",
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}
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author = "J.A. Levine and S. Jadhav and H. Bhatia and V.
Pascucci and P.-T. Bremer",
title = "A Quantized Boundary Representation of {2D}
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journal = "Computer Graphics Forum",
volume = "31",
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pages = "945--954",
year = "2012",
month = "June",
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author = "S. Lew and C. Wolters and K. Lee and S. Makeig and
G. Worrell and R.S. MacLeod",
title = "Epileptogenic Source Localization For Open Skull
Head Model of Epilepsy By Independent Component
Analysis And Inverse Dipole Fit Method",
booktitle = "1st Annual Mountain West Biomedical Engineering
Conference",
year = "2005",
keywords = "source localization, EEG, ICA, dipole fit, ncrr,
forward problems inverse problems forward
simulation inverse solutions, inverse eeg, eeg,
ica",
}
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author = "S. Lew and C. Wolters and A. Anwander and S.
Makeig and R.S. MacLeod",
title = "Low Resolution Conductivity Estimation to Improve
Source Localization",
booktitle = "New Frontiers in Biomagnetism. Proceedings of the
15th International Conference on Biomagnetism,
Vancouver, BC, Canada, August 21-25, 2006.",
volume = "1300",
pages = "149--152",
year = "2007",
series = "International Congress Series",
month = "June",
keywords = "forward problems inverse problems forward
simulation inverse solutions, source localization,
ncrr",
url = "http://www.sci.utah.edu/publications/lew07/Lew_ICB2006.pdf",
}
@Article{SCI:Lew2008a,
author = "S. Lew and C.H. Wolters and A. Anwander and S.
Makeig and R.S. Macleod",
title = "Improved EEG Source Analysis Using Low-Resolution
Conductivity Estimation in a Four-Compartment
Finite Element Head Model",
journal = "Human Brain Mapping",
volume = "31",
year = "2008",
month = "December",
url = "http://www.sci.utah.edu/publications/lew08/LewEtAl_HumanBrainMapping_2009.pdf",
}
@Article{SCI:Lew2009a,
author = "S. Lew and C.H. Wolters and T. Dierkes and C.
R{\"o}er and R.S. MacLeod",
title = "Accuracy and run-time comparison for different
potential approaches and iterative solvers in
finite element method based EEG source analysis",
journal = "Applied Numerical Mathematics",
volume = "59",
pages = "1970--1988",
year = "2009",
url = "http://www.sci.utah.edu/publications/lew09/Lew_ANM2009.pdf",
}
@Article{SCI:Lew2009b,
author = "S. Lew and C.H. Wolters and A. Anwander and S.
Makeig and R.S. MacLeod",
title = "Improved EEG Source Analysis Using Low-Resolution
Conductivity Estimation in a Four-Compartment
Finite Element Head Model",
journal = "Human Brain Mapping",
volume = "30",
pages = "2862--2878",
year = "2009",
keywords = "EEG, source analysis, realistic four-compartment
head modeling, in vivo conductivity estimation,
brain and skull conductivity, cerebrospinal fluid,
simulated annealing, finite element method,
somatosensory-evoked potentials, T1- and
PD-weighted MRI",
url = "http://www.sci.utah.edu/publications/lew09/Lew_HBM2009.pdf",
}
@Article{SCI:Lew2014a,
author = "J.D. Lewis and A.C. Evans and J.R. Pruett and K.
Botteron and L. Zwaigenbaum and A. Estes and G.
Gerig and L. Collins and P. Kostopoulos and R.
McKinstry and S. Dager and S. Paterson and R.
Schultz and M. Styner and H. Hazlett and J. Piven
and IBIS network",
title = "Network inefficiencies in autism spectrum disorder
at 24 months",
journal = "Translational Psychiatry",
volume = "4",
number = "5",
pages = "e388",
year = "2014",
publisher = "Nature Publishing Group",
month = "May",
doi = "10.1038/tp.2014.24",
keywords = "autism, infant siblings, connectivity, network
analysis, efficiency",
url = "http://www.sci.utah.edu/publications/Lew2014a/Lewis_TranslPsy2014.pdf",
}
@InProceedings{SCI:Lex2010a,
author = "A. Lex and M. Streit and E. Kruijff and D.
Schmalstieg",
title = "Caleydo: Design and Evaluation of a Visual
Analysis Framework for Gene Expression Data in its
Biological Context",
booktitle = "Proceeding of the IEEE Symposium on Pacific
Visualization (PacificVis '10)",
pages = "57--64",
year = "2010",
isbn = "424466856",
doi = "10.1109/PACIFICVIS.2010.5429609",
url = "http://www.sci.utah.edu/publications/Lex2010a/05429609.pdf",
}
@Article{SCI:Lex2010b,
author = "A. Lex and M. Streit and C. Partl and K. Kashofer
and D. Schmalstieg",
title = "Comparative Analysis of Multidimensional,
Quantitative Data",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "16",
number = "6",
pages = "1027--1035",
year = "2010",
url = "http://www.sci.utah.edu/publications/Lex2010b/2010_infovis_matchmaker.pdf",
}
@Article{SCI:Lex2011a,
author = "A. Lex and H. Schulz and M. Streit and C. Partl
and D. Schmalstieg",
title = "VisBricks: Multiform Visualization of Large,
Inhomogeneous Data",
journal = "IEEE Transactions on Visualization and Computer
Graphics (InfoVis '11)",
volume = "17",
number = "12",
year = "2011",
url = "http://www.sci.utah.edu/publications/Lex2011a/2011_infovis_visbricks.pdf",
}
@Article{SCI:Lex2012a,
author = "A. Lex and M. Streit and H. Schulz and C. Partl
and D. Schmalstieg and P.. Park and N.
Gehlenborg",
title = "StratomeX: Visual Analysis of Large-Scale
Heterogeneous Genomics Data for Cancer Subtype
Characterization ",
journal = "Computer Graphics Forum (EuroVis '12)",
volume = "31",
number = "3",
pages = "1175--1184",
year = "2012",
issn = "0167-7055",
doi = "10.1111/j.1467-8659.2012.03110.x",
url = "http://www.sci.utah.edu/publications/Lex2012a/2012_eurovis_stratomex.pdf",
}
@Article{SCI:Lex2013a,
author = "A. Lex and C. Partl and D. Kalkofen and M. Streit
and A. Wasserman and S. Gratzl and D. Schmalstieg
and H. Pfister",
title = "Entourage: Visualizing Relationships between
Biological Pathways using Contextual Subsets",
journal = "IEEE Transactions on Visualization and Computer
Graphics (InfoVis '13)",
volume = "19",
number = "12",
pages = "2536--2545",
year = "2013",
issn = "1077-2626",
doi = "10.1109/TVCG.2013.154",
url = "http://www.sci.utah.edu/publications/Lex2013a/2013_infovis_entourage.pdf",
}
@Article{SCI:Lex2014a,
author = "A. Lex and N. Gehlenborg and H. Strobelt and R.
Vuillemot and and H. Pfister",
title = "UpSet: Visualization of Intersecting Sets",
journal = "IEEE Transactions on Visualization and Computer
Graphics (InfoVis '14)",
volume = "20",
number = "12",
pages = "1983--1992",
year = "2014",
issn = "1077-2626",
url = "http://www.sci.utah.edu/publications/Lex2014a/2014_infovis_upset.pdf",
}
@InProceedings{SCI:Li2003a,
author = "G. Li and U.D. Bordoloi and H. Shen",
title = "Chameleon: An Interactive Texture-based Rendering
Framework for Visualizing Three-dimensional Vector
Fields",
booktitle = "Proceedings of {IEEE} Visualization 2003",
pages = "32",
year = "2003",
month = "Oct",
keywords = "scalar field methods, vector field methods, tensor
field methods, atmospherics weather meterology,
scientific visualization",
url = "http://www.sci.utah.edu/publications/li03/chameleon2003.pdf",
}
@InProceedings{SCI:Li2006a,
author = "G. Li and X. Tricoche and C.D. Hansen",
title = "GPUFLIC: Interactive and Accurate Dense
Visualization of Unsteady Flows",
booktitle = "Proceedings of Euro Vis 2006",
pages = "29--34",
year = "2006",
url = "http://www.sci.utah.edu/publications/li06/eurovis06.pdf",
}
@InProceedings{SCI:Li2006b,
author = "G. Li and X. Tricoche and C.D. Hansen",
title = "Survey of Texture-based Techniques in Flow
Visualization",
booktitle = "VIsualization of Large and Unstructured Data Sets
- Applications in Geospatial Planning, Modeling,
and Engineering",
pages = "11--21",
year = "2006",
series = "Lecture Notes in Informatics - Visualization of
Large and Unstructured Data Sets. First workshop of
the DFG's International Research Training Group",
edition = "GI-Edition",
month = "June",
location = "Dagstuhl, Germany",
}
@TechReport{SCI:Li2007a,
author = "G.-S. Li and X. Tricoche and C.D. Hansen",
title = "Visualizing Unsteady Flows on Surfaces Using
Spherical Parameterization",
number = "UUSCI-2007-013",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "vector field methods, cardiac heart, bioelectric
fields",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-013.pdf",
}
@Article{SCI:Li2008a,
author = "G.-S. Li and X. Tricoche and D. Weiskopf and C.D.
Hansen",
title = "Flow Charts: Visualization of Vector Fields on
Arbitrary Surfaces",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "14",
number = "5",
pages = "1--14",
year = "2008",
month = "September/October",
url = "http://www.sci.utah.edu/publications/li08/flowcharts.pdf",
}
@Article{SCI:Li2008b,
author = "G.-S. Li and X. Tricoche and C.D. Hansen",
title = "Physically-based Dye Advection for Flow
Visualization",
journal = "Computer Graphics Forum",
volume = "27",
number = "3",
pages = "727--734",
year = "2008",
editor = "A. Vilanova and A. Telea and G. Scheuermann and T.
Moeller",
publisher = "Wiley-Blackwell",
month = "May",
doi = "10.1111/j.1467-8659.2008.01201.x",
url = "http://www.sci.utah.edu/publications/Li2008b/dyeadvection.pdf",
}
@Article{SCI:Li2008c,
author = "J. Li and D. Xiu",
title = "On Numerical Properties of the Ensemble Kalman
Filter for Data Assimilation",
journal = "Computer Methods in Applied Mechanics and
Engineering",
volume = "197",
number = "43--44",
pages = "3574--3583",
year = "2008",
doi = "10.1016/j.cma.2008.03.022",
keywords = "Data assimilation, Uncertainty quantification,
Ensemble Kalman filter",
url = "http://www.sci.utah.edu/publications/li08/Li_CMAME2008.pdf",
}
@Article{SCI:Li2009a,
author = "J. Li and D. Xiu",
title = "A Generalized Polynomial Chaos Based Ensemble
Kalman Filter with High Accuracy",
journal = "Journal of Computational Physics",
volume = "228",
number = "15",
pages = "5454--5469",
year = "2009",
doi = "10.1016/j.jcp.2009.04.029",
keywords = "Kalman filter, Data assimilation, Polynomial
chaos, Uncertainty quantification",
url = "http://www.sci.utah.edu/publications/li09/Li_JCP2009.pdf",
}
@Article{SCI:Li2010b,
author = "J. Li and D. Xiu",
title = "Evaluation of Failure Probability via Surrogate
Models",
journal = "Journal of Computational Physics",
volume = "229",
number = "23",
pages = "8966--8980",
year = "2010",
doi = "10.1016/j.jcp.2010.08.022",
keywords = "Failure probability, Sampling, Polynomial chaos,
Stochastic computation",
url = "http://www.sci.utah.edu/publications/li10/Li_JCP2010.pdf",
}
@Article{SCI:Li2011a,
author = "G. Li and R. Palmer and M. DeLisi and G.
Gopalakrishnan and R.M. Kirby",
title = "Formal Specification of {MPI} 2.0: Case Study in
Specifying a Practical Concurrent Programming
{API}",
journal = "Science of Computer Programming",
volume = "76",
pages = "65--81",
year = "2011",
doi = "10.1016/j.scico.2010.03.007",
url = "http://www.sci.utah.edu/publications/li11/Li_SCP2011.pdf",
}
@Article{SCI:Li2011b,
author = "J. Li and J. Li and D. Xiu",
title = "An Efficient Surrogate-based Method for Computing
Rare Failure Probability",
journal = "Journal of Computational Physics",
volume = "230",
number = "24",
pages = "8683--8697",
year = "2011",
doi = "10.1016/j.jcp.2011.08.008",
keywords = "Rare events, Failure probability, Importance
sampling, Cross-entropy",
url = "http://www.sci.utah.edu/publications/li11/Li_JCP2011.pdf",
}
@Article{SCI:Li2012a,
author = "J. Li and D. Xiu",
title = "Computation of Failure Probability Subject to
Epistemic Uncertainty",
journal = "SIAM Journal on Scientific Computing",
volume = "34",
number = "6",
pages = "A2946--A2964",
year = "2012",
doi = "10.1137/120864155",
keywords = "failure probability, uncertainty quantification,
epistemic uncertainty, relative entropy",
url = "http://www.sci.utah.edu/publications/li12/Li_SIAM_JSC2012.pdf",
}
@Article{SCI:Lil2015a,
author = "O. A. von Lilienfeld and R. Ramakrishanan and M.
and A. Knoll",
title = "Fourier Series of Atomic Radial Distribution
Functions: A Molecular Fingerprint for Machine
Learning Models of Quantum Chemical Properties",
journal = "International Journal of Quantum Chemistry",
year = "2015",
publisher = "Wiley Online Library",
url = "http://www.sci.utah.edu/publications/Lil2015a/lilienfield2015.pdf",
}
@InProceedings{SCI:Lin2001a,
author = "P. Lindstrom and V. Pascucci",
title = "Visualization of Large Terrains Made Easy",
booktitle = "Proceedings of the 12th Annual {IEEE} Conference
on Visualization ({VIS}-01)",
pages = "363--370, 574",
year = "2001",
organization = "IEEE Computer Society",
month = "October 21-26",
location = "San Diego, CA",
note = "UCRL-JC-144753",
}
@Article{SCI:Lin2002a,
author = "P. Lindstrom and V. Pascucci",
title = "Terrain Simplification Simplified: A General
Framework for View-Dependent Out-of-Core
Visualization",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "8",
number = "3",
pages = "239--254",
year = "2002",
month = "July-September",
note = "UCRL-JC-147847",
}
@InProceedings{SCI:Lin2002b,
author = "L. Linsen and V. Pascucci and M.A. Duchaineau and
B. Hamann and K.I. Joy",
title = "Hierarchical Representation of Time-varying Volume
Data with 4th-root-of-2 Subdivision and
Quadrilinear {B}-spline Wavelets",
booktitle = "Proceedings of Tenth Pacific Conference on
Computer Graphics and Applications",
pages = "346--355",
year = "2002",
location = "Beijing, China",
note = "UCRL-JC-151063",
}
@InProceedings{SCI:Lin2004a,
author = "L. Linsen and V. Pascucci and M.A. Duchaineau and
B. Hamann and K.I. Joy",
title = "Wavelet-Based Multiresolution with
N-th-Root-of-2",
booktitle = "Geometric Modeling, Dagstuhl 2002. Proceedings of
the Dagstuhl Seminar on Geometric Modeling",
year = "2004",
address = "Dagstuhl, Germany",
month = "May",
note = "UCRL-PROC-208699",
}
@InCollection{SCI:Lin2004b,
author = "L. Linsen and J.T. Gray and V. Pascucci and M.A.
Duchaineau and B. Hamann and K.I. Joy",
title = "Hierarchical Large-scale Volume Representation
with 3rd-root-of-2 Subdivision and Trivariate
B-spline Wavelets",
booktitle = "Geometric Modeling for Scientific Visualization",
pages = "359--377",
year = "2004",
editor = "G. Brunnett and B. Hamann and H. Mueller",
publisher = "Springer-Verlag",
doi = "10.1007/978-3-662-07443-5_22",
}
@InProceedings{SCI:Lin2004c,
author = "L. Linsen and V. Pascucci and M.A. Duchaineau and
B. Hamann and K.I. Joy",
title = "Wavelet-Based Multiresolution with
n-th-root-of-2",
booktitle = "Proceedings of Geometric Modeling, Dagstuhl
2002",
year = "2004",
month = "May",
location = "Dagstuhl, Germany",
note = "UCRL-PROC-208699",
}
@InProceedings{SCI:Lin2008a,
author = "L. Lins and D. Koop and E.W. Anderson and S.P.
Callahan and E. Santos and C.E. Scheidegger and J.
Freire and C.T. Silva",
title = "Examining Statistics of Workflow Evolution
Provenance: A First Study",
booktitle = "Proceedings of the 20th International Conference
on Scientific and Statistical Database Management
(SSDBM)",
pages = "573--579",
year = "2008",
doi = "10.1007/978-3-540-69497-7_40",
keywords = "vistrails, provenance, workflow management",
url = "http://www.sci.utah.edu/publications/lins08/ssdbm08.pdf",
}
@Article{SCI:Lin2008b,
author = "W. Lin and Q. Zhu and W. Gao and Y. Chen and C.-H.
Toh and M. Styner and G. Gerig and J.K. Smith and
B. Biswal and J. Gilmore",
title = "Functional Connectivity Magnetic Resonance Imaging
Reveals Cortical Functional Connectivity in the
Developing Brain",
journal = "American Journal of Neuroradiology",
volume = "29",
pages = "1883--1889",
year = "2008",
month = "Fall",
keywords = "ucnia",
url = "http://www.sci.utah.edu/publications/lin08/Functional_Connectivity_MRI.pdf",
}
@TechReport{SCI:Lin2011a,
author = "L. Lins and D. Koop and J. Freire and C.T.
Silva",
title = "DEFOG: A System for Data-Backed Visual
Composition",
number = "UUSCI-2011-003",
year = "2011",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2011-003.pdf",
}
@InProceedings{SCI:Liu2009a,
author = "Z. Liu and H. Zhu and B.L. Marks and L.M. Katz and
C.B. Goodlett and G. Gerig and M. Styner",
title = "Voxel-wise group analysis of {DTI}",
booktitle = "Proceedings of the {IEEE} International Symposium
on Biomedical Imaging: From Nano to Macro, 2009",
pages = "807--810",
year = "2009",
doi = "10.1109/ISBI.2009.5193172",
url = "http://www.sci.utah.edu/publications/liu09/Liu_ISBI2009.pdf",
}
@Article{SCI:Liu2010a,
author = "W. Liu and P. Zhu and J.S. Anderson and D.
Yurgelun-Todd and P.T. Fletcher",
title = "Spatial Regularization of Functional Connectivity
Using High-Dimensional Markov Random Fields",
journal = "Medical Image Computing and Computer-Assisted
Intervention (MICCAI 2010)",
volume = "14",
pages = "363--370",
year = "2010",
pmid = "20879336",
url = "http://www.sci.utah.edu/publications/liu10/MRF_connectivity_miccai2010.pdf",
}
@Article{SCI:Liu2010b,
author = "Z. Liu and C. Goodlett and G. Gerig and M.
Styner",
title = "Evaluation of DTI Property Maps as Basis of DTI
Atlas Building",
journal = "SPIE Medical Imaging",
volume = "7623, 762325",
year = "2010",
month = "February",
doi = "10.1117/12.844911",
}
@Article{SCI:Liu2010c,
author = "Z. Liu and Y. Wang and G. Gerig and S. Gouttard
and R. Tao and T. Fletcher and M.A. Styner",
title = "Quality control of diffusion weighted images",
journal = "SPIE Medical Imaging",
volume = "7628, 76280J",
year = "2010",
month = "February",
doi = "10.1117/12.844748",
}
@Article{SCI:Liu2011a,
author = "W. Liu and S. Awate and J. Anderson and D.
Yurgelun-Todd and P.T. Fletcher",
title = "Monte Carlo expectation maximization with hidden
Markov models to detect functional networks in
resting-state fMRI",
journal = "Machine Learning in Medical Imaging",
volume = "7009/2011",
pages = "59--66",
year = "2011",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-24319-6_8",
url = "http://www.sci.utah.edu/publications/liu11/Liu_MLMI2011.pdf",
}
@InProceedings{SCI:Liu2012a,
author = "T. Liu and E. Jurrus and M. Seyedhosseini and M.
Ellisman and T. Tasdizen",
title = "Watershed Merge Tree Classification for Electron
Microscopy Image Segmentation",
booktitle = "Proceedings of the 21st International Conference
on Pattern Recognition (ICPR)",
pages = "133--137",
year = "2012",
url = "http://www.sci.utah.edu/publications/liu12/Liu_ICPR2012.pdf",
}
@InProceedings{SCI:Liu2012b,
author = "S. Liu and J.A. Levine and P.-T. Bremer and V.
Pascucci",
title = "Gaussian Mixture Model Based Volume
Visualization",
booktitle = "Proceedings of the {IEEE} Large-Scale Data
Analysis and Visualization Symposium 2012",
pages = "73--77",
year = "2012",
note = "Received Best Paper Award",
doi = "10.1109/LDAV.2012.6378978",
keywords = "Uncertainty Visualization, Volume Rendering,
Gaussian Mixture Model, Ensemble Visualization",
url = "http://www.sci.utah.edu/publications/liu12/Liu_LDAV2012.pdf",
}
@InProceedings{SCI:Liu2012c,
author = "W. Liu and S. Awate and P.T. Fletcher",
title = "Group Analysis of Resting-State {fMRI} by
Hierarchical Markov Random Fields",
booktitle = "Medical Image Computing and Computer-Assisted
Intervention – {MICCAI} 2012",
volume = "7512",
pages = "189--196",
year = "2012",
series = "Lecture Notes in Computer Science ({LNCS})",
isbn = "978-3-642-33453-5",
doi = "10.1007/978-3-642-33454-2_24",
url = "http://www.sci.utah.edu/publications/liu12/Liu_MICCAI2012.pdf",
}
@InProceedings{SCI:Liu2013a,
author = "T. Liu and M. Seyedhosseini and M. Ellisman and T.
Tasdizen",
title = "Watershed Merge Forest Classification for Electron
Microscopy Image Stack Segmentation",
booktitle = "Proceedings of the 2013 International Conference
on Image Processing",
year = "2013",
url = "http://www.sci.utah.edu/publications/Liu2013a/Liu_ICIP2013.pdf",
}
@Article{SCI:Liu2014a,
author = "W. Liu and S.P. Awate and J.S. Anderson and P.T.
Fletcher",
title = "A functional network estimation method of
resting-state {fMRI} using a hierarchical Markov
random field",
title_url =
"http://www.sciencedirect.com/science/article/pii/S1053811914004698",
journal = "NeuroImage",
volume = "100",
pages = "520--534",
year = "2014",
issn = "1053-8119",
doi = "10.1016/j.neuroimage.2014.06.001",
keywords = "Resting-state functional MRI, Segmentation,
Functional connectivity, Hierarchical Markov random
field, Bayesian",
url = "http://www.sci.utah.edu/publications/Liu2014a/Liu_Neuroimage2014.pdf",
}
@TechReport{SCI:Liu2014b,
author = "Shusen Liu and Bei Wang and J.J. Thiagarajan and
P.-T. Bremer and V. Pascucci",
title = "Visual Exploration of High-Dimensional Data:
Subspace Analysis through Dynamic Projections",
number = "UUSCI-2014-003",
year = "2014",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "High-dimensional data, Subspace, Dynamic
projection",
url = "http://www.sci.utah.edu/publications/Liu2014b/UUSCI-2014-003.pdf",
}
@Article{SCI:Liu2014c,
author = "S. Liu and Bei Wang and P.-T. Bremer and V.
Pascucci",
title = "Distortion-Guided Structure-Driven Interactive
Exploration of High-Dimensional Data",
journal = "Computer Graphics Forum",
volume = "33",
number = "3",
pages = "101--110",
year = "2014",
publisher = "Wiley-Blackwell",
month = "June",
url = "http://www.sci.utah.edu/publications/Liu2014c/Liu_Distortion_Interactive_2014.pdf",
}
@InProceedings{SCI:Liu2014d,
author = "Shusen Liu and Bei Wang and J.J. Thiagarajan and
P.-T. Bremer and V. Pascucci",
title = "Multivariate Volume Visualization through Dynamic
Projections",
booktitle = "Proceedings of the {IEEE} Symposium on Large Data
Analysis and Visualization ({LDAV})",
year = "2014",
url = "http://www.sci.utah.edu/publications/Liu2014d/Liu_paper102.pdf",
}
@Article{SCI:Liu2014e,
author = "T. Liu and C. Jones and M. Seyedhosseini and T.
Tasdizen",
title = "A modular hierarchical approach to 3D electron
microscopy image segmentation",
journal = "Journal of Neuroscience Methods",
volume = "226",
number = "15",
pages = "88--102",
year = "2014",
month = "April",
doi = "10.1016/j.jneumeth.2014.01.022",
keywords = "Image segmentation, Electron microscopy,
Hierarchical segmentation, Semi-automatic
segmentation, Neuron reconstruction",
url = "http://www.sci.utah.edu/publications/Liu2014e/Liu_JNM2014.pdf",
}
@Conference{SCI:Liu2015a,
author = "S. Liu and D. Maljovec and Bei Wang and P. T.
Bremer and V. Pascucci",
title = "Visualizing High-Dimensional Data: Advances in the
Past Decade",
booktitle = "State of The Art Report",
year = "2015",
organization = "Eurographics Conference on Visualization
(EuroVis)",
url = "http://www.sci.utah.edu/publications/Liu2015a/Vis_HD_STAR_BeiWang_2015.pdf",
}
@Article{SCI:Liu2015b,
author = "S. Liu and Bei Wang and J. J. Thiagarajan and P.
T. Bremer and V. Pascucci",
title = "Visual Exploration of High-Dimensional Data
through Subspace Analysis and Dynamic
Projections",
journal = "Computer Graphics Forum",
volume = "34",
number = "3",
pages = "271--280",
year = "2015",
publisher = "Wiley-Blackwell",
month = "June",
doi = "10.1111/cgf.12639",
url = "http://www.sci.utah.edu/publications/Liu2015b/Subspace_Dynamic_Projection_BeiWang_2015.pdf",
}
@Article{SCI:Liu2016a,
author = "T. Liu and S.M. Seyedhosseini and T. Tasdizen",
title = "Image Segmentation Using Hierarchical Merge
Tree",
journal = "IEEE Transactions on Image Processing",
volume = "25",
number = "10",
pages = "4596--4607",
year = "2016",
publisher = "IEEE",
month = "Oct",
doi = "10.1109/tip.2016.2592704",
url = "http://www.sci.utah.edu/publications/Liu2016a/07515198.pdf",
}
@InCollection{SCI:Liu2016b,
author = "T. Liu and M. Zhang and M. Javanmardi and N.
Ramesh and T. Tasdizen",
title = "SSHMT: Semi-supervised Hierarchical Merge Tree for
Electron Microscopy Image Segmentation",
title_url =
"https://link.springer.com/chapter/10.1007%2F978-3-319-46448-0_9#citeas",
booktitle = "Lecture Notes in Computer Science",
volume = "9905",
pages = "144--159",
year = "2016",
publisher = "Springer International Publishing",
doi = "10.1007/978-3-319-46448-0_9",
}
@Article{SCI:Liu2018a,
author = "S. Liu and P.T. Bremer and J.J. Thiagarajan and V.
Srikumar and B. Wang and Y. Livnat and V.
Pascucci",
title = "Visual Exploration of Semantic Relationships in
Neural Word Embeddings",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "24",
number = "1",
pages = "553--562",
year = "2018",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/tvcg.2017.2745141",
url = "http://www.sci.utah.edu/publications/Liu2018a/08019864.pdf",
}
@InCollection{SCI:Liv2000,
author = "Y. Livnat and S.G. Parker and C.R. Johnson",
title = "Fast Isosurface Extraction Methods for Large Image
Data Sets",
booktitle = "Handbook of Medical Imaging",
pages = "731--745",
year = "2000",
editor = "A.N. Bankman",
publisher = "Academic Press",
address = "San Diego, CA",
month = "Nov",
keywords = "scalar field methods, isosurface extraction,
remote visualization, remote isosurface
visualization, scientific visualization",
url = "http://www.sci.utah.edu/publications/hmip_00/paper_final.ps",
url = "http://www.sci.utah.edu/publications/hmip_00/paper_final.ps.gz",
url = "http://www.sci.utah.edu/publications/hmip_00/paper_final.pdf",
}
@InProceedings{SCI:Liv2001,
author = "Y. Livnat and C.D. Hansen and S.G. Parker and C.R.
Johnson",
title = "Isosurface extraction for large-scale datasets",
booktitle = "Proceedings of Scientific Visualization
-Dagstuhl`2000",
year = "2001",
editor = "F. Post",
keywords = "scalar field methods, isosurface extraction,
scientific visualization",
url = "http://www.sci.utah.edu/publications/yarden01/dagstuhl00.pdf",
}
@TechReport{SCI:Liv2002b,
author = "Y. Livnat and X. Cavin and C.D. Hansen",
title = "{PHASE}: Progressive Hardware Assisted IsoSurface
Extraction Framework",
number = "UUSCI-2002-001",
year = "2002",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "isosurface extraction, scalar field methods",
url = "http://www.sci.utah.edu/publications/yarden02/UUSCI-2002-001.pdf",
}
@TechReport{SCI:Liv2003a,
author = "Y. Livnat and C.D. Hansen",
title = "Dynamic View Dependent Isosurface Extraction",
number = "UUSCI-2003-004",
year = "2003",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scalar field methods, isosurface extraction",
url = "http://www.sci.utah.edu/publications/yarden03/UUSCI-2003-004.pdf",
}
@InProceedings{SCI:Liv2004a,
author = "Y. Livnat and X. Tricoche",
title = "Interactive Point Based Isosurface Extraction",
booktitle = c-VIS2004,
pages = "457--464",
year = "2004",
keywords = "scalar field methods, isosurface extraction,
parallel visualization, visible human, point based
methods, hybrid surface representation, ncrr",
url = "http://www.sci.utah.edu/publications/yarden04/pisa.pdf",
}
@InCollection{SCI:Liv2005a,
author = "Y. Livnat",
title = "Accelerated Isosurface Extraction Approaches",
booktitle = "The Visualization Handbook",
pages = "39--55",
year = "2005",
editor = "C.D. Hansen and C.R. Johnson",
publisher = "Elsevier",
isbn = "0-12-387582-X",
keywords = "scalar field methods, isosurface extraction",
url = "http://www.sci.utah.edu/publications/yarden05/ch02_livnat.pdf",
}
@InProceedings{SCI:Liv2005b,
author = "Y. Livnat and J. Agutter and S. Moon and R.F.
Erbacher and S. Foresti",
title = "A Visualization Paradigm for Network Intrusion
Detection",
booktitle = "{IEEE} Workshop on Information Assurance and
Security 2005",
pages = "30--37",
year = "2005",
month = "June",
keywords = "network security visualization, interfaces,
intrusion detection, visalert",
url = "http://www.sci.utah.edu/publications/yarden05/VisAlert.pdf",
}
@InProceedings{SCI:Liv2005c,
author = "Y. Livnat and J. Agutter and S. Moon and S.
Foresti",
title = "Visual Correlation for Situational Awareness",
booktitle = c-IVIS2005,
pages = "13",
year = "2005",
month = "October",
keywords = "network security visualization, interfaces,
intrusion detection, visalert, visaware,",
url = "http://www.sci.utah.edu/publications/yarden05/VisAware.pdf",
}
@TechReport{SCI:Liv2005d,
author = "Y. Livnat and X. Tricoche",
title = "Shadows for Incomplete Point-based Isosurfaces",
number = "UUSCI-2005-001",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "isosurface extraction, remote visualization,
remote isosurface visualization",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-001.pdf",
}
@TechReport{SCI:Liv2006a,
author = "O.E. Livne",
title = "Clustering on Single Refinement Level:
Berger-Rigoustos Algorithm",
number = "UUSCI-2006-001",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-001.pdf",
}
@TechReport{SCI:Liv2006b,
author = "O.E. Livne",
title = "Minimum and Maximum Patch Size Clustering on a
Single Refinement Level",
number = "UUSCI-2006-002",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-002.pdf",
}
@TechReport{SCI:Liv2006c,
author = "O.E. Livne",
title = "Efficient Update of Persistent Patches in the
Berger Rigoutsous Algorithm",
number = "UUSCI-2006-003",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-003.pdf",
}
@TechReport{SCI:Liv2006d,
author = "O.E. Livne",
title = "Clustering Patches for Multi-Level Refined Grids:
a Hierarchical Approach",
number = "UUSCI-2006-004",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-004.pdf",
}
@TechReport{SCI:Liv2006e,
author = "O.E. Livne",
title = "ShockTube Problem - Status Report 1 Uni-Level
Experiments",
number = "UUSCI-2006-005",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-005.pdf",
}
@TechReport{SCI:Liv2006f,
author = "O.E. Livne",
title = "ICE Algorithm and the Davis Advection Scheme",
number = "UUSCI-2006-006",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-006.pdf",
}
@TechReport{SCI:Liv2006g,
author = "O.E. Livne",
title = "ICE Algorithm for the Shocktube Problem",
number = "UUSCI-2006-007",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-007.pdf",
}
@InCollection{SCI:Liv2007a,
author = "Y. Livnat and S.G. Parker and C.R. Johnson",
title = "Fast Isosurface Extraction Methods for Large Image
Data Sets",
booktitle = "Handbook of Medical Imaging: Processing and
Analysis",
year = "2007",
editor = "Isaac Bankman",
chapter = "44",
publisher = "Academic Press",
edition = "2nd Edition",
keywords = "isosurface extraction, large dataset
visualization",
url = "http://www.sci.utah.edu/publications/livnat07/Livnat_Handbook_MI_Ch44.pdf",
}
@InCollection{SCI:Liv2008a,
author = "Y. Livnat and S.G. Parker and C.R. Johnson",
title = "Fast Isosurface Extraction Methods for Large Image
Data Sets",
booktitle = "Handbook of Medical Image Processing and
Analysis",
pages = "801--816",
year = "2008",
editor = "Isaac N. Bankman",
chapter = "47",
publisher = "Elsevier",
edition = "2nd edition",
note = "(to appear)",
url = "http://www.sci.utah.edu/publications/livnat08/Large-scale-isosurface08.pdf",
}
@InProceedings{SCI:Liv2010a,
author = "Y. Livnat and P. Gesteland and J. Benuzillo and W.
Pettey and D. Bolton and F. Drews and H. Kramer and
M. Samare",
title = "A Novel Workbench for Epidemic investigation and
Analysis of Search Strategies in public health
practice",
booktitle = "Proceedings of AMIA 2010 Annual Symposium",
pages = "647--651",
year = "2010",
url = "http://www.sci.utah.edu/publications/livnat10/Epinome_AMIA_2010.pdf",
}
@Article{SCI:Liv2012a,
author = "Y. Livnat and T.-M. Rhyne and M. Samore",
title = "Epinome: A Visual-Analytics Workbench for
Epidemiology Data",
journal = "{IEEE} Computer Graphics and Applications",
volume = "32",
number = "2",
pages = "89--95",
year = "2012",
issn = "0272-1716",
doi = "10.1109/MCG.2012.31",
url = "http://www.sci.utah.edu/publications/livnat12/Livnat_Epinome-CGA.pdf",
}
@InProceedings{SCI:Liv2013a,
author = "Y. Livnat and E. Jurrus and A.V. Gundlapalli and
P. Gestland",
title = "The CommonGround visual paradigm for
biosurveillance",
booktitle = "Proceedings of the 2013 IEEE International
Conference on Intelligence and Security Informatics
(ISI)",
pages = "352--357",
year = "2013",
isbn = "978-1-4673-6214-6",
doi = "10.1109/ISI.2013.6578857",
keywords = "biosurveillance, visualization, interactive
exploration, situational awareness",
url = "http://www.sci.utah.edu/publications/livnat13/Livnat_CommonGround2013.pdf",
}
@Article{SCI:Liv96,
author = "Y. Livnat and H.W. Shen and C.R. Johnson",
title = "A Near Optimal Isosurface Extraction Algorithm
Using the Span Space",
journal = "{IEEE} Transactions on Visual Computer Graphics",
volume = "2",
number = "1",
pages = "73--84",
year = "1996",
keywords = "scalar field methods, isosurface extraction,
scientific visualization",
url = "http://www.sci.utah.edu/publications/yarden96/tvcg96.pdf",
}
@InProceedings{SCI:Liv98,
author = "Y. Livnat and C.D. Hansen",
title = "View Dependent Isosurface Extraction",
booktitle = "{IEEE} Visualization '98",
pages = "175--180",
year = "1998",
month = "Oct",
keywords = "scalar field methods, isosurface extraction,
remote isosurface visualization",
url = "http://www.sci.utah.edu/publications/yarden98/wise.pdf",
}
@TechReport{SCI:Liv99a,
author = "Y. Livnat",
title = "{NOISE}, {WISE} and {SAGE}: Algorithms for Rapid
Isosurface Extraction",
number = "UUSCI-1999-001",
year = "1999",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
month = "December",
keywords = "scalar field methods, isosurface extraction",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-1999-001.pdf",
}
@InProceedings{SCI:Liz2008a,
author = "M. Lizier and J.F. Shepherd and L.G. Nonato and J.
Comba and C.T. Silva",
title = "Comparing Techniques for Tetrahedral Mesh
Generation",
booktitle = "Proceedings of the Inaugural International
Conference of the Engineering Mechanics Institute
({EM} 2008)",
pages = "(accepted)",
year = "2008",
url = "http://www.sci.utah.edu/publications/lizier08/meshing-comp.pdf",
}
@InProceedings{SCI:Liz2010a,
author = "M.A.S. Lizier and M.F. Siqueira and J.D. Daniels
II and C.T. Silva and L.G. Nonato",
title = "Template-based Remeshing for Image
Decomposition",
booktitle = "Proceedings of the 23rd SIBGRAPI Conference on
Graphics, Patterns and Images",
pages = "95--102",
year = "2010",
url = "http://www.sci.utah.edu/publications/lizier10/Lizier_SIBGRAPI2010.pdf",
}
@Article{SCI:Lju2016a,
author = "P. Ljung and J. Kr{\"u}ger and E. Gr{\"o}ller and M.
Hadwiger and C. D. Hansen and and A. Ynnerman",
title = "State of the Art in Transfer Functions for Direct
Volume Rendering",
journal = "Computer Graphics Forum",
volume = "35",
number = "3",
pages = "669--691",
year = "2016",
publisher = "Wiley-Blackwell",
month = "June",
doi = "10.1111/cgf.12934",
url = "http://www.sci.utah.edu/publications/Lju2016a/Transfer-Function-Design-2016.pdf",
}
@Article{SCI:Lom1999a,
author = "I. Lomtev and R.M. Kirby and G.E. Karniadakis",
title = "A Discontinuous Galerkin ALE Method for
Compressible Viscous Flows in Moving Domains",
journal = "Journal of Computational Physics",
volume = "155",
pages = "128--159",
year = "1999",
}
@InProceedings{SCI:Lor2001a,
author = "P. Lorenzen and S. Joshi and G. Gerig and E.
Bullitt",
title = "Tumor-Induced Structural Radiometric Asymmetry in
Brain Images",
booktitle = "Workshop on Mathematical Methods in Biomedical
Image Analysis (MMBIA)",
pages = "163--170",
year = "2001",
month = "2001",
url = "http://www.sci.utah.edu/publications/lorenzen01/MMBIA01-Lorenzen-brain.pdf",
}
@InProceedings{SCI:Lor2003a,
author = "P. Lorenzen and S. Joshi",
title = "High-Dimensional Multi-modal Image Registration",
booktitle = "Proceedings of the Workshop on Biomedical Image
Registration",
pages = "234--243",
year = "2003",
url = "http://www.sci.utah.edu/publications/lorenzen03/WBIR03_Lorenzen.pdf",
}
@InProceedings{SCI:Lor2004a,
author = "P. Lorenzen and B. Davis and S. Joshi",
title = "Model Based Symmetric Information Theoretic Large
Deformation Multi-Modal Image Registration",
booktitle = "Proceedings of the International Symposium on
Biomedical Imaging (ISBI)",
pages = "720--723",
year = "2004",
month = "April",
location = "Piscataway, NJ",
url = "http://www.sci.utah.edu/publications/lorenzen04/ISBI04-Lorenzen-MultiModal.pdf",
}
@InProceedings{SCI:Lor2005a,
author = "P. Lorenzen and B. Davis and S. Joshi",
title = "Unbiased Atlas Formation via Large Deformations
Metric Mapping",
booktitle = "Med Image Comput Comput Assist Interv Int Conf Med
Image Comput Comput Assist Interv (MICCAI)",
volume = "8 (Pt. 2)",
pages = "411--418",
year = "2005",
editor = "J.S. Duncan and G. Gerig",
url = "http://www.sci.utah.edu/publications/lorenzen05/MICCAI05_Lorenzen.pdf",
}
@InProceedings{SCI:Lor2006a,
author = "L. Lorenzo and R.S. MacLeod and R.T. Whitaker and
G. Adluru and E.V.R. DiBella",
title = "Level Sets and Shape Models for Segmentation of
Cardiac Perfusion MRI",
booktitle = c-SPIEMI2006,
volume = "6144",
pages = "1320--1331",
year = "2006",
keywords = "ip image processing signal processing,
segmentation, cardiac heart, ncrr, ip gp image
processing goemetry processing",
url = "http://www.sci.utah.edu/publications/adluru06/SPIE_06.pdf",
}
@Article{SCI:Lor2006b,
author = "P. Lorenzen and M.W. Prastawa and B. Davis and G.
Gerig and E. Bullitt and S. Joshi",
title = "Multi-Modal Image Set Registration and Atlas
Formation",
journal = "Med Image Anal",
volume = "10",
number = "3",
pages = "440--451",
year = "2006",
month = "June",
url = "http://www.sci.utah.edu/publications/lorenzen06/Lorenzen-MedIA-2006.pdf",
}
@InProceedings{SCI:Lu2002a,
author = "A. Lu and J. Taylor and M. Hartner and D. Ebert
and C.D. Hansen",
title = "Hardware-Accelerated Interactive Illustrative
Stipple Drawing of Polygonal Objects",
booktitle = c-VMV2002,
pages = "61--68",
year = "2002",
month = "November",
location = "Erlangen, Germany",
url = "http://www.sci.utah.edu/publications/lu02/stipple_VMV_2002.pdf",
}
@InProceedings{SCI:Lu2002b,
author = "A. Lu and C.J. Morris and D. Ebert and P.
Rheingans and C.D. Hansen",
title = "Non-Photorealistic Volume Rendering Using
Stippling Techniques",
booktitle = c-VIS2002,
pages = "211--218",
year = "2002",
location = "Boston, MA",
note = "Awarded Best Paper at the conference",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/lu02/vis_stipple.pdf",
}
@Article{SCI:Lu2003a,
author = "A. Lu and C.J. Morris and J. Taylor and D.S. Ebert
and C.D. Hansen and P. Rheingans and M. Hartner",
title = "Illustrative Interactive Stipple Rendering",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "9",
number = "2",
pages = "127--138",
year = "2003",
month = "April",
keywords = "scalar field methods, scientific visualization",
url = "http://www.sci.utah.edu/publications/lu03/Lu_TVCG2003.pdf",
}
@Article{SCI:Lu2003b,
author = "C. Lu and S. Pizer and S. Joshi",
title = "A Markov Random Field Approach to Multi-scale
Shape Analysis",
journal = "Scale Space Methods in Computer Vision",
pages = "416--431",
year = "2003",
editor = "LD Griffin and M Lillholm",
url = "http://www.sci.utah.edu/publications/lu03/ScaleSpace03_Lu_shape.pdf",
}
@Article{SCI:Lu2005a,
author = "H. Lu and M. Berzins and C.E. Goodyer and P.K.
Jimack",
title = "High Order Discontinuous Galerkin Method for EHL
Line Contact Problems",
journal = "Communication in Numerical Methods in
Engineering",
volume = "21",
number = "11",
pages = "643--650",
year = "2005",
keywords = "computational mechanics, EHL",
url = "http://www.sci.utah.edu/publications/lu05/LBGJ05.pdf",
}
@InProceedings{SCI:Lu2006a,
author = "H. Lu and M. Berzins and C.E. Goodyer and P.K.
Jimack and M. Walkley",
title = "Adaptive High-order Finite Element Solution of
Transient Elastohydrodynamic Lubrication
Problems",
booktitle = "Proc. IMechE Part J: J. Engrg. Tribology",
volume = "220",
pages = "215--225",
year = "2006",
keywords = "high-order DG, adaptivity, EHL, line contact,
transient",
url = "http://www.sci.utah.edu/publications/lu06/LBGJW06.pdf",
}
@Article{SCI:Lu2006b,
author = "H. Lu and M. Berzins and P.K. Jimack",
title = "Application of the Adaptive Discontinuous Galerkin
Method to Problems in Elastohydrodynamic
Lubrication",
journal = "Innovation in Engineering Computational
Technology",
pages = "169--191",
year = "2006",
editor = "B.H.V. Topping and G. Montero and R. Montenegro",
publisher = "Saxe-Coburg Publications, Stirling",
keywords = "computational mechanics, EHL",
url = "http://www.sci.utah.edu/publications/lu06/LBJ06.pdf",
}
@PhdThesis{SCI:Lu2006c,
author = "H. Lu",
title = "High Order Finite Element Solution of
Elastohydrodynamic Lubrication Problems",
year = "2006",
school = "School of Computing, University of Leeds",
note = "Advisor: Martin Berzins",
url = "http://www.sci.utah.edu/publications/Lu2006c/HLu_PhDTheis2006.pdf",
}
@Article{SCI:Lu2012a,
author = "H. Lu and M. Berzins and C.E. Goodyer and P.K.
Jimack",
title = "Adaptive High-Order Discontinuous Galerkin
Solution of Elastohydrodynamic Lubrication Point
Contact Problems",
journal = "Advances in Engineering Software",
volume = "45",
number = "1",
pages = "313--324",
year = "2012",
doi = "10.1016/j.advengsoft.2011.10.006",
keywords = "Elastohydrodynamic lubrication, Discontinuous
Galerkin, High polynomial degree, h-adaptivity,
Nonlinear systems",
url = "http://www.sci.utah.edu/publications/lu12/Lu_LBGJ2012.pdf",
}
@Article{SCI:Luc2003a,
author = "D. Lucor and D. Xiu and C.-H. Su and G.E.
Karniadakis",
title = "Predictability and Uncertainty in CFD",
journal = "International Journal for Numerical Methods in
Fluids",
volume = "43",
number = "5",
pages = "483--505",
year = "2003",
doi = "10.1002/fld.500",
keywords = "computational fluid dynamics, polynomial chaos,
Wiener–Hermite functionals, incompressible
flows",
url = "http://www.sci.utah.edu/publications/lucor03/Lucor_IJNMF2003.pdf",
}
@Article{SCI:Lui2007a,
author = "J. Luitjens and M. Berzins and T.C. Henderson",
title = "Parallel Space Filling Curve Generation Through
Sorting",
journal = "Journal of Concurrency and Computation",
volume = "19",
number = "10",
pages = "1387--1402",
year = "2007",
url = "http://www.sci.utah.edu/publications/luitjens07/Concurrency2007JL.pdf",
}
@InCollection{SCI:Lui2007b,
author = "J. Luitjens and B. Worthen and M. Berzins and T.C.
Henderson",
title = "Scalable Parallel AMR for the Uintah Multiphysics
Code",
booktitle = "Petascale Computing Algorithms and Applications",
year = "2007",
editor = "D. Bader",
publisher = "Chapman and Hall/CRC",
keywords = "uintah",
url = "http://www.sci.utah.edu/publications/luitjens07/2008_Luitjens_UintahMultiphysicsCode.pdf",
}
@Article{SCI:Lui2007c,
author = "J. Luitjens and M. Berzins and T. Henderson",
title = "Parallel space-filling curve generation through
sorting",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "19",
number = "10",
pages = "1387--1402",
year = "2007",
month = "July",
doi = "10.1002/cpe.1179",
url = "http://www.sci.utah.edu/publications/Lui2007c/Luitjens_CCPE2007.pdf",
}
@TechReport{SCI:Lui2008a,
author = "J. Luitjens and Q. Meng and M. Berzins and T.
Henderson",
title = "Improving the Load Balance of Parallel Adaptive
Mesh Refined Simulations",
number = "UUSCI-2008-007",
year = "2008",
institution = "University of Utah School of Computing",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-007.pdf",
}
@InCollection{SCI:Lui2008b,
author = "J. Luitjens and B. Worthen and M. Berzins and T.
Henderson",
title = "Scalable Parallel AMR for the Uintah Multiphysics
Code",
booktitle = "Petascale Computing Algorithms and Applications",
pages = "67--82",
year = "2008",
chapter = "4",
publisher = "CRC Press LLC.",
url = "http://www.sci.utah.edu/publications/Lui2008b/Luitjens_Uintah_Multiphysics_Code2008.pdf",
}
@TechReport{SCI:Lui2009a,
author = "J. Luitjens and M. Berzins",
title = "Uintah: A Scalable Adaptive Framework for Emerging
Petascale Platforms",
number = "UUSCI-2009-002",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2009-002.pdf",
}
@InProceedings{SCI:Lui2010a,
author = "J. Luitjens and M. Berzins",
title = "Improving the Performance of Uintah: A Large-Scale
Adaptive Meshing Computational Framework",
booktitle = "Proceedings of the 24th {IEEE} International
Parallel and Distributed Processing Symposium
({IPDPS10})",
pages = "1--10",
year = "2010",
location = "Atlanta, GA",
doi = "10.1109/IPDPS.2010.5470437",
keywords = "csafe, c-safe, scirun, uintah, fires, explosions,
simulation",
url = "http://www.sci.utah.edu/publications/luitjens10/Luitjens_ipdps2010.pdf",
}
@InBook{SCI:Lui2010b,
author = "J. Luitjens and J. Guilkey and T. Harman and B.
Worthen and S.G. Parker",
title = "Adaptive Computations in the Uintah Framework",
booktitle = "Advanced Computational Infastructures for
Parallel/Distributed Adapative Applications",
year = "2010",
chapter = "1",
publisher = "Wiley Press",
url = "http://www.sci.utah.edu/publications/luitjens10/Luitjens_Uintah2010a.pdf",
}
@PhdThesis{SCI:Lui2010c,
author = "J. Luitjens",
title = "The Scalability of Parallel Adaptive Mesh
Refinement Within Uintah",
year = "2010",
school = "School of Computing, University of Utah",
url = "http://www.sci.utah.edu/publications/Lui2010c/Luitjens_PhDThesis2010.pdf",
}
@Article{SCI:Lui2011a,
author = "J. Luitjens and M. Berzins",
title = "Scalable parallel regridding algorithms for
block-structured adaptive mesh renement",
journal = "Concurrency And Computation: Practice And
Experience",
volume = "23",
number = "13",
pages = "1522--1537",
year = "2011",
publisher = "John Wiley \& Sons, Ltd.",
issn = "1532--0634",
doi = "10.1002/cpe.1719",
keywords = "adaptive mesh refinement, regridding, remeshing,
scalability",
url = "http://www.sci.utah.edu/publications/Lui2011a/Luitjens-Berzins_CCPE2011.pdf",
}
@PhdThesis{SCI:Lui2011b,
author = "J.P. Luitjens",
title = "The Scalability of Parallel Adaptive Mesh
Refinement Within Uintah",
year = "2011",
school = "School of Computing, University of Utah",
note = "Advisor: Martin Berzins",
url = "http://www.sci.utah.edu/publications/Lui2011b/JLuitjens_PhDThesis2011.pdf",
}
@Article{SCI:Lui2011c,
author = "J. Luitjens and M. Berzins",
title = "Scalable parallel regridding algorithms for
block-structured adaptive mesh refinement",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "23",
number = "13",
pages = "1522--1537",
year = "2011",
month = "September",
doi = "10.1002/cpe.1719",
url = "http://www.sci.utah.edu/publications/Lui2011c/Luitjens_CCPE2011.pdf",
}
@InProceedings{SCI:Luj2004a,
author = "T.J. Lujan and M.S. Dalton and S.P. Lake and B.J.
Ellis and T.D. Rosenberg and J.A. Weiss",
title = "{ACL} Injury Alters {MCL} Strain During
Anterior-Posterior but not Varus-Valgus Loading",
booktitle = c-ORS2004,
volume = "29",
pages = "1272",
year = "2004",
month = "March",
location = "San Francisco, CA",
}
@Article{SCI:Luj2005a,
author = "T.J. Lujan and S.P. Lake and T.A. Plaizier and
B.J. Ellis and J.A. Weiss",
title = "Simultaneous Measurement of Three-Dimensional
Joint Kinematics and Tissue Strains with Optical
Methods",
journal = "ASME Journal of Biomechanical Engineering",
volume = "127",
pages = "193--197",
year = "2005",
keywords = "computational biomechanics, computational
mechanics",
url = "http://www.sci.utah.edu/publications/lujan05/lujan_jbme_2005.pdf",
}
@Article{SCI:Luj2006a,
author = "T.J. Lujan and M.S. Dalton and B.M. Thompson B.J.
Ellis and J.A. Weiss",
title = "Effect of ACL Deficiency on MCL Strains and Joint
Kinematics",
journal = "Journal of Biomechanical Engineering",
pages = "(in press)",
year = "2006",
month = "November",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/lujan06/lujan_jbme_2007.pdf",
}
@Article{SCI:Luj2006b,
author = "T.J. Lujan and C.J. Underwood and H.B. Henninger
and B.M. Thompson and J.A. Weiss",
title = "Effect of Dermatan Sulfate Glycosaminoglycans on
the Quasi-Static Material Properties of the Human
Medial Collateral Ligament",
journal = "Journal of Orthopaedic Research",
pages = "(in press)",
year = "2006",
month = "October",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/lujan06/lujan_JOR_2007.pdf",
}
@Article{SCI:Luj2007a,
author = "T.J. Lujan and M.S. Dalton and B.M. Thompson and
B.J. Ellis and J.A. Weiss",
title = "Effect of ACL Deficiency on MCL Strains and Joint
Kinematics",
journal = "Journal of Biomechanical Engineering",
volume = "129",
number = "3",
pages = "386--392",
year = "2007",
url = "http://www.sci.utah.edu/publications/lujan07/lujan_jbme_2007.pdf",
}
@Article{SCI:Luj2007b,
author = "T.J. Lujan and C.J. Underwood and H.B. Henninger
and B.M. Thompson and J.A. Weiss",
title = "Effect of Dermatan Sulfate Glycosaminoglycans on
the Quasi-Static Material Properties of the Human
Medial Collateral Ligament",
journal = "Journal of Orthopaedic Research",
volume = "25",
number = "7",
pages = "894--903",
year = "2007",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/lujan07/lujan_JOR_2007.pdf",
}
@Article{SCI:Luj2008a,
author = "T.J. Lujan and C.J. Underwood and N.T. Jacobs and
J.A. Weiss",
title = "Contribution of Glycosaminoglycans to Viscoelastic
Tensile Behavior of Human Ligament",
journal = "Journal of Applied Physiology",
volume = "106",
number = "2",
pages = "423--431",
year = "2008",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/lujan08/lujan_jap_2009.pdf",
}
@InProceedings{SCI:Luk2002a,
author = "E. Luke and C.D. Hansen",
title = "Semotus Visum: A Flexible Remote Visualization
Framework",
booktitle = c-VIS2002,
pages = "61--68",
year = "2002",
location = "Boston, MA",
url = "http://www.sci.utah.edu/publications/luke02/Vis02-luke-hansen-2002.pdf",
}
@Article{SCI:Ly2020a,
author = "C. Ly and C. Vachet and I. Schwerdt and E. Abbott
and A. Brenkmann and L.W. McDonald and T.
Tasdizen",
title = "Determining uranium ore concentrates and their
calcination products via image classification of
multiple magnifications",
title_url = "https://doi.org/10.1016/j.jnucmat.2020.152082",
journal = "Journal of Nuclear Materials",
year = "2020",
}
@Article{SCI:Lya2012a,
author = "A.E. Lyall and S. Woolson and H.M. Wolf and B.D.
Goldman and J.S. Reznick and R.M. Hamer and W. Lin
and M. Styner and G. Gerig and J.H. Gilmore",
title = "Prenatal isolated mild ventriculomegaly is
associated with persistent ventricle enlargement at
ages 1 and 2",
journal = "Early Human Development",
pages = "(in press)",
year = "2012",
publisher = "Elsevier",
url = "http://www.sci.utah.edu/publications/lyall12/MVM-Lyall-Gilmore-Elsevier-03-26-2012.pdf",
}
@Article{SCI:Ma2001,
author = "K. Ma and S.G. Parker",
title = "Massively Parallel Software Rendering for
Visualizing Large-Scale DataSets",
journal = j-TVCG,
pages = "72--83",
year = "2001",
month = "July/August",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, scientific
visualization",
url = "http://www.sci.utah.edu/publications/ma01/ma2001.pdf",
}
@InProceedings{SCI:Ma93a,
author = "K.L. Ma and J. Painter and C.D. Hansen and M.
Krogh",
title = "A Data Distributed, Parallel Algorithm for
Ray-Traced Volume Rendering",
booktitle = "Proceedings of the Parallel Rendering Symposium
1993",
pages = "15--22",
year = "1993",
month = "October",
location = "San Jose, Ca.",
keywords = "scalar field methods, volume rendering, parallel
visualization",
}
@TechReport{SCI:Ma93b,
author = "K.L. Ma and J.S. Painter and C.D. Hansen and M.F.
Krogh",
title = "A Data Distributed Parallel Algorithm for
Ray-Traced Volume Rendering",
pages = "15--22",
year = "1993",
institution = "Institute for Computer Applications in Science
and Engineering, {NASA} Langley Research Center",
type = "{ICASE} Report",
month = "August",
location = "Hampton, VA",
keywords = "volume rendering, parallel visualization,
interactive rt distributed interactive ray tracing
dirt",
}
@Article{SCI:Ma94a,
author = "K.L. Ma and J. Painter and C.D. Hansen and M.
Krogh",
title = "Parallel Volume Rendering Using Binary-Swap
Compositing",
journal = "{IEEE} Computer Graphics and Applications",
volume = "14",
number = "4",
pages = "59--68",
year = "1994",
}
@TechReport{SCI:Maa2009a,
author = "S.A. Maas and B.J. Ellis and D.S. Rawlins and J.A.
Weiss",
title = "A Comparison of FEBio, ABAQUS, and NIKE3D Results
for a Suite of Verification Problems",
number = "UUSCI-2009-009",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "mrl, MRL, FEBio, ABAQUS, NIKE3D",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2009-009.pdf",
}
@TechReport{SCI:Maa2011a,
author = "S.A. Maas and B.J. Ellis and D.S. Rawlins and L.T.
Edgar and C.R. Henak and J.A. Weiss",
title = "Implementation and Verification of a
Nodally-Integrated Tetrahedral Element in FEBio",
number = "UUSCI-2011-007",
year = "2011",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "MRL",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2011-007.pdf",
}
@Article{SCI:Maa2012a,
author = "S.A. Maas and B.J. Ellis and G.A. Ateshian and
J.A. Weiss",
title = "{FEBio:} Finite elements for biomechanics",
journal = "Journal of Biomechanical Engineering",
volume = "134",
number = "1",
pages = "011005",
year = "2012",
doi = "10.1115/1.4005694",
pmid = "22482660",
url = "http://www.sci.utah.edu/publications/maas12/Maas_jbme_2012.pdf",
}
@Article{SCI:Mac2001a,
author = "R.S. MacLeod and B. Yilmaz and B. Taccardi and
B.B. Punske and Y. Serina and D.H. Brooks",
title = "Direct and Inverse Methods for Cardiac Mapping
Using Multielectrode Catheter Measurements",
journal = "Journal of Biomedizinische Technik",
volume = "46(supp)",
pages = "207--209",
year = "2001",
keywords = "ncrr, map3d, cardiac heart, scientific
visualization, forward problems inverse problems
forward simulation inverse solutions finite
elements",
}
@Article{SCI:Mac2001b,
author = "R.S. MacLeod and B.B. Punske and B. Yilmaz and S.
Shome and B. Taccardi",
title = "The Role of Heart Rate in Myocardial Ischemia From
Restricted Coronary Perfusion",
journal = j-JE,
volume = "34 (supp)",
pages = "43--51",
year = "2001",
note = "ISCE conference paper",
keywords = "ncrr, map3d, cardiac heart, scientific
visualization",
url = "http://www.sci.utah.edu/publications/macleod_isce01/isce01.pdf",
}
@Article{SCI:Mac2002a,
author = "R.S. MacLeod and Q. Ni and B. Taccardi",
title = "Modeling Cardiac Bioelectricity in Realistic
Volumes: How Real is Real?",
journal = "Einthoven 2002",
pages = "45-56",
year = "2002",
editor = "M.J. Schalij and M.J. Janse and A. van Oosterom
and H.J.J. Wellens and E.E. van der Wall",
institution = "The Einthoven Foundation",
location = "Leiden",
keywords = "NCRR, forward problems inverse problems forward
simulation inverse solutions finite elements,
biopse, cardiac heart, ncrr, scientific
computing",
url = "http://www.sci.utah.edu/publications/macleod02/MacLeod-EInthoven2002.pdf",
}
@InProceedings{SCI:Mac2002b,
author = "R.S. MacLeod and E.D. DiBella and B.B. Punske and
E.K. Jeong",
title = "Multimodal Imaging of Cardiac Activation,
Perfusion, and Ischemia",
booktitle = "14th Annual Research Symposium of the Medical
Imaging Research Laboratory",
year = "2002",
keywords = "NCRR, forward problems inverse problems forward
simulation inverse solutions finite elements,
forward simulation, map3d, biopse, cardiac heart,
ncrr, scientific computing",
}
@InProceedings{SCI:Mac2004a,
author = "R.S. Macleod and D.M. Weinstein and J.D. de St.
Germain and D.H. Brooks and C.R. Johnson and S.G.
Parker",
title = "SCIRun/BioPSE: Integrated Problem Solving
Environment for Bioelectric Field Problems and
Visualization",
booktitle = "Proceedings of the Int. Symp. on Biomed. Imag.",
pages = "640--643",
year = "2004",
month = "April",
location = "Arlington, Va",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions, scirun, biopse",
url = "http://www.sci.utah.edu/publications/macleod04/paper-utah.pdf",
}
@Article{SCI:Mac2005a,
author = "R.S. MacLeod and B. Yilmaz and B.B. Punske and B.
Taccardi and D.H. Brooks",
title = "Epicardial Activation Mapping from Multielectrode
Venous Catheters",
journal = j-JE,
pages = "(in press)",
year = "2005",
keywords = "cardiac heart, ncrr",
}
@Article{SCI:Mac2005b,
author = "R.S. MacLeod and S. Shome and J.G. Stinstra and
B.P. Punske and B. Hopenfeld",
title = "Mechanisms of Ischemia-Induced ST-Segment
Changes",
journal = j-JE,
volume = "38(4 Suppl)",
pages = "8--13",
year = "2005",
month = "November",
keywords = "ncrr",
}
@Article{SCI:Mac2005c,
author = "R.S. MacLeod",
title = "Mechanisms of ischemia-induced {ST}-segment
changes",
journal = "Journal of Electrocardiology",
volume = "38",
number = "4 ",
pages = "8--13",
year = "2005",
publisher = "Elsevier",
month = "Oct",
doi = "10.1016/j.jelectrocard.2005.06.095",
keywords = "cardiac heart, ncrr",
}
@Article{SCI:Mac2005e,
author = "R.S. MacLeod and F. Kornreich and A. van Oosterom
and P. Rautaharju and R. Selvester and G. Wagner
and C. Zywietz",
title = "Report of the First Virtual Visualization of the
Reconstructed Electrocardiographic Display
Symposium",
journal = "Journal of Electrocardiology",
volume = "38",
pages = "385--399",
year = "2005",
url = "http://www.sci.utah.edu/publications/macleod05/FredSymposium-final.pdf",
}
@Article{SCI:Mac2009a,
author = "R.S. MacLeod and J.G. Stinstra and S. Lew and R.T.
Whitaker and D.J. Swenson and M.J. Cole and J.
Kr{\"u}ger and D.H. Brooks and C.R. Johnson",
title = "Subject-specific, multiscale simulation of
electrophysiology: a software pipeline for
image-based models and application examples",
journal = "Philosophical Transactions of The Royal Society A,
Mathematical, Physical \& Engineering Sciences",
volume = "367",
number = "1896",
pages = "2293--2310",
year = "2009",
url = "http://www.sci.utah.edu/publications/Mac2009a/MacLeod_TRSA2009.pdf",
}
@InCollection{SCI:Mac2011a,
author = "R.S. MacLeod and J.J.E. Blauer",
title = "Atrial Fibrillation",
booktitle = "Multimodal Cardiovascular Imaging: Principles and
Clinical Applications",
year = "2011",
editor = "O. Pahlm and G. Wagner",
chapter = "25",
publisher = "McGraw Hill",
isbn = "0071613463",
keywords = "ablation, carma, cvrti, 5P41-RR012553-10",
url = "http://www.sci.utah.edu/publications/macleod13/MacLeod_AfibChapter2013.pdf",
}
@InProceedings{SCI:Mac91a,
author = "R.S. MacLeod and C.R. Johnson and P.R. Ershler",
title = "Construction of an Inhomogeneous Model of the
Human Torso for Use in Computational
Electrocardiography",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
13th Annual International Conference",
pages = "688--689",
year = "1991",
publisher = "{IEEE} Press",
}
@InProceedings{SCI:Mac92c,
author = "R.S. MacLeod and C.R. Johnson and M.A. Matheson",
title = "Visualization Tools for Computational
Electrocardiology",
booktitle = "Visualization in Biomedical Computing",
pages = "433--444",
year = "1992",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart, pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/macleod92/MacLeod_VBC1992.pdf",
}
@InProceedings{SCI:Mac92d,
author = "R.S. MacLeod and C.R. Johnson and M.A. Matheson",
title = "Visualization of cardiac bioelectricity --- a case
study",
booktitle = "{IEEE} Visualization `92",
pages = "411--418",
year = "1992",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scalar field methods, vector field methods, cardiac
heart",
}
@InProceedings{SCI:Mac92e,
author = "R.S. MacLeod and C.R. Johnson and M.J. Gardner
B.M.",
title = "Localization of Ischemia during Coronary
Angioplasty using Body Surface Potential Mapping
and an Electrocardiographic Inverse Solution",
booktitle = "Computers in Cardiology",
pages = "251--254",
year = "1992",
publisher = "{IEEE} Press",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
}
@Article{SCI:Mac93,
author = "R.S. MacLeod and C.R. Johnson and M.A. Matheson",
title = "Visualization of Bioelectric Fields",
journal = "{IEEE} Computer Graphics and Applications",
volume = "14",
pages = "10--12",
year = "1993",
month = "Jul",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scalar field methods, vector field methods",
}
@InProceedings{SCI:Mac93b,
author = "R.S. MacLeod and C.R. Johnson",
title = "Map3d: Interactive Scientific Visualization for
Bioengineering Data",
booktitle = "Proceedings of the {IEEE} Engineering in Medicine
and Biology Society 15th Annual International
Conference",
pages = "30--31",
year = "1993",
publisher = "{IEEE} Press",
keywords = "map3d, neuro brain, cardiac heart, scientific
visualization",
url = "http://www.sci.utah.edu/publications/macleod93/embs93.pdf",
}
@TechReport{SCI:Mac94d,
author = "R.S. MacLeod and P.R. Ershler and C.R. Johnson
M.A.",
title = "Map3d: Scientific Visualization Program for
Multichannel Time Series Data on Unstructured,
Three-Dimensional Meshes. Program User's Guide",
number = "UUCS-94-016",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "computational pde pdes computational partial
differential equations evaporation, map3d, cardiac
heart, scientific visualization",
url = "http://www.sci.utah.edu/publications/macleod94/tr-map3d.ps",
url = "http://www.sci.utah.edu/publications/macleod94/tr-map3d.ps.Z",
}
@TechReport{SCI:Mac94e,
author = "R.S. MacLeod and C.R. Johnson and P.R. Ershler",
title = "Construction of a Human Torso Model from Magnetic
Resonance Images for Problems in Computational
Electrocardiography",
number = "UUCS-94-017",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
computational pde pdes computational partial
differential equations evaporation, cardiac heart,
scientific computing",
url = "http://www.sci.utah.edu/publications/macleod94/tr-mridoc.ps",
url = "http://www.sci.utah.edu/publications/macleod94/tr-mridoc.ps.Z",
}
@InProceedings{SCI:Mag2004a,
author = "M. Magnor and G. Kindlmann and C.D. Hansen and N.
Duric",
title = "Constrained Inverse Volume Rendering for Planetary
Nebulae",
booktitle = c-VIS2004,
pages = "83--90",
year = "2004",
keywords = "scalar field methods, volume rendering, simian,
inverse constrained volume rendering",
url = "http://www.sci.utah.edu/publications/magnor04/Magnor_Vis2004.pdf",
}
@Article{SCI:Mah2010a,
author = "C. Mahnkopf and T.J. Badger and N.S. Burgon and M.
Daccarett and T.S. Haslam and C.T. Badger and C.J.
McGann and N. Akoum and E. Kholmovski and R.S.
Macleod and N.F. Marrouche",
title = "Evaluation of the left atrial substrate in
patients with lone atrial fibrillation using
delayed-enhanced {MRI}: implications for disease
progression and response to catheter ablation",
journal = "Heart Rhythm",
volume = "7",
number = "10",
pages = "1475--1481",
year = "2010",
pmid = "20601148",
keywords = "af, atrial fibrillation, ablation",
url = "http://www.sci.utah.edu/publications/mahnkopf10/mahnkopf2010.pdf",
}
@Article{SCI:Mak2009a,
author = "C.B. Maks and C.R. Butson and B.L. Walter and J.L.
Vitek and C.C. McIntyre",
title = "Deep brain stimulation activation volumes and
their association with neurophysiological mapping
and therapeutic outcomes",
journal = "Journal of Neurology, Neurosurgery, and
Psychiatry",
volume = "80",
number = "6",
pages = "659--666",
year = "2009",
month = "June",
issn = "1468-330X",
doi = "10.1136/jnnp.2007.126219",
keywords = "Brain Mapping, Brain Mapping: methods,
Cerebral,Cerebral: physiology, Computer-Assisted,
Computer-Assisted: methods, Deep Brain Stimulation,
Deep Brain Stimulation: methods, Diffusion Magnetic
Resonance Imaging, Diffusion Magnetic Resonance
Imaging: methods, Dominance, Electrodes, Humans,
Image Processing, Imaging, Implanted, Magnetic
Resonance Imaging, Magnetic Resonance Imaging:
methods, Nerve Net, Nerve Net: physiopathology,
Neurologic Examination, Neurons, Neurons:
physiology, Parkinson Disease, Parkinson Disease:
physiopathology, Parkinson Disease: therapy,
Substantia Nigra, Substantia Nigra:
physiopathology, Subthalamic Nucleus, Subthalamic
Nucleus: physiopathology, Synaptic Transmission,
Synaptic Transmission: physiology, Thalamus,
Thalamus: physiopathology, Three-Dimensional,
Tomography, Treatment Outcome, X-Ray Computed,
X-Ray Computed: methods",
url = "http://www.sci.utah.edu/publications/Mak2009a/Maks_JNNP2009.pdf",
}
@Article{SCI:Mal2007a,
author = "M. Malik and Y. Birnbaum and R.S. MacLeod and V.
Shusterman",
title = "Markers of impaired repolarization",
journal = "Journal of Electrocardiology",
volume = "40",
number = "1",
pages = "S54--S57",
year = "2007",
month = "January",
}
@InProceedings{SCI:Mal2013a,
author = "D. Maljovec and Bei Wang and V. Pascucci and P.-T.
Bremer and M.Pernice and D. Mandelli and R.
Nourgaliev",
title = "Exploration of High-Dimensional Scalar Function
for Nuclear Reactor Safety Analysis and
Visualization",
booktitle = "Proceedings of the 2013 International Conference
on Mathematics and Computational Methods Applied to
Nuclear Science \& Engineering ({M\&C})",
pages = "712-723",
year = "2013",
keywords = "high-dimensional data analysis, computational
topology, nuclear reactor safety analysis,
visualization",
url = "http://www.sci.utah.edu/publications/Mal2013a/Maljovec_HighDim_ReactorSafety2013.pdf",
}
@InProceedings{SCI:Mal2013b,
author = "D. Maljovec and Bei Wang and D. Mandelli and P.-T.
Bremer and V. Pascucci",
title = "Adaptive Sampling Algorithms for Probabilistic
Risk Assessment of Nuclear Simulations",
booktitle = "Proceedings of the 2013 International Topical
Meeting on Probabilistic Safety Assessment and
Analysis ({PSA} 2013)",
year = "2013",
note = "First runner-up for Best Student Paper Award",
keywords = "high-dimensional data analysis, computational
topology, nuclear reactor safety analysis,
visualization",
url = "http://www.sci.utah.edu/publications/maljovec13/Maljovec_Adaptive_Sampling2013.pdf",
}
@InProceedings{SCI:Mal2013c,
author = "D. Maljovec and Bei Wang and D. Mandelli and P.-T.
Bremer and V. Pascucci",
title = "Analyze Dynamic Probabilistic Risk Assessment Data
through Clustering",
booktitle = "Proceedings of the 2013 International Topical
Meeting on Probabilistic Safety Assessment and
Analysis ({PSA} 2013)",
year = "2013",
url = "http://www.sci.utah.edu/publications/maljovec13/Maljovec_DPRA_Clustering2013.pdf",
}
@Article{SCI:Mal2013d,
author = "D. Maljovec and Bei Wang and A. Kupresanin and G.
Johannesson and V. Pascucci and P.-T. Bremer",
title = "Adaptive Sampling with Topological Scores",
journal = "Int. J. Uncertainty Quantification",
volume = "3",
number = "2",
pages = "119--141",
year = "2013",
publisher = "Begell House",
doi =
"10.1615/int.j.uncertaintyquantification.2012003955",
url = "http://www.sci.utah.edu/publications/Mal2013d/Maljovec_IJUQ2013.pdf",
}
@TechReport{SCI:Mal2014a,
author = "D. Maljovec and Bei Wang and J. Moeller and V.
Pascucci",
title = "Topology-Based Active Learning",
number = "UUSCI-2014-001",
year = "2014",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/Mal2014a/UUSCI-2014-001.pdf",
}
@InProceedings{SCI:Mal2014b,
author = "D. Maljovec and S. Liu and Bei Wang and V.
Pascucci and P.-T. Bremer and D. Mandelli and C.
Smith",
title = "Analyzing Simulation-Based {PRA} Data Through
Clustering: a {BWR} Station Blackout Case Study",
booktitle = "Proceedings of the Probabilistic Safety Assessment
\& Management conference ({PSAM})",
year = "2014",
keywords = "{PRA}, computational topology, clustering,
high-dimensional analysis",
url = "http://www.sci.utah.edu/publications/Mal2014b/Maljovec_BWR_Study_2014.pdf",
}
@Article{SCI:Mal2016a,
author = "D. Maljovec and S. Liu and Bei Wang and V.
Pascucci and P. T. Bremer and D. Mandelli and C.
Smith.",
title = "Analyzing Simulation-Based PRA Data Through
Traditional and Topological Clustering: A BWR
Station Blackout Case Study",
journal = "Reliability Engineering \& System Safety",
volume = "145",
pages = "262--276",
year = "2016",
publisher = "Elsevier",
month = "January",
doi = "10.1016/j.ress.2015.07.001",
url = "http://www.sci.utah.edu/publications/Mal2016a/RESS_BWR_BeiWang_2015.pdf",
}
@InProceedings{SCI:Man2011a,
author = "J. Mandel and J.D. Beezley and A. Kochanski and
V.Y. Kondratenko and L. Zhang and E. Anderson and
J. Daniels II and C.T. Silva and C.R. Johnson",
title = "A wildland fire modeling and visualization
environment",
title_url =
"http://ams.confex.com/ams/9FIRE/webprogram/Paper192277.html",
booktitle = "Proceedings of the Ninth Symposium on Fire and
Forest Meteorology",
pages = "(published online)",
year = "2011",
keywords = "vistrails, wildland fire modeling, openwfm.org",
url = "http://www.sci.utah.edu/publications/mandel11/Mandel_9fire2011.pdf",
}
@InProceedings{SCI:Man2014a,
author = "D. Mandelli and C. Smith and T. Riley and J.
Nielsen and J. Schroeder and C. Rabiti and A.
Alfonsi and J. Cogliati and R. Kinoshita and V.
Pascucci and Bei Wang and D. Maljovec",
title = "Overview of New Tools to Perform Safety Analysis:
{BWR} Station Black Out Test Case",
booktitle = "Proceedings of the Probabilistic Safety Assessment
\& Management conference ({PSAM})",
year = "2014",
url = "http://www.sci.utah.edu/publications/Man2014a/Mandelli_Overview_Tools_2014.pdf",
}
@Misc{SCI:Map3d,
author = "{CIBC}",
year = "2015",
note = "map3d: Interactive scientific visualization tool
for bioengineering data. Scientific Computing and
Imaging Institute ({SCI}), Download from:
http://www.sci.utah.edu/cibc/software.html",
keywords = "Map3d, CIBC",
}
@Article{SCI:Mar2002a,
author = "W. Martin and E. Reinhard and P. Shirly and S.G.
Parker and W. Thompson",
title = "Temporally Coherent Interactive Ray Tracing",
journal = "Journal of Graphics Tools",
volume = "7",
number = "2",
pages = "41--48",
year = "2002",
keywords = "rtrt real-time ray tracing, interactive rt
distributed interactive ray tracing dirt",
url = "http://www.sci.utah.edu/publications/martin02/Temporally_Coherent_Inter_Raytracing.pdf",
}
@TechReport{SCI:Mar2006a,
author = "H. Marmanis and C.W. Hamman and R.M. Kirby",
title = "A One-Dimensional Model of the Navier-Stokes",
number = "UUSCI-2006-012",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = ", navier-stokes",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-012.pdf",
}
@InProceedings{SCI:Mar2008a,
author = "T. Martin and E. Cohen and R.M. Kirby",
title = "Volumetric Parameterization and Trivariate
B-spline Fitting using Harmonic Functions",
booktitle = "Proceedings of ACM Solid and Physical Modeling",
pages = "269-280",
year = "2008",
location = "Stony Brook, NY",
note = "Awarded Best Paper",
url = "http://www.sci.utah.edu/publications/martin08/martin_spm08.pdf",
}
@Article{SCI:Mar2009a,
author = "H.G. Martinez and S.I. Prajapati and C.A. Estrada
and F. Jimenez and M.P. Quinones and I. Wu and A.
Bahadur and A. Sanderson and C.R. Johnson and M.
Shim and C. Keller and S.S. Ahuja",
title = "Microscopic Computed Tomography Based Virtual
Histology for Visualization and Morphometry of
Atherosclerosis in Diabetic Apolipoprotein E Mutant
Mice",
journal = "Circulation: Journal of the American Heart
Association",
volume = "120",
number = "9",
pages = "821--822",
year = "2009",
keywords = "virtual histology, diabetes, tomography,
morphometry",
url = "http://www.sci.utah.edu/publications/martinez09/Prajapati-etal-CIRCULATION.pdf",
}
@Article{SCI:Mar2009b,
author = "H. Martinez and S. Prajapati and C. Estrada and F.
Jimenez and I. Wu and A. Bahadur and A. Sanderson
and C.R. Johnson and M. Shim and C. Keller and S.
Ahuja",
title = "Microscopic Computed Tomography–Based Virtual
Histology for Visualization and Morphometry of
Atherosclerosis in Diabetic Apolipoprotein E Mutant
Mice",
journal = "Circulation",
volume = "120",
number = "821--822",
year = "2009",
url = "http://www.sci.utah.edu/publications/martinez09/Martinez_Circulation2009.pdf",
}
@Article{SCI:Mar2009c,
author = "Y. Marzouk and D. Xiu",
title = "A Stochastic Collocation Approach to Bayesian
Inference in Inverse Problems",
journal = "Communications in Computational Physics",
volume = "6",
number = "4",
pages = "826--847",
year = "2009",
doi = "10.4208/cicp.2009.v6.p826",
keywords = "Inverse problems, Bayesian inference, stochastic
collocation, generalized polynomial",
url = "http://www.sci.utah.edu/publications/marzouk09/Marzouk_CiCP2009.pdf",
}
@InProceedings{SCI:Mar2010a,
author = "C. Marc and C. Vachet and J.E. Blocher and G.
Gerig and J.H. Gilmore and M.A. Styner",
title = "Changes of MR and DTI appearance in early human
brain development",
booktitle = "Proceedings of SPIE Medical Imaging 7623,
762324",
year = "2010",
doi = "10.1117/12.844912",
}
@Article{SCI:Mar2011a,
author = "T. Martin and E. Cohen and R.M. Kirby",
title = "Direct Isosurface Visualization of Hex-Based
High-Order Geometry and Attribute
Representations",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "PP",
number = "99",
pages = "1--14",
year = "2011",
issn = "1077-2626",
doi = "10.1109/TVCG.2011.103",
url = "http://www.sci.utah.edu/publications/martin11/Martin_TVCG2011.pdf",
}
@Article{SCI:Mar2012a,
author = "T. Martin and G. Chen and S. Musuvathy and E.
Cohen and C.D. Hansen",
title = "Generalized Swept Mid-structure for Polygonal
Models",
journal = "Computer Graphics Forum",
volume = "31",
number = "2 part 4",
pages = "805--814",
year = "2012",
publisher = "Wiley-Blackwell",
month = "May",
doi = "10.1111/j.1467-8659.2012.03061.x",
keywords = "scidac, kaust",
url = "http://www.sci.utah.edu/publications/Mar2012a/Martin_gsm_EG2012.pdf",
}
@InProceedings{SCI:Mas2004a,
author = "A. Mascarenhas and M. Isenburg and V. Pascucci and
J. Snoeyink",
title = "Encoding Volumetric Meshes For Streaming
Isosurface Extraction",
booktitle = "Proceedings of the International Symposium on 3D
Data Processing, Visualization, and Transmission
(3DPVT)",
pages = "293--300",
year = "2004",
month = "September",
note = "UCRL-PROC-208696",
}
@InProceedings{SCI:Max2003a,
author = "N. Max and P. Williams and C.T. Silva and R.
Cook",
title = "Volume Rendering for Curvilinear and Unstructured
Grids",
booktitle = "Proceedings of Computer Graphics International,
2003",
pages = "210--215",
year = "2003",
isbn = "0-7695-1946-6",
issn = "1530-1052",
url = "http://www.sci.utah.edu/publications/max03/cgi2003.pdf",
}
@InProceedings{SCI:Mcc2001a,
author = "J. McCorquodale and J.D. de St. Germain and S.G.
Parker and C.R. Johnson",
title = "The Uintah Parallelism Infrastructure: A
Performance Evaluation on the SGI Origin 2000",
booktitle = c-HPC2001,
year = "2001",
month = "Mar",
location = "Seattle",
keywords = "scirun, uintah, csafe, sgi",
url = "http://www.sci.utah.edu/publications/hpc01-dav/hpc01.pdf",
}
@InProceedings{SCI:Mcc2004a,
author = "P. McCormick and J. Inman and J. Ahrens and G.
Roth and C.D. Hansen",
title = "Hardware-Accelerated System for Quantitatively
Driven Visualization and Analysis",
booktitle = c-VIS2004,
pages = "171--178",
year = "2004",
keywords = "volume rendering, hardware acceleration,
visualization systems, multivariate
visualization",
url = "http://www.sci.utah.edu/publications/mccormick04/vis04-scout04.pdf",
}
@Article{SCI:Mcc2013a,
author = "R.K. McClure and M. Styner and J.A. Lieberman and
S. Gouttard and G. Gerig and X. Shi and H. Zhu",
title = "Localized differences in caudate and hippocampal
shape associated with schizophrenia but not
antipsychotic type",
journal = "Psychiatry Research: Neuroimaging",
volume = "211",
number = "1",
pages = "1--10",
year = "2013",
month = "January",
doi = "10.1016/j.pscychresns.2012.07.001",
pmcid = "PMC3557605",
url = "http://www.sci.utah.edu/publications/mcclure12/Mcclure_PRN2012.pdf",
}
@Article{SCI:Mcc99a,
author = "P. McCormick and C.D. Hansen and E. Angel",
title = "The Deferred Accumulation Buffer",
journal = "Journal for Graphics Tools",
volume = "4",
number = "3",
pages = "35--46",
year = "1999",
}
@Article{SCI:Mcd2012a,
author = "K.S. McDowell and F. Vadakkumpadan and R. Blake
and J. Blauer and G. Plank and R.S. MacLeod and
N.A. Trayanova",
title = "Methodology for patient-specific modeling of
atrial fibrosis as a substrate for atrial
fibrillation",
journal = "Journal of Electrocardiology",
volume = "45",
number = "6",
pages = "640--645",
year = "2012",
doi = "10.1016/j.jelectrocard.2012.08.005",
pmid = "22999492",
pmcid = "PMC3515859",
keywords = "Patient-specific modeling, Computational model,
Atrial fibrillation, Atrial fibrosis",
url = "http://www.sci.utah.edu/publications/mcdowell12/McDowell_JEC2012.pdf",
}
@Article{SCI:Mcd2013a,
author = "K.S. McDowell and F. Vadakkumpadan and R. Blake
and J. Blauer and G.t Plank and R.S. MacLeod and
N.A. Trayanova",
title = "Mechanistic Inquiry into the Role of Tissue
Remodeling in Fibrotic Lesions in Human Atrial
Fibrillation",
journal = "Biophysical Journal",
volume = "104",
pages = "2764--2773",
year = "2013",
doi = "10.1016/j.bpj.2013.05.025",
pmid = "23790385",
pmcid = "PMC3686346",
url = "http://www.sci.utah.edu/publications/mcdowell13/McDowell_Biophysical2013.pdf",
}
@Article{SCI:Mcd2015a,
author = "K.S. McDowell and S. Zahid and F. Vadakkumpadan
and J.J. Blauer and R.S. MacLeod and N.A.
Trayanova",
title = "Virtual Electrophysiological Study of Atrial
Fibrillation in Fibrotic Remodeling",
journal = "PLoS ONE",
volume = "10",
number = "2",
pages = "e0117110",
year = "2015",
month = "February",
doi = "10.1371/journal.pone.0117110",
url = "http://www.sci.utah.edu/publications/Mcd2015a/McDowell_PLoSONE2015.pdf",
}
@Article{SCI:Mcd2015b,
author = "K. S. McDowell and S. Zahid and F. Vadakkumpadan
and J. Blauer and R. S. MacLeod and N. A.
Trayanova",
title = "Virtual Electrophysiological Study of Atrial
Fibrillation in Fibrotic Remodeling",
journal = "PLoS ONE",
volume = "10",
number = "2",
pages = "1-16",
year = "2015",
publisher = "Public Library of Science",
month = "May",
doi = "doi.org/10.1371/journal.pone.0117110",
url = "http://www.sci.utah.edu/publications/Mcd2015b/journal.pone.0117110.PDF",
}
@Article{SCI:Mcg2008a,
author = "C.J. McGann and E.G. Kholmovski and R.S. Oakes and
J.J. Blauer and M. Daccarett and N. Segerson and
K.J. Airey and N. Akoum and E. Fish and T.J. Badger
and E.V. DiBella and D.L. Parker and R.S. MacLeod
and N.F. Marrouche",
title = "New Magnetic Resonance Imaging-Based Method for
Defining the Extent of Left Atrial Wall Injury
After the Ablation of Atrial Fibrillation",
journal = "Journal of the American College of Cardiology",
volume = "52",
number = "15",
pages = "1263--1271",
year = "2008",
month = "Oct 7",
url = "http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf",
}
@Article{SCI:Mcg2011a,
author = "C.J. McGann and E.G. Kholmovski and J.J. Blauer
and S. Vijayakumar and T.S. Haslam and J.E. Cates
and E.V. DiBella and N.S. Burgon and B. Wilson and
A.J. Alexander and M.W. Prastawa and M. Daccarett
and G. Vergara and N.W. Akoum and D.L. Parker and
R.S. MacLeod and N.F. Marrouche",
title = "Dark Regions of No-Reflow on Late Gadolinium
Enhancement Magnetic Resonance Imaging Result in
Scar Formation After Atrial Fibrillation
Ablation",
journal = "Journal of the American College of Cardiology",
volume = "58",
number = "2",
pages = "177--185",
year = "2011",
doi = "10.1016/j.jacc.2011.04.008",
pmid = "21718914",
url = "http://www.sci.utah.edu/publications/mcgann11/McGann_JACC2011.pdf",
}
@Article{SCI:Mcg2013a,
author = "C. McGann and N. Akoum and A. Patel and E.
Kholmovski and P. Revelo and K. Damal and B. Wilson
and J. Cates and A. Harrison and R. Ranjan and N.S.
Burgon and T. Greene and D. Kim and E.V.R. DiBella
and D. Parker and R.S. MacLeod and N.F.
Marrouche",
title = "Atrial Fibrillation Ablation Outcome is Predicted
by Left Atrial Remodeling on {MRI}",
journal = "Circulation: Arrhythmia and Electrophysiology",
year = "2013",
month = "December",
note = "Published online before print.",
doi = "10.1161/CIRCEP.113.000689",
keywords = "atrial fibrillation arrhythmia, catheter ablation,
magnetic resonance imaging, remodeling, outcome",
url = "http://www.sci.utah.edu/publications/mcgann13/McGann_Circ2013.pdf",
}
@Article{SCI:Mcg2014a,
author = "C. McGann and N. Akoum and A. Patel and E.
Kholmovski and P. Revelo and K. Damal and B. Wilson
and J. Cates and A. Harrison and R. Ranjan and N.S.
Burgon and T. Greene and D. Kim and E.V. Dibella
and D. Parker and R.S. MacLeod and N.F.
Marrouche",
title = "Atrial fibrillation ablation outcome is predicted
by left atrial remodeling on {MRI}",
journal = "Circ Arrhythm Electrophysiol",
volume = "7",
number = "1",
pages = "23--30",
year = "2014",
doi = "10.1161/CIRCEP.113.000689",
pmid = "24363354",
}
@InCollection{SCI:Mci2006a,
author = "L.C. McInnes and B.A. Allan and R. Armstrong and
S.J. Benson and D.E. Bernholdt and T.L. Dahlgren
and L.F. Diachin and M. Krishnan and J.A. Kohl and
J.W. Larson and S. Lefantzi and J. Nieplocha and B.
Norris and S.G. Parker and J. Ray and S. Zhou",
title = "Parallel {PDE}-Based Simulations Using the Common
Component Architecture",
booktitle = "Numerical Solution of Partial Differential
Equations on Parallel Computers",
pages = "327--284",
year = "2006",
editor = "A.M. Bruaset and P. Bjorstad and A. Tveito",
series = "Lecture Notes in Computational Science and
Engineering",
publisher = "Springer",
isbn = "3-540-29076-1",
keywords = "computational pde pdes computational partial
differential equations, cca, simulation, parallel
computing",
}
@Article{SCI:Mci2014a,
author = "G. McInerny and M. Chen and R. Freeman and D.
Gavaghan and M.D. Meyer and F. Rowland and D.
Spiegelhalter and M. Steganer and G. Tessarolo and
J. Hortal",
title = "Information Visualization for Science and Policy:
Engaging Users and Avoiding Bias",
journal = "Trends in Ecology \& Evolution",
volume = "29",
number = "3",
pages = "148--157",
year = "2014",
doi = "10.1016/j.tree.2014.01.003",
url = "http://www.sci.utah.edu/publications/Mci2014a/McInerny_InfoVisForScienceAndPolicy2014.pdf",
}
@Article{SCI:Mck2014a,
author = "S. McKenna and D. Mazur and J. Agutter and M.D.
Meyer",
title = "Design Activity Framework for Visualization
Design",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
year = "2014",
keywords = "Design, frameworks, process, cybersecurity, nested
model, decisions, models, evaluation,
visualization",
url = "http://www.sci.utah.edu/publications/Mck2014a/McKenna_TVCG2014.pdf",
}
@Article{SCI:Mck2015a,
author = "S. McKenna and M. Meyer and C. Gregg and S.
Gerber",
title = "s-CorrPlot: An Interactive Scatterplot for
Exploring Correlation",
title_url = "http://dx.doi.org/10.1080/10618600.2015.1021926",
journal = "Journal of Computational and Graphical
Statistics",
year = "2015",
doi = "10.1080/10618600.2015.1021926",
url = "http://www.sci.utah.edu/publications/Mck2015a/McKenna_CompGraphStat15.pdf",
}
@Article{SCI:Mck2017a,
author = "S. McKenna and A. Lex and M. Meyer",
title = "Worksheets for Guiding Novices through the
Visualization Design Process",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Mck2017a/1709.05723.pdf",
}
@Article{SCI:Mcl2013a,
author = "T. McLoughlin and M.W. Jones and R.S. Laramee and
R. Malki and I. Masters and C.D. Hansen",
title = "Similarity Measures for Enhancing Interactive
Streamline Seeding",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "19",
number = "8",
pages = "1342--1353",
year = "2013",
issn = "1077-2626",
doi = "10.1109/TVCG.2012.150",
pmid = "23744264",
url = "http://www.sci.utah.edu/publications/Mcl2013a/McLoughlin_TVCG2013.pdf",
}
@Article{SCI:Mea2006a,
author = "S. Means and A.J. Smith and J. Shepherd and J.
Shadid and J. Fowler and R. Wojcikiewicz and T.
Mazel and G.D. Smith and B.S. Wilson",
title = "Reaction Diffusion Modeling of Calcium Dynamics
with Realistic ER Geometry",
journal = j-BJ,
volume = "91",
pages = "537--557",
year = "2006",
month = "March",
url = "http://www.sci.utah.edu/publications/means06/means_biophysj_2006.pdf",
}
@InProceedings{SCI:Mel2006a,
author = "I. Melatti and R. Palmer and G. Sawaya and Y. Yang
and R.M. Kirby and G. Gopalakrishnan",
title = "Parallel and Distributed Model Checking in Eddy",
booktitle = "Model Checking Software: Proceedings of the 13th
International SPIN Workshop ({SPIN} 2006)",
volume = "3925/2006",
pages = "108--125",
year = "2006",
location = "Austria",
url = "http://www.sci.utah.edu/publications/melatti06/melatti_SPIN06.pdf",
}
@TechReport{SCI:Men2008a,
author = "Q. Meng and J. Luitjens and M. Berzins",
title = "A Comparison of Load Balancing Algorithms for AMR
in Uintah",
number = "UUSCI-2008-006",
year = "2008",
institution = "University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-006.pdf",
}
@TechReport{SCI:Men2010a,
author = "Q. Meng and J. Luitjens and M. Berzins",
title = "Dynamic Task Scheduling for Scalable Parallel AMR
in the Uintah Framework",
number = "UUSCI-2010-001",
year = "2010",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "csafe, c-safe, uintah, scirun, fluid structure,
amr, mpm",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2010-001.pdf",
}
@InProceedings{SCI:Men2010b,
author = "Q. Meng and J. Luitjens and M. Berzins",
title = "Dynamic Task Scheduling for the Uintah
Framework",
booktitle = "Proceedings of the 3rd {IEEE} Workshop on
Many-Task Computing on Grids and Supercomputers
({MTAGS10})",
pages = "1--10",
year = "2010",
doi = "10.1109/MTAGS.2010.5699431",
url = "http://www.sci.utah.edu/publications/Men2010b/Meng_TaskSchedulingUintah2010.pdf",
}
@InProceedings{SCI:Men2011a,
author = "Q. Meng and M. Berzins and J. Schmidt",
title = "Using Hybrid Parallelism to improve memory use in
Uintah",
booktitle = "Proceedings of the TeraGrid 2011 Conference",
year = "2011",
publisher = "ACM",
month = "July",
location = "Salt Lake City, Utah",
doi = "10.1145/2016741.2016767",
keywords = "Uintah, C-SAFE, parallel computing",
url = "http://www.sci.utah.edu/publications/Men2011a/Meng_Tgrid11.pdf",
}
@TechReport{SCI:Men2012a,
author = "Q. Meng and M. Berzins",
title = "Scalable Large-scale Fluid-structure Interaction
Solvers in the Uintah Framework via Hybrid
Task-based Parallelism Algorithms",
number = "UUSCI-2012-004",
year = "2012",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "uintah, csafe",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2012-004.pdf",
}
@InProceedings{SCI:Men2012b,
author = "Q. Meng and A. Humphrey and M. Berzins",
title = "The Uintah Framework: A Unified Heterogeneous Task
Scheduling and Runtime System",
booktitle = "Digital Proceedings of The International
Conference for High Performance Computing,
Networking, Storage and Analysis",
pages = "2441--2448",
year = "2012",
note = "SC’12 –2nd International Workshop on
Domain-Specific Languages and High-Level Frameworks
for High Performance Computing, WOLFHPC 2012",
doi = "10.1109/SCC.2012.6674233",
url = "http://www.sci.utah.edu/publications/Men2012b/uintah-wolfhpc12.pdf",
}
@Article{SCI:Men2012c,
author = "Q. Meng and J. Hall and H. Rutigliano and X. Zhou
and B.R. Sessions and R. Stott and K. Panter and
C.J. Davies and R. Ranjan and D. Dosdall and R.S.
MacLeod and N. Marrouche and K.L. White and Z. Wang
and I.A. Polejaeva",
title = "30 Generation of Cloned Transgenic Goats with
Cardiac Specific Overexpression of Transforming
Growth Factor β1",
journal = "Reproduction, Fertility and Development",
volume = "25",
number = "1",
pages = "162--163",
year = "2012",
doi = "10.1071/RDv25n1Ab30",
url = "http://www.sci.utah.edu/publications/meng12/Meng_RFD2012.pdf",
}
@TechReport{SCI:Men2013a,
author = "Q. Meng and A. Humphrey and J. Schmidt and M.
Berzins",
title = "Preliminary Experiences with the Uintah Framework
on Intel Xeon Phi and Stampede",
number = "UUSCI-2013-002",
year = "2013",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "Uintah, hybrid parallelism, scalability, parallel,
adaptive, MIC, Xeon Phi, heterogeneous systems,
Stampede, co-processor",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2013-002.pdf",
}
@TechReport{SCI:Men2013c,
author = "Q. Meng and A. Humphrey and J. Schmidt and M.
Berzins",
title = "Investigating Applications Portability with the
Uintah DAG-based Runtime System on PetaScale
Supercomputers",
number = "UUSCI-2013-003",
year = "2013",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "Uintah, hybrid parallelism, scalability, parallel,
adaptive, MIC, Xeon Phi, heterogeneous systems,
Stampede, co-processor",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2013-003.pdf",
}
@InProceedings{SCI:Men2013d,
author = "Q. Meng and A. Humphrey and J. Schmidt and M.
Berzins",
title = "Investigating Applications Portability with the
Uintah {DAG-based} Runtime System on {PetaScale}
Supercomputers",
booktitle = "Proceedings of SC13: International Conference for
High Performance Computing, Networking, Storage and
Analysis",
pages = "96:1--96:12",
year = "2013",
isbn = "978-1-4503-2378-9",
doi = "10.1145/2503210.2503250",
keywords = "Blue Gene/Q, GPU, Xeon Phi, adaptive, application,
co-processor, heterogeneous systems, hybrid
parallelism, parallel, scalability, software,
uintah, NETL",
url = "http://www.sci.utah.edu/publications/meng13/Meng_SC2013.pdf",
}
@InProceedings{SCI:Men2013e,
author = "Q. Meng and A. Humphrey and J. Schmidt and M.
Berzins",
title = "Preliminary Experiences with the Uintah Framework
on Intel Xeon Phi and Stampede",
booktitle = "Proceedings of the Conference on Extreme Science
and Engineering Discovery Environment: Gateway to
Discovery ({XSEDE} 2013)",
pages = "48:1--48:8",
year = "2013",
location = "San Diego, California",
doi = "10.1145/2484762.2484779",
keywords = "MIC, Xeon Phi, adaptive, co-processor,
heterogeneous systems, hybrid parallelism,
parallel, scalability, stampede, uintah, c-safe",
url = "http://www.sci.utah.edu/publications/meng13/Meng_XSEDE2013.pdf",
}
@Article{SCI:Men2014b,
author = "Q. Meng and M. Berzins",
title = "Scalable large-scale fluid-structure interaction
solvers in the Uintah framework via hybrid
task-based parallelism algorithms",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "26",
number = "7",
pages = "1388--1407",
year = "2014",
month = "May",
doi = "10.1002/cpe",
keywords = "MPI, threads, Uintah, many core, lock free,
fluid-structure interaction, c-safe",
url = "http://www.sci.utah.edu/publications/Men2014b/Meng_CCPE2013.pdf",
}
@PhdThesis{SCI:Men2014c,
author = "Qingyu Meng",
title = "Large-Scale Distributed Runtime System for
{DAG}-Based Computational Framework",
year = "2014",
school = "School of Computing, University of Utah",
month = "August",
note = "Ph.D. in Computer Science, advisor Martin
Berzins",
url = "http://www.sci.utah.edu/publications/Men2014c/Qingyu_Meng_PhDThesis2014.pdf",
}
@InProceedings{SCI:Mer2008a,
author = "S. Mergen and C. Heuser and J. Freire",
title = "Querying Structured Information Sources on the
Web",
booktitle = "Proceedings of the 10th International Conference
on Information Integration and Web-based
Applications and Services",
pages = "470--476",
year = "2008",
url = "http://www.sci.utah.edu/publications/mergen08/p470-mergen.pdf",
}
@Article{SCI:Mer2008b,
author = "D. Merck and G. Tracton and R. Saboo and J. Levy
and E. Chaney and S. Pizer and S. Joshi",
title = "Training models of anatomic shape variability",
journal = "Medical Physics",
volume = "35",
number = "8",
pages = "3584--3596",
year = "2008",
pmid = "18777919",
url = "http://www.sci.utah.edu/publications/merck08/Merck_MedPhy2008.pdf",
}
@Article{SCI:Mer2014a,
author = "J. Mercer and B. Pandian and A. Lex and N. Bonneel
and and H. Pfister",
title = "Mu-8: Visualizing Differences between Proteins and
their Families ",
journal = "BMC Proceedings",
volume = "8",
number = "Suppl 2",
pages = "S5",
year = "2014",
month = "Aug",
issn = "1753-6561",
doi = "10.1186/1753-6561-8-S2-S5",
url = "http://www.sci.utah.edu/publications/Mer2014a/2014_bmc_mu8.pdf",
}
@InProceedings{SCI:Mes2015a,
author = "F. Mesadi and M. Cetin and T. Tasdizen",
title = "Disjunctive Normal Shape and Appearance Priors
with Applications to Image Segmentation",
title_url =
"https://link.springer.com/chapter/10.1007%2F978-3-319-24574-4_84",
booktitle = "Lecture Notes in Computer Science",
pages = "703--710",
year = "2015",
publisher = "Springer International Publishing",
isbn = "978-3-319-24574-4",
doi = "10.1007/978-3-319-24574-4_84",
}
@InProceedings{SCI:Mes2016a,
author = "F. Mesadi and M. Cetin and T. Tasdizen",
title = "Disjunctive normal level set: An efficient
parametric implicit method",
booktitle = "2016 IEEE International Conference on Image
Processing (ICIP)",
year = "2016",
publisher = "IEEE",
month = "September",
doi = "10.1109/icip.2016.7533171",
url = "http://www.sci.utah.edu/publications/Mes2016a/07533171.pdf",
}
@Article{SCI:Mes2018a,
author = "Image segmentation using disjunctive normal
Bayesian shape and appearance models",
title = "F. Mesadi, E. Erdil, M. Cetin, T. Tasdizen",
journal = "IEEE Transactions on Medical Imaging",
volume = "37",
number = "1",
pages = "293--305",
year = "2018",
publisher = "IEEE",
month = "Jan",
doi = "10.1109/tmi.2017.2756929",
url = "http://www.sci.utah.edu/publications/Mes2018a/08051060.pdf",
}
@TechReport{SCI:Mey2005a,
author = "M.D. Meyer and H. Pfister and C.D. Hansen and C.R.
Johnson",
title = "Image-Based Volume Rendering with Opacity Light
Fields",
number = "UUSCI-2005-002",
year = "2005",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scalar field methods, volume rendering, image
based volume rendering ibvr",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2005-002.pdf",
}
@InProceedings{SCI:Mey2005b,
author = "M.D. Meyer and P. Georgel and R.T. Whitaker",
title = "Robust Particle Systems for Curvature Dependent
Sampling of Implicit Surfaces",
booktitle = "In Proceedings of the International Conference on
Shape Modeling and Applications (SMI)",
pages = "124--133",
year = "2005",
month = "June",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/miriah05/smi05meyer.pdf",
}
@Article{SCI:Mey2007a,
author = "M.D. Meyer and B. Nelson and R.M. Kirby and R.T.
Whitaker",
title = "Particle Systems for Efficient and Accurate Finite
Element Visualization",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "13",
number = "5",
pages = "1015--1026",
year = "2007",
keywords = "finite elements, particle systems",
url = "http://www.sci.utah.edu/publications/meyer07/tvcg07meyer.pdf",
}
@Article{SCI:Mey2007b,
author = "M.D. Meyer and R.M. Kirby and R.T. Whitaker",
title = "Topology, Accuracy, and Quality of Isosurface
Meshes Using Dynamic Particles",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "13",
number = "6",
pages = "1704--1711",
year = "2007",
publisher = "IEEE",
month = "Nov",
keywords = "scalar field methods",
url = "http://www.sci.utah.edu/publications/Mey2007b/vis07meyer.pdf",
}
@Article{SCI:Mey2008a,
author = "M.D. Meyer and R.T. Whitaker and R.M. Kirby and C.
Ledergerber and H. Pﬁster",
title = "Particle-based Sampling and Meshing of Surfaces in
Multimaterial Volumes",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "14",
number = "6",
pages = "1539--1546",
year = "2008",
url = "http://www.sci.utah.edu/publications/meyer08/Meyer_VCG2008.pdf",
}
@PhdThesis{SCI:Mey2008b,
author = "M.D. Meyer",
title = "Dynamic Particle Systems for Adaptive Sampling of
Implicit Surfaces",
year = "2008",
school = "School of Computing, University of Utah",
url = "http://www.sci.utah.edu/publications/meyer08/Meyer_dissertation2008.pdf",
}
@Article{SCI:Mey2009a,
author = "M.D. Meyer and T. Munzner and H. Pfister",
title = "{MizBee}: A Multiscale Synteny Browser",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics (Proceedings of {InfoVis} 2009)",
volume = "15",
number = "6",
pages = "897--904",
year = "2009",
note = "Honorable Mention for Best Paper Award",
url = "http://www.sci.utah.edu/publications/meyer09/Meyer_Mizbee2009.pdf",
}
@Article{SCI:Mey2010a,
author = "M.D. Meyer and T. Munzner and A. DePace and H.
Pfister",
title = "{MulteeSum}: A Tool for Comparative Spatial and
Temporal Gene Expression Data",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics (Proceedings of {InfoVis} 2010)",
volume = "16",
number = "6",
pages = "908--917",
year = "2010",
url = "http://www.sci.utah.edu/publications/meyer10/Meyer_multeesum2010.pdf",
}
@Article{SCI:Mey2010b,
author = "M.D. Meyer and B. Wong and M. Styczynski and T.
Munzner and H. Pfister",
title = "Pathline: A Tool for Comparative Functional
Genomics",
journal = "Computer Graphics Forum",
volume = "29",
number = "3",
pages = "1043--1052",
year = "2010",
publisher = "Wiley-Blackwell",
month = "Aug",
doi = "10.1111/j.1467-8659.2009.01710.x",
url = "http://www.sci.utah.edu/publications/Mey2010b/Meyer_Pathline2010.pdf",
}
@InProceedings{SCI:Mey2012a,
author = "M.D. Meyer and M. Sedlmair and T. Munzner",
title = "The Four-Level Nested Model Revisited: Blocks and
Guidelines",
booktitle = "Workshop on {BEyond} time and errors: novel
evaLuation methods for Information Visualization
({BELIV}), {IEEE} {VisWeek} 2012",
year = "2012",
url = "http://www.sci.utah.edu/publications/meyer12/Meyer_BELIV2012.pdf",
}
@Article{SCI:Mey2014a,
author = "M.D. Meyer and M. Sedlmair and P.S. Quinan and T.
Munzner",
title = "The Nested Blocks and Guidelines Model",
journal = "Journal of Information Visualization, Special
Issue on Evaluation ({BELIV})",
year = "2014",
url = "http://www.sci.utah.edu/publications/Mey2014a/Meyer_BELIV2014.pdf",
}
@Article{SCI:Mil1994a,
author = "M.I. Miller and S. Joshi and D.R. Maffitt and J.G.
McNally and U. Grenander",
title = "Membranes, Mitochondria and Amoebae: Shape
Models",
journal = "Journal of Applied Statistics",
volume = "21",
number = "1, 2",
pages = "141--163",
year = "1994",
editor = "Kanti Mardia",
}
@Article{SCI:Mil1997a,
author = "M. Miller and A. Banerjee and G. Christensen and
S. Joshi and N. Khaneja and U. Grenander and L.
Matejic",
title = "Statistical Methods in Computational Anatomy",
journal = "Stat Methods Med Res",
volume = "6",
number = "3",
pages = "267--299",
year = "1997",
month = "September",
}
@InProceedings{SCI:Mil1997b,
author = "M.I. Miller and S. Joshi",
title = "Discussion of Mathematics for Object Recognition
Shape, Invariance and Deformations",
booktitle = "Proceedings of the Workshop on Mathematics for
Object Recognition Shape, Invariance and
Deformations",
year = "1997",
editor = "L. Younes",
month = "November",
}
@InProceedings{SCI:Mil1999a,
author = "M. Miller and C.D. Hansen and C.R. Johnson",
title = "The {SCIR}un Problem Solving Environment:
Implementation within a Distributed Environment",
booktitle = "Ninth {SIAM} Conference on Parallel Processing for
Scientific Computing",
year = "1999",
note = "extended abstract",
keywords = "scirun, ncrr",
url = "http://www.sci.utah.edu/publications/siam99/siam99c.pdf",
}
@Article{SCI:Mil1999b,
author = "M.I. Miller and S.C. Joshi and G.E. Christensen",
title = "Large Deformation Fluid Diffeomorphisms For
Landmark and Image Matching",
journal = "Brain Warping",
pages = "115--131",
year = "1999",
editor = "A. W. Toga and John Mazziotta",
}
@InProceedings{SCI:Mil2001,
author = "M. Miller and C. Moulding and J. Dongarra and C.R.
Johnson",
title = "Grid-enabling Problem Solving Environments: A Case
Study of {SCIR}un and Netsolv",
booktitle = c-HPC2001,
pages = "98--103",
year = "2001",
series = "2001 Advanced Simulation Technologies
Conference",
organization = "Society for Modeling and Simulation
International",
month = "April",
keywords = "scirun, netsolv, grid",
}
@InProceedings{SCI:Mil2006a,
author = "P. Miller and P.-T. Bremer and W. Cabot and A.
Cook and D. Laney and A. Mascarenhas and V.
Pascucci",
title = "Application of Morse Theory to Analysis of
Rayleigh-Taylor Topology",
booktitle = "10th International Workshop on the Physics of
Compressible Turbulent Mixing",
year = "2006",
}
@InProceedings{SCI:Mil2009a,
author = "M. Milanic and V. Jazbinsek and D.F. Wang and J.
Sinstra and R.S. Macleod and D.H. Brooks and R.
Hren",
title = "Evaluation of Approaches of Solving
Electrocardiographic Imaging Problem",
booktitle = "Proceeding of Computers in Cardiology 2010",
year = "2009",
month = "September",
location = "Park City, Utah",
url = "http://www.sci.utah.edu/publications/milanic09/Milanic_CinC2009.pdf",
}
@Article{SCI:Mil2014a,
author = "M. Milani{\vc} and V. Jazbin{\vs}ek and R.S. MacLeod and
D.H. Brooks and R. Hren",
title = "Assessment of regularization techniques for
electrocardiographic imaging",
journal = "Journal of electrocardiology",
volume = "47",
number = "1",
pages = "20--28",
year = "2014",
doi = "10.1016/j.jelectrocard.2013.10.004",
url = "http://www.sci.utah.edu/publications/Mil2014a/Melanic_JEC2014.pdf",
}
@InCollection{SCI:Mil98a,
author = "M. Miller and C.D. Hansen and C.R. Johnson",
title = "Simulation Steering with {SCIRun} in a Distributed
Memory Environment",
booktitle = "Applied Parallel Computing, 4th International
Workshop, {PARA'98}",
journal = "Lecture Notes in Computer Science,
Springer-Verlag",
volume = "1541",
pages = "366--376",
year = "1998",
editor = "B. Kagstrom and J. Dongarra and E. Elmroth and J.
Wasniewski",
series = "Lecture Notes in Computer Science",
publisher = "Springer-Verlag",
address = "Berlin",
keywords = "scirun",
url = "http://www.sci.utah.edu/publications/miller98/para98.ps.gz",
url = "http://www.sci.utah.edu/publications/miller98/para98.ps",
url = "http://www.sci.utah.edu/publications/miller98/hpdc98_abs.pdf",
}
@InProceedings{SCI:Mil98b,
author = "M. Miller and C.D. Hansen and S.G. Parker and C.R.
Johnson",
title = "Simulation Steering with {SCIR}un in a Distributed
Memory Environment",
booktitle = "Seventh {IEEE} International Symposium on High
Performance Distributed Computing (HPDC-7)",
year = "1998",
month = "Jul",
url = "http://www.sci.utah.edu/publications/miller98/hpdc98_abs.ps.Z",
url = "http://www.sci.utah.edu/publications/miller98/hpdc98_abs.ps",
url = "http://www.sci.utah.edu/publications/miller98/hpdc98_abs.pdf",
}
@Article{SCI:Mio2009a,
author = "S. Miocinovic and S.F. Lempka and G.S. Russo and
C.B. Maks and C.R. Butson and K.E. Sakaie and J.L.
Vitek and C.C. McIntyre",
title = "Experimental and theoretical characterization of
the voltage distribution generated by deep brain
stimulation",
journal = "Experimental Neurology",
volume = "216",
number = "1",
pages = "166--176",
year = "2009",
publisher = "Elsevier Inc.",
month = "March",
issn = "1090--2430",
doi = "10.1016/j.expneurol.2008.11.024",
pmid = "19118551",
url = "http://www.sci.utah.edu/publications/Mio2009a/Miocinovic_ExpNeurol2009.pdf",
}
@TechReport{SCI:Mir2009a,
author = "H. Mirzaee and C. Eskilsson and S.J. Sherwin and
R.M. Kirby",
title = "Comparison of Consistent Integration Versus
Adaptive Quadrature for Taming Aliasing Errors",
number = "UUSCI-2009-008",
year = "2009",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2009-008.pdf",
}
@Article{SCI:Mir2010a,
author = "H. Mirzaee and J.K. Ryan and R.M. Kirby",
title = "Quantificiation of Errors Introduced in the
Numerical Approximation and Implementation of
Smoothness-Increasing Accuracy Conserving (SIAC)
Filtering of Discontinuous Galerkin (DG) Fields",
journal = "Journal of Scientific Computing",
volume = "45",
pages = "447-470",
year = "2010",
url = "http://www.sci.utah.edu/publications/mirzaee10/Mirzaee_JSC2010.pdf",
}
@Article{SCI:Mir2011a,
author = "H. Mirzaee and Liangyue and J.K. Ryan and R.M.
Kirby",
title = "Smoothness-Increasing Accuracy-Conserving ({SIAC})
Postprocessing for Discontinuous Galerkin Solutions
Over Structured Triangular Meshes",
journal = "{SIAM} Journal of Numerical Analysis",
volume = "49",
number = "5",
pages = "1899--1920",
year = "2011",
url = "http://www.sci.utah.edu/publications/mirzaee11/Mirzaee_JNA2011.pdf",
}
@Article{SCI:Mir2011b,
author = "H. Mirzaee and J.K. Ryan and R.M. Kirby",
title = "Efficient Implementation of Smoothness-Increasing
Accuracy-Conserving ({SIAC}) Filters for
Discontinuous Galerkin Solutions",
journal = "Journal of Scientific Computing",
pages = "(in press)",
year = "2011",
doi = "10.1007/s10915-011-9535-x",
url = "http://www.sci.utah.edu/publications/mirzaee11/Mirzaee_JSC2011.pdf",
}
@Article{SCI:Mir2014a,
author = "M. Mirzargar and R. Whitaker and R. M. Kirby",
title = "Curve Boxplot: Generalization of Boxplot for
Ensembles of Curves",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "20",
number = "12",
pages = "2654-63",
year = "2014",
publisher = "IEEE",
month = "December",
url = "http://www.sci.utah.edu/publications/Mir2014a/curve-boxplot-2.pdf",
}
@Article{SCI:Mir2017a,
author = "M. Mirzargar and A. Jallepalli and J.K. Ryan and
R.M. Kirby",
title = "Hexagonal Smoothness-Increasing
Accuracy-Conserving Filtering",
journal = "Journal of Scientific Computing",
volume = "73",
number = "2-3",
pages = "1072--1093",
year = "2017",
publisher = "Springer Nature",
month = "Aug",
doi = "10.1007/s10915-017-0517-5",
url = "http://www.sci.utah.edu/publications/Mir2017a/Mirzargar2017_Article_HexagonalSmoothness-Increasing.pdf",
}
@Article{SCI:Mir2017b,
author = "M. Mirzargar and R.T. Whitaker and R.M. Kirby",
title = "Exploration of Heterogeneous Data Using Robust
Similarity",
journal = "CoRR",
year = "2017",
url = "http://www.sci.utah.edu/publications/Mir2017b/1710.02862.pdf",
}
@Article{SCI:Mlo2011a,
author = "M.J. Mlodzianoski and J.M. Schreiner and S.P.
Callahan and K. Smolková and A. Dlasková and J.
{\vS}antorová and P. Ježek and J. Bewersdorf",
title = "Sample drift correction in 3D fluorescence
photoactivation localization microscopy",
journal = "Optics Express",
volume = "19",
number = "16",
pages = "15009--15019",
year = "2011",
doi = "10.1364/OE.19.015009",
url = "http://www.sci.utah.edu/publications/mlodzianoski11/Mlodzianoski_OptExpress2011.pdf",
}
@InProceedings{SCI:Moo2005a,
author = "S.M. Moore and R.E. Debski and B. Ellis and P.J.
McMahon and J.A. Weiss",
title = "All Three Regions of the Inferior Glenohumeral
Ligament Contribute to Anterior Stability",
booktitle = "Proceedings, 51st Annual Orthopaedic Research
Society Meeting",
volume = "30",
pages = "804",
year = "2005",
keywords = "computational biomechanics, mrl",
url = "http://www.sci.utah.edu/publications/moore05/moore_ORS_05.pdf",
}
@Unpublished{SCI:Moo2006a,
author = "C.R. Johnson and R. Moorhead and T. Munzner and H.
Pfister and P. Rheingans and T. Yoo",
title = "{NIH/NSF} Visualization Research Challenges Report
Summary",
pages = "66-73",
year = "2006",
note = "{NIH/NSF}",
url = "http://www.sci.utah.edu/publications/Moo2006a/NIH-NSF-VRC-Report-Final.pdf",
}
@Article{SCI:Moo2009a,
author = "S.M. Moore and B.J. Ellis and J.A. Weiss and P.J.
McMahon and R.E. Debski",
title = "The Glenohumeral Capsule Should be Evaluated as a
Sheet of Fibrous Tissue: A Validated Finite Element
Model",
journal = "Annals of Biomedical Engineering",
volume = "38",
number = "1",
pages = "66--76",
year = "2009",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/moore09/Moore_ABE_2009.pdf",
}
@Article{SCI:Mor2008a,
author = "L. Moreau and B. Lud{\"a}scher and I. Altintas and
R. Barga and S. Bowers and S.P. Callahan and G.
Chin Jr. and B. Clifford and S. Cohen and S.
Cohen-Boulakia and S. Davidson and E. Deelman and
L. Digiampietri and I. Foster and J. Freire and J.
Frew and J. Futrelle and T. Gibson and Y. Gil and
C. Goble and J. Golbeck and P. Groth and D. A.
Holland and S. Jiang and J. Kim and D. Koop and A.
Krenek and T. McPhillips and G. Mehta and S. Miles
and D. Metzger and S. Munroe and J. Myers and B.
Plale and N. Podhorszki and V. Ratnakar and E.
Santos and C.E. Scheidegger and K. Schuchardt and
M. Seltzer and Y. L. Simmhan and C.T. Silva and P.
Slaughter and E. Stephan and R. Stevens and D. Turi
and H.T. Vo and M. Wilde and J. Zhao and Y. Zhao",
title = "The First Provenance Challenge",
journal = "Concurrency and Computation: Practice and
Experience",
volume = "20",
number = "5",
pages = "409--418",
year = "2008",
month = "April",
keywords = "vistrails, provenance, workflow management",
}
@Article{SCI:Mor2008b,
author = "L. Moreau and J. Freire and J. Futrelle and R.E.
McGrath and J. Myers and P. Paulson",
title = "The Open Provenance Model: An Overview",
journal = "Provenance and Annotation of Data and Processes",
pages = "323--326",
year = "2008",
series = "Lecture Notes in Computer Science (LNCS)",
isbn = "978-3-540-89964-8",
keywords = "provenance, vistrails",
url = "http://www.sci.utah.edu/publications/moreau08/Moreau_LNCS2008.pdf",
}
@Article{SCI:Mor2016b,
author = "K. Moreland and C. Sewell and W. Usher and L. Lo
and J. Meredith and D. Pugmire and J. Kress and H.
Schroots and K. Ma and H. Childs and M. Larsen and
C. Chen and R. Maynard and B. Geveci",
title = "VTK-m: Accelerating the Visualization Toolkit for
Massively Threaded Architectures",
journal = "IEEE Computer Graphics and Applications",
volume = "36",
number = "3",
pages = "48--58",
year = "2016",
month = "May",
issn = "0272-1716",
doi = "10.1109/MCG.2016.48",
url = "http://www.sci.utah.edu/publications/Mor2016b/07466740.pdf",
}
@Article{SCI:Mos2009a,
author = "M.W. Mosconi and H. Cody-Hazlett and M.D. Poe and
G. Gerig and R. Gimpel-Smith and J. Piven",
title = "Longitudinal study of amygdala volume and joint
attention in 2- to 4-year-old children with
autism",
journal = "Arch Gen Psychiatry",
volume = "66",
number = "5",
pages = "509--516",
year = "2009",
pmid = "19414710",
url = "http://www.sci.utah.edu/publications/mosconi09/Mosconi_GenPsy2009.pdf",
}
@Article{SCI:Muk2008a,
author = "N. Mukherjee and C. Kang and H.M. Wolfe and B.S.
Hertzberg and J.K. Smith and W. Lin and G. Gerig
and R.M. Hamer and J.H. Gilmore",
title = "Discordance of Prenatal and Neonatal Brain
Development in Twins",
journal = "Early Human Development",
pages = "(in press)",
year = "2008",
month = "August",
keywords = "ucnia",
url = "http://www.sci.utah.edu/publications/mukherjee08/Twin_Discordance.pdf",
}
@Article{SCI:Muk2009a,
author = "N. Mukherjee and C. Kang and H.M. Wolfe and B.S.
Hertzberg and J.K. Smith and W. Lin and G. Gerig
and R.M. Hamer and J.H. Gilmore",
title = "Discordance of Prenatal and Neonatal Brain
Development in Twins",
journal = "Early Human Development",
volume = "85",
number = "3",
pages = "171--175",
year = "2009",
pmid = "18804925",
url = "http://www.sci.utah.edu/publications/mukherjee09/Mukherjee_EHD2009.pdf",
}
@InProceedings{SCI:Mul2009a,
author = "H M{\"u}ller and R Reihs and S Sauer and K Zatloukal
and M Streit and A Lex and B Schlegl and D
Schmalstieg",
title = "Connecting Genes with Diseases",
booktitle = "Information Visualisation, 2009 13th International
Conference",
pages = "323--330",
year = "2009",
month = "July",
doi = "10.1109/IV.2009.86",
url = "http://www.sci.utah.edu/publications/Mul2009a/2009_ivbi_connecting-genes.pdf",
}
@Unpublished{SCI:Mun2006a,
author = "T. Munzner and C.R. Johnson and R. Moorhead and H.
Pfister and P. Rheingans and T.S. Yoo",
title = "{NIH-NSF} Visualization Research Challenges Report
Summary",
pages = "20--24",
year = "2006",
month = "March/April",
note = "{NIH-NSF}",
keywords = "forward problems inverse problems forward
simulation inverse solutions, bioelectric fields",
url = "http://www.sci.utah.edu/publications/Mun2006a/Vis_Viewpoints06.pdf",
}
@Article{SCI:Mur2011a,
author = "C. Muralidhara and A.M. Gross and R.R. Gutell and
O. Alter",
title = "Tensor Decomposition Reveals Concurrent
Evolutionary Convergences and Divergences and
Correlations with Structural Motifs in Ribosomal
{RNA}",
journal = "{PLoS} {ONE}",
volume = "6",
number = "4",
pages = "e18768",
year = "2011",
publisher = "Public Library of Science",
month = "April",
doi = "10.1371/journal.pone.0018768",
url = "http://www.sci.utah.edu/publications/muralidhara11/Muralidhara_PLoSOne2011.pdf",
url = "http://www.sci.utah.edu/publications/muralidhara11/Muralidhara_PLoSOne2011-appendix.pdf",
}
@InProceedings{SCI:Mur2012a,
author = "P. Muralidharan and P.T. Fletcher",
title = "Sasaki Metrics for Analysis of Longitudinal Data
on Manifolds",
booktitle = "Proceedings of the 2012 {IEEE} conference on
Computer Vision and Pattern Recognition ({CVPR})",
pages = "1027--1034",
year = "2012",
doi = "10.1109/CVPR.2012.6247780",
url = "http://www.sci.utah.edu/publications/muralidharan12/Muralidharan_sasaki2012.pdf",
}
@InProceedings{SCI:Mur2014a,
author = "P. Muralidharan and J. Fishbaugh and H.J. Johnson
and S. Durrleman and J.S. Paulsen and G. Gerig and
P.T. Fletcher",
title = "Diffeomorphic Shape Trajectories for Improved
Longitudinal Segmentation and Statistics",
booktitle = "Proceedings of Medical Image Computing and
Computer Assisted Intervention ({MICCAI})",
year = "2014",
url = "http://www.sci.utah.edu/publications/Mur2014a/Muralidharan_MICCAI2014.pdf",
}
@InProceedings{SCI:Mur2016a,
author = "P. Muralidharan and J. Fishbaugh and E. Y. Kim and
H. J. Johnson and J. S. Paulsen and G. Gerig and P.
T. Fletcher",
title = "Bayesian Covariate Selection in Mixed Effects
Models for Longitudinal Shape Analysis",
booktitle = "International Symposium on Biomedical Imaging
(ISBI)",
year = "2016",
publisher = "IEEE",
month = "April",
doi = "10.1109/isbi.2016.7493352",
url = "http://www.sci.utah.edu/publications/Mur2016a/paper.pdf",
}
@InProceedings{SCI:Nag2002a,
author = "S.S. Nagarajan and O. Portniaguine and K. Sekihara
and D. Hwang and C.R. Johnson",
title = "Performance of a Minimum-Support Imaging Method
for Biomagnetic Source Localization",
booktitle = c-EMBS2002,
volume = "3",
pages = "2006-2007",
year = "2002",
month = "October",
location = "Houston",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions finite elements,
biopse, scientific computing",
}
@Article{SCI:Nag2006a,
author = "S. Nagarajan and O. Portniaguine and D. Hwang and
C.R. Johnson and K. Sekihara",
title = "Controlled Support MEG Imaging",
journal = "NeuroImage",
volume = "15;33",
number = "3",
pages = "878--885",
year = "2006",
keywords = "forward problems inverse problems forward
simulation inverse solutions, inverse meg, finite
elements, ip image processing signal processing",
url = "http://www.sci.utah.edu/publications/nagarajan06/controlledsupport_neuroimage.pdf",
}
@InProceedings{SCI:Nai2007a,
author = "D. Nain and M. Styner and M. Niethammer and J.J.
Levitt and M.E. Shenton and G. Gerig and A. Bobick
and A. Tannenbaum",
title = "Statistical Shape Analysis of Brain Structures
Using Spherical Wavelets",
booktitle = "Proceedings of the 4th {IEEE} International
Symposium on Biomedical Imaging: From Nano to Macro
({ISBI} 2007)",
pages = "209--212",
year = "2007",
publisher = "{IEEE} Press",
url = "http://www.sci.utah.edu/publications/nain07/Nain_ISBI2007a.pdf",
}
@Article{SCI:Nar2011a,
author = "A. Narayan and D. Xiu",
title = "Distributional Sensitivity for Uncertainty
Quantification",
journal = "Communications in Computational Physics",
volume = "10",
number = "1",
pages = "140--160",
year = "2011",
doi = "10.4208/cicp.160210.300710a",
keywords = "Uncertainty quantification, epistemic uncertainty,
distributional sensitivity, generalized polynomial
chaos",
url = "http://www.sci.utah.edu/publications/narayan11/Narayan_CiCP2011.pdf",
}
@Article{SCI:Nar2012a,
author = "A. Narayan and D. Xiu",
title = "Stochastic Collocation Methods on Unstructured
Grids in High Dimensions via Interpolation",
journal = "SIAM Journal on Scientific Computing",
volume = "34",
number = "3",
pages = "A1729–-A1752",
year = "2012",
doi = "10.1137/110854059",
keywords = "stochastic collocation, polynomial chaos,
interpolation, orthogonal polynomials",
url = "http://www.sci.utah.edu/publications/narayan12/Narayan_SIAM_JSC2012.pdf",
}
@Article{SCI:Nar2012b,
author = "A. Narayan and Y. Marzouk and D. Xiu",
title = "Sequential Data Assimilation with Multiple
Models",
journal = "Journal of Computational Physics",
volume = "231",
number = "19",
pages = "6401--6418",
year = "2012",
doi = "10.1016/j.jcp.2012.06.002",
keywords = "Uncertainty quantification, Data assimilation,
Kalman filter, Model averaging",
url = "http://www.sci.utah.edu/publications/narayan12/Narayan_JCP2012.pdf",
}
@Article{SCI:Nar2017a,
author = "A. Narayan and J. Jakeman and T. Zhou",
title = "A Christoffel function weighted least squares
algorithm for collocation approximations",
journal = "Mathematics of Computation",
volume = "86",
number = "306",
pages = "1913--1947",
year = "2017",
issn = "0025-5718, 1088-6842",
doi = "10.1090/mcom/3192",
url = "http://www.sci.utah.edu/publications/Nar2017a/1412.4305.pdf",
}
@Article{SCI:Nas1999a,
author = "J. Nash and P. Dew and M. Berzins",
title = "Using SADTs to Support Irregular Computational
Problems",
journal = "International Symposium on Parallel Architectures,
Algorithms, and Networks",
pages = "338--344",
year = "1999",
publisher = "IEEE Computer Society",
address = "Los Alamitos, CA, USA",
issn = "1087-4089",
doi = "10.1109/ISPAN.1999.778961",
url = "http://www.sci.utah.edu/publications/nash99/NASHDEWMB99.pdf",
}
@InCollection{SCI:Nas1999b,
author = "J. Nash and M. Berzins and P. Selwood",
title = "A Structured SADT Approach to the Support of a
Parallel Adaptive 3D CFD Code",
booktitle = "Euro-Par'99 Parallel Processing",
pages = "651--658",
year = "1999",
publisher = "Springer Nature",
doi = "10.1007/3-540-48311-x_91",
url = "http://www.sci.utah.edu/publications/Nas1999b/4609_001.pdf",
}
@InProceedings{SCI:Nat2005a,
author = "V. Natarajan and V. Pascucci",
title = "Volumetric Data Analysis Using Morse-Smale
Complexes",
booktitle = "Proceedings of the International Conference Shape
Modeling and Applications",
pages = "320--325",
year = "2005",
editor = "A.G. Belyaev and A.A. Pasko and M. Spagnuolo",
organization = "IEEE Computer Society",
month = "June",
}
@Article{SCI:Nat2006a,
author = "V. Natarajan and Y. Wang and P.-T. Bremer and V.
Pascucci and B. Hamann",
title = "Segmenting Molecular Surfaces",
journal = "Computer Aided Geometric Design",
volume = "23",
number = "6",
pages = "495--509",
year = "2006",
series = "Special Issue on Applications of Geometric
Modeling in the Life Sciences",
note = "(To appear)",
}
@Misc{SCI:NCRTools,
author = "{SCI} Institute",
year = "2015",
note = "{NCR} Toolset: A collection of software tools for
the reconstruction and visualization of neural
circuitry from electron microscopy data. Scientific
Computing and Imaging Institute ({SCI}). Download
from: http://www.sci.utah.edu/software.html",
keywords = "NCR Toolset, neural circuit reconstruction,
electron microscopy data",
}
@Article{SCI:Nei2014a,
author = "J.A. Nielsen and B.A. Zielinski and P.T. Fletcher
and A.L. Alexander and N. Lange and E.D. Bigler and
J.E. Lainhart and J.S. Anderson",
title = "Abnormal lateralization of functional connectivity
between language and default mode regions in
autism",
journal = "Molecular Autism",
volume = "5",
number = "1",
pages = "8",
year = "2014",
doi = "10.1186/2040-2392-5-8",
keywords = "brain lateralization, brain asymmetry, autism,
autism spectrum disorder, language, functional
magnetic resonance imaging, functional
connectivity",
url = "http://www.sci.utah.edu/publications/Nei2014a/Neilsen_MolecularAutism2014.pdf",
}
@Article{SCI:Nel2006a,
author = "B. Nelson and R.M. Kirby",
title = "Ray-Tracing Polymorphic Multi-Domain Spectral/hp
Elements for Isosurface Rendering",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "12",
number = "1",
pages = "114--125",
year = "2006",
url = "http://www.sci.utah.edu/publications/nelson06/Nelson_VCG06.pdf",
}
@Article{SCI:Nel2011a,
author = "B. Nelson and R. Haimes and R.M. Kirby",
title = "{GPU}-Based Interactive Cut-Surface Extraction
From High-0rder Finite Element Fields",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({IEEE} Visualization Issue)",
volume = "17",
number = "12",
pages = "1803--1811",
year = "2011",
url = "http://www.sci.utah.edu/publications/nelson11/GPU-BasedInteractiveCut-SurfaceExtractionFromHigh-OrderFiniteElementFields.pdf",
}
@Article{SCI:Nel2012a,
author = "B. Nelson and E. Liu and R.M. Kirby and R.
Haimes",
title = "ElVis: A System for the Accurate and Interactive
Visualization of High-Order Finite Element
Solutions",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "18",
number = "12",
pages = "2325--2334",
year = "2012",
month = "Dec",
doi = "10.1109/TVCG.2012.218",
url = "http://www.sci.utah.edu/publications/Nel2012a/Nelson_ElVis_TVCG2012.pdf",
}
@Article{SCI:Nem2006a,
author = "O. Nemitz and M. Rumpf and T. Tasdizen and R.T.
Whitaker",
title = "Anisotropic Curvature Motion for Structure
Enhancing Smoothing of 3D MR Angiography Data",
journal = "Journal of Mathematical Imaging and Vision",
volume = "27",
number = "3",
pages = "217--229",
year = "2006",
month = "April",
}
@Article{SCI:Nem2007a,
author = "O. Nemitz and T. Tasdizen and M. Rumpf and R.T.
Whitaker",
title = "Anisotropic Curvature Motion for Structure
Enhancing Smoothing of 3D MR Angiography Data",
journal = "Journal of Mathematical Imaging and Vision",
volume = "7",
number = "3",
pages = "217--229",
year = "2007",
doi = "10.1007/s10851-006-0645-2",
keywords = "cardiac heart",
}
@Article{SCI:Nes2014a,
author = "K.A. Nestor and J.D. Jones and C.R. Butson and T.
Morishita and C.E. Jacobson and D.A. Peace and D.
Chen and K.D. Foote and M.S. Okun",
title = "Coordinate-based lead location does not predict
Parkinson's disease deep brain stimulation
outcome",
journal = "PloS One",
volume = "9",
number = "4",
pages = "e93524",
year = "2014",
month = "January",
issn = "1932-6203",
doi = "10.1371/journal.pone.0093524",
pmid = "24691109",
url = "http://www.sci.utah.edu/publications/Nes2014a/Nestor_PlosOne2014.pdf",
}
@Article{SCI:New2007a,
author = "E.P. Newren and A.L. Fogelson and R.D. Guy and
R.M. Kirby",
title = "Unconditionally Stable Discretizations of the
Immersed Boundary Equations",
journal = "Journal of Computational Physics",
volume = "222",
number = "2",
pages = "702--719",
year = "2007",
url = "http://www.sci.utah.edu/publications/newren07/Kirby-18.pdf",
}
@Article{SCI:New2007b,
author = "E.P. Newren and A.L. Fogelson and R.D. Guy and
R.M. Kirby",
title = "Unconditionally Stable Discretizations of the
Immersed Boundary Equations",
journal = "Journal of Computational Physics",
volume = "222",
number = "2",
pages = "702--719",
year = "2007",
month = "March",
}
@Article{SCI:New2008a,
author = "E.P. Newren and A.L. Fogelson and R.D. Guy and
R.M. Kirby",
title = "A Comparison of Implicit Solvers for the Immersed
Boundary Equations",
journal = "Computer Methods in Applied Mechanics and
Engineering",
volume = "197",
number = "25--28",
pages = "2290--2304",
year = "2008",
doi = "10.1016/j.cma.2007.11.030",
url = "http://www.sci.utah.edu/publications/newren08/CompImplicitSolvers.pdf",
}
@Article{SCI:Ngu2008a,
author = "H. Nguyen and T. Nguyen and J. Freire",
title = "Learning to Extract Form Labels",
journal = "Proceedings of the VLDB Endowment",
volume = "1",
number = "1",
pages = "684--694",
year = "2008",
publisher = "VLDB Endowment",
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doi = "10.14778/1453856.1453931",
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author = "H. Nguyen and E.Y. Kang and J. Freire",
title = "Automatically Extracting Form Labels",
booktitle = "Proceedings of the 2008 {IEEE} 24th International
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pages = "1498--1500",
year = "2008",
url = "http://www.sci.utah.edu/publications/nguyen08/label-extraction-icde2008.pdf",
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author = "Q.C. Nguyen and M. Sajjadi and M. McCullough and
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author = "T. Nielsen and R.B. West and S.C. Linn and O.
Alter and M.A. Knowling and J. O'Connell and S. Zhu
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pages = "1301–-1307",
year = "2002",
month = "April",
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booktitle = "Eurographics Conference on Visualization (EuroVis)
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author = "C. Nobre and M. Streit and A. Lex",
title = "Juniper: A Tree+ Table Approach to Multivariate
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author = "C. Nuber and E.C. LaMar and V. Pascucci and B.
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year = "2003",
editor = "Georges-Pierre Bonneau AND Stefanie Hahmann AND
Charles D. Hansen",
publisher = "Association for Computing Machinery",
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author = "E.M. Nurgat and M. Berzins and L.E. Scales",
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Segerson and M. Daccarett and J. Windfelder and
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N.F. Marrouche",
title = "Detection and quantification of left atrial
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author = "T. Ochotta and C.E. Scheidegger and J. Schreiner
and Y. Lima and R.M. Kirby and C.T. Silva",
title = "A Unified Projection Operator for Moving Least
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number = "UUSCI-2007-006",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-006.pdf",
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author = "T. Ochotta and D. Saupe",
title = "Image-Based Surface Compression",
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pages = "1647--1663",
year = "2008",
url = "http://www.sci.utah.edu/publications/ochotta08/OcSa06.pdf",
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author = "J.T. Oden and J. Fish and C.R. Johnson and A. Laub
and D. Srolovitz and T. Belytschko and T.J.R.
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title = "{NSF} Blue Ribbon Panel Report on Simulation Based
Engineering Science",
year = "2006",
note = "NSF Report",
url = "http://www.sci.utah.edu/publications/Ode2006a/TO_SBES_Debrief_050306.pdf",
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author = "J.T. Oden and O. Ghattas and J.L. King and B.I.
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year = "2011",
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author = "I. Oguz and J. Cates and P.T. Fletcher and R.T.
Whitaker and D. Cool and S. Aylward and M.
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title = "Cortical Correspondence using Entropy-Based
Particle Systems and Local Features",
booktitle = "5th {IEEE} International Symposium on Biomedical
Imaging: From Nano to Macro, 2008. (ISBI 2008)",
pages = "1637--1640",
year = "2008",
url = "http://www.sci.utah.edu/publications/oguz08/Oguz_ISBI2008.pdf",
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author = "I. Oguz and M. Niethammer and J. Cates and R.T.
Whitaker and P.T. Fletcher and C. Vachet and M.
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series = "Lecture Notes in Computer Science (LCNS)",
doi = "10.1007/978-3-642-02498-6_54",
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author = "I. Oguz and M. Farzinfar and J. Matsui and F.
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year = "2014",
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author = "I. OguzI and J. Cates and M. Datar and B. Paniagua
and T. Fletcher and C. Vachet and M. Styner and R.
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title = "Entropy-based particle correspondence for shape
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journal = "International Journal of Computer Assisted
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author = "D.C.B. de Oliveira and Z. Rakamaric and G.
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Berzins",
title = "Crash Early, Crash Often, Explain Well: Practical
Formal Correctness Checking of Million-core Problem
Solving Environments for {HPC}",
booktitle = "Proceedings of the 35th International Conference
on Software Engineering ({ICSE} 2013)",
pages = "(accepted)",
year = "2013",
keywords = "Uintah",
url = "http://www.sci.utah.edu/publications/oliveira13/deOliveira_ICSEWS2013.pdf",
}
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author = "D.C.B. de Oliveira and A. Humphrey and Q. Meng and
Z. Rakamaric and M. Berzins and G.
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title = "Systematic Debugging of Concurrent Systems Using
Coalesced Stack Trace Graphs",
booktitle = "Proceedings of the 27th International Workshop on
Languages and Compilers for Parallel Computing
({LCPC})",
year = "2014",
month = "September",
url = "http://www.sci.utah.edu/publications/Oli2014a/Oliveira_LCPC2014.pdf",
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title = "A Tensor Higher-Order Singular Value Decomposition
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publisher = "Proceedings of the National Academy of Sciences",
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L.S. Drury and J.F.X. Diffley and O. Alter",
title = "Global Effects of DNA Replication and DNA
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Berzins",
title = "OpenMP 4 Fortran Modernization of WSM6 for KNL",
booktitle = "Proceedings of the Practice and Experience in
Advanced Research Computing 2017 on Sustainability,
Success and Impact",
number = "12",
pages = "12:1--12:8",
year = "2017",
series = "PEARC17",
publisher = "ACM",
isbn = "978-1-4503-5272-7",
doi = "10.1145/3093338.3093387",
url = "http://www.sci.utah.edu/publications/Oue2017b/a12-Ouermi.pdf",
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author = "T.A.J. Ouermi and A. Knoll and R.M. Kirby and M.
Berzins",
title = "Optimization Strategies for WRF Single-Moment
6-Class Microphysics Scheme (WSM6) on Intel
Microarchitectures",
booktitle = "Proceedings of the fifth international symposium
on computing and networking (CANDAR 17). Awarded
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year = "2017",
publisher = "IEEE",
url = "http://www.sci.utah.edu/publications/Oue2017c/bare_conf.pdf",
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author = "T.A.J and Ouermi and R. M. Kirby and and M.
Berzins",
title = "Performance Optimization Strategies for WRF
Physics Schemes Used in Weather Modeling",
journal = "International Journal of Networking and
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volume = "8",
number = "2",
pages = "301--327",
year = "2018",
publisher = "IJNC ",
doi = "10.15803/ijnc.8.2_301",
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@Misc{SCI:Oue2020a,
author = "T. A. J. Ouermi and R. M. Kirby and M. Berzins",
title = "Numerical Testing of a New Positivity-Preserving
Interpolation Algorithm",
subtitle = "arXiv",
year = "2020",
url = "http://www.sci.utah.edu/publications/Oue2020a/ppi_testing.pdf",
}
@Article{SCI:Pai2009a,
author = "A.R.C. Paiva and I. Park and J.C. Principe",
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author = "A.R.C. Paiva and T. Tasdizen",
title = "Fast Semi-Supervised Image Segmentation by Novelty
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year = "2010",
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doi = "10.1109/ICASSP.2010.5495333",
url = "http://www.sci.utah.edu/publications/paiva10/Paiva_ICASSP2010.pdf",
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@InCollection{SCI:Pai2010b,
author = "A.R.C. Paiva and I. Park and J.C. Principe",
title = "Inner products for representation and learning in
the spike train domain",
booktitle = "Statistical Signal Processing for Neuroscience and
Neurotechnology",
pages = "265--309",
year = "2010",
editor = "Karim G. Oweiss",
chapter = "8",
publisher = "Elsevier",
doi = "10.1016/b978-0-12-375027-3.00008-9",
url = "http://www.sci.utah.edu/publications/Pai2010b/2010d.pdf",
}
@InCollection{SCI:Pai2010c,
author = "A.R.C. Paiva and I. Park and J.C. Principe",
title = "Optimization in Reproducing Kernel Hilbert Spaces
of Spike Trains",
booktitle = "Computational Neuroscience",
pages = "3--29",
year = "2010",
editor = "W. Chaovalitwongse et al.",
publisher = "Springer",
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doi = "10.1007/978-0-387-88630-5_1",
url = "http://www.sci.utah.edu/publications/Pai2010c/Paiva_2010a.pdf",
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author = "A.R.C. Paiva and I. Park and J.C. Principe",
title = "A comparison of binless spike train measures",
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volume = "19",
number = "3",
pages = "405--419",
year = "2010",
url = "http://www.sci.utah.edu/publications/paiva10/Paiva_2010b.pdf",
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author = "A.R.C. Paiva and T. Tasdizen",
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year = "2010",
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year = "2010",
location = "Istanbul, Turkey",
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Gopalakrishnan and R.M. Kirby",
title = "Gauss: A Framework for Verifying Scientific
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booktitle = "Proceeding of the Software Model Checking
Workshop",
year = "2005",
month = "July",
location = "Edinburgh, Scotland",
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author = "R. Palmer and S. Barrus and Y. Yang and G.
Gopalakrishnan and R.M. Kirby",
title = "Gauss: A Framework for Verifying Scientific
Computing Software",
journal = "Electronic Notes on Theoretical Computer Science
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pages = "95--106",
year = "2006",
month = "February",
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@InProceedings{SCI:Pal2007a,
author = "R. Palmer and G. Gopalakrishnan and R.M. Kirby",
title = "Semantics Driven Dynamic Partial-Order Reduction
of MPI-based Parallel Programs",
booktitle = "Proceedings of Parallel and Distributed Systems:
Testing and Debugging (PADTAD)",
year = "2007",
location = "London, UK",
note = "Awarded Best Paper",
keywords = "parallel visualization",
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author = "R. Palmer and M. DeLisi and G. Gopalakrishnan and
R.M. Kirby",
title = "An Approach to Formalization and Analysis of
Message Passing Libraries",
booktitle = "Proceedings of the 12th International Workshop on
Formal Methods for Industrial Critical Systems
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volume = "4916/2008",
pages = "164--181",
year = "2008",
location = "Berlin, Germany",
note = "Awarded Best Paper.",
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Anderson and P.T. Fletcher and B. Wang",
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Architecture Underlying Autism Using
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@Article{SCI:Pan2009a,
author = "Y. Pan and R.T. Whitaker and A. Cheryauka and D.
Ferguson",
title = "Feasibility of GPU-Assisted Iterative Image
Reconstruction for Mobile C-ARM CT",
booktitle = "Proceedings of SPIE Medical Imaging 2009",
journal = "Progress in biomedical optics and imaging",
volume = "10",
number = "3",
year = "2009",
issn = "1605-7422",
url = "http://www.sci.utah.edu/publications/pan09/GPU_RECON_A4.pdf",
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@InProceedings{SCI:Pan2009b,
author = "Y. Pan and W.-K. Jeong and R.T. Whitaker",
title = "Markov Surfaces: A Probabilistic Framework for
User-Assisted Three Dimensional Image
Segmentation",
booktitle = "Proceedings of MICCAI 2009 workshop on
Probabilistic Models for Medical Image Analysis",
year = "2009",
location = "London, UK",
url = "http://www.sci.utah.edu/publications/pan09/Pan_MICCAI2009.pdf",
}
@InProceedings{SCI:Pan2010a,
author = "Y. Pan and R.T. Whitaker and A. Cheryauka and D.
Ferguson",
title = "Regularized {3D} Iterative Reconstruction on a
Mobile {C-ARM} {CT}",
booktitle = "Proceedings of The First {CT} Meeting",
pages = "(accepted)",
year = "2010",
location = "Salt Lake City, UT",
keywords = "Cone-beam CT, iterative reconstruction, SART, GPU,
TV regularization",
url = "http://www.sci.utah.edu/publications/pan10/Pan_First_CT_Meeting.pdf",
}
@InProceedings{SCI:Pan2010b,
author = "Y. Pan and R.T. Whitaker and A. Cheryauka and D.
Ferguson",
title = "TV-regularized Iterative Image Reconstruction on a
Mobile C-ARM CT",
booktitle = "Proceedings of SPIE Medical Imaging 2010",
volume = "7622",
pages = "(published online)",
year = "2010",
location = "San Diego, CA",
doi = "10.1117/12.844398",
url = "http://www.sci.utah.edu/publications/pan10/Pan_SPIE2010.pdf",
}
@Article{SCI:Pan2011a,
author = "Y. Pan and W.-K. Jeong and R.T. Whitaker",
title = "Markov surfaces: A probabilistic framework for
user-assisted three-dimensional image
segmentation",
journal = "Computer Vision and Image Understanding",
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number = "10",
pages = "1375--1383",
year = "2011",
url = "http://www.sci.utah.edu/publications/pan11/Pan_markovsurface2012.pdf",
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author = "B. Paniagua and L. Bompard and J. Cates and R.T.
Whitaker and M. Datar and C. Vachet and M.
Styner",
title = "Combined {SPHARM-PDM} and entropy-based particle
systems shape analysis framework",
booktitle = "Medical Imaging 2012: Biomedical Applications in
Molecular, Structural, and Functional Imaging",
year = "2012",
publisher = "SPIE Intl Soc Optical Eng",
month = "March",
doi = "10.1117/12.911228",
pmid = "24027625",
pmcid = "PMC3766973",
url = "http://www.sci.utah.edu/publications/Pan2012a/Paniagua_SPIE2012.pdf",
}
@InProceedings{SCI:Pan2013a,
author = "B. Paniagua and O. Emodi and J. Hill and J.
Fishbaugh and L.A. Pimenta and S.R. Aylward and E.
Andinet and G. Gerig and J. Gilmore and J.A. van
Aalst and M. Styner",
title = "3D of brain shape and volume after cranial vault
remodeling surgery for craniosynostosis correction
in infants",
booktitle = "Proceedings of SPIE 8672, Medical Imaging 2013:
Biomedical Applications in Molecular, Structural,
and Functional Imaging, 86720V",
year = "2013",
doi = "10.1117/12.2006524",
url = "http://www.sci.utah.edu/publications/paniagua13/Paniagua_SPIE2013.pdf",
}
@InProceedings{SCI:Pan2013b,
author = "B. Paniagua and A. Lyall and J.-B. Berger and C.
Vachet and R.M. Hamer and S. Woolson and W. Lin and
J. Gilmore and M. Styner",
title = "Lateral ventricle morphology analysis via mean
latitude axis",
booktitle = "Proceedings of SPIE 8672, Biomedical Applications
in Molecular, Structural, and Functional Imaging,
86720M",
year = "2013",
doi = "10.1117/12.2006846",
pmid = "23606800",
pmcid = "PMC3630372",
url = "http://www.sci.utah.edu/publications/paniagua13/Paniagua_SPIE2013b.pdf",
}
@TechReport{SCI:Pan98a,
author = "J. Pan and C.G.W. Sheppard and A. Tindall and M.
Berzins and S.V. Pennington and J.M. Ware",
title = "End Gas Inhomogeneity, Autoignition and Knock",
number = "982616",
year = "1998",
institution = "SAE",
type = "SAE meeting technical report",
location = "San Fransisco, CA",
url = "http://www.sci.utah.edu/publications/pan98/SAE982616.pdf",
}
@InProceedings{SCI:Pao1993a,
author = "A. Paoluzzi and V. Pascucci and M. Vicentino",
title = "{PLASM} Functional Approach to Design:
Representation of Geometry",
booktitle = "Proceedings of the Fifth International Conference
on Computer-Aided Design Futures ({CAAD} Futures
'93)",
pages = "127--141",
year = "1993",
editor = "U. Flemming and S. Van Wyk",
publisher = "North-Holland",
}
@InProceedings{SCI:Pao1993b,
author = "A. Paoluzzi and V. Pascucci and M. Vicentino",
title = "Un linguaggio di progettazione orientato al Solid
Modeling ({A} Design Language oriented to Solid
Modeling)",
booktitle = "Atti del convegno IcoGraphics '93",
pages = "60--66",
year = "1993",
publisher = "Mondadori Informatica",
address = "Milano, Italy",
month = "March",
note = "In Italian",
}
@Article{SCI:Pao1995a,
author = "A. Paoluzzi and V. Pascucci and M. Vicentino",
title = "Geometric Programming: A Programming Approach to
Geometric Design",
journal = "ACM Transactions on Graphics",
volume = "14",
number = "3",
pages = "266--306",
year = "1995",
month = "July",
}
@InProceedings{SCI:Pao1995b,
author = "A. Paoluzzi and V. Pascucci",
title = "Building Design Programming with a Functional
Language",
booktitle = "Proceedings of 6th Conference on Computing in
Civil and Building Engineering",
year = "1995",
publisher = "AA Balkema, Rotterdam",
month = "July",
location = "Berlin, Germany",
}
@InProceedings{SCI:Pao1995c,
author = "A. Paoluzzi and V. Pascucci and C. Sansoni",
title = "Prototype Shape Modeling with a Design Language",
booktitle = "Proceedings of the Sixth Int. Conf. on
Computer-Aided Architectural Design Futures",
pages = "59--78",
year = "1995",
editor = "Milton Tan and Robert Teh",
series = "The Global Design Studio",
address = "Centre for Advanced Studies in Architecture,
National University of Singapore",
}
@Book{SCI:Pao2003a,
author = "A. Paoluzzi and V. Pascucci and M. Vicentino and
C. Baldazzi and S. Protuesi",
title = "Geometric Programming for Computer Aided Design",
year = "2003",
publisher = "John Wiley \& Sons",
month = "June",
}
@InProceedings{SCI:Pao2004a,
author = "A. Paoluzzi and V. Pascucci and G. Scorzelli",
title = "Progressive BSP Representation and Boolean
Operations for Dimension-Independent Polyhedra",
booktitle = "ACM Symposium on Solid Modeling",
pages = "203-211",
year = "2004",
month = "June",
note = "UCRL-PROC-208679",
}
@InProceedings{SCI:Par1995a,
author = "S.G. Parker and C.R. Johnson",
title = "{SCIR}un: A Scientific Programming Environment for
Computational Steering",
booktitle = "Proceedings of the 1995 ACM/IEEE Conference on
Supercomputing",
booktitle_url = "http://doi.acm.org/10.1145/224170.224354",
number = "52",
year = "1995",
series = "Supercomputing '95",
publisher = "ACM",
address = "New York, NY, USA",
location = "San Diego, California, USA",
isbn = "0-89791-816-9",
doi = "10.1145/224170.224354",
keywords = "steering, interactive, dataflow, visual
programming, scientific computing",
url = "http://www.sci.utah.edu/publications/Par1995a/Parker_SCIRun_SC1995.pdf",
}
@InCollection{SCI:Par1997a,
author = "S.G. Parker and D.M. Weinstein and C.R. Johnson",
title = "The {SCIR}un Computational Steering Software
System",
booktitle = "Modern Software Tools in Scientific Computing",
pages = "1--40",
year = "1997",
editor = "E. Arge and A.M. Bruaset and H.P. Langtangen",
publisher = "Birkhauser Press",
address = "Boston",
keywords = "scirun, problem solving environments, ncrr,
scientific visualization, pse pses problem solving
envoronment, bioelectric fields",
url = "http://www.sci.utah.edu/publications/Par1997a/Parker_SCIRun1997.pdf",
}
@InProceedings{SCI:Par2000a,
author = "S.G. Parker and M. Miller and C.D. Hansen and C.R.
Johnson",
title = "Computational Steering and the {SCIR}un Integrated
Problem Solving Environment",
booktitle = "Proceedings of Dagstuhl 1997 Workshop on
Scientific Visualization",
pages = "257--266",
year = "2000",
editor = "Hans Hagen and Greg Nielson and Frits Post",
note = "Invited and peer reviewed",
keywords = "ncrr, scirun",
url = "http://www.sci.utah.edu/publications/sparker00/scivis97.pdf",
}
@Article{SCI:Par2002a,
author = "S.G. Parker",
title = "Interactive Ray Tracing on a Supercomputer",
journal = "In Practical Parallel Rendering",
year = "2002",
editor = "A. Chalmers and E. Reinhard",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, scientific
visualization, rtrt",
}
@InProceedings{SCI:Par2002b,
author = "S.G. Parker",
title = "A Component-Based Architecture for Parallel
Multi-physics PDE Simulation",
booktitle = c-ICCS2002,
volume = "2331",
pages = "719--734",
year = "2002",
}
@Article{SCI:Par2003b,
author = "S.G. Parker",
title = "{C-SAFE} Uses Linux {HPCC} in Fire Research",
journal = "Syllabus, Technology for Higher Education",
volume = "16",
number = "7",
year = "2003",
month = "Feburary",
keywords = "uintah, csafe c-safe, pse, problem solving
environments",
url = "http://www.sci.utah.edu/publications/Par2003b/2003_Parker_Linux_HPCC_in_Fire_Research.pdf",
}
@Article{SCI:Par2006a,
author = "S.G. Parker",
title = "A Component-Based Architecture for Parallel
Multi-physics PDE Simulation",
journal = "Future Generation Computer Systems (FGCS)",
volume = "22",
number = "1-2",
pages = "204--216",
year = "2006",
publisher = "Elsevier",
keywords = "forward simulation, computational pde pdes
computational partial differential equations,
parallel visualization",
url = "http://www.sci.utah.edu/publications/sparker06/science.pdf",
}
@InCollection{SCI:Par2006b,
author = "S.G. Parker and K. Zhang and K. Damevski and C.R.
Johnson",
title = "Integrating Component-Based Scientific Computing
Software",
booktitle = "Parallel Processing for Scientific Computing",
pages = "271--288",
year = "2006",
editor = "M.A. Heroux and P. Raghavan and H.D. Simon",
publisher = "{SIAM} Press",
isbn = "0-89871-619-5",
url = "http://www.sci.utah.edu/publications/sparker06/SIAM-PSE-Book05.pdf",
}
@Article{SCI:Par2006c,
author = "S.G. Parker and J. Guilkey and T. Harman",
title = "A Component-based Parallel Infrastructure for the
Simulation of Fluid Structure Interaction",
journal = "Engineering with Computers",
volume = "22",
number = "3-4",
pages = "277--292",
year = "2006",
publisher = "Springer London",
keywords = "fluid structure problems, mpm material point
method, parallel computing, csafe c-safe",
}
@InProceedings{SCI:Par2006d,
author = "S.G. Parker",
title = "Composition of Components in Multiphysics
Applications",
booktitle = "Proceedings of the 12th SIAM Conference on
Parallel Processing for Scientific Computing",
year = "2006",
location = "San Francisco, CA",
note = "Presented at the Minisymposium on Parallel Dynamic
Data Management Infrastructures for Scientific \&
Engineering Applications",
keywords = "csafe c-safe",
}
@InProceedings{SCI:Par2006e,
author = "S.G. Parker",
title = "Component-Based Multi-Physics Simulations of Fires
and Explosions",
booktitle = "Proceedings of the 12th SIAM Conference on
Parallel Processing for Scientific Computing",
year = "2006",
location = "San Francisco, CA",
note = "Presented at the Minisymposium on Parallel Dynamic
Data Management Infrastructures for Scientific \&
Engineering Applications",
keywords = "csafe c-safe",
}
@InProceedings{SCI:Par2006f,
author = "S.G. Parker",
title = "Why do Software Engineering Methods Fail for
HPC?",
booktitle = "Presented at Architectures and Algorithms for
Petascale Computing",
volume = "Seminar 06071",
year = "2006",
month = "February",
location = "Schloss Dagstuhl, Germany",
}
@InCollection{SCI:Par2006g,
author = "S. Parker and K. Zhang and C. Damevski and C.R.
Johnson",
title = "Integrating Component-Based Scientific Computing
Software",
booktitle = "Parallel Processing for Scientific Computing",
pages = "271--288",
year = "2006",
editor = "M.A. Heroux and P. Raghavan and H.D. Simon",
publisher = "SIAM",
month = "January",
url = "http://www.sci.utah.edu/publications/Par2006g/Parker_Int-Comp-Based-Sci-Comp-Software2005.pdf",
}
@InProceedings{SCI:Par2007a,
author = "S.G. Parker and S. Boulos and J. Bigler and A.
Robison",
title = "RTSL: a Ray Tracing Shading Language",
booktitle = "In 2007 {IEEE}/Eurographics Symposium on
Interactive Ray Tracing",
pages = "149--160",
year = "2007",
keywords = "rt ray tracing",
}
@Article{SCI:Par2007b,
author = "S.G. Parker and R. Armstrong and D. Bernholdt and
T. Dahlgren and T. Epperly and J. Kenny and M.
Krishnan and G. Kumfert and J. Larson and L.C.
McInnes and J. Nieplocha and J. Ray and S.
Shasharina",
title = "Enabling Advanced Scientific Computing Software",
journal = "CTWatch Quarterly",
volume = "3",
number = "4",
year = "2007",
}
@InCollection{SCI:Par2009a,
author = "S.G. Parker and K. Damevski and A. Khan and A.
Swaminathan and C.R. Johnson",
title = "The SCIJump Framework for Parallel and Distributed
Scientific Computing",
booktitle = "Advanced Computational Infrastructures for
Parallel and Distributed Adaptive Applications",
pages = "149--170",
year = "2009",
editor = "Manish Parashar and Xiaolin Li and Sumir
Chandra",
publisher = "Wiley-Blackwell",
doi = "10.1002/9780470558027.ch9",
url = "http://www.sci.utah.edu/publications/Par2009a/Parker_SCIJump-chapter2011.pdf",
}
@InProceedings{SCI:Par2012a,
author = "C Partl and A Lex and M Streit and D Kalkofen and
K Kashofer and D Schmalstieg",
title = "enRoute: Dynamic Path Extraction from Biological
Pathway Maps for In-Depth Experimental Data
Analysis",
booktitle = "Proceedings of the IEEE Symposium on Biological
Data Visualization (BioVis '12)",
pages = "107--114",
year = "2012",
publisher = "IEEE",
doi = "10.1109/BioVis.2012.6378600",
url = "http://www.sci.utah.edu/publications/Par2012a/2012_biovis_enroute.pdf",
}
@Article{SCI:Par2013a,
author = "C. Partl and A. Lex and M. Streit and D. Kalkofen
and K. Kashofer and D. Schmalstieg",
title = "enRoute: Dynamic Path Extraction from Biological
Pathway Maps for Exploring Heterogeneous
Experimental Datasets",
journal = "BMC Bioinformatics",
volume = "14",
number = "Suppl 19",
year = "2013",
month = "Nov",
issn = "1471-2105",
doi = "10.1186/1471-2105-14-S19-S3",
url = "http://www.sci.utah.edu/publications/Par2013a/2013_bmc_enroute.pdf",
}
@Article{SCI:Par2014a,
author = "B.R. Parmar and T.R. Jarrett and N.S. Burgon and
E.G. Kholmovski and N.W. Akoum and N. Hu and R.S.
Macleod and N.F. Marrouche and R. Ranjan",
title = "Comparison of Left Atrial Area Marked Ablated in
Electroanatomical Maps with Scar in MRI",
journal = "Journal of Cardiovascular Electrophysiology",
year = "2014",
doi = "10.1111/jce.12357",
keywords = "atrial fibrillation, magnetic resonance imaging,
radiofrequency ablation",
url = "http://www.sci.utah.edu/publications/Par2014a/Parmar_jce12357.pdf",
}
@Article{SCI:Par2014b,
author = "Christian Partl and Alexander Lex and Marc Streit
and Hendrik Strobelt and Anne-Mai Wasserman and
Hanspeter Pfister and and Dieter Schmalstieg",
title = "ConTour: Data-Driven Exploration of
Multi-Relational Datasets for Drug Discovery",
journal = "IEEE Transactions on Visualization and Computer
Graphics (VAST '14)",
volume = "20",
number = "12",
pages = "1883--1892",
year = "2014",
issn = "1077-2626",
doi = "10.1109/TVCG.2014.2346752",
url = "http://www.sci.utah.edu/publications/Par2014b/2014_vast_contour.pdf",
}
@Article{SCI:Par2015a,
author = "B.R. Parmar and T.R. Jarrett and E.G. Kholmovski
and N. Hu and D. Parker and R.S. MacLeod and N.F.
Marrouche and R. Ranjan",
title = "Poor scar formation after ablation is associated
with atrial fibrillation recurrence",
title_url = "http://www.ncbi.nlm.nih.gov/pubmed/26455362",
journal = "Journal of Interventional Cardiac
Electrophysiology",
volume = "44",
number = "3",
pages = "247-256",
year = "2015",
month = "December",
}
@Article{SCI:Par2016a,
author = "C. Partl and S. Gratzl and M. Streit and A.
Wassermann and H. Pfister and D. Schmalstieg and A.
Lex",
title = "Pathfinder: Visual Analysis of Paths in Graphs",
journal = "Computer Graphics Forum (EuroVis '16)",
volume = "35",
number = "3",
pages = "71-80",
year = "2016",
month = "jun",
issn = "1467-8659",
doi = "10.1111/cgf.12883",
url = "http://www.sci.utah.edu/publications/Par2016a/2016_eurovis_pathfinder.pdf",
}
@TechReport{SCI:Par93a,
author = "J. Parker and M. Berzins and J.M. Cameron and K.A.
Collins and C.M. Sawyer",
title = "Final Report on SERC/DTI Parallel Applications
Programme Collaboration Between EPCC, Rolls Royce
ands Leeds University",
year = "1993",
institution = "Edinburgh Parallel Computing Centre",
month = "September",
}
@TechReport{SCI:Par94,
author = "S.G. Parker and D.M. Weinstein and C.R. Johnson",
title = "A Morphing Algorithm for Generating Near Optimal
Grids: Applications in Computational Medicine",
number = "UUCS-94-014",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "computational pde pdes computational partial
differential equations evaporation, scientific
computing",
url = "http://www.sci.utah.edu/publications/sparker94/uu_tech.mm.ps",
url = "http://www.sci.utah.edu/publications/sparker94/uu_tech.mm.ps.Z",
}
@TechReport{SCI:Par94b,
author = "S.G. Parker and C.R. Johnson",
title = "Interactive Manipulation of Contour Data Using the
Layers Program - User Guide",
number = "UUCS-94-014",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = ", pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/sparker94/layers.ps",
}
@Article{SCI:Par96a,
author = "S.G. Parker and C.R. Johnson",
title = "{SCIR}un: Applying Interactive Computer Graphics
to Scientific Problems",
journal = "{SIGGRAPH} (applications/demo)",
year = "1996",
keywords = "scirun, scientific computing, scientific
visualization",
url = "http://www.sci.utah.edu/publications/sparker96/siggraph96.ps",
}
@Article{SCI:Par97b,
author = "S.G. Parker and D.M. Beazley and C.R. Johnson",
title = "Computational Steering Software Systems and
Strategies",
journal = "{IEEE} Computational Science and Engineering",
volume = "4",
number = "4",
pages = "50--59",
year = "1997",
keywords = "scirun, pse, problem solving environments",
url = "http://www.sci.utah.edu/publications/sparker97/ieee_cse96.ps.Z",
}
@InProceedings{SCI:Par98a,
author = "S.G. Parker and P. Shirley and Y. Livnat and C.D.
Hansen and P.-P. Sloan",
title = "Interactive Ray Tracing for Isosurface
Extraction",
booktitle = "{IEEE} Visualization '98",
pages = "233--238",
year = "1998",
month = "October",
keywords = "scalar field methods, isosurface extraction,
parallel visualization, interactive rt distributed
interactive ray tracing dirt",
url = "http://www.sci.utah.edu/publications/viz98/iso.pdf",
}
@TechReport{SCI:Par98b,
author = "S.G. Parker and P. Shirley and B. Smits",
title = "Single Sample Soft Shadows",
number = "UUCS-98-019",
year = "1998",
institution = "University of Utah",
type = "School of Computing Technical Report",
month = "October",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, scientific
visualization, rtrt",
}
@InProceedings{SCI:Par98c,
author = "S.G. Parker and M. Miller and C.D. Hansen and C.R.
Johnson and P.-P. Sloan",
title = "An Integrated Problem Solving Environment: The
{SCIR}un Computational Steering System",
booktitle = "31st Hawaii International Conference on System
Sciences ({HICSS}-31)",
volume = "VII",
pages = "147--156",
year = "1998",
editor = "H. El-Rewini",
publisher = pub-IEEE,
month = "January",
keywords = "scirun",
url = "http://www.sci.utah.edu/publications/hicss98/hicss98_color.ps.gz",
url = "http://www.sci.utah.edu/publications/hicss98/hicss98_color.ps.gz",
url = "http://www.sci.utah.edu/publications/hicss98/hicss98_color.ps.gz",
}
@Article{SCI:Par99a,
author = "S.G. Parker and M. Parker and Y. Livnat and P.P.
Sloan and C.D. Hansen and P. Shirley",
title = "Interactive Ray Tracing for Volume
Visualization",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "5",
number = "3",
pages = "238--250",
year = "1999",
month = "July-September",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, visible human,
scientific visualization",
url = "http://www.sci.utah.edu/publications/ieee_tvcg99/tvcg99.ps.gz",
url = "http://www.sci.utah.edu/publications/ieee_tvcg99/tvcg99.pdf",
}
@InProceedings{SCI:Par99b,
author = "S.G. Parker and P. Shirley and Y. Livnat and C.D.
Hansen and P.-P. Sloan and M. Parker",
title = "Interacting with Gigabyte Volume Datasets on the
Origin 2000",
booktitle = "The 41st Annual Cray User's Group Conference",
year = "1999",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, scientific
visualization, rtrt",
url = "http://www.sci.utah.edu/publications/sparker99/rtrt.ps.gz",
url = "http://www.sci.utah.edu/publications/sparker99/rtrt.pdf",
}
@InProceedings{SCI:Par99c,
author = "S.G. Parker and W. Martin and P.-P. Sloan and P.
Shirley and B. Smits and C.D. Hansen",
title = "Interactive Ray Tracing",
booktitle = "Symposium on Interactive 3D Graphics: Interactive
3D",
pages = "119--126",
year = "1999",
month = "April 26-28",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, scientific
visualization, rtrt",
url = "http://www.sci.utah.edu/publications/sparker99/rtrt.pdf",
url = "http://www.sci.utah.edu/publications/sparker99/rtrt.ps.gz",
}
@InProceedings{SCI:Pas1992a,
author = "A. Pascucci and V. Pascucci",
title = "Uso del calcolatore nella produzione, elaborazione
ed archiviazione di proiezioni parallele (Using the
computer for generating, processing and archiving
parallel projections)",
booktitle = "Atti del convegno L'immagine nel rilievo",
pages = "540--561",
year = "1992",
editor = "C. Cundari",
publisher = "Gangemi",
}
@InProceedings{SCI:Pas1995a,
author = "V. Pascucci and V. Ferrucci and A. Paoluzzi",
title = "Dimension-independent convex-cell based {HPC}:
representation scheme and implementation issues",
booktitle = "SMA '95: Proceedings of the Third Symposium on
Solid Modeling and Applications",
pages = "163--174",
year = "1995",
organization = "ACM",
month = "May",
note = "held May 17-19, 1995 in Salt Lake City, Utah",
}
@Article{SCI:Pas1996a,
author = "V. Pascucci and V. Ferrucci and A. Paoluzzi",
title = "Dimension-Independent Convex-Cell Based HPC:
Skeletons and Product",
journal = "International Journal of Shape Modeling",
volume = "2",
pages = "37--67",
year = "1996",
}
@InProceedings{SCI:Pas2000a,
author = "V. Pascucci and C.L. Bajaj",
title = "Time Critical Isosurface Refinement and
Smoothing",
booktitle = "Proceedings of the {ACM/IEEE} Volume Visualization
and Graphics Symposium 2000",
pages = "33--42",
year = "2000",
month = "October",
location = "Salt lake City, Utah",
note = "UCRL-JC-139628",
}
@InProceedings{SCI:Pas2001a,
author = "V. Pascucci and R.J. Frank",
title = "Global Static Indexing for Real-time Exploration
of Very Large Regular Grids",
booktitle = "Proceedings of Supercomputing 2001",
year = "2001",
organization = "ACM",
month = "Nov",
note = "UCRL-JC-144754",
}
@InProceedings{SCI:Pas2001b,
author = "V. Pascucci",
title = "On the Topology of the Level Sets of a Scalar
Field",
booktitle = "Proceedings of the 13th Canadian Conference on
Computational Geometry",
pages = "141--144",
year = "2001",
month = "August",
note = "UCRL-JC-142262",
}
@InProceedings{SCI:Pas2002b,
author = "V. Pascucci and K. Cole-McLaughlin",
title = "Efficient Computation of the Topology of Level
Sets",
booktitle = "Proceedings of IEEE Conference on Visualization
({VIS}-02)",
pages = "187--194",
year = "2002",
month = "October",
location = "Boston, MA",
note = "UCRL-JC-149277",
}
@InProceedings{SCI:Pas2002c,
author = "V. Pascucci",
title = "Slow Growing Subdivision ({SGS}) in Any Dimension:
Towards Removing the Curse Of Dimensionality",
booktitle = "Proceedings of Eurographics 2002",
pages = "451--460",
year = "2002",
month = "September",
location = "Saabruken, Germany",
note = "UCRL-ID-144257",
}
@InProceedings{SCI:Pas2002d,
author = "V. Pascucci",
title = "Slow Growing Volumetric Subdivision for 3D
Volumetric Data",
booktitle = "{SIGGRAPH} 2002 Technical Sketches",
year = "2002",
}
@Article{SCI:Pas2003a,
author = "V. Pascucci and K. Cole-McLaughlin",
title = "Parallel Computation of the Topology of Level
Sets",
journal = "Algorithmica",
volume = "38",
number = "1",
pages = "249--268",
year = "2003",
month = "October",
}
@InProceedings{SCI:Pas2003b,
author = "V. Pascucci and D.E. Laney and R. Frank and G.
Scorzelli and L. Linsen and B. Hamann and F.
Gygi",
title = "Real-Time Monitoring of Large Scientific
Simulations",
booktitle = "Proceedings of the 18-th annual ACM Symposium on
Applied Computing",
pages = "194--198",
year = "2003",
month = "March",
location = "Melbourne, Florida",
note = "UCRL-JC-151094",
}
@InCollection{SCI:Pas2003g,
author = "V. Pascucci and R. J. Frank",
title = "Hierarchical Indexing for Out-of-Core Access to
Multi-Resolution Data",
booktitle = "Mathematics and Visualization",
pages = "225--241",
year = "2003",
editor = "G.Farin and B. Hamann and H. Hagen",
publisher = "Springer-Verlag",
note = "UCRL-JC-140581",
doi = "10.1007/978-3-642-55787-3_14",
}
@InProceedings{SCI:Pas2004b,
author = "V. Pascucci",
title = "Isosurface Computation Made Simple: Hardware
Acceleration, Adaptive Refinement and Tetrahedral
Stripping",
booktitle = "Proceedings of the Joint Eurographics - {IEEE}
{TVCG} Symposium on Visualization (VisSym)",
pages = "293--300",
year = "2004",
month = "May",
note = "UCRL-CONF-202459",
}
@InCollection{SCI:Pas2006g,
author = "V. Pascucci",
title = "Topology Diagrams of Scalar Fields in Scientific
Visualisation",
booktitle = "Topological Data Structures for Surfaces",
pages = "121--129",
year = "2006",
editor = "Sanjay Rana and Jo Wood",
publisher = "Wiley-Blackwell",
month = "May",
note = "UCRL-BOOK-200013",
doi = "10.1002/0470020288.ch8",
}
@Article{SCI:Pas2007a,
author = "V. Pascucci and G. Scorzelli and P.-T. Bremer and
A. Mascarenhas",
title = "Robust On-line Computation of Reeb Graphs:
Simplicity and Speed",
journal = "ACM Transactions on Graphics: ACM SIGGRAPH 2007
Papers",
pages = "1057--1066",
year = "2007",
publisher = "ACM Press",
address = "New York, NY, USA",
}
@Book{SCI:Pas2011a,
author = "Valerio Pascucci and Xavier Tricoche and Hans
Hagen and Julien Tierny",
title = "Topological Methods in Data Analysis and
Visualization: Theory, Algorithms, and Applications
(Mathematics and Visualization)",
title_url =
"http://www.amazon.com/Topological-Methods-Data-Analysis-Visualization/dp/3642150136/ref=sr_1_5?ie=UTF8\&s=books\&qid=1296389542\&sr=1-5",
year = "2011",
publisher = "Springer",
isbn = "978-3642150135",
}
@InCollection{SCI:Pas2012a,
author = "V. Pascucci and G. Scorzelli and B. Summa and
P.-T. Bremer and A. Gyulassy and C. Christensen and
S. Philip and S. Kumar",
title = "The {ViSUS} Visualization Framework",
booktitle = "High Performance Visualization: Enabling
Extreme-Scale Scientific Insight",
year = "2012",
editor = "E. Wes Bethel and Hank Childs (LBNL) and Charles
Hansen (UofU)",
chapter = "19",
series = "Chapman and Hall/{CRC} Computational Science",
publisher = "Chapman and Hall/{CRC}",
url = "http://www.sci.utah.edu/publications/pascucci12/Pascucci_Visus_ch19.pdf",
}
@InProceedings{SCI:Pas2013a,
author = "V. Pascucci and P.-T. Bremer and A. Gyulassy and
G. Scorzelli and C. Christensen and B. Summa and S.
Kumar",
title = "Scalable Visualization and Interactive Analysis
Using Massive Data Streams",
booktitle = "Cloud Computing and Big Data",
volume = "23",
pages = "212--230",
year = "2013",
series = "Advances in Parallel Computing",
publisher = "IOS Press",
keywords = "Visualization, data analysis, topological data
analysis, Parallel I/O",
url = "http://www.sci.utah.edu/publications/Pas2013a/ViSUS_book_chapter.pdf",
}
@TechReport{SCI:Pas2020a,
author = "V. Pascucci and I. Altintas and J. Fortes and I.
Foster and H. Gu and S. Hariri and D. Stanzione and
M. Taufer and X. Zhao",
title = "Report from the NSF Workshop on Smart
Cyberinfrastructure 2020",
year = "2020",
institution = "NSF",
url = "http://www.sci.utah.edu/publications/Pas2020a/UUSCI-2020-001.pdf",
}
@Article{SCI:Pat2013a,
author = "Y. Pathak and B.H. Kopell and A. Szabo and C.
Rainey and H. Harsch and C.R. Butson",
title = "The role of electrode location and stimulation
polarity in patient response to cortical
stimulation for major depressive disorder",
journal = "Brain Stimulation",
volume = "6",
number = "3",
pages = "254--260",
year = "2013",
publisher = "Elsevier Ltd.",
month = "July",
issn = "1935-861X",
doi = "10.1016/j.brs.2012.07.001",
keywords = "cortical stimulation",
url = "http://www.sci.utah.edu/publications/Pat2013a/Pathak_BrainStim2013.pdf",
}
@Article{SCI:Pat2016a,
author = "Y. Pathak and O. Salami and S. Baillet and Z. Li
and C.R. Butson",
title = "Longitudinal Changes in Depressive Circuitry in
Response to Neuromodulation Therapy",
journal = "Frontiers in Neural Circuits",
volume = "10",
year = "2016",
publisher = "rontiers Media SA",
month = "July",
doi = "10.3389/fncir.2016.00050",
url = "http://www.sci.utah.edu/publications/Pat2016a/pathak_2016.pdf",
}
@Article{SCI:Pau2010a,
author = "F.V. Paulovich and C.T. Silva and L.G. Nonato",
title = "Two-Phase Mapping for Projecting Massive Data
Sets",
booktitle = "{IEEE} Tr",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "16",
number = "6",
pages = "1281--1290",
year = "2010",
month = "Nov",
doi = "10.1109/TVCG.2010.207",
url = "http://www.sci.utah.edu/publications/Pau2010a/Paulovich_TVCG2010.pdf",
}
@InProceedings{SCI:Peg2006a,
author = "V. Pegoraro and S.G. Parker",
title = "Physically-Based Realistic Fire Rendering",
booktitle = "Proceedings of the 2006 Eurographics Workshop on
Natural Phenomena",
pages = "51--59",
year = "2006",
keywords = "predictive ray tracing flame radiation,
rtcenter",
url = "http://www.sci.utah.edu/publications/vpegorar06/PhysicallyBasedRealisticFireRendering.pdf",
}
@InProceedings{SCI:Peg2008a,
author = "V. Pegoraro and I. Wald and S.G. Parker",
title = "Sequential Monte Carlo Adaptation in
Low-Anisotropy Participating Media",
booktitle = "Proceedings of the 19th Eurographics Symposium on
Rendering",
pages = "1097--1104",
year = "2008",
url = "http://www.sci.utah.edu/publications/pegoraro08/SequentialMonteCarloAdaptationInLowAnisotropyParticipatingMedia.pdf",
}
@InProceedings{SCI:Peg2008b,
author = "V. Pegoraro and C. Brownlee and P.S. Shirley and
S.G. Parker",
title = "Towards Interactive Global Illumination Effects
via Sequential Monte Carlo Adaptation",
booktitle = "Proceedings of the 3rd {IEEE} Symposium on
Interactive Ray Tracing",
pages = "107--114",
year = "2008",
url = "http://www.sci.utah.edu/publications/pegoraro08/TowardsInteractiveGlobalIlluminationEffectsViaSequentialMonteCarloAdaptation.pdf",
}
@Article{SCI:Peg2009a,
author = "V. Pegoraro and S.G. Parker",
title = "An Analytical Solution to Single Scattering in
Homogeneous Participating Media",
journal = "Computer Graphics Forum (Proceedings of the 30th
Eurographics Conference)",
volume = "28",
number = "2",
pages = "329--335",
year = "2009",
url = "http://www.sci.utah.edu/publications/pegoraro09/Pegoraro_CGF09.pdf",
}
@InProceedings{SCI:Peg2009b,
author = "V. Pegoraro and M. Schott and S.G. Parker",
title = "An Analytical Approach to Single Scattering for
Anisotropic Media and Light Distributions",
booktitle = "Proceedings of the 35th Graphics Interface
Conference",
pages = "71--77",
year = "2009",
url = "http://www.sci.utah.edu/publications/pegoraro09/Pegoraro_GIF09.pdf",
}
@Article{SCI:Peg2010a,
author = "V. Pegoraro and M. Schott and S.G. Parker",
title = "A Closed-Form Solution to Single Scattering for
General Phase Functions and Light Distributions",
journal = "Computer Graphics Forum",
volume = "29",
number = "4",
pages = "1365--1374",
year = "2010",
publisher = "Wiley-Blackwell",
month = "Aug",
doi = "10.1111/j.1467-8659.2010.01732.x",
url = "http://www.sci.utah.edu/publications/Peg2010a/Pegoraro_EGSR2010.pdf",
}
@Article{SCI:Pen2012a,
author = "Z. Peng and E. Grundy and R.S. Laramee and G. Chen
and N. Croft",
title = "Mesh-Driven Vector Field Clustering and
Visualization: An Image-Based Approach",
journal = "IEEE Transactions on Visualization and Computer
Graphics, 2011",
volume = "18",
number = "2",
pages = "283--298",
year = "2012",
month = "February",
doi = "10.1109/TVCG.2011.25",
keywords = "Vector Field Visualization, Clustering,
Feature-based, Surfaces",
url = "http://www.sci.utah.edu/publications/Pen2012a/Peng_TVCG2011.pdf",
}
@Article{SCI:Pen94b,
author = "S.V. Pennington and M. Berzins",
title = "New {NAG} Library Software for First-Order Partial
Differential Equations",
journal = "{ACM} Transactions on Mathematical Software",
volume = "20",
number = "1",
pages = "63--99",
year = "1994",
month = "March",
url = "http://www.sci.utah.edu/publications/berzins94/ACMTOMSp63-pennington.pdf",
}
@InProceedings{SCI:Per2006a,
author = "S. Pervez and G. Gopalakrishnan and R.M. Kirby and
R. Thakur and W. Gropp",
title = "Formal Verification of Programs that use MPI
One-Sided Communications",
booktitle = "Proceedings of EuroPVM-MPI 2006",
year = "2006",
month = "September 17-20",
location = "Bonn, Germany",
}
@InProceedings{SCI:Per2007a,
author = "S. Pervez and G. Gopalakrishnan and R.M. Kirby and
R. Palmer and R. Thakur and W. Gropp",
title = "Practical Model Checking Method for Verifying
Correctness of MPI Programs",
booktitle = "Recent Advances in Parallel Virtual Machine and
Message Passing Interface - Proceedings of
EuroPVM-MPI 2007",
volume = "4757/2007",
pages = "344--353",
year = "2007",
location = "Paris, France",
}
@InProceedings{SCI:Per2012a,
author = "D. Perry and A. Morris and N. Burgon and C. McGann
and R.S. MacLeod and J. Cates",
title = "Automatic classification of scar tissue in late
gadolinium enhancement cardiac MRI for the
assessment of left-atrial wall injury after
radiofrequency ablation",
booktitle = "{SPIE} Proceedings",
volume = "8315",
pages = "(published online)",
year = "2012",
doi = "10.1117/12.910833",
pmid = "24236224",
pmcid = "PMC3824273",
url = "http://www.sci.utah.edu/publications/perry12/Perry_SPIE2012.pdf",
}
@Article{SCI:Per2014a,
author = "A. J. Perez and M. Seyedhosseini and T. J.
Deerinck and E. A. Bushong and S. Panda and T.
Tasdizen and M. H. Ellisman",
title = "A workflow for the automatic segmentation of
organelles in electron microscopy image stacks",
journal = "Frontiers in Neuroanatomy",
volume = "8",
number = "126",
year = "2014",
doi = "10.3389/fnana.2014.00126",
}
@Article{SCI:Per2014b,
author = "A. Perez and M. Seyedhosseini and T. Tasdizen and
M. Ellisman",
title = "Automated workflows for the morphological
characterization of organelles in electron
microscopy image stacks (LB72)",
journal = "The FASEB Journal",
volume = "28",
number = "1 Supplement LB72",
year = "2014",
month = "April",
}
@InProceedings{SCI:Pes2004a,
author = "S. Pesco and P. Lindstrom and V. Pascucci and C.T.
Silva",
title = "Implicit Occluders",
booktitle = c-VVIS2004,
pages = "47--54",
year = "2004",
url = "http://www.sci.utah.edu/publications/pesco04/Pesco04_ImplicitOccluders.pdf",
}
@InProceedings{SCI:Pet2011a,
author = "T. Peterka and R. Ross and A. Gyulassy and V.
Pascucci and W. Kendall and H.-W. Shen and T.-Y.
Lee and A. Chaudhuri",
title = "Scalable Parallel Building Blocks for Custom Data
Analysis",
booktitle = "Proceedings of the 2011 {IEEE} Symposium on
Large-Scale Data Analysis and Visualization
({LDAV})",
pages = "105--112",
year = "2011",
month = "October",
doi = "10.1109/LDAV.2011.6092324",
url = "http://www.sci.utah.edu/publications/Pet2011a/Peterka_LDAV2011.pdf",
}
@InProceedings{SCI:Pet2012a,
author = "J.R. Peterson and J.C. Beckvermit and T. Harman
and M. Berzins and C.A. Wight",
title = "Multiscale Modeling of High Explosives for
Transportation Accidents",
booktitle = "Proceedings of the 1st Conference of the Extreme
Science and Engineering Discovery Environment:
Bridging from the eXtreme to the campus and
beyond",
year = "2012",
doi = "10.1145/2335755.2335828",
url = "http://www.sci.utah.edu/publications/peterson12/Peterson_XSEDE2012.pdf",
}
@Article{SCI:Pet2012b,
author = "J. Peterson and C. Wight",
title = "An Eulerian-Lagrangian Computational Model for
Deagration and Detonation of High Explosives",
journal = "Combustion and Flame",
volume = "159",
number = "7",
pages = "2491--2499",
year = "2012",
doi = "10.1016/j.combustflame.2012.02.006",
url = "http://www.sci.utah.edu/publications/Pet2012b/Peterson_CF2012.pdf",
}
@Article{SCI:Pet2013a,
author = "J.R. Peterson and C.A. Wight and M. Berzins",
title = "Applying high-performance computing to petascale
explosive simulations",
journal = "Procedia Computer Science",
year = "2013",
keywords = "Energetic Material Hazards, Uintah, MPM, ICE,
MPMICE, Scalable Parallelism, C-SAFE",
url = "http://www.sci.utah.edu/publications/peterson13/Peterson_JRP-ICCS2013.pdf",
}
@TechReport{SCI:Pet2015f,
author = "B. Peterson and N. Xiao and J. Holmen and S.
Chaganti and A. Pakki and J. Schmidt and D.
Sunderland and A. Humphrey and M. Berzins",
title = "Developing Uintah’s Runtime System For
Forthcoming Architectures",
title_url =
"http://respa15.rice.edu/files/2015/11/9-2csbfkt.pdf",
subtitle = "Refereed paper presented at the RESPA 15 Workshop
at SuperComputing 2015 Austin Texas",
year = "2015",
institution = "SCI Institute",
url = "http://www.sci.utah.edu/publications/Pet2015f/9-2csbfkt.pdf",
}
@InProceedings{SCI:Pet2015g,
author = "B. Peterson and H. K. Dasari and A. Humphrey and
J.C. Sutherland and T. Saad and M. Berzins",
title = "Reducing overhead in the Uintah framework to
support short-lived tasks on GPU-heterogeneous
architectures",
booktitle = "Proceedings of the 5th International Workshop on
Domain-Specific Languages and High-Level Frameworks
for High Performance Computing (WOLFHPC'15)",
pages = "4:1-4:8",
year = "2015",
publisher = "ACM",
doi = "10.1145/2830018.2830023",
url = "http://www.sci.utah.edu/publications/Pet2015g/wolfhpc-sc15.pdf",
}
@InProceedings{SCI:Pet2017a,
author = "B. Peterson and A. Humphrey and J. Schmidt and M.
Berzins",
title = "Addressing Global Data Dependencies in
Heterogeneous Asynchronous Runtime Systems on GPUs.
Awarded Best Paper",
booktitle = "Proceedings of the Third International Workshop on
Extreme Scale Programming Models and Middleware -
ESPM2'17",
year = "2017",
publisher = "ACM",
doi = "10.1145/3152041.3152082",
url = "http://www.sci.utah.edu/publications/Pet2017a/a1-peterson.pdf",
}
@InProceedings{SCI:Pet2017b,
author = "S. Petruzza and A. Venkat and A. Gyulassy and G.
Scorzelli and F. Federer and A. Angelucci and V.
Pascucci and P. T. Bremer",
title = "ISAVS: Interactive Scalable Analysis and
Visualization System",
booktitle = "ACM SIGGRAPH Asia 2017 Symposium on
Visualization",
year = "2017",
publisher = "ACM Press",
doi = "10.1145/3139295.3139299",
url = "http://www.sci.utah.edu/publications/Pet2017b/ISAVS_Interactive_Scalable_Analysis_and_Visualizat.pdf",
}
@Article{SCI:Pet2018a,
author = "B. Peterson and A. Humphrey and J. Holmen T.
Harman and M. Berzins and D. Sunderland and H.C.
Edwards",
title = "Demonstrating GPU Code Portability and Scalability
for Radiative Heat Transfer Computations",
journal = "Journal of Computational Science",
year = "2018",
publisher = "Elsevier BV",
month = "June",
issn = "1877-7503",
doi = "10.1016/j.jocs.2018.06.005",
url = "http://www.sci.utah.edu/publications/Pet2018a/jocs17-2.pdf",
}
@Article{SCI:Pet2018b,
author = "B. Peterson and A. Humphrey and D. Sunderland and
J. Sutherland and T. Saad and H. Dasari and M.
Berzins",
title = "Automatic Halo Management for the Uintah
GPU-Heterogeneous Asynchronous Many-Task Runtime",
journal = "International Journal of Parallel Programming",
year = "2018",
month = "Dec",
issn = "1573-7640",
doi = "10.1007/s10766-018-0619-1",
url = "http://www.sci.utah.edu/publications/Pet2018b/IJPP-final_submission.pdf",
}
@InProceedings{SCI:Pet2018c,
author = "S. Petruzza and A. Gyulassy and V. Pascucci and
and P. T. Bremer",
title = "A Task-Based Abstraction Layer for User
Productivity and Performance Portability in
Post-Moore’s Era Supercomputing",
booktitle = "3RD INTERNATIONAL WORKSHOP ON POST-MOORE’S ERA
SUPERCOMPUTING (PMES)",
year = "2018",
url = "http://www.sci.utah.edu/publications/Pet2018c/ws_pmes109s1-file1.pdf",
}
@InProceedings{SCI:Pet2018d,
author = "S. Petruzza and A. Gyulassy and V. Pascucci and
and P. T. Bremer",
title = "A Task-Based Abstraction Layer for User
Productivity and Performance Portability in
Post-Moore’s Era Supercomputing",
booktitle = "3RD INTERNATIONAL WORKSHOP ON POST-MOORE’S ERA
SUPERCOMPUTING (PMES)",
year = "2018",
url = "http://www.sci.utah.edu/publications/Pet2018d/ws_pmes109s1-file1.pdf",
}
@PhdThesis{SCI:Pet2019a,
author = "B. Peterson",
title = "Portable and Performant GPU/Heterogeneous
Asynchronous Many-task Runtime System",
subtitle = "Ph.D. Dissertation",
year = "2019",
school = "University of Utah, School of Computing",
month = "Dec",
url = "http://www.sci.utah.edu/publications/Pet2019a/bradpeterson-thesis.pdf",
}
@Article{SCI:Pfi2001a,
author = "H. Pfister and B. Lorensen and C. Bajaj and G.
Kindlmann and W. Schroeder and L.S. Avila and K.M.
Raghu and R. Machiraju and J. Lee",
title = "The transfer function bake-off",
journal = "IEEE Computer Graphics and Applications",
volume = "21",
number = "1",
pages = "16--22",
year = "2001",
publisher = "IEEE",
doi = "10.1109/38.920623",
url = "http://www.sci.utah.edu/publications/Pfi2001a/The Transfer Function Bake-Off.pdf",
}
@InProceedings{SCI:Pha2004a,
author = "N.S. Phatak and J.L. McCann and Q. Sun and S.E.
Kim and D.L. Parker and E.K. Jeong and R.K. Sanders
and A.I. Veress and J.A. Weiss",
title = "Noninvasive Measurement of Ligament Strain",
booktitle = c-ORS2004,
volume = "29",
pages = "893",
year = "2004",
month = "March",
location = "San Francisco, {CA}",
keywords = "forward problems inverse problems forward
simulation inverse solutions, finite elements,
computational mechanics, computational
biomechanics, ip image processing signal
processing, segmentation, warping, deformable image
registration",
}
@Article{SCI:Pha2007a,
author = "N.S. Phatak and Q. Sun and S.-E. Kim and D.L.
Parker and R.K. Sanders and A.I. Veress and B.J.
Ellis and J.A. Weiss",
title = "Noninvasive Determination of Ligament Strain with
Deformable Image Registration",
journal = "Annals of Biomedical Engineering",
volume = "35",
number = "7",
pages = "1175--1187",
year = "2007",
month = "February",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/phatak07/phatak_abme_2007.pdf",
}
@Article{SCI:Pha2008a,
author = "N.S. Phatak and S.A. Maas and A.I. Veress and N.A.
Pack and E.V.R. Di Bella and J.A. Weiss",
title = "Strain measurement in the left ventricle during
systole with deformable image registration",
journal = "Medical Image Analysis",
pages = "(in press)",
year = "2008",
}
@Article{SCI:Pha2009a,
author = "N.S. Phatak and S.A. Maas and A.I. Veress and N.A.
Pack and E.V. DiBella and J.A. Weiss",
title = "Strain Measurement in the Left Ventricle During
Systole with Deformable Image Registration",
journal = "Medical Image Analysi",
volume = "13",
number = "2",
pages = "354--361",
year = "2009",
keywords = "mrl, cardiology",
url = "http://www.sci.utah.edu/publications/phatak09/phatak_med_image_anal_2009.pdf",
}
@InProceedings{SCI:Phi2011a,
author = "S. Philip and B. Summa and P.-T. Bremer and and V.
Pascucci",
title = "Parallel Gradient Domain Processing of Massive
Images",
booktitle = "Proceedings of the 2011 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "11--19",
year = "2011",
url = "http://www.sci.utah.edu/publications/philip11/parallel-panorama.pdf",
}
@InProceedings{SCI:Phi2011b,
author = "S. Philip and B. Summa and P-T Bremer and V.
Pascucci",
title = "Hybrid CPU-GPU Solver for Gradient Domain
Processing of Massive Images",
booktitle = "Proceedings of 2011 International Conference on
Parallel and Distributed Systems (ICPADS)",
pages = "244--251",
year = "2011",
url = "http://www.sci.utah.edu/publications/philip11/hybrid-panorama.pdf",
}
@InProceedings{SCI:Phi2013a,
author = "S. Philip and B. Summa and J. Tierny and P.-T.
Bremer and V. Pascucci",
title = "Scalable Seams for Gigapixel Panoramas",
booktitle = "Proceedings of the 2013 Eurographics Symposium on
Parallel Graphics and Visualization",
pages = "25--32",
year = "2013",
note = "Awarded Best Paper!",
doi = "10.2312/EGPGV/EGPGV13/025-032",
url = "http://www.sci.utah.edu/publications/philip13/Philip_EGPGV2013.pdf",
}
@Article{SCI:Phi2015a,
author = "J. M. Phillips and Bei Wang and Y. Zheng",
title = "Geometric Inference on Kernel Density Estimates",
journal = "CoRR",
volume = "abs/1307.7760",
year = "2015",
url = "http://www.sci.utah.edu/publications/Phi2015a/KDE_Geomtric_Inference_BeiWang_2015.pdf",
}
@InProceedings{SCI:Pil2010a,
author = "T.A. Pilcher and J.D. Tate and J.G. Stinstra and
E.V. Saarel and M.D. Puchalski and and R.S.
MacLeod",
title = "Partially extracted defibrillator coils and pacing
leads alter defibrillation thresholds",
booktitle = "Proceedings of the 15th International Academy of
Cardiology World Congress of Cardiology",
year = "2010",
url = "http://www.sci.utah.edu/publications/pilcher10/Pilcher_2010.pdf",
}
@Article{SCI:Piz2001a,
author = "S. Pizer and S. Joshi and P.T. Fletcher and M.
Styner and G. Tracton and Z. Chen",
title = "Segmentation of Single-Figure Objects by
Deformable M-reps",
journal = "Medical Image Computing and Computer-Assisted
Intervention (MICCAI)",
pages = "862--871",
year = "2001",
editor = "WJ Niessen and MA Viergever",
publisher = "New York",
month = "October",
url = "http://www.sci.utah.edu/publications/pizer01/MICCAI01-Pizer-defmreps.pdf",
}
@Article{SCI:Piz2003a,
author = "S.M. Pizer and G. Gerig and S. Joshi and S.
Aylward",
title = "Multiscale Medial Shape-Based Analysis of Image
Objects",
journal = "Proceedings of the IEEE",
volume = "91",
number = "10",
pages = "1670--1679",
year = "2003",
editor = "C. Roux and J.K. Udupa",
publisher = "IEEE",
month = "October",
doi = "10.1109/jproc.2003.817876",
url = "http://www.sci.utah.edu/publications/Piz2003a/IEEEproc03_Pizer_multimed.pdf",
}
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author = "S.M. Pizer and P.T. Fletcher and Y. Fridman and
D.S. Fritsch and A.G. Gash and J.M. Glotzer and S.
Joshi and A. Thall and G. Tracton and P. Yushkevich
and E.L. Chaney",
title = "Deformable {M-Reps} for {3D} Medical Image
Segmentation",
journal = "International Journal of Computer Vision - Special
{UNC-MIDAG} issue",
volume = "55",
number = "2",
pages = "85--106",
year = "2003",
editor = "O Faugeras and K Ikeuchi and J Ponce",
publisher = "Kluwer Academic",
month = "November-December",
url = "http://www.sci.utah.edu/publications/pizer03/IJCV03-Pizer-mreps.pdf",
}
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author = "S.M. Pizer and P.T. Fletcher and A. Thall and M.
Styner and G. Gerig and S. Joshi",
title = "Object Models in Multiscale Intrinsic Coordinates
via M-reps",
journal = "Image and Vision Computing, Special Issue on
Generative Model-based Vision",
volume = "21",
number = "1",
pages = "5--15",
year = "2003",
month = "January",
url = "http://www.sci.utah.edu/publications/pizer03/GMBV02_Pizer.pdf",
}
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author = "S.M. Pizer and P.T. Fletcher and S. Joshi and A.G.
Gash and J. Stough and A. Thall and G. Tracton and
E. Chaney",
title = "A Method and Software for Segmentation of Anatomic
Object Ensembles by Deformable M-Reps",
journal = "Med Phys",
volume = "32",
number = "5",
pages = "1335--1345",
year = "2005",
month = "May",
url = "http://www.sci.utah.edu/publications/pizer05/MEDPHYS05_Pizer_defmrep.pdf",
}
@InProceedings{SCI:Piz2005b,
author = "S.M. Pizer and J.Y. Jeong and C. Lu and K. Muller
and S. Joshi",
title = "Estimating the Statistics of Multi-Object Anatomic
Geometry Using Inter-Object Relationships",
booktitle = "Proceedings of International Workshop on Deep
Structure, Singularities and Computer Vision
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pages = "60--71",
year = "2005",
editor = "O.F. Olsen and L. Florack and A Kuijper",
month = "June",
url = "http://www.sci.utah.edu/publications/pizer05/DSSCV05_Pizer_Jeong.pdf",
}
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author = "S. Pizer and M. Styner and T. Terriberry and R.
Broadhurst and S. Joshi and E. Chaney and P.T.
Fletcher",
title = "Statistical Applications with Deformable M-Reps",
booktitle = "Computational Imaging and Vision",
pages = "269--308",
year = "2008",
publisher = "Springer",
doi = "10.1007/978-1-4020-8658-8_9",
url = "http://www.sci.utah.edu/publications/Piz2008g/Pizer_MRMAA2009.pdf",
}
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R. Stott and K.E. Panter and P.M. Lee and A.J. Van
Wettere and J.R. Stevens and Z. Wang and R.S.
Macleod and N.F. Marrouche and K.L. White",
title = "Increased Susceptibility to Atrial Fibrillation
Secondary to Atrial Fibrosis in Transgenic Goats
Expressing Transforming Growth Factor-β1",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "27",
number = "10",
pages = "1220--1229",
year = "2016",
publisher = "Wiley-Blackwell",
month = "Aug",
doi = "10.1111/jce.13049",
url = "http://www.sci.utah.edu/publications/Pol2016a/POLEJAEVA_et_al-2016.pdf",
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author = "S.P. Ponnapalli and M.A. Saunders and C.F. Van
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author = "S. P. Ponnapalli and M. W. Bradley and K. Devine
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title = "Retrospective clinical trial experimentally
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month = "Sep",
keywords = "ncrr, forward problems inverse problems forward
simulation inverse solutions finite elements,
focusing inversion, scirun, biopse, scientific
computing",
url = "http://www.sci.utah.edu/publications/nfsi01-oleg/nfsi01-oleg.ps.gz",
url = "http://www.sci.utah.edu/publications/nfsi01-oleg/nfsi01-oleg.ps",
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year = "2002",
month = "September - October",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
focusing inversion, biopse, neuro brain, scientific
computing",
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year = "2003",
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keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
scientific computing",
}
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Computer Graphics and Visualization ({IADIS})
2008",
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author = "K. Potter and A. Wilson and P.-T. Bremer and D.
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pmid = "23543120",
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keywords = "visualization, probability density function,
cumulative density function, generalized polynomial
chaos, stochastic Galerkin methods, stochastic
collocation methods",
url = "http://www.sci.utah.edu/publications/potter12/Potter_IJUQ2012.pdf",
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author = "K. Potter and P. Rosen and C.R. Johnson",
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series = "IFIP Advances in Information and Communication
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publisher = "Springer",
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keywords = "scidac, netl, uncertainty visualization",
url = "http://www.sci.utah.edu/publications/potter11/Potter_IFIP2011.pdf",
}
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title = "Personalized Virtual-heart Technology for Guiding
the Ablation of Infarct-related Ventricular
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A.D. McCulloch and G.R. Mirams and G.E. Morley and
S. Nattel and D. Noble and S.P. Olesen and A.V.
Panfilov and N.A. Trayanova and U. Ravens and S.
Richard and D.S. Rosenbaum and Y. Rudy and F. Sachs
and F.B. Sachse and D.A. Saint and U. Schotten and
O. Solovyova and P. Taggart and L. Tung and A.
Varr{\`o} and P.G. Volders and K. Wang and J.N.
Weiss and E. Wettwer and E. White and R. Wilders
and R.L. Winslow and P. Kohl",
title = "Minimum Information about a Cardiac
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reporting for model reproducibility,
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pages = "4--10",
year = "2011",
publisher = "Elsevier",
month = "October",
doi = "10.1016/j.pbiomolbio.2011.07.001",
pmcid = "PMC3190048",
keywords = "Minimum Information Standard; Cardiac
electrophysiology; Data sharing; Reproducibility;
Integration; Computational modelling",
url = "http://www.sci.utah.edu/publications/Qui2011a/MICEE_ PBMB2011.pdf",
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author = "E.J. Rainis and S.A. Maas and H.B. Henninger and
P.J. McMahon and J.A. Weiss and R.E. Debski",
title = "Material properties of the axillary pouch of the
glenohumeral capsule: Is isotropic material
symmetry appropriate?",
journal = "Journal of Biomechanical Engineering",
volume = "131",
number = "13",
pages = "(7 pages)",
year = "2009",
keywords = "mrl",
url = "http://www.sci.utah.edu/publications/rainis09/Rainis_JBME2009.pdf",
}
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author = "M. Raj and M. Mirzargar and R. Kirby and R.
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year = "2015",
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@Article{SCI:Raj2016a,
author = "M. Raj and M. Mirzargar and R. Kirby and R.
Whitaker and J. Preston",
title = "Evaluating Shape Alignment via Ensemble
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journal = "IEEE Computer Graphics and Applications",
volume = "36",
number = "3",
pages = "60--71",
year = "2016",
publisher = "IEEE",
month = "May",
doi = "10.1109/mcg.2015.70",
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}
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author = "S.D. Ramsey and M. Bertram and C.D. Hansen",
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2003)",
pages = "117--222",
year = "2003",
location = "Honolulu",
url = "http://www.sci.utah.edu/publications/ramsey03/IASTED03_ramsey.pdf",
}
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author = "M. Ramanath and J. Freire and J. Haritsa and P.
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year = "2004",
keywords = "ip image processing signal processing, tone
mapping, temporal tone mapping, adaptive temporal
tone mapping, undergrad",
url = "http://www.sci.utah.edu/publications/ramsey04/attm.pdf",
}
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pages = "273--284",
year = "2005",
publisher = "IEEE Computer Society",
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}
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booktitle = "9th IEEE International Symposium on Biomedical
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pages = "206--209",
year = "2012",
doi = "10.1109/ISBI.2012.6235520",
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booktitle = "2014 IEEE International Conference on Image
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year = "2014",
publisher = "IEEE",
month = "Oct",
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year = "2015",
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booktitle = "2018 IEEE 15th International Symposium on
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year = "2018",
publisher = "IEEE",
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title = "Identification and Acute Targeting of Gaps in
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journal = "Circulation: Arrhythmia and Electrophysiology",
volume = "5",
pages = "1130--1135",
year = "2012",
doi = "10.1161/CIRCEP.112.973164",
pmid = "23071143",
pmcid = "PMC3691079",
url = "http://www.sci.utah.edu/publications/ranjan12/Ranjan_Circulation2012.pdf",
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}
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booktitle = "Proceedings of the Tenth {SIAM} Conference on
Parallel Processing for Scientific Computing",
year = "2001",
month = "March 12-14",
location = "Portsmouth, Virginia",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, uintah, fire pool,
csafe c-safe",
}
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title = "Micromechanical models of helical superstructures
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year = "2010",
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url = "http://www.sci.utah.edu/publications/reese10/reese_jbme_2010.pdf",
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author = "S.P. Reese",
title = "Multiscale structure-function relationships in the
mechanical behavior of tendon and ligament",
year = "2012",
school = "Department of Bioengineering, University of
Utah",
note = "Ph.D. Thesis",
url = "http://www.sci.utah.edu/publications/reese12/ShawnReese_Dissertation.pdf",
}
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year = "2003",
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publisher = "Springer-Verlag New York, Inc.",
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pmid = "22661796",
pmcid = "PMC3364594",
keywords = "Interactive 3-D scene exploration, Navigation,
Occlusions, User study, Visual interfaces",
url = "http://www.sci.utah.edu/publications/Ros2011b/Rosen_CGI2011.pdf",
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author = "P. Rosen and V. Popescu",
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pages = "151--158",
year = "2012",
keywords = "Rendering, Shadow Algorithms, Adaptive Sampling",
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in Medicine and Life Sciences",
year = "2013",
url = "http://www.sci.utah.edu/publications/rosen13/Rosen_EuroVis2013.pdf",
}
@Article{SCI:Ros2013b,
author = "P. Rosen",
title = "A Visual Approach to Investigating Shared and
Global Memory Behavior of {CUDA} Kernels",
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publisher = "Wiley-Blackwell",
month = "June",
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author = "P. Rosen and B. Burton and K. Potter and C.R.
Johnson",
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booktitle = "Visualization in Medicine and Life Sciences III",
pages = "49--69",
year = "2016",
publisher = "Springer Nature",
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booktitle = "Proceeding of the 2014 Joint Annual Meeting
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pages = "(accepted)",
year = "2014",
url = "http://www.sci.utah.edu/publications/rousset14/ISMRM_2014_KidneyMotionCorrection_Abstract.pdf",
}
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author = "U. R{\"u}de and K. Willcox and L. C. McInnes and H.
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Turner and V. Voevodin and B. Wohlmuth and C. S.
Woodward",
title = "Research and Education in Computational Science
and Engineering",
subtitle = "Report from a workshop sponsored by the Society
for Industrial and Applied Mathematics (SIAM) and
the European Exascale Software Initiative
(EESI-2)",
year = "2016",
month = "Aug",
url = "http://www.sci.utah.edu/publications/Rud2016a/1610.02608v3.pdf",
}
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Johnson and K. E. Jordan and D. E. Keyes and R.
Krause and V. Kumar and S. Mayer and J. Meza and K.
M. Mrken and J. T. Oden and L. Petzold and P.
Raghavan and S. M. Shontz and A. Trefethen and P.
Turner and V. Voevodin and B. Wohlmuth and and C.
S. Woodward",
title = "Research and Education in Computational Science
and Engineering",
journal = "SIAM Review",
volume = "60",
number = "3",
pages = "707--754",
year = "2018",
publisher = "SIAM",
month = "Jan",
doi = "10.1137/16m1096840",
url = "http://www.sci.utah.edu/publications/Rue2018a/1610.02608.pdf",
}
@Article{SCI:Rul2008a,
author = "M. Rullmann and A. Anwander and M. Dannhauer and
S.K. Warfield and F.H. Duffy and C.H. Wolters",
title = "{EEG} Source Analysis of Epileptiform Activity
Using a 1mm Anisotropic Hexahedra Finite Element
Head Model.",
journal = "NeuroImage",
volume = "44",
number = "2",
pages = "399--410",
year = "2008",
doi = "10.1016/j.neuroimage.2008.09.009",
url = "http://www.sci.utah.edu/publications/rullmann08/RullmannEtAl_NeuroImage2008.pdf",
}
@Article{SCI:Run2013a,
author = "A. Rungta and B. Summa and D. Demir and P.-T.
Bremer and V. Pascucci",
title = "{ManyVis}: Multiple Applications in an Integrated
Visualization Environment",
journal = "IEEE Transactions on Visualization and Computer
Graphics ({TVCG})",
volume = "19",
number = "12",
pages = "2878--2885",
year = "2013",
month = "December",
url = "http://www.sci.utah.edu/publications/Run2013a/Rungta_manyvis2013.pdf",
}
@Article{SCI:Rut2015a,
author = "H. J.V. Rutherford and G. Gerig and S. Gouttard
and M. N. Potenza and L. C. Mayes",
title = "Investigating maternal brain structure and its
relationship to substance use and motivational
systems",
journal = "Yale Journal of Biology and Medicine, in print",
year = "2015",
url = "http://www.sci.utah.edu/publications/Rut2015a/helena_yale_2015.pdf",
}
@InProceedings{SCI:Ryd96a,
author = "G.J. Ryder and M. Berzins and T.H.C. Childs",
title = "Modelling Simple Feature Creation in Selective
Laser Sintering",
booktitle = "Proc 7th Symposium on Solid Free Form
Fabrication",
pages = "567--574",
year = "1996",
editor = "J.W. Barlow et al.",
location = "University of Texas at Austin",
url = "http://www.sci.utah.edu/publications/ryder96/1996-65-Ryder.pdf",
}
@Book{SCI:Sac2004b,
author = "F. B. Sachse",
title = "Computational Cardiology: Modeling of Anatomy,
Electrophysiology, and Mechanics",
year = "2004",
series = "LNCS 2966",
publisher = "Springer",
address = "Berlin, Heidelberg, New York",
}
@InProceedings{SCI:Sac2005a,
author = "F. Sachse and M. Cole and R.M. Kirby and X.
Tricoche and C.R. Johnson",
title = "Advanced Modeling and Visualization of
Cardiothoracic Electrical Fields",
booktitle = "Proceedings of 13th Medicine Meets Virtual Reality
(MMVR13)",
year = "2005",
url = "http://www.sci.utah.edu/publications/sachse05/Sachse_Mod_Card_Elec_Fields2005.pdf",
}
@TechReport{SCI:Sad2007a,
author = "N. Sadeghi and T. Tasdizen and N.L. Foster and
A.Y. Wang and S. Minoshima and A.P. Lieberman.",
title = "Automatic Classification of Alzheimers Disease vs.
Frontotemporal Dementia: A Decision Tree Approach
with FDG-PET",
number = "UUSCI-2007-016",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "alzheimers, dementia, automatic disease
classification, decision trees",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-016.pdf",
}
@InProceedings{SCI:Sad2008a,
author = "N. Sadeghi and N.L. Foster and A.Y. Wang and S.
Minoshima and A.P. Lieberman and T. Tasdizen",
title = "Automatic Classification of Alzheimer",
booktitle = "Proceedings of {IEEE} International Symposium on
Biomedical Imaging ({ISBI} 2008): From Nano to
Macro",
pages = "408--411",
year = "2008",
doi = "10.1109/ISBI.2008.4541019",
keywords = "PET, alzheimers, dementia, automatic
classification",
url = "http://www.sci.utah.edu/publications/sadeghi08/Sadeghi_ISBI2008.pdf",
}
@InProceedings{SCI:Sad2010a,
author = "N. Sadeghi and M.W. Prastawa and J.H. Gilmore and
W. Lin and G. Gerig",
title = "Spatio-Temporal Analysis of Early Brain
Development",
booktitle = "Proceedings {IEEE} Asilomar Conference on Signals,
Systems and Computers",
pages = "777--781",
year = "2010",
doi = "10.1109/ACSSC.2010.5757670",
url = "http://www.sci.utah.edu/publications/sadeghi10/sadeghi_asilomar2010.pdf",
}
@Article{SCI:Sad2010b,
author = "N. Sadeghi and M.W. Prastawa and J.H. Gilmore and
W. Lin and G. Gerig",
title = "Towards Analysis of Growth Trajectory through
Multi-modal Longitudinal MR Imaging",
journal = "SPIE Medical Imaging 2010: Image Processing",
volume = "7623, 76232U",
pages = "(published online)",
year = "2010",
editor = "Benoit M. Dawant and David R. Haynor",
month = "March",
doi = "10.1117/12.844526",
url = "http://www.sci.utah.edu/publications/sadeghi10/SPIE2010_Sadeghi_EarlyLongitudinal.pdf",
}
@InProceedings{SCI:Sad2011a,
author = "N. Sadeghi and M.W. Prastawa and P.T. Fletcher and
J.H. Gilmore and W. Lin and G. Gerig",
title = "Statistical Growth Modeling of Longitudinal
{DT-MRI} for Regional Characterization of Early
Brain Development",
booktitle = "Proceedings of the Medical Image Computing and
Computer Assisted Intervention ({MICCAI}) 2011
Workshop on Image Analysis of Human Brain
Development",
pages = "1507--1510",
year = "2011",
doi = "10.1109/ISBI.2012.6235858",
keywords = "namic",
url = "http://www.sci.utah.edu/publications/sadeghi/Sadeghi_MICCIA2011.pdf",
}
@InProceedings{SCI:Sad2012a,
author = "N. Sadeghi and M.W. Prastawa and P.T. Fletcher and
J.H. Gilmore and W. Lin and G. Gerig",
title = "Statistical Growth Modeling of Longitudinal
{DT-MRI} for Regional Characterization of Early
Brain Development",
booktitle = "Proceedings of {IEEE} {ISBI} 2012",
pages = "1507--1510",
year = "2012",
doi = "10.1109/ISBI.2012.6235858",
url = "http://www.sci.utah.edu/publications/sadeghi12/Sadeghi_ISBI_2012-final-subm.pdf",
}
@InProceedings{SCI:Sad2013a,
author = "N. Sadeghi and M.W. Prastawa and P.T. Fletcher and
C. Vachet and Bo Wang and J.H. Gilmore and G.
Gerig",
title = "Multivariate Modeling of Longitudinal {MRI} in
Early Brain Development with Confidence Measures",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "1400--1403",
year = "2013",
doi = "10.1109/ISBI.2013.6556795",
url = "http://www.sci.utah.edu/publications/sadeghi13/Sadeghi_ISBI2013.pdf",
}
@Article{SCI:Sad2013b,
author = "N. Sadeghi and M.W. Prastawa and P.T. Fletcher and
J. Wolff and J.H. Gilmore and G. Gerig",
title = "Regional characterization of longitudinal {DT-MRI}
to study white matter maturation of the early
developing brain",
journal = "NeuroImage",
volume = "68",
pages = "236--247",
year = "2013",
month = "March",
doi = "10.1016/j.neuroimage.2012.11.040",
pmid = "23235270",
url = "http://www.sci.utah.edu/publications/sadeghi12/Sadeghi_Neuroimage2012.pdf",
}
@InProceedings{SCI:Sad2013c,
author = "N. Sadeghi and C. Vachet and M. Prastawa and J.
Korenberg and G. Gerig",
title = "Analysis of Diffusion Tensor Imaging for Subjects
with Down Syndrome",
booktitle = "Proceedings of the 19th Annual Meeting of the
Organization for Human Brain Mapping {OHBM}",
pages = "(in print)",
year = "2013",
url = "http://www.sci.utah.edu/publications/sadeghi13/Sadeghi_HBM2013.pdf",
url = "http://www.sci.utah.edu/publications/sadeghi13/Sadeghi_HBM2013_Table2Correction.pdf",
}
@PhdThesis{SCI:Sad2013d,
author = "N. Sadeghi",
title = "Modeling and Analysis of Longitudinal Multimodal
Magnetic Resonance Imaging: Application to Early
Brain Development",
year = "2013",
school = "Department of Bioengineering, University of
Utah",
month = "December",
note = "Ph.D. Thesis",
keywords = "autism, brain development, image analysis",
url = "http://www.sci.utah.edu/publications/sadeghi13/Sadeghi_PhDdissertation2013.pdf",
}
@InProceedings{SCI:Sad2014a,
author = "N. Sadeghi and J.H. Gilmore and W. Lin and G.
Gerig",
title = "Normative Modeling of Early Brain Maturation from
Longitudinal {DTI} Reveals Twin-Singleton
Differences",
booktitle = "Proceeding of the 2014 Joint Annual Meeting
{ISMRM-ESMRMB}",
pages = "(accepted)",
year = "2014",
url = "http://www.sci.utah.edu/publications/sadeghi14/sadeghi_ISMRM2014_abstract7869.pdf",
}
@InProceedings{SCI:Sad2014b,
author = "N. Sadeghi and P.T. Fletcher and M. Prastawa and
J.H. Gilmore and G. Gerig",
title = "Subject-specific prediction using nonlinear
population modeling: Application to early brain
maturation from {DTI}",
booktitle = "Proceedings of Medical Image Computing and
Computer-Assisted Intervention ({MICCAI} 2014)",
year = "2014",
url = "http://www.sci.utah.edu/publications/Sad2014b/Sadeghi_MICCAI2014.pdf",
}
@Article{SCI:Sad2015a,
author = "N. Sadeghi and J. H. Gilmore and G. Gerig",
title = "Modeling Brain Growth and Development",
journal = "Brain",
volume = "1",
pages = "429-436",
year = "2015",
doi = " 10.1016/B978-0-12-397025-1.00314-6",
url = "http://www.sci.utah.edu/publications/Sad2015a/sadeghi_brain2015.pdf",
}
@Article{SCI:Sah2019a,
author = "D. Sahasrabudhe and M. Berzins and J. Schmidt",
title = "Node failure resiliency for Uintah without
checkpointing",
journal = "Concurrency and Computation: Practice and
Experience",
pages = "e5340",
year = "2019",
doi = "doi:10.1002/cpe.5340",
url = "http://www.sci.utah.edu/publications/Sah2019a/00_Uintah_Resiliency.pdf",
}
@InProceedings{SCI:Sah2019b,
author = "D. Sahasrabudhe and E. T. Phipps and S.
Rajamanickam and M. Berzins",
title = "A Portable SIMD Primitive using Kokkos for
Heterogeneous Architectures",
booktitle = "Sixth Workshop on Accelerator Programming Using
Directives (WACCPD)",
year = "2019",
url = "http://www.sci.utah.edu/publications/Sah2019b/portable_simd.pdf",
}
@InProceedings{SCI:Sah2020a,
author = "D. Sahasrabudhe and M. Berzins",
title = "Improving Performance of the Hypre Iterative
Solver for Uintah Combustion Codes on Manycore
Architectures Using MPI Endpoints and Kernel
Consolidation",
booktitle = "Computational Science -- ICCS 2020, 20th
International Conference, Amsterdam, The
Netherlands, June 3–5, 2020, Proceedings, Part
I",
pages = "175--190",
year = "2020",
publisher = "Springer International Publishing",
isbn = "978-3-030-50371-0",
url = "http://www.sci.utah.edu/publications/Sah2020a/hypre.pdf",
}
@InProceedings{SCI:Sah2020b,
author = "D. Sahasrabudhe and R. Zambre and A.
Chandramowlishwaran and M. Berzins",
title = "Optimizing the Hypre solver for manycore and GPU
architectures",
booktitle = "Journal of Computational Science",
pages = "101279",
year = "2020",
publisher = "Springer International Publishing",
isbn = "978-3-030-50371-0",
issn = "1877-7503",
doi = "https://doi.org/10.1016/j.jocs.2020.101279",
url = "http://www.sci.utah.edu/publications/Sah2020b/00_main.pdf",
}
@Article{SCI:Saj2015a,
author = "M. Sajjadi and M. Seyedhosseini and and T.
Tasdizen",
title = "Nonlinear Regression with Logistic Product Basis
Networks",
journal = "IEEE Signal Processing Letters",
volume = "22",
number = "8",
pages = "1011--1015",
year = "2015",
publisher = "IEEE",
month = "Aug",
doi = "10.1109/lsp.2014.2380791",
url = "http://www.sci.utah.edu/publications/Saj2015a/06985567.pdf",
}
@Article{SCI:Saj2016a,
author = "M. Sajjadi and S.M. Seyedhosseini and T.
Tasdizen",
title = "Disjunctive Normal Networks",
journal = "Neurocomputing",
volume = "218",
pages = "276--285",
year = "2016",
publisher = "Elsevier BV",
month = "Dec",
doi = "10.1016/j.neucom.2016.08.047",
url = "http://www.sci.utah.edu/publications/Saj2016a/1-s2.0-S0925231216309432-main.pdf",
}
@Article{SCI:Saj2016b,
author = "M. Sajjadi and M. Javanmardi and T. Tasdizen",
title = "Regularization With Stochastic Transformations and
Perturbations for Deep Semi-Supervised Learning",
journal = "CoRR",
volume = "abs/1606.04586",
year = "2016",
url = "http://www.sci.utah.edu/publications/Saj2016b/1606.04586.pdf",
}
@InProceedings{SCI:Saj2016c,
author = "M. Sajjadi and M. Javanmardi and T. Tasdizen",
title = "Mutual exclusivity loss for semi-supervised deep
learning",
booktitle = "2016 IEEE International Conference on Image
Processing (ICIP)",
year = "2016",
publisher = "IEEE",
month = "September",
url = "http://www.sci.utah.edu/publications/Saj2016c/07532690.pdf",
}
@Article{SCI:Sal2011a,
author = "B. Salter and B. Wang and M. Sadinski and S.
Ruhnau and V. Sarkar and J. Hinkle and Y. Hitchcock
and K. Kokeny and S. Joshi",
title = "WE-E-BRC-06: Comparison of Two Methods of
Contouring Internal Target Volume on Multiple 4DCT
Data Sets from the Same Subjects: Maximum Intensity
Projection and Combination of 10 Phases",
journal = "Medical Physics",
volume = "38",
number = "6",
pages = "3820",
year = "2011",
url = "http://www.sci.utah.edu/publications/salter11/Salter_MedPhys_WE-E-BRC-06.pdf",
}
@Article{SCI:Sal2015b,
author = "A. P. Salzwedel and K. M. Grewen and C. Vachet and
G. Gerig and W. Lin and and W. Gao",
title = "Prenatal Drug Exposure Affects Neonatal Brain
Functional Connectivity",
journal = "The Journal of Neuroscience",
volume = "35",
number = "14",
pages = "5860-5869",
year = "2015",
month = "April",
doi = "10.1523/JNEUROSCI.4333-14.2015",
url = "http://www.sci.utah.edu/publications/Sal2015b/salzwedel_jns_2015.pdf",
}
@InProceedings{SCI:Sam2002a,
author = "A.A. Samsonov and R.T. Whitaker and C.R.
Johnson",
title = "Noise-Adaptive Nonlinear Filtering Technique for
{SENSE}-Reconstructed Images",
booktitle = c-ISMRM2002,
pages = "74",
year = "2002",
location = "Honolulu",
keywords = "ncrr, ip image processing signal processing,
imaging, bisti",
url = "http://www.sci.utah.edu/publications/samsonov02/ismrm2002_1.pdf",
}
@InProceedings{SCI:Sam2002b,
author = "A.A. Samsonov and C.R. Johnson",
title = "Noise-Adaptive Anisotropic Diffusion Filtering of
{MRI} Images Reconstructed by {SENSE}
({SENS}itivity Encoding) Method",
booktitle = c-ISBI2002,
pages = "701--704",
year = "2002",
month = "July",
location = "Washington DC",
keywords = "ncrr, bisti",
url = "http://www.sci.utah.edu/publications/samsonov02/isbi2002.pdf",
}
@InProceedings{SCI:Sam2002c,
author = "A.A. Samsonov and R.T. Whitaker and E.G.
Kholmovski and C.R. Johnson",
title = "Parametric Method for Correction of Intensity
Inhomogeneity in {MRI} Data",
booktitle = c-ISMRM2002,
pages = "154",
year = "2002",
location = "Honolulu",
keywords = "NCRR, ip image processing signal processing, neuro
brain, ncrr, imaging, bisti",
url = "http://www.sci.utah.edu/publications/samsonov02/ismrm02_abs2.pdf",
}
@InProceedings{SCI:Sam2002d,
author = "A.A. Samsonov and E.G. Kholmovski",
title = "Method for Quality Improvement of Images
Reconstructed From Sensitivity-Encoded Data",
booktitle = c-ISMRM2002,
pages = "2408",
year = "2002",
location = "Honolulu",
keywords = "ip image processing signal processing, neuro
brain, ncrr, imaging, bisti",
url = "http://www.sci.utah.edu/publications/samsonov02/ismrm02_abs3.pdf",
}
@InProceedings{SCI:Sam2003a,
author = "A.A. Samsonov and E.G. Kholmovski and C.R.
Johnson",
title = "Image Reconstruction from Sensitivity Encoded
{MRI} Data Using Extrapolated Iterations of
Parallel Projections Onto Convex Sets",
booktitle = "{SPIE} Medical Imaging",
volume = "5032",
pages = "1829--1838",
year = "2003",
keywords = "NCRR, ip image processing signal processing, ncrr,
scientific computing, bisti",
url = "http://www.sci.utah.edu/publications/samsonov03/spie2003.pdf",
}
@InProceedings{SCI:Sam2003b,
author = "A.A. Samsonov and E.G. Kholmovski and C.R.
Johnson",
title = "Determination of the Sampling Density Compensation
Function Using a Point Spread Function Modeling
Approach and Gridding Approximation",
booktitle = "Proceedings of 11th Annual Meeting of the
International Society for Magnetic Resonance in
Medicine ({ISMRM})",
pages = "477",
year = "2003",
location = "Toronto",
keywords = "ip image processing signal processing, neuro
brain, ncrr, scientific computing, bisti",
url = "http://www.sci.utah.edu/publications/samsonov03/ismrm03_abs1.pdf",
}
@InProceedings{SCI:Sam2003c,
author = "A.A. Samsonov and E.G. Kholmovski and C.R.
Johnson",
title = "A Modified {POCSENSE} Technique for Accelerated
Iterative Reconstruction from Sensitivity Encoded
{MRI} Data",
booktitle = "Proceedings of 11th Annual Meeting of the
International Society for Magnetic Resonance in
Medicine ({ISMRM})",
pages = "477",
year = "2003",
location = "Toronto",
keywords = "ip image processing signal processing, neuro
brain, ncrr, scientific computing, bisti",
url = "http://www.sci.utah.edu/publications/samsonov03/ismrm03_abs3.pdf",
}
@InProceedings{SCI:Sam2004a,
author = "A.A. Samsonov and C.R. Johnson.",
title = "Removal of Intensity Bias in Magnitude Spin-Echo
{MRI} Images by Nonlinear Diffusion Filtering",
booktitle = c-MI2004,
volume = "5370",
pages = "743--752",
year = "2004",
location = "San Diego, CA",
keywords = "ip image processing signal processing, tensor
field methods, diffusion tensor imaging, vector
field methods, scientific visualization, fire pool,
forward problems inverse problems forward
simulation inverse solutions finite elements, ncrr,
bisti",
url = "http://www.sci.utah.edu/publications/samsonov04/spie2004.pdf",
}
@InProceedings{SCI:Sam2004c,
author = "A.A. Samsonov and C.R. Johnson",
title = "Non-Cartesian {POCSENSE}",
booktitle = c-ISMRM2004,
pages = "2648",
year = "2004",
location = "Kyoto, Japan",
keywords = "ip image processing signal processing, neuro
brain, ncrr, scientific computing, POCSENSE,
pocsense, bisti",
url = "http://www.sci.utah.edu/publications/samsonov04/ISMRM04_01.pdf",
}
@InProceedings{SCI:Sam2004d,
author = "A.A. Samsonov and C.R. Johnson",
title = "Unbiased Nonlinear Filtering of Fast Spin Echo
{MRI} Images",
booktitle = c-ISMRM2004,
pages = "760",
year = "2004",
location = "Kyoto, Japan",
keywords = "ip image processing signal processing, neuro
brain, ncrr, scientific computing, mri, bisti",
url = "http://www.sci.utah.edu/publications/samsonov04/ISMRM04_03.pdf",
}
@InProceedings{SCI:Sam2004e,
author = "A.A. Samsonov and E.G. Kholmovski and C.R.
Johnson",
title = "Phase-Constrained Reconstruction of
Sensitivity-Encoded {MRI} Data with {POCSENSE}",
booktitle = c-ISMRM2004,
pages = "2647",
year = "2004",
location = "Kyoto, Japan",
keywords = "ip image processing signal processing, neuro
brain, ncrr, scientific computing, mri, POCSENSE,
pocsense, bisti",
url = "http://www.sci.utah.edu/publications/samsonov04/ISMRM04_02.pdf",
}
@Article{SCI:Sam2004f,
author = "A.A. Samsonov and C.R. Johnson",
title = "Noise-Adaptive Nonlinear Diffusion Filtering of
{MR} Images with Spatially Varying Noise Levels",
journal = j-MRM,
volume = "52",
pages = "798--806",
year = "2004",
keywords = "ip image processing signal processing,
segmentation, ncrr, bisti, Anisotropid Diffusion
Filtering, MRI, Robust Statistics, SENSE,
anisotropid diffusion filtering, mri, robust
statistics, sense",
url = "http://www.sci.utah.edu/publications/samsonov04/AnisotropicFilterSENSE.pdf",
}
@Article{SCI:Sam2004g,
author = "A.A. Samsonov and E.G. Kholmovski and D.L. Parker
and C.R. Johnson",
title = "{POCSENSE}: {POCS}-based reconstruction for
sensitivity encoded {MRI}",
journal = j-MRM,
volume = "52",
pages = "1397--1406",
year = "2004",
keywords = "pocsense, ncrr, bisti",
url = "http://www.sci.utah.edu/publications/samsonov04/pocsense.pdf",
}
@InProceedings{SCI:Sam2004h,
author = "A.A. Samsonov and C.R. Johnson",
title = "Multicoil {MRI} Artifacts Correction Using
Parallel Pocs",
booktitle = c-ISMRM2004,
year = "2004",
keywords = "ncrr, bisti",
}
@InProceedings{SCI:Sam2005a,
author = "A.A. Samsonov and E.V.R. DiBella and P. Kellman
and E.G. Kholmovski and C.R. Johnson",
title = "Adaptive k-t {BLAST}/k-t {SENSE} for Accelerating
Cardiac Perfusion {MRI}",
booktitle = c-SCMR2005,
pages = "277--278",
year = "2005",
keywords = "cardiac heart, ncrr, cardiac perfusion mri,
reduced acquisition, adaptive filtering, k-t blast,
k-t sense, tsense, bisti",
url = "http://www.sci.utah.edu/publications/samsonov05/scmr05.pdf",
}
@InProceedings{SCI:Sam2005b,
author = "A.A. Samsonov and E.G. Kh{\"o}lmovski and C.R.
Johnson",
title = "{POCS}-Enhanced Parallel {MRI} Correction of {MR}
Image Artifacts",
booktitle = "Proc. Intl. Soc. Mag. Reson.",
pages = "690",
year = "2005",
note = "Abstract",
url = "http://www.sci.utah.edu/publications/samsonov05/Samsonov_ISMR2005.pdf",
}
@Article{SCI:Sam2010a,
author = "A.A. Samsonov and J.V. Velikina and Y.K. Jung and
E.G. Kholmovski and C.R. Johnson and W.F. Block",
title = "POCS-enhanced correction of motion artifacts in
parallel MRI",
journal = "Magnetic Resonance in Medicine",
volume = "63",
number = "4",
pages = "1104--1110",
year = "2010",
month = "May",
url = "http://www.sci.utah.edu/publications/samsonov10/Samsonov_POCS2010.pdf",
}
@Article{SCI:Sam2011a,
author = "R. Samuel and H.J. Sant and F. Jiao and C.R.
Johnson and B.K. Gale",
title = "Microfluidic laminate-based phantom for diffusion
tensor-magnetic resonance imaging",
journal = "Journal of Micromech. Microeng.",
volume = "21",
pages = "095027--095038",
year = "2011",
doi = "10.1088/0960-1317/21/9/095027",
url = "http://www.sci.utah.edu/publications/samuel11/Samuel_JMM2011.pdf",
}
@TechReport{SCI:San2003a,
author = "A.R. Sanderson and C.R. Johnson",
title = "Display of Vector Fields Using a
Reaction-Diffusion Model",
number = "UUSCI-2003-002",
year = "2003",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
month = "June",
keywords = "fusion tokamak nimrod, vector field methods,
scirun, scirun fusion, fusion tokamak, scientific
visualization",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2003-002.pdf",
}
@InProceedings{SCI:San2004a,
author = "A.R. Sanderson and C.R. Johnson and R.M. Kirby",
title = "Display of Vector Fields Using a Reaction
Diffusion Model",
booktitle = c-VIS2004,
pages = "115--122",
year = "2004",
keywords = "tensor field methods, stress tensor, strain
tensor, LIC, lic, vector field methods, ncrr",
url = "http://www.sci.utah.edu/publications/allen04/sanderson_et_al_final_267.pdf",
}
@Article{SCI:San2006a,
author = "A.R. Sanderson and R.M. Kirby and C.R. Johnson and
L. Yang",
title = "Advanced Reaction-Diffusion Models for Texture
Synthesis",
journal = "Journal of Graphics Tools",
volume = "11",
number = "3",
pages = "47--71",
year = "2006",
url = "http://www.sci.utah.edu/publications/allen06/Sanderson_JGT_2006.pdf",
}
@InProceedings{SCI:San2006c,
author = "A.R. Sanderson and X. Tricoche and C. Garth and S.
Kruger and C. Sovinec and E. Held and J. Breslau",
title = "Detection of Magnetic Nulls in Toroidal
Geometry",
booktitle = "Proceedings of the 48th Annual Meeting of the
Division of Plasma Physics",
year = "2006",
keywords = "fusion",
}
@InProceedings{SCI:San2006d,
author = "A.R. Sanderson and X. Tricoche and C. Garth and S.
Kruger and C. Sovinec and E. Held and J. Breslau",
title = "Visualizing Patterns in the Poincare Plot of a
Magnetic Field",
booktitle = "{IEEE} Visualization Conference 2006 Compendium",
year = "2006",
keywords = "fusion",
url = "http://www.sci.utah.edu/publications/sanderson06/Sanderson_Vis_06.pdf",
url = "http://www.sci.utah.edu/publications/sanderson06/Sanderson_Vis06_Poster.pdf",
}
@InProceedings{SCI:San2008b,
author = "E. Santos and L. Lins and J.P. Ahrens and J.
Freire and C.T. Silva",
title = "A First Study on Clustering Collections of
Workflow Graphs",
booktitle = "Proceedings of the Second International Provenance
and Annotation Workshop (IPAW 2008)",
pages = "160--173",
year = "2008",
keywords = "vistrails, workflows, provenance",
url = "http://www.sci.utah.edu/publications/santos08/ipaw2008b.pdf",
}
@InProceedings{SCI:San2009a,
author = "E. Santos and D. Koop and H.T. Vo and E. Anderson
and J. Freire and C.T. Silva",
title = "Using Workflow Medleys to Streamline Exploratory
Tasks",
booktitle = "21st International Conference on Scientific and
Statistical Database Management (SSDBM)",
pages = "292--301",
year = "2009",
url = "http://www.sci.utah.edu/publications/santos09/medleys-ssdbm2009.pdf",
}
@Article{SCI:San2009b,
author = "E. Santos and L. Lins and J.P. Ahrens and J.
Freire and C.T. Silva",
title = "{VisMashup:} Streamlining the Creation of Custom
Visualization Applications",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics, Proceedings of the 2009 {IEEE}
Visualization Conference",
volume = "15",
number = "6",
pages = "1539--1546",
year = "2009",
month = "Sept/Oct",
doi = "10.1109/TVCG.2009.195",
url = "http://www.sci.utah.edu/publications/santos09/Santos_mashup-vis2009.pdf",
}
@Article{SCI:San2009c,
author = "A.R. Sanderson and M.D. Meyer and R.M. Kirby and
C.R. Johnson",
title = "A Framework for Exploring Numerical Solutions of
Advection Reaction Diffusion Equations using a GPU
Based Approach",
journal = "Journal of Computing and Visualization in
Science",
volume = "12",
pages = "155--170",
year = "2009",
doi = "10.1007/s00791-008-0086-0",
url = "http://www.sci.utah.edu/publications/sanderson09/Sanderson_CVS2009.pdf",
}
@InProceedings{SCI:San2010a,
author = "Allen R. Sanderson and Scott Kruger and and
Stephane Either",
title = "Visualization and Analysis Tools for Assisting in
Evaluating Fusion Simulations",
booktitle = "Proceedings of the Sherwood Fusion Theory
Conference",
year = "2010",
url = "http://www.sci.utah.edu/publications/sanderson10/ARS_Sherwood2010.pdf",
url = "http://www.sci.utah.edu/publications/sanderson10/ARS_SherwoodPoster2010.pdf",
}
@Article{SCI:San2010b,
author = "A.R. Sanderson and G. Chen and X. Tricoche and D.
Pugmire and S. Kruger and J. Breslau",
title = "Analysis of Recurrent Patterns in Toroidal
Magnetic Fields",
journal = "IEEE Transactions on Visualization and Computer
Graphics",
volume = "16",
number = "6",
pages = "1431-1440",
year = "2010",
publisher = "IEEE",
month = "Nov",
doi = "10.1109/tvcg.2010.133",
url = "http://www.sci.utah.edu/publications/San2010b/ARS_Fusion_Vis2010.pdf",
}
@InProceedings{SCI:San2012a,
author = "A.R. Sanderson and B. Whitlock and O. Reubel and
H. Childs and G.H. Weber and Prabhat and K. Wu",
title = "A System for Query Based Analysis and
Visualization",
booktitle = "Proceedings of the Third International Eurovis
Workshop on Visual Analytics {EuroVA} 2012",
pages = "25--29",
year = "2012",
month = "June",
url = "http://www.sci.utah.edu/publications/sanderson12/Sanderson_EuroVA_2012.pdf",
}
@InProceedings{SCI:San2012b,
author = "A.R. Sanderson and G. Chen and X. Tricoche and E.
Cohen",
title = "Understanding Quasi-Periodic Fieldlines and Their
Topology in Toroidal Magnetic Fields",
booktitle = "Topological Methods in Data Analysis and
Visualization II",
pages = "125--140",
year = "2012",
editor = "R. Peikert and H. Carr and H. Hauser and R.
Fuchs",
publisher = "Springer",
doi = "10.1007/478-3-642-23175-9",
keywords = "fusion",
}
@InProceedings{SCI:San2014a,
author = "A.R. Sanderson",
title = "An Alternative Formulation of Lyapunov Exponents
for Computing Lagrangian Coherent Structures",
booktitle = "Proceedings of the 2014 {IEEE} Pacific
Visualization Symposium ({PacificVis})",
year = "2014",
location = "Yokahama Japan",
url = "http://www.sci.utah.edu/publications/San2014a/Sanderson_PacificVis2014_ShortNote.pdf",
}
@Article{SCI:San2015a,
author = "S. Sankaranarayanan and T.E. Schomay and K.A.
Aiello and O. Alter",
title = "Tensor GSVD of patient- and platform-matched tumor
and normal DNA copy-number profiles uncovers
chromosome arm-wide patterns of tumor-exclusive
platform-consistent alterations encoding for cell
transformation and predicting ovarian cancer
survival",
journal = "PLoS ONE",
volume = "10",
number = "e121396",
year = "2015",
doi = "10.1371/journal.pone.0121396",
}
@Article{SCI:San2018a,
author = "A. Sanderson and A. Humphrey and J. Schmidt and R.
Sisneros",
title = "Coupling the Uintah Framework and the VisIt
Toolkit for Parallel In Situ Data Analysis and
Visualization and Computational Steering",
journal = "High Performance Computing",
year = "2018",
month = "June",
url = "http://www.sci.utah.edu/publications/San2018a/InSituVisWorkShop.pdf",
}
@InProceedings{SCI:San2018b,
author = "A. Sanderson and X. Tricoche",
title = "Exploration of periodic flow fields",
booktitle = "18th International Symposium on Flow
Visualization",
year = "2018",
url = "http://www.sci.utah.edu/publications/San2018b/ISFV18_PeriodicFlowFields.pdf",
}
@InProceedings{SCI:San2019a,
author = "A. Sanderson and A. Humphrey and J. Schmidt and R.
Sisneros and and M. Papka",
title = " In situ visualization of performance metrics in
multiple domains",
booktitle = "2019 IEEE/ACM International Workshop on
Programming and Performance Visualization Tools
(ProTools)",
year = "2019",
publisher = "IEEE",
month = "Nov",
doi = "10.1109/protools49597.2019.00014",
url = "http://www.sci.utah.edu/publications/San2019a/Sanderson_SC_ProTools19.pdf",
}
@MastersThesis{SCI:Saq2013a,
author = "Nazmus Saquib",
title = "Visualizing Intrinsic Isosurface Variation due to
Uncertainty Through Heat Kernel Signatures",
year = "2013",
school = "University of Utah School of Computing",
note = "Master of Science Thesis, Computational
Engineering and Science ({CES}) Program",
url = "http://www.sci.utah.edu/publications/saquib13/Saquib_thesis.pdf",
}
@Article{SCI:Sar2012a,
author = "V. Sarkar and Brian Wang and J. Hinkle and V.J.
Gonzalez and Y.J. Hitchcock and P. Rassiah-Szegedi
and S. Joshi and B.J. Salter",
title = "Dosimetric evaluation of a virtual image-guidance
alternative to explicit 6 degree of freedom robotic
couch correction",
journal = "Practical Radiation Oncology",
volume = "2",
number = "2",
pages = "122--137",
year = "2012",
url = "http://www.sci.utah.edu/publications/sarkar12/Sarkar_PRO2012.pdf",
}
@Article{SCI:Sat2009a,
author = "D. Sato and Y. Xie and J.N. Weiss and Z. Qu and A.
Garfinkel and A.R. Sanderson",
title = "Acceleration of Cardiac Tissue Simulation with
Graphic Processing Units",
journal = "Medical and Biological Engineering and
Computing",
year = "2009",
note = "Published online Aug 5, 2009",
doi = "10.1007/s11517-0",
url = "http://www.sci.utah.edu/publications/Sat2009a/Sato_MBEC2009.pdf",
}
@InProceedings{SCI:Sch1999a,
author = "G. Scheuermann and X. Tricoche and H. Hagen",
title = "C1-Interpolation for Vector Field Topology
Visualization",
booktitle = "Proceeding IEEE Visualization 1999",
pages = "271--278",
year = "1999",
url = "http://www.sci.utah.edu/publications/scheuermann99/interpolation.pdf",
}
@Article{SCI:Sch2000a,
author = "G. Scheuermann and W. Kollmann and X. Tricoche and
T. Wischgoll",
title = "Evolution of Topology in Axi-Symmetric and 3D
Viscous Flows",
journal = "Numerical Simulations of Incompressible Flows",
pages = "622--643",
year = "2000",
publisher = "World Scientific Publishing, New Jersey",
url = "http://www.sci.utah.edu/publications/scheuermann00/evolution.pdf",
}
@Article{SCI:Sch2001a,
author = "L.M. Schultz and C.R. Butson and G.A. Clark",
title = "Post-light potentiation at type B to A
photoreceptor connections in Hermissenda",
journal = "Neurobiology of Learning and Memory",
volume = "76",
number = "1",
pages = "7--32",
year = "2001",
month = "July",
url = "http://www.sci.utah.edu/publications/schultz01/Schultz2001_PLP.pdf",
}
@InProceedings{SCI:Sch2003a,
author = "J. Schpok and J. Simons and D.S. Ebert and C.D.
Hansen",
title = "A Real-Time Cloud Modeling, Rendering, and
Animation System",
booktitle = "{ACM} Symposium on Computer Animation",
pages = "160--166",
year = "2003",
location = "San Diego",
url = "http://www.sci.utah.edu/publications/schpok03/scaclouds.pdf",
}
@InProceedings{SCI:Sch2004a,
author = "U. Schmitt and C.H. Wolters and A. Anwander and T.
Knoesche",
title = "STR: A New Spatio-Temporal Approach for Accurate
and Efficient Current Density Reconstruction",
booktitle = c-BIOMAG2004,
pages = "591--592",
year = "2004",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr",
}
@InCollection{SCI:Sch2005a,
author = "G. Scheuermann and X. Tricoche",
title = "Topological Methods for Flow Visualization",
booktitle = "The Visualization Handbook",
pages = "341--356",
year = "2005",
editor = "C.D. Hansen and C.R. Johnson",
publisher = "Elsevier",
isbn = "0-12-387582-X",
keywords = "ncrr, vector field methods, aerodynamics",
url = "http://www.sci.utah.edu/publications/scheuermann05/ch17_scheuermann.pdf",
}
@InProceedings{SCI:Sch2005b,
author = "C. Scheidegger and S. Fleishman and C.T. Silva.",
title = "Triangulating Point-Set Surfaces With Bounded
Error",
booktitle = "Proceedings of the Third Eurographics/ACM
Symposium on Geometry Processing",
pages = "63--72",
year = "2005",
publisher = "Eurographics Association",
isbn = "3-905673-24-X",
url = "http://www.sci.utah.edu/publications/cscheid05/tpss.pdf",
}
@Article{SCI:Sch2005c,
author = "C. Scheidegger and J. Comba and R. Cunha.",
title = "Practical CFD Simulations on the GPU Using SMAC",
journal = "Computer Graphics Forum",
volume = "24",
number = "4",
pages = "715--728",
year = "2005",
keywords = "cfd computational fluid dynamics",
url = "http://www.sci.utah.edu/publications/cscheid05/smac-cgf.pdf",
}
@TechReport{SCI:Sch2006a,
author = "J. Schreiner and C.E. Scheidegger and S. Fleishman
and C.T. Silva",
title = "Direct (Re)Meshing for Efficient Surface
Processing",
number = "UUSCI-2006-013",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "ip image processing signal processing, surface
processing",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-013.pdf",
}
@Article{SCI:Sch2006b,
author = "J. Schreiner and C.E. Scheidegger and S. Fleishman
and C.T. Silva",
title = "Direct (Re)Meshing for Efficient Surface
Processing",
journal = "Computer Graphics Forum",
volume = "25",
number = "3",
pages = "527--536",
year = "2006",
publisher = "Wiley-Blackwell",
month = "Sep",
doi = "10.1111/j.1467-8659.2006.00972.x",
keywords = "ip image processing signal processing, surface
processing, ip gp image processing goemetry
processing, meshing",
url = "http://www.sci.utah.edu/publications/Sch2006b/direct_remeshing.pdf",
}
@Article{SCI:Sch2006c,
author = "J. Schreiner and C.E. Scheidegger and C.T.
Silva",
title = "High-Quality Extraction of Isosurfaces from
Regular and Irregular Grids",
journal = "IEEE Trans. Vis. Comp. Graph.",
volume = "12",
number = "5",
pages = "1205--1212",
year = "2006",
}
@InProceedings{SCI:Sch2006d,
author = "T. Schultz and B. Burgeth and J. Weickert",
title = "Flexible Segmentation and Smoothing of {DT-MRI}
Fields Through a Customizable Structure Tensor",
booktitle = "Advances in Visual Computing",
volume = "4291",
pages = "455--464",
year = "2006",
editor = "G. Bebis and R. Boyle and B. Parvin and D. Koracin
and P. Remagnino and A. V. Nefian and M. Gopi and
V. Pascucci and J. Zara and J. Molineros and H.
Theisel and T. Malzbender",
series = "Lecture Notes in Computer Science",
publisher = "Springer",
keywords = "tensor field methods, diffusion tensor imaging,
ncrr",
}
@InProceedings{SCI:Sch2007b,
author = "C.E. Scheidegger and H.T. Vo and D. Koop and J.
Freire and C.T. Silva",
title = "Querying and Creating Visualizations by Analogy",
booktitle = "Proceeding of {IEEE} Visualization 2007",
pages = "1560--1567",
year = "2007",
keywords = "vistrails, vacet",
url = "http://www.sci.utah.edu/publications/scheidegger07/vis_by_analogy.pdf",
}
@Article{SCI:Sch2008a,
author = "C.E. Scheidegger and D. Koop and E. Santos and
H.T. Vo and S.P. Callahan and J. Freire and C.T.
Silva.",
title = "Tackling the Provenance Challenge One Layer at a
Time",
journal = "Concurrency Computat.: Pract. Exper.",
volume = "20",
number = "5",
pages = "473--483",
year = "2008",
keywords = "vistrails, provenance, , vistrails, vacet",
url = "http://www.sci.utah.edu/publications/scheidegger07/tackling.pdf",
}
@InProceedings{SCI:Sch2008b,
author = "C.E. Scheidegger and H.T. Vo and D. Koop and J.
Freire and C.T. Silva",
title = "Querying and Re-Using Workflows with
{VisTrails}",
booktitle = "Proceedings of the 2008 {ACM} {SIGMOD}
International Conference on Management of Data",
pages = "1251--1254",
year = "2008",
doi = "10.1145/1376616.1376747",
keywords = "vistrails, provenance, workflows",
}
@TechReport{SCI:Sch2008c,
author = "J.A. Schmidt",
title = "Uintah Application Development",
number = "UUSCI-2008-005",
year = "2008",
institution = "University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-005.pdf",
}
@TechReport{SCI:Sch2008d,
author = "M. Schott and V. Pegoraro and C.D. Hansen and K.
Boulanger and J. Stratton and K. Bouatouch",
title = "A Directional Occlusion Shading Model for
Interactive Direct Volume Rendering",
number = "UUSCI-2008-009",
year = "2008",
institution = "University of Utah Scientific Computing and
Imaging Institute",
type = "SCI Technical Report",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2008-009.pdf",
}
@Article{SCI:Sch2008e,
author = "C.E. Scheidegger and J. Schreiner and B. Duffy and
H. Carr and C.T. Silva",
title = "Revisiting Histograms and Isosurface Statistics",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics (Proceedings of {IEEE} Visualization
2008)",
volume = "14",
number = "6",
pages = "1659--1666",
year = "2008",
doi = "10.1109/TVCG.2008.160",
url = "http://www.sci.utah.edu/publications/scheidegger08/vis2008c.pdf",
}
@Article{SCI:Sch2009a,
author = "M. Schott and V. Pegoraro and C.D. Hansen and K.
Boulanger and K. Bouatouch",
title = "A Directional Occlusion Shading Model for
Interactive Direct Volume Rendering",
journal = "Computer Graphics Forum",
volume = "28",
number = "3",
pages = "855--862",
year = "2009",
publisher = "Wiley-Blackwell",
month = "jun",
doi = "10.1111/j.1467-8659.2009.01464.x",
url = "http://www.sci.utah.edu/publications/Sch2009a/EuroVis09DirectionalOcclusionShading.pdf",
}
@PhdThesis{SCI:Sch2009b,
author = "J.M. Schreiner",
title = "Uniform and Adaptive (Re)meshing of Surfaces",
year = "2009",
school = "School of Computing, University of Utah",
month = "June",
note = "Ph.D. Thesis",
keywords = "meshing, mesh generation",
url = "http://www.sci.utah.edu/publications/schreiner09/JohnSchreiner_dissertation.pdf",
}
@InProceedings{SCI:Sch2010a,
author = "J. Schmidt and M. Berzins",
title = "Development of the Uintah Gateway for
Fluid-Structure-Interaction Problems",
booktitle = "Proceedings of the Teragrid 2010 Conference",
year = "2010",
publisher = "ACM",
doi = "10.1145/1838574.1838591",
keywords = "Uintah, csafe",
url = "http://www.sci.utah.edu/publications/Sch2010a/UintahGateway.pdf",
}
@TechReport{SCI:Sch2010b,
author = "C.E. Scheidegger and T. Etiene and L.G. Nonato and
C.T. Silva",
title = "Edge Flows: Stratified Morse Theory for Simple,
Correct Isosurface Extraction",
number = "UUSCI-2010-002",
year = "2010",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2010-002.pdf",
}
@TechReport{SCI:Sch2010c,
author = "M. Schott and P. Grosset and T. Martin and V.
Pegoraro and C.D. Hansen",
title = "Depth of Field Effects for Interactive Direct
Volume Rendering",
number = "UUSCI-2010-005",
year = "2010",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2010-005.pdf",
}
@Article{SCI:Sch2010d,
author = "C. Schlimper and O. Nemitz and U. Dorenbeck and J.
Scorzin and R.T. Whitaker and T. Tasdizen and M.
Rumpf and K. Schaller",
title = "Restoring three-dimensional magnetic resonance
angiography images with mean curvature motion",
journal = "Neurological Research",
volume = "32",
number = "1",
pages = "87--93",
year = "2010",
month = "February",
note = "Epub 2009 Nov 26",
doi = "10.1179/016164110X12556180206077",
pmid = "19941735",
url = "http://www.sci.utah.edu/publications/schlimper10/Schlimper_NeuroRes2010.pdf",
}
@Article{SCI:Sch2011a,
author = "M. Schott and A.V.P. Grosset and T. Martin and V.
Pegoraro and S.T. Smith and C.D. Hansen",
title = "Depth of Field Effects for Interactive Direct
Volume Rendering",
journal = "Computer Graphics Forum",
volume = "30",
number = "3",
pages = "941--950",
year = "2011",
editor = "H. Hauser and H. Pfister and J.J. van Wijk",
publisher = "Wiley-Blackwell",
month = "jun",
doi = "10.1111/j.1467-8659.2011.01943.x",
url = "http://www.sci.utah.edu/publications/Sch2011a/Schott_EuroVis11.pdf",
url = "http://www.sci.utah.edu/publications/Sch2011a/Schott_EuroVis11DepthOfFieldDVRVideo.mov",
}
@InProceedings{SCI:Sch2011b,
author = "M. Schulz and J.A. Levine and P.-T. Bremer and T.
Gamblin and V. Pascucci",
title = "Interpreting Performance Data Across Intuitive
Domains",
booktitle = "International Conference on Parallel Processing",
pages = "206--215",
year = "2011",
publisher = "IEEE",
location = "Taipei, Taiwan",
doi = "10.1109/ICPP.2011.60",
url = "http://www.sci.utah.edu/publications/schulz11/Schulz_ICPP2011.pdf",
}
@InProceedings{SCI:Sch2012a,
author = "M. Schott and T. Martin and A.V.P. Grosset and C.
Brownlee and Thomas Hollt and B.P. Brown and S.T.
Smith and C.D. Hansen",
title = "Combined Surface and Volumetric Occlusion
Shading",
booktitle = "Proceedings of Pacific Vis 2012",
pages = "169--176",
year = "2012",
doi = "10.1109/PacificVis.2012.6183588",
keywords = "scidac, vacet, kaust, nvidia",
url = "http://www.sci.utah.edu/publications/schott12/Schott_PacificVis2012.pdf",
}
@TechReport{SCI:Sch2012b,
author = "J. Schmidt and M. Berzins and J. Thornock and T.
Saad and J. Sutherland",
title = "Large Scale Parallel Solution of Incompressible
Flow Problems using Uintah and hypre",
number = "UUSCI-2012-002",
year = "2012",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
keywords = "uintah, csafe",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2012-002.pdf",
}
@Article{SCI:Sch2013a,
author = "M. Schott and T. Martin and A.V.P. Grosset and
S.T. Smith and C.D. Hansen",
title = "Ambient Occlusion Effects for Combined Volumes and
Tubular Geometry",
journal = "IEEE Transactions on Visualization and Computer
Graphics (TVCG)",
volume = "19",
number = "6",
pages = "913--926",
year = "2013",
note = "Selected as Spotlight paper for June 2013 issue",
doi = "10.1109/TVCG.2012.306",
keywords = "Volume rendering, ambient occlusion, stream
tubes",
url = "http://www.sci.utah.edu/publications/schott13/Schott_TVCG2013.pdf",
}
@Article{SCI:Sch2013b,
author = "P.T. Scheffel and H.B. Henninger and R.T. Burks",
title = "Relationship of the intercondylar roof and the
tibial footprint of the {ACL:} implications for
{ACL} reconstruction",
journal = "American Journal of Sports Medicine",
volume = "41",
number = "2",
pages = "396--401",
year = "2013",
doi = "10.1177/0363546512467955",
url = "http://www.sci.utah.edu/publications/scheffel13/Scheffel_AmJSportsMed2013.pdf",
}
@InProceedings{SCI:Sch2013c,
author = "J. Schmidt and M. Berzins and J. Thornock and T.
Saad and J. Sutherland",
title = "Large Scale Parallel Solution of Incompressible
Flow Problems using Uintah and hypre",
booktitle = "2013 13th {IEEE/ACM} International Symposium on
Cluster, Cloud and Grid Computing {(CCGrid)}",
pages = "458--465",
year = "2013",
keywords = "Uintah, hypre, parallelism, scalability, linear
equations",
url = "http://www.sci.utah.edu/publications/schmidt13/Schmidt_CCGRID2013.pdf",
}
@Article{SCI:Sch2018a,
author = "I. .J Schwerdt and A. Brenkmann and S. Martinson
and B. D. Albrecht and S. Heffernan and M. R.
Klosterman and T. Kirkham and T. Tasdizen and L. W.
McDonald IV",
title = "Nuclear proliferomics: A new field of study to
identify signatures of nuclear materials as
demonstrated on alpha-UO3",
journal = "Talanta",
volume = "186",
pages = "433--444",
year = "2018",
publisher = "Elsevier BV",
month = "Aug",
doi = "10.1016/j.talanta.2018.04.092",
url = "http://www.sci.utah.edu/publications/Sch2018a/1-s2.0-S0039914018304508-main.pdf",
}
@InCollection{SCI:Sch95a,
author = "J.A. Schmidt and C.R. Johnson and J.C. Eason and
R.S. MacLeod",
title = "Applications of Automatic Mesh Generation and
Adaptive Methods in Computational Medicine",
booktitle = "Modeling, Mesh Generation, and
AdaptiveMethodsforPartial Differential Equations",
pages = "367--390",
year = "1995",
editor = "I. Babuska and J.E. Flaherty and W.D. Henshaw and
J.E. Hopcroft and J.E. Oliger and T. Tezduyar",
publisher = "Springer-Verlag",
keywords = "computational pde pdes computational partial
differential equations evaporation, adaptive mesh
generation, scientific computing",
url = "http://www.sci.utah.edu/publications/schmidt95/ima93_5.ps",
url = "http://www.sci.utah.edu/publications/schmidt95/ima93_5.ps.Z",
}
@InProceedings{SCI:Sch95b,
author = "J.A. Schmidt and C.R. Johnson",
title = "Defibsim: An Interactive Defibrillation Device
Design Tool",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
17th Annual International Conference",
pages = "305--306",
year = "1995",
publisher = "{IEEE} Press",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
url = "http://www.sci.utah.edu/publications/schmidt95/embs95_2.ps",
url = "http://www.sci.utah.edu/publications/schmidt95/embs95_2.ps.Z",
}
@InProceedings{SCI:Sch95c,
author = "J.A. Schmidt and C.R. Johnson and R.S. MacLeod",
title = "An Interactive Computer Model for Defibrillation
Device Design",
booktitle = "International Congress on Electrocardiology",
pages = "160--161",
year = "1995",
publisher = "ICE",
keywords = "forward problems inverse problems forward
simulation inverse solutions finite elements,
cardiac heart",
url = "http://www.sci.utah.edu/publications/schmidt95/ice95.ps",
url = "http://www.sci.utah.edu/publications/schmidt95/ice95.ps.Z",
}
@Misc{SCI:SciInst,
year = "2015",
note = "Scientific Computing and Imaging Institute
({SCI}), University of Utah, www.sci.utah.edu",
keywords = "SCI Institute",
}
@Misc{SCI:SCIRun,
author = "{SCI} Institute",
year = "2015",
note = "{SCIRun}: A Scientific Computing Problem Solving
Environment, Scientific Computing and Imaging
Institute ({SCI}), Download from:
http://www.scirun.org",
keywords = "SCIRun, CIBC",
}
@Article{SCI:Sed2012a,
author = "M. Sedlmair and M.D. Meyer and T. Munzner",
title = "Design Study Methodology: Reflections from the
Trenches and the Stacks",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "18",
number = "12",
pages = "2431--2440",
year = "2012",
note = "Honorable Mention for Best Paper Award.",
url = "http://www.sci.utah.edu/publications/sedlmair12/Sedlmair_InfoVis2012.pdf",
}
@Article{SCI:Seg2009a,
author = "N.M. Segerson and M. Daccarett and T.J. Badger and
A. Shabaan and N. Akoum and E.N. Fish and S. Rao
and N.S. Burgon and Y. Adjei-Poku and E.G.
Kholmovski and S. Vijayakumar and E.V.R. Dibella
and R.S. Macleod and N.F. Marrouche",
title = "Magnetic Resonance Imaging-Confirmed Ablative
Debulking of the Left Atrial Posterior Wall and
Septum for Treatment of Persistent Atrial
Fibrillation: Rationale and Initial Experience",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "21",
number = "2",
pages = "126--132",
year = "2009",
keywords = "atrial fibrillation, radiofrequency ablation,
debulking, magnetic resonance imaging, delayed
enhancement, complex fractionated electrograms",
url = "http://www.sci.utah.edu/publications/segerson09/Segerson_JCEP2009.pdf",
}
@Article{SCI:Seg2010a,
author = "N.M. Segerson and M. Daccarett and T.J. Badger and
A. Shabaan and N. Akoum and E.N. Fish and S. Rao
and N.S. Burgon and Y. Adjei-Poku and E. Kholmovski
and S. Vijayakumar and E.V. DiBella and R.S.
MacLeod and N.F. Marrouche",
title = "Magnetic resonance imaging-confirmed ablative
debulking of the left atrial posterior wall and
septum for treatment of persistent atrial
fibrillation: rationale and initial experience",
journal = "Journal of Cardiovascular Electrophysiology",
volume = "21",
number = "2",
pages = "126--132",
year = "2010",
pmid = "19804549",
keywords = "cvrti",
url = "http://www.sci.utah.edu/publications/segerson10/Segerson_JCardElect2010.pdf",
}
@Misc{SCI:Seg3D,
author = "{CIBC}",
year = "2015",
note = "{Seg3D}: Volumetric Image Segmentation and
Visualization. Scientific Computing and Imaging
Institute ({SCI}), Download from:
http://www.seg3d.org",
keywords = "Seg3D, CIBC",
}
@InProceedings{SCI:Sel1998a,
author = "P.Selwood and M.Berzins and J. Nash and P.M.
Dew",
title = "Portable Parallel Adaptation of Unstructured
Tetrahedral Meshes",
booktitle = "Proceedings of Irregular 98 Conference",
volume = "1457",
pages = "56--67",
year = "1998",
editor = "A. Ferreira et al.",
series = "Lecture Notes in Computer Science (LNCS)",
publisher = "Springer",
url = "http://www.sci.utah.edu/publications/selwood98/Selwood_Irregular98.pdf",
}
@InProceedings{SCI:Sel96a,
author = "P. Selwood and N.A. Verhoeven and J.M. Nash and M.
Berzins and N.P. Weatherill and P.M. Dew and K.
Morgan",
title = "Parallel Mesh Generation and Adaptivity :
Partitioning and Analysis",
booktitle = "Parallel {C.F.D.}- Proc. of Parallel {CFD} 96
Conference",
year = "1997",
editor = "A.Ecer and J.Periaux and N.Satufoka and
P.Schiano",
publisher = "Elesvier Science {BV}",
month = "May",
location = "Capri, Italy",
isbn = "0-444 823271",
}
@Article{SCI:Sel97a,
author = "P. Selwood and M. Berzins and P.M. Dew",
title = "3D Parallel Mesh Adaptivity: Data Structures and
Algorithms",
journal = "Proc. of {SIAM} Conf. on Parallel Processing for
Scientific Computing",
pages = "(CD-Rom)",
year = "1997",
month = "March",
location = "Minneapolis, MN, USA",
isbn = "0-89871-395-1",
url = "http://www.sci.utah.edu/publications/selwood97/d-parallel-mesh-adaptivity.pdf",
}
@Article{SCI:Sel99a,
author = "P. Selwood and M. Berzins",
title = "Portable Parallel Adaptation of Unstructured
Tetrahedral Meshes",
journal = "Concurrency",
volume = "11",
number = "13",
pages = "1--22",
year = "1999",
url = "http://www.sci.utah.edu/publications/selwood99/concur99.pdf",
}
@InProceedings{SCI:Ser2002a,
author = "Y. Serinagaoglu and D.H. Brooks and R.S.
MacLeod",
title = "Including Sparse Noisy Epicardial Potential
Measurements Into Bayesian Inverse
Electrocardiography",
booktitle = "Proceedings of EMBC 2002",
year = "2002",
keywords = "forward problems inverse problems forward
simulation inverse solutions, cardiac heart,
ncrr",
url = "http://www.sci.utah.edu/publications/yesim02/ysd_embc_2002.pdf",
}
@Article{SCI:Ser2002b,
author = "Y. Serinagaoglu and R.S. MacLeod and B. Yilmaz and
D.H. Brooks",
title = "Multielectrode Venous Catheter Mapping as a High
Quality Constraint for Electrocardiographic Inverse
Solution",
journal = j-JE,
volume = "35 (supplement)",
year = "2002",
keywords = "forward problems inverse problems forward
simulation inverse solutions, cardiac heart,
ncrr",
url = "http://www.sci.utah.edu/publications/yesim02/ysd_jecg_2002.pdf",
}
@InProceedings{SCI:Ser2003a,
author = "Y. Serinagaoglu and D.H. Brooks and R.S.
MacLeod",
title = "Prior Model Selection for Bayesian Inverse
Electrocardiography",
booktitle = "Proceedings of the NFSI Conference 2003",
year = "2003",
location = "Chieti, Italy",
keywords = "forward problems inverse problems forward
simulation inverse solutions, cardiac heart,
ncrr",
url = "http://www.sci.utah.edu/publications/yesim03/ysd_nfsi_2003.pdf",
}
@InProceedings{SCI:Ser2003b,
author = "Y. Serinagaoglu and R.S. MacLeod and D.H.
Brooks",
title = "A Bayesian Approach to Inclusion and Performance
Analysis of Using Extra Information in Bioelectric
Inverse Problems",
booktitle = "Proceedings of the {IEEE} International Conference
on Image Processing",
year = "2003",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr",
url = "http://www.sci.utah.edu/publications/yesim03/ysd_icip_2003.pdf",
}
@Article{SCI:Ser2003c,
author = "Y. Serinagaoglu and D.H. Brooks and R.S.
MacLeod",
title = "Combining Numerical and Physiological Constraints
in Inverse Electrocardiography",
journal = j-IJBEM,
volume = "5",
number = "1",
pages = "215--217",
year = "2003",
keywords = "map3d, cardiac heart, ncrr, scientific
visualization, forward problems inverse problems
forward simulation inverse solutions",
url = "http://www.sci.utah.edu/publications/yesim03/ICE03-yesim.pdf",
}
@Article{SCI:Ser2005a,
author = "Y. Serinagaoglu and D.H. Brooks and R.S.
MacLeod",
title = "Bayesian Solutions and Performance Analysis in
Bioelectric Inverse Problems",
journal = j-BME,
volume = "52",
number = "6",
pages = "1009--1020",
year = "2005",
month = "June",
keywords = "ncrr, cibc",
url = "http://www.sci.utah.edu/publications/serinagaoglu05/Serinagaoglu_TBE2005.pdf",
}
@Article{SCI:Ser2006a,
author = "Y. Serinagaoglu and D.H. Brooks and R.S.
MacLeod",
title = "Improved Performance of {B}ayesian Solutions for
Inverse Electrocardiography Using Multiple
Information Sources",
journal = j-BME,
volume = "53",
number = "10",
pages = "2024--2034",
year = "2006",
month = "October",
keywords = "forward problems inverse problems forward
simulation inverse solutions, ncrr, cibc,
simulation math modeling",
url = "http://www.sci.utah.edu/publications/serinagaoglu06/Serinagaoglu_IEEETBME2006.pdf",
}
@Article{SCI:Ses2017a,
author = "P. Seshadri and A. Narayan and S. Mahadevan",
title = "Effectively Subsampled Quadratures for Least
Squares Polynomial Approximations",
journal = "SIAM/ASA Journal on Uncertainty Quantification",
pages = "1003--1023",
year = "2017",
month = "Jan",
url = "http://www.sci.utah.edu/publications/Ses2017a/1601.05470.pdf",
}
@InProceedings{SCI:Sey2010a,
author = "M. Seyedhosseini and A.R.C. Paiva and T.
Tasdizen",
title = "Image Parsing with a Three-State Series Neural
Network Classifier",
booktitle = "Proc. {IEEE} Intl. Conference on Pattern
Recognition",
pages = "4508--4511",
year = "2010",
location = "Istanbul, Turkey",
doi = "10.1109/ICPR.2010.1095",
url = "http://www.sci.utah.edu/publications/seyedhosseini10/Seyedhosseini_2010a.pdf",
}
@TechReport{SCI:Sey2011a,
author = "M. Seyedhosseini and A.R.C. Paiva and T.
Tasdizen",
title = "Multi-scale Series Contextual Model for Image
Parsing",
number = "UUSCI-2011-004",
year = "2011",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2011-004.pdf",
}
@InProceedings{SCI:Sey2011b,
author = "M. Seyedhosseini and A.R.C. Paiva and T.
Tasdizen",
title = "Fast {AdaBoost} training using weighted novelty
selection",
booktitle = "Proc. {IEEE} Intl. Joint Conf. on Neural
Networks",
pages = "1245--1250",
year = "2011",
address = "San Jose, CA, USA",
month = "August",
url = "http://www.sci.utah.edu/publications/seyedhosseini11/Seyedhosseini_NeuralNet2011.pdf",
url = "http://www.sci.utah.edu/publications/seyedhosseini11/Seyedhosseini_NeuralNet2011-poster.pdf",
}
@InProceedings{SCI:Sey2011c,
author = "M. Seyedhosseini and R. Kumar and E. Jurrus and R.
Guily and M. Ellisman and H. Pfister and T.
Tasdizen",
title = "Detection of Neuron Membranes in Electron
Microscopy Images using Multi-scale Context and
Radon-like Features",
booktitle = "Medical Image Computing and Computer-Assisted
Intervention – MICCAI 2011",
volume = "6891",
pages = "670--677",
year = "2011",
series = "Lecture Notes in Computer Science (LNCS)",
doi = "10.1007/978-3-642-23623-5_84",
url = "http://www.sci.utah.edu/publications/seyedhosseini11/Seyedhosseini_MICCAI2011.pdf",
}
@InProceedings{SCI:Sey2013a,
author = "M. Seyedhosseini and M. Ellisman and T.
Tasdizen",
title = "Segmentation of Mitochondria in Electron
Microscopy Images using Algebraic Curves",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "860--863",
year = "2013",
doi = "10.1109/ISBI.2013.6556611",
url = "http://www.sci.utah.edu/publications/seyedhosseini13/Seyedhosseini_ISBI2013.pdf",
}
@Article{SCI:Sey2013b,
author = "M. Seyedhosseini and T. Tasdizen",
title = "Multi-class Multi-scale Series Contextual Model
for Image Segmentation",
journal = "{IEEE} Transactions on Image Processing",
volume = "PP",
number = "99",
year = "2013",
doi = "10.1109/TIP.2013.2274388",
url = "http://www.sci.utah.edu/publications/seyedhosseini13/Seyedhosseini_MCMS2013.pdf",
}
@InProceedings{SCI:Sey2013c,
author = "M. Seyedhosseini and M. Sajjadi and T. Tasdizen",
title = "Image Segmentation with Cascaded Hierarchical
Models and Logistic Disjunctive Normal Networks",
booktitle = "Proceedings of the {IEEE} International Conference
on Computer Vison ({ICCV} 2013)",
pages = "(accepted)",
year = "2013",
url = "http://www.sci.utah.edu/publications/seyedhosseini13/Seyedhosseini_ICCV2013.pdf",
}
@Article{SCI:Sey2014a,
author = "M. Seyedhosseini and T. Tasdizen",
title = "Disjunctive normal random forests",
journal = "Pattern Recognition",
year = "2014",
month = "September",
doi = "10.1016/j.patcog.2014.08.023",
keywords = "Random forest, Decision tree, Classifier,
Supervised learning, Disjunctive normal form",
}
@Article{SCI:Sey2014b,
author = "M. Seyedhosseini and T. Tasdizen",
title = "Scene Labeling with Contextual Hierarchical
Models",
journal = "CoRR",
volume = "abs/1402.0595",
year = "2014",
url = "http://www.sci.utah.edu/publications/Sey2014b/Seyedhosseini_ArXiv2014.pdf",
}
@Article{SCI:Sey2015a,
author = "M. Seyedhosseini and T. Tasdizen",
title = "Disjunctive normal random forests",
journal = "Pattern Recognition",
volume = "48",
number = "3",
pages = "976--983",
year = "2015",
publisher = "Elsevier BV",
month = "March",
doi = "10.1016/j.patcog.2014.08.023",
url = "http://www.sci.utah.edu/publications/Sey2015a/randomforests2015.pdf",
}
@Article{SCI:Sey2015b,
author = "S.M. Seyedhosseini and S. Shushruth and T. Davis
and J.M. Ichida and P.A. House and B. Greger and A.
Angelucci and T. Tasdizen",
title = "Informative features of local field potential
signals in primary visual cortex during natural
image stimulation",
journal = "Journal of Neurophysiology",
volume = "113",
number = "5",
pages = "1520--1532",
year = "2015",
publisher = "American Physiological Society",
month = "March",
doi = "10.1152/jn.00278.2014",
url = "http://www.sci.utah.edu/publications/Sey2015b/jn.00278.2014.pdf",
}
@Article{SCI:Sey2016a,
author = "S.M. Seyedhosseini and T. Tasdizen",
title = "Semantic Image Segmentation with Contextual
Hierarchical Models",
journal = "IEEE Transactions on Pattern Analysis and Machine
Intelligence",
volume = "38",
number = "5",
pages = "951--964",
year = "2016",
publisher = "IEEE",
month = "May",
doi = "10.1109/tpami.2015.2473846",
url = "http://www.sci.utah.edu/publications/Sey2016a/07226830.pdf",
}
@InProceedings{SCI:Sha2000a,
author = "A. Shamir and V. Pascucci and C.L. Bajaj",
title = "Multi-Resolution Dynamic Meshes with Arbitrary
Deformations",
booktitle = "Proceedings of {IEEE} Conference on Visualization
({VIS}-00)",
pages = "423--430",
year = "2000",
location = "Salt lake City, Utah",
note = "UCRL-JC-139680",
}
@InProceedings{SCI:Sha2001a,
author = "A. Shamir and V. Pascucci",
title = "Temporal and Spatial Level of Details for Dynamic
Meshes",
booktitle = "Proceedings of the ACM Symposium on Virtual
Reality Software and Technology 2001",
year = "2001",
organization = "ACM",
month = "November",
location = "Banff Center, Canada",
}
@InProceedings{SCI:Sha2008a,
author = "S. Sharma and S. Vakkalanka and G. Gopalakrishnan
and R.M. Kirby and R. Thakur and W. Gropp",
title = "A Formal Approach to Detect Functionally
Irrelevant Barriers in {MPI} Programs",
booktitle = "Proceedings of EuroPVM-MPI 2008",
volume = "5205",
pages = "265--273",
year = "2008",
month = "September",
location = "Dublin, Ireland",
doi = "10.1007/978-3-540-87475-1_36",
}
@InProceedings{SCI:Sha2012a,
author = "A. Sharma and S. Durrleman and J.H. Gilmore and G.
Gerig",
title = "Longitudinal Growth Modeling of Discrete-Time
Functions with Application to {DTI} Tract Evolution
in Early Neurodevelopment",
booktitle = "Proceedings of {IEEE} {ISBI} 2012",
pages = "1397--1400",
year = "2012",
doi = "10.1109/ISBI.2012.6235829",
url = "http://www.sci.utah.edu/publications/sharma12/Sharma_ISBI2012.pdf",
}
@InProceedings{SCI:Sha2013a,
author = "A. Sharma and P.T. Fletcher and J.H. Gilmore and
M.L. Escolar and A. Gupta and M. Styner and G.
Gerig",
title = "Spatiotemporal Modeling of Discrete-Time
Distribution-Valued Data Applied to {DTI} Tract
Evolution in Infant Neurodevelopment",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "684--687",
year = "2013",
doi = "10.1109/ISBI.2013.6556567",
url = "http://www.sci.utah.edu/publications/sharma13/Sharma_isbi2013.pdf",
}
@InProceedings{SCI:Sha2014a,
author = "A. Sharma and P.T. Fletcher and J.H. Gilmore and
M.L. Escolar and A. Gupta and M. Styner and G.
Gerig",
title = "Parametric Regression Scheme for Distributions:
Analysis of {DTI} Fiber Tract Diffusion Changes in
Early Brain Development",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "(accepted)",
year = "2014",
keywords = "linear regression, distribution-valued data,
spatiotemporal growth trajectory, DTI, early
neurodevelopment",
url = "http://www.sci.utah.edu/publications/sharma14/Sharma_ISBI2014.pdf",
}
@Misc{SCI:ShapeWorks,
author = "{SCI} Institute",
year = "2015",
note = "{ShapeWorks}: An open-source tool for constructing
compact statistical point-based models of ensembles
of similar shapes that does not rely on specific
surface parameterization. Scientific Computing and
Imaging Institute ({SCI}). Download from:
http://www.sci.utah.edu/software/shapeworks.html",
keywords = "ShapeWorks, shape works, modeling",
}
@Article{SCI:She2004a,
author = "H.-W. Shen and G.-S. Li and U. Bordoloi",
title = "Interactive Visualization of Three-Dimensional
Vector Fields with Flexible Appearance Control",
journal = "{IEEE} Transactions on Visualization and Computer
Graphics",
volume = "10",
number = "4",
pages = "434--445",
year = "2004",
keywords = "vector field methods",
url = "http://www.sci.utah.edu/publications/shen04/tvcg04.pdf",
}
@TechReport{SCI:She2006a,
author = "J.F. Shepherd",
title = "Hexahedral Mesh Generation Constraints",
number = "UUSCI-2006-010",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-010.pdf",
}
@TechReport{SCI:She2006b,
author = "J.F. Shepherd and C.J. Tuttle and C.T. Silva and
Y. Zhang",
title = "Quality Improvement and Feature Capture in
Hexahedral Meshes",
number = "UUSCI-2006-029",
year = "2006",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "feature capture, hexahedral meshes, adaptive mesh
generation",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2006-029.pdf",
}
@Article{SCI:She2006c,
author = "S.J. Sherwin and R.M. Kirby and J. Peiro and R.L.
Taylor and O.C. Zienkiewicz",
title = "On 2D Elliptic Discontinuous Galerkin Methods",
journal = "International Journal of Numerical Methods in
Engineering",
volume = "65",
number = "5",
pages = "752--784",
year = "2006",
url = "http://www.sci.utah.edu/publications/sherwin06/Sherwin_J-NumMethEng06.pdf",
}
@PhdThesis{SCI:She2007b,
author = "J.F. Shepherd",
title = "Topologic and Geometric Constraint-Based
Hexahedral Mesh Generation",
year = "2007",
school = "School of Computing, University of Utah",
month = "May",
keywords = "meshing, mesh generation",
url = "http://www.sci.utah.edu/publications/shepherd07/thesis.pdf",
}
@TechReport{SCI:She2007c,
author = "J.F. Shepherd and C.R. Johnson",
title = "Hexahedral Mesh Generation for Biomedical Models
in SCIRun",
number = "UUSCI-2007-008",
year = "2007",
institution = "University of Utah",
type = "{SCI} Institute Technical Report",
keywords = "scirun, ncrr, mesh generation",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2007-008.pdf",
}
@Article{SCI:She2008a,
author = "J.F. Shepherd and C.R. Johnson",
title = "Hexahedral Mesh Generation Constraints",
journal = "Journal of Engineering with Computers",
volume = "24",
number = "3",
pages = "195--213",
year = "2008",
keywords = "meshing",
url = "http://www.sci.utah.edu/publications/shepherd07/EWC_hex_constraints.pdf",
}
@Article{SCI:She2009a,
author = "J.F. Shepherd and C.R. Johnson",
title = "Hexahedral Mesh Generation for Biomedical Models
in SCIRun",
journal = "Engineering with Computers",
volume = "25",
number = "1",
pages = "97--114",
year = "2009",
url = "http://www.sci.utah.edu/publications/shepherd09/Shepherd_EngComp2009.pdf",
}
@InProceedings{SCI:She94a,
author = "H.W. Shen and P.B. Gharpure and C.R. Johnson",
title = "Visualization of 3-D wave prorogation in the heart
- a new technique",
booktitle = "{IEEE} Engineering in Medicine and Biology Society
16th Annual International Conference",
pages = "684--685",
year = "1994",
publisher = "{IEEE} Press",
keywords = "scalar field methods, vector field methods,
cardiac heart, scientific visualization",
}
@TechReport{SCI:She94b,
author = "H.W. Shen and C.R. Johnson",
title = "Semi-automatic image segmentation: A bimodel
thresholding approach",
number = "UUCS-94-019",
year = "1994",
institution = "University of Utah",
type = "School of Computing Technical Report",
keywords = "ip image processing signal processing,
segmentation, imaging",
url = "http://www.sci.utah.edu/publications/shen94/shen95_1.ps",
}
@InProceedings{SCI:She94c,
author = "H.W. Shen and C.R. Johnson",
title = "Differential volume rendering: A fast alogrithm
for scalar field animation",
booktitle = "Visualization 94",
pages = "180--187",
year = "1994",
publisher = "{IEEE} Press",
keywords = "computational pde pdes computational partial
differential equations evaporation, scalar field
methods, volume rendering",
url = "http://www.sci.utah.edu/publications/shen94/vis94_7.ps",
url = "http://www.sci.utah.edu/publications/shen94/vis94_7.ps.Z",
}
@InProceedings{SCI:She95a,
author = "H.W. Shen and C.R. Johnson",
title = "Sweeping Simplices: A Fast Iso-surface Extraction
Algorithm for Unstructured Grids",
booktitle = "{IEEE} Visualization `95",
pages = "143--150",
year = "1995",
publisher = "{IEEE} Press",
keywords = "scalar field methods, isosurface extraction,
scientific computing, scientific visualization",
url = "http://www.sci.utah.edu/publications/shen95/vis95_9.ps",
url = "http://www.sci.utah.edu/publications/shen95/vis95_9.ps.Z",
}
@InProceedings{SCI:She96a,
author = "H.W. Shen and C.R. Johnson and K.L. Ma",
title = "Global and Local Vector Field Visualization Using
Enhanced Line Integral Convolution",
booktitle = "Symposium on Volume Visualization",
pages = "63--70",
year = "1996",
publisher = "{IEEE} Press",
keywords = "vector field methods, scientific visualization",
url = "http://www.sci.utah.edu/publications/shen96/lic.ps",
}
@InProceedings{SCI:She96b,
author = "H.W. Shen and C.D. Hansen and Y. Livnat and C.R.
Johnson",
title = "Isosurfacing in Span Space with Utmost
Efficiency",
booktitle = "{IEEE} Visualization `96",
pages = "287--294",
year = "1996",
publisher = "{IEEE} Press",
keywords = "scalar field methods, isosurface extraction,
scientific visualization",
url = "http://www.sci.utah.edu/publications/shen96/issue.pdf",
}
@Article{SCI:Shi2005a,
author = "Y.T. Shiu and J.A. Weiss and J.B. Hoying and M.N.
Iwamoto and I.S. Joung and C.T. Quam",
title = "The Role of Mechanical Stresses in Angiogenesis",
journal = j-CRBME,
volume = "33",
number = "5",
pages = "431--510",
year = "2005",
keywords = "angiogenesis, computational biomechanics,
computational mechanics",
url = "http://www.sci.utah.edu/publications/shiu05/shiu_crbe_2005.pdf",
}
@Article{SCI:Shi2009a,
author = "F. Shi and P.T. Yap and Y. Fan and J.Z. Cheng and
L.L. Wald and G. Gerig and W. Lin and D. Shen",
title = "Cortical Enhanced Tissue Segmentation of Neonatal
Brain MR Images Acquired by a Dedicated Phased
Array Coil",
journal = "Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern
Recognition",
pages = "39--45",
year = "2009",
pmid = "20862268",
url = "http://www.sci.utah.edu/publications/shi09/Shi_nihms188810.pdf",
}
@Article{SCI:Shi2011a,
author = "F. Shi and D. Shen and P.-T. Yap and Y. Fan and
J.-Z. Cheng and H. An and L.L. Wald and G. Gerig
and J.H. Gilmore and W. Lin",
title = "CENTS: Cortical Enhanced Neonatal Tissue
Segmentation",
journal = "Human Brain Mapping HBM",
volume = "32",
number = "3",
pages = "382--396",
year = "2011",
month = "March",
note = "ePub 5 Aug 2010",
doi = "10.1002/hbm.21023",
pmid = "20690143",
url = "http://www.sci.utah.edu/publications/shi2011/Shi_HBM2011a.pdf",
}
@InProceedings{SCI:Shi2013a,
author = "Y. Shi and G. Roger and C. Vachet and F. Budin and
E. Maltbie and A. Verde and M. Hoogstoel and J.-B.
Berger and M. Styner",
title = "Software-based diffusion MR human brain phantom
for evaluating fiber-tracking algorithms",
booktitle = "Proceedings of {SPIE} 8669, Medical Imaging 2013:
Image Processing, 86692A",
year = "2013",
doi = "10.1117/12.2006113",
pmid = "24357914",
pmcid = "PMC3865235",
url = "http://www.sci.utah.edu/publications/Shi2013a/Shi_SPIE2013_86692A.pdf",
}
@Article{SCI:Sho2007a,
author = "S. Shome and R.L. Lux and B.B. Punske and R.S.
MacLeod",
title = "Ischemic Preconditioning Protects Against
Arrhythmogenesis Through Maintenance of Both Active
as well as Passive Electrical Properties in
Ischemic Canine Hearts",
journal = "Journal of Electrocardiology",
volume = "40",
number = "6 supp",
pages = "S150--S159",
year = "2007",
month = "Nov-Dec",
}
@Article{SCI:Sho2007b,
author = "S. Shome and J.G. Stinstra and C Henriquez and
R.S. Macleod",
title = "Influence of Extracellular Potassium and Reduced
Extracellular Space on Conduction Velocity During
Acute Ischemia: A Simulation Study",
journal = "Journal of Electrocardiology",
volume = "40",
number = "4",
pages = "S5--S6",
year = "2007",
}
@Article{SCI:Sho2013a,
author = "S. Short and J.T. Elison and B.D. Goldman and M.
Styner and H. Gu and M. Connelly and E. Maltbie and
S. Woolson and W. Lin and G. Gerig and J.S. Reznick
and J.H. Gilmore",
title = "Associations Between White Matter Microstructure
and Infants' Working Memory",
journal = "Neuroimage",
volume = "64",
number = "1",
pages = "156--166",
year = "2013",
publisher = "Elsvier",
month = "January",
doi = "10.1016/j.neuroimage.2012.09.021",
pmid = "22989623",
url = "http://www.sci.utah.edu/publications/short12/Short_NIMG-12-1102R1.pdf",
}
@Article{SCI:Shv2008a,
author = "A.G. Shvedko and M.D. Warren and S. Shome and J.G.
Stinstra and A.V. Zaitsev",
title = "Influence of the Skeletal Muscle Activity on Time
and Frequency Domain Properties of the Body Surface
{ECG} During Evolving Ventricular Fibrillation in
the Pig",
journal = "Resuscitation",
volume = "78",
number = "2",
pages = "215--223",
year = "2008",
month = "May 24",
doi = "10.1016/j.resuscitation.2008.03.010",
keywords = "inverse ECG, electrocardiology, heart",
}
@Article{SCI:Sib2013a,
author = "S.C. Sibole and S.A. Maas and J.P. Halloran and
J.A. Weiss and A. Erdemir",
title = "Evaluation of a post-processing approach for
multiscale analysis of biphasic mechanics of
chondrocytes",
journal = "Computer Methods in Biomechanical and Biomedical
Engineering",
volume = "16",
number = "10",
pages = "1112--1126",
year = "2013",
doi = "10.1080/10255842.2013.809711",
pmid = "23809004",
}
@Article{SCI:Sil2005a,
author = "C.T. Silva and J.L.D. Comba and S.P. Callahan and
F.F. Bernardon",
title = "A Survey of GPU-Based Volume Rendering of
Unstructured Grids",
journal = "Revista de Informatica Teorica e Aplicada",
volume = "12",
number = "2",
pages = "9--29",
year = "2005",
issn = "01034308",
keywords = "volume rendering",
url = "http://www.sci.utah.edu/publications/csilva2005/gputet_survey.pdf",
}
@Article{SCI:Sil2007a,
author = "C.T. Silva and J. Freire and S.P. Callahan",
title = "Provenance for Visualizations: Reproducibility and
Beyond",
journal = "IEEE Computing in Science and Engineering",
volume = "9",
number = "5",
pages = "82--89",
year = "2007",
keywords = "vistrails, provenance, workflow management",
url = "http://www.sci.utah.edu/publications/silva07/Silva_ProvenanceForVis.pdf",
}
@Article{SCI:Sil2008a,
author = "C.T. Silva and J. Tohline",
title = "Guest Editorial: Special Issue on Computational
Provenance",
journal = "Computing in Science and Engineering",
volume = "10",
number = "3",
pages = "9--10",
year = "2008",
url = "http://www.sci.utah.edu/publications/silva08/cise2008e.pdf",
}
@Article{SCI:Sil2008b,
author = "C.T. Silva and J. Freire",
title = "Software Infrastructure for Exploratory
Visualization and Data Analysis: Past, Present and
Future",
journal = "Journal of Physics: Conference Series (SciDAC 2008
Conference)",
volume = "125",
year = "2008",
url = "http://www.sci.utah.edu/publications/silva08/jpconf8_125_012100.pdf",
}
@InProceedings{SCI:Sil2010a,
author = "C. Silva and E. Anderson and E. Santos and J.
Freire",
title = "Using VisTrails and Provenance for Teaching
Scientific Visualization",
booktitle = "EUROGRAPHICS 2010 Educator Program",
year = "2010",
note = "Awarded Best Paper!",
keywords = "vistrails, provenance, workflows",
url = "http://www.sci.utah.edu/publications/silva10/vistrails-teaching-eurographics2010.pdf",
}
@InProceedings{SCI:Sim2002a,
author = "J. Simpson and A.R. Sanderson and E. Luke and K.
Balling and R. Coffey",
title = "Collaborative Remote Visualization",
booktitle = c-ACMSC2002,
year = "2002",
month = "November",
location = "Baltimore, Maryland",
keywords = "undergrad, esp, remote visualization,
collaborative remote visualization, scientific
visualization",
url = "http://www.sci.utah.edu/publications/simpson02/CRV-2.pdf",
}
@InProceedings{SCI:Sim2002b,
author = "J. Simpson and A.R. Sanderson and E. Luke and K.
Balling and R. Coffey",
title = "Collaborative Remote Visualization",
booktitle = "Presented before the Utah State Legislature",
year = "2002",
keywords = "undergrad, esp, remote visualization,
collaborative remote visualization, scientific
visualization",
url = "http://www.sci.utah.edu/publications/simpson02/CRV-1.pdf",
}
@Article{SCI:Sim2004a,
author = "J. Simpson and S.J. Balling",
title = "{ANNOT3D} and Packaging of 3D Visualizations for
Educational Purposes",
journal = c-MMVR2004,
pages = "(in press)",
year = "2004",
month = "January",
location = "Newport Beach, {CA}",
keywords = "scalar field methods, annot3d, vr virtual reality
haptics, undergrad",
}
@Article{SCI:Sin2010a,
author = "N.P. Singh and P.T. Fletcher and J.S. Preston and
L. Ha and R. King and J.S. Marron and M. Wiener and
S. Joshi",
title = "Multivariate Statistical Analysis of Deformation
Momenta Relating Anatomical Shape to
Neuropsychological Measures",
journal = "Medical Image Computing and Computer-Assisted
Intervention – MICCAI 2010, Lecture Notes in
Computer Science (LCNS)",
volume = "6363/2010",
pages = "529-537",
year = "2010",
doi = "10.1007/978-3-642-15711-0_66",
pmid = "20879441",
url = "http://www.sci.utah.edu/publications/singh10/Singh_MICCAI2010.pdf",
}
@InProceedings{SCI:Sin2012a,
author = "N.P. Singh and A.Y. Wang and P. Sankaranarayanan
and P.T. Fletcher and S. Joshi",
title = "Genetic, Structural and Functional Imaging
Biomarkers for Early Detection of Conversion from
{MCI} to {AD}",
booktitle = "Proceedings of Medical Image Computing and
Computer-Assisted Intervention {MICCAI} 2012",
volume = "7510",
pages = "132--140",
year = "2012",
doi = "10.1007/978-3-642-33415-3_17",
keywords = "adni",
url = "http://www.sci.utah.edu/publications/singh12/Singh_MICCAI2012.pdf",
}
@InProceedings{SCI:Sin2013a,
author = "N.P. Singh and J. Hinkle and S. Joshi and P.T.
Fletcher",
title = "A Vector Momenta Formulation of Diffeomorphisms
for Improved Geodesic Regression and Atlas
Construction",
booktitle = "Proceedings of the 2013 {IEEE} 10th International
Symposium on Biomedical Imaging ({ISBI})",
pages = "1219--1222",
year = "2013",
note = "Received Best Student Paper Award",
doi = "10.1109/ISBI.2013.6556700",
keywords = "{LDDMM}, Geodesic regression, Atlas, Vector
Momentum",
url = "http://www.sci.utah.edu/publications/singh13/Singh_ISBI2013.pdf",
}
@InProceedings{SCI:Sin2013b,
author = "N.P. Singh and J. Hinkle and S. Joshi and P.T.
Fletcher",
title = "A Hierarchical Geodesic Model for Diffeomorphic
Longitudinal Shape Analysis",
booktitle = "Proceedings of the International Conference on
Information Processing in Medical Imaging
({IPMI})",
pages = "(accepted)",
year = "2013",
series = "Lecture Notes in Computer Science ({LNCS})",
url = "http://www.sci.utah.edu/publications/singh13/Singh_IPMI2013.pdf",
}
@InProceedings{SCI:Sin2014a,
author = "N.P. Singh and J. Hinkle and S. Joshi and P.T.
Fletcher",
title = "An Efficient Parallel Algorithm for Hierarchical
Geodesic Models in Diffeomorphisms",
booktitle = "Proceedings of the 2014 {IEEE} International
Symposium on Biomedical Imaging ({ISBI})",
pages = "(accepted)",
year = "2014",
keywords = "{LDDMM}, {HGM}, Vector Momentum, Diffeomorphisms,
Longitudinal Analysis",
url = "http://www.sci.utah.edu/publications/singh14/Singh_ISBI2014.pdf",
}
@Article{SCI:Sir2005a,
author = "S. Sirisup and G.E. Karniadakis and D. Xiu and
I.G. Kevrekidis",
title = "Equation-free/Galerkin-free POD-assisted
Computation of Incompressible Flows",
journal = "Journal of Computational Physics",
volume = "207",
number = "2",
pages = "568--587",
year = "2005",
doi = "10.1016/j.jcp.2005.01.024",
url = "http://www.sci.utah.edu/publications/sirisup05/Sirisup_JCP2005.pdf",
}
@Article{SCI:Ske1990a,
author = "R.D. Skeel and M. Berzins",
title = "A Method for the Spatial Discretisation of
Parabolic Equations",
journal = "{SIAM} Journal on Scientific Computing",
volume = "11",
number = "1",
pages = "1--32",
year = "1990",
month = "January",
url = "http://www.sci.utah.edu/publications/Ske1990a/Skeel_JSC1990.pdf",
}
@TechReport{SCI:Skr2013a,
author = "P. Skraba and Bei Wang and G. Chen and P. Rosen",
title = "2D Vector Field Simplification Based on
Robustness",
number = "UUSCI-2013-004",
year = "2013",
institution = "SCI Institute, University of Utah",
type = "SCI Technical Report",
url = "http://www.sci.utah.edu/publications/SCITechReports/UUSCI-2013-004.pdf",
}
@InProceedings{SCI:Skr2014a,
author = "P. Skraba and Bei Wang and G. Chen and P. Rosen",
title = "{2D} Vector Field Simplification Based on
Robustness",
booktitle = "Proceedings of the 2014 {IEEE} Pacific
Visualization Symposium",
year = "2014",
series = "{PacificVis}",
note = "Awarded Best Paper!",
keywords = "vector field, topology-based techniques, flow
visualization",
url = "http://www.sci.utah.edu/publications/skraba14/Skraba_PV2014.pdf",
}
@InCollection{SCI:Skr2014b,
author = "P. Skraba and Bei Wang",
title = "Interpreting Feature Tracking Through the Lens of
Robustness",
booktitle = "Mathematics and Visualization",
pages = "19-37",
year = "2014",
publisher = "Springer",
doi = "10.1007/978-3-319-04099-8_2",
url = "http://www.sci.utah.edu/publications/Skr2014b/Feature_Tracking_Robustness_BeiWang_2013.pdf",
}
@InProceedings{SCI:Skr2014c,
author = "P. Skraba and Bei Wang",
title = "Approximating Local Homology from Samples",
booktitle = "Proceedings 25th Annual ACM-SIAM Symposium on
Discrete Algorithms (SODA)",
pages = "174-192",
year = "2014",
url = "http://www.sci.utah.edu/publications/Skr2014c/Sampling_LocalHomology_BeiWang_2014.pdf",
}
@Article{SCI:Skr2015a,
author = "P. Skraba and Bei Wang and G. Chen and P. Rosen",
title = "Robustness-Based Simplification of 2D Steady and
Unsteady Vector Fields",
journal = "IEEE Transactions on Visualization and Computer
Graphics (to appear)",
year = "2015",
url = "http://www.sci.utah.edu/publications/Skr2015a/Robustness_Unsteady_VF_BeiWang_2015.pdf",
}
@Misc{SCI:SLASH,
author = "{SLASH}",
year = "2015",
note = "{SLASH}: A hybrid system for high-throughput
segmentation of large neuropil datasets, SLASH is
funded by the National Institute of Neurological
Disorders and Stroke (NINDS) grant
5R01NS075314-03.",
keywords = "SLASH, SCI",
}
@InProceedings{SCI:Sle1996a,
author = "P.A. Sleigh and M. Berzins and P.H. Gaskell",
title = "A Reliable and Accurate Technique for the
Modelling of Complex Hydraulic Flows",
booktitle = "Proceedings of the First International Symposium
on Finite Volumes for Complex Applications",
pages = "635--642",
year = "1996",
location = "Hermes, Paris",
isbn = "2-86601-556-8",
url = "http://www.sci.utah.edu/publications/Sle1996a/Sleigh_FVCA1996.pdf",
}
@InProceedings{SCI:Sle95a,
author = "P.A. Sleigh and P.H. Gaskell and M. Berzins and
J.M. Ware and N.G. Wright",
title = "A Reliable and Accurate Technique for the
Modelling of Practically Occurring Open Channel
Flow",
booktitle = "Proceedings of the Ninth International Conference
on Numerical Methods in Laminar and Turbulent
Flow",
pages = "881--892",
year = "1995",
publisher = "Pineridge Press",
}
@Article{SCI:Sle98a,
author = "P.A. Sleigh and M. Berzins and P.H. Gaskell and
N.G. Wright",
title = "An Unstructured Finite Volume Algorithm for
Predicting Flow in Rivers and Estuaries",
journal = "Computers and Fluids",
volume = "27",
number = "4",
pages = "479--508",
year = "1998",
url = "http://www.sci.utah.edu/publications/sleigh98/CompFluids27.pdf",
}
@InProceedings{SCI:Slo97,
author = "P.P.J. Sloan and M.F. Cohen and S.J. Gortler",
title = "Time Critical Lumigraph Rendering",
booktitle = "1997 Symposium on Interactive 3D Graphics",
year = "1997",
month = "Apr",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt",
url = "http://www.sci.utah.edu/publications/sloan97/si3d.ps.gz",
}
@InProceedings{SCI:Slo98,
author = "P.P.J. Sloan and D.M. Weinstein and J.D.
Brederson",
title = "Importance Driven Texture Coordinate
Optimization",
booktitle = "Eurographics 98",
year = "1998",
month = "Sep",
keywords = ", scientific visualization",
url = "http://www.sci.utah.edu/publications/sloan98/eg98.pdf",
url = "http://www.sci.utah.edu/publications/sloan98/eg98CP.pdf",
}
@InProceedings{SCI:Slo99,
author = "P.P. Sloan and C.D. Hansen",
title = "Parallel Lumigraph Reconstruction",
booktitle = "Parallel Visualization and Graphics Symposium
1999",
pages = "7--14",
year = "1999",
month = "October",
keywords = "parallel visualization, interactive rt distributed
interactive ray tracing dirt, rtrt, scientific
visualization",
url = "http://www.sci.utah.edu/publications/sloan99/pvg99.ps.gz",
url = "http://www.sci.utah.edu/publications/sloan99/pvg99.ps",
}
@InProceedings{SCI:Smi1996a,
author = "J.D.B. Smith and A.S. Tomlin and M. Berzins and V.
Pennington and M.J. Pilling",
title = "Modelling the effects of Concentrated Emissions
Sources on Tropospheric Ozone",
booktitle = "Proceedings of the 3rd Workshop on Modelling of
Chemical Reaction Systems",
year = "1996",
month = "July",
location = "Heidelberg, Germany",
howpublished = "Published on CD-ROM",
isbn = "3-932217-00-4",
url = "http://www.sc