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Updated August 28, 2024 12:06

2024

[Ada2024a] J. Adams, K. Iyer, S. Elhabian.
**“Weakly Supervised Bayesian Shape Modeling from Unsegmented Medical Images,”** Subtitled **“arXiv:2405.09697v1,”** 2024.

[Ada2024b] J. Adams, S. Elhabian.
**“Point2SSM++: Self-Supervised Learning of Anatomical Shape Models from Point Clouds,”** Subtitled **“arXiv:2405.09707v1,”** 2024.

[Ath2024a] T. M. Athawale, B. Triana, T. Kotha, D. Pugmire, P. Rosen.
**“A Comparative Study of the Perceptual Sensitivity of Topological Visualizations to Feature Variations,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 30, No. 1, pp. 1074-1084. Jan, 2024.

DOI: 10.1109/TVCG.2023.3326592

[Azi2024a] A.Z.B. Aziz, M.S.T. Karanam, T. Kataria, S.Y. Elhabian.
**“EfficientMorph: Parameter-Efficient Transformer-Based Architecture for 3D Image Registration,”** Subtitled **“arXiv preprint arXiv:2403.11026,”** 2024.

[Bas2024a] Z. Bastiani, R.M. Kirby, J. Hochhalter, S. Zhe.
**“Complexity-Aware Deep Symbolic Regression with Robust Risk-Seeking Policy Gradients,”** Subtitled **“arXiv:2406.06751,”** 2024.

[Bei2024a] J.W. Beiriger, W. Tao, Z. Irgebay, J. Smetona, L. Dvoracek, N. Kass, A. Dixon, C. Zhang, M. Mehta, R. Whitaker, J. Goldstein.
**“A Longitudinal Analysis of Pre-and Post-Operative Dysmorphology in Metopic Craniosynostosis,”** In *The Cleft Palate Craniofacial Journal*, Sage, 2024.

DOI: 10.1177/10556656241237605

[Ber2024a] M. Berzins.
**“COMPUTATIONAL ERROR ESTIMATION FOR THE MATERIAL POINT METHOD IN 1D AND 2D,”** In *VIII International Conference on Particle-Based Methods, PARTICLES 2023*, 2024.

[Ber2024b] C.C. Berggren, D. Jiang, Y.F. Wang, J.A. Bergquist, L. Rupp, Z. Liu, R.S. MacLeod, A. Narayan, L. Timmins.
**“Influence of Material Parameter Variability on the Predicted Coronary Artery Biomechanical Environment via Uncertainty Quantification,”** Subtitled **“arXiv preprint arXiv:2401.15047,”** 2024.

[Can2024a] O. Cankur, A. Tomar, D. Nichols, C. Scully-Allison, K. Isaacs, A. Bhatele.
**“Automated Programmatic Performance Analysis of Parallel Programs,”** Subtitled **“arXiv:2401.13150v1,”** 2024.

[Cha2024a] A.M. Chalifoux, L. Gibb, K.N. Wurth, T. Tenner, T. Tasdizen, L. MacDonald.
**“Morphology of uranium oxides reduced from magnesium and sodium diuranate,”** In *Radiochimica Acta*, Vol. 112, No. 2, pp. 73-84. 2024.

[Che2024a] N. Cheng, O.A. Malik, Y. Xu, S. Becker, A. Doostan, A. Narayan.
**“Subsampling of Parametric Models with Bifidelity Boosting,”** In *Journal on Uncertainty Quantificatio.*, ACM, 2024.

[Che2024b] Y. Chen, Y. Ji, A. Narayan, Z. Xu.
**“TGPT-PINN: Nonlinear model reduction with transformed GPT-PINNs,”** Subtitled **“arXiv preprint arXiv:2403.03459,”** 2024.

[Coo2024a] M. Cooley, S. Zhe, R.M. Kirby, V. Shankar.
**“Polynomial-Augmented Neural Networks (PANNs) with Weak Orthogonality Constraints for Enhanced Function and PDE Approximation,”** Subtitled **“arXiv preprint arXiv:2406.02336,”** 2024.

[Dai2024a] H. Dai, S. Joshi.
**“Refining Skewed Perceptions in Vision-Language Models through Visual Representations,”** Subtitled **“arXiv preprint arXiv:2405.14030,”** 2024.

[Das2024a] S. Dasetty, T.C. Bidone, A.L. Ferguson.
**“Data-driven prediction of αIIbβ3 integrin activation pathways using nonlinear manifold learning and deep generative modeling,”** In *Biophysical Journal*, Vol. 123, 2024.

[Don2024a] J. Dong, E. Kwan, J.A. Bergquist, B.A. Steinberg, D.J. Dosdall, E. DiBella, R.S. MacLeod, T.J. Bunch, R. Ranjan.
**“Ablation-induced left atrial mechanical dysfunction recovers in weeks after ablation,”** In *Journal of Interventional Cardiac Electrophysiology*, Springer, 2024.

[Eck2024a] K. Eckelt, K. Gadhave, A. Lex, M. Streit.
**“Loops: Leveraging Provenance and Visualization to Support Exploratory Data Analysis in Notebooks,”** In *Computer Graphics Forum*, 2024.

[Fer2024a] A. Ferrero, E. Ghelichkhan, H. Manoochehri, M.M. Ho, D.J. Albertson, B.J. Brintz, T. Tasdizen, R.T. Whitaker, B. Knudsen.
**“HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification,”** In *Modern Pathology*, Vol. 37, No. 4, 2024.

[Gar2024a] S. Garg, J. Zhang, R. Pitchumani, M. Parashar, B. Xie, S. Kannan.
**“CrossPrefetch: Accelerating I/O Prefetching for Modern Storage,”** In *29th ACM International Conference on Architectural Support for Programming Languages and Operating Systems*, ACM, 2024.

[Gho2024a] S. Ghorbany, M. Hu, S. Yao, C. Wang, Q.C. Nguyen, X. Yue, M. Alirezaei, T. Tasdizen, M Sisk.
**“Examining the role of passive design indicators in energy burden reduction: Insights from a machine learning and deep learning approach,”** In *Building and Environment*, Elsevier, 2024.

[Han2024a] M. Han, J. Li, S. Sane, S. Gupta, B. Wang, S. Petruzza, C.R. Johnson.
**“Interactive Visualization of Time-Varying Flow Fields Using Particle Tracing Neural Networks,”** Subtitled **“arXiv preprint arXiv:2312.14973,”** 2024.

[Ho2024a] M.M. Ho, S. Dubey, Y. Chong, B. Knudsen, T. Tasdizen.
**“F2FLDM: Latent Diffusion Models with Histopathology Pre-Trained Embeddings for Unpaired Frozen Section to FFPE Translation,”** Subtitled **“arXiv:2404.12650v1,”** 2024.

[Ho2024b] M.M. Ho, E. Ghelichkhan, Y. Chong, Y. Zhou, B.S. Knudsen, T. Tasdizen.
**“DISC: Latent Diffusion Models with Self-Distillation from Separated Conditions for Prostate Cancer Grading,”** Subtitled **“arXiv:2404.13097,”** 2024.

[Hoe2024a] T. Hoefler, M. Copik, P. Beckman, A. Jones, I. Foster, M. Parashar, D. Reed, M. Troyer, T. Schulthess, D. Ernst, J. Dongarra.
**“XaaS: Acceleration as a Service to Enable Productive High-Performance Cloud Computing,”** Subtitled **“arXiv:2401.04552v1,”** 2024.

[Hol2024a] J. K. Holmen , M. Garcıa, A. Bagusetty, V. Madananth, A. Sanderson,, M. Berzins.
**“Making Uintah Performance Portable for Department of Energy Exascale Testbeds,”** In *Euro-Par 2023: Parallel Processing*, pp. 1--12. 2024.

[Hua2024a] Q. Huang, J. Le, S. Joshi, J. Mendes, G. Adluru, E. DiBella.
**“Arterial Input Function (AIF) Correction Using AIF Plus Tissue Inputs with a Bi-LSTM Network,”** In *Tomography*, Vol. 10, pp. 660-673. 2024.

[Hua2024b] X. Huang, H. Miao, A. Townsend, K. Champley, J. Tringe, V. Pascucci, P.T. Bremer.
**“Bimodal Visualization of Industrial X-Ray and Neutron Computed Tomography Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2024.

DOI: 10.1109/TVCG.2024.3382607

[Isa2024a] K.E. Isaacs, H. Kaiser.
**“Halide Code Generation Framework in Phylanx,”** In *Euro-Par 2022: Parallel Processing Workshops *, Springer, 2024.

[Iye2024a] K. Iyer, J. Adams, S.Y. Elhabian.
**“SCorP: Statistics-Informed Dense Correspondence Prediction Directly from Unsegmented Medical Images,”** Subtitled **“arXiv preprint arXiv:2404.17967,”** 2024.

[Joh2024a] J Johnson, L McDonald, T Tasdizen.
**“Improving uranium oxide pathway discernment and generalizability using contrastive self-supervised learning,”** In *Computational Materials Science*, Vol. 223, Elsevier, 2024.

[Jos2024a] O. Joshi, T. Skóra, A. Yarema, R.D. Rabbitt, T.C. Bidone.
**“Contributions of the individual domains of αIIbβ3 integrin to its extension: Insights from multiscale modeling ,”** In *Cytoskeleton*, 2024.

[Kat2024a] T. Kataria, B. Knudsen, S.Y. Elhabian.
**“StainDiffuser: MultiTask Dual Diffusion Model for Virtual Staining,”** Subtitled **“arXiv preprint arXiv:2403.11340,”** 2024.

[Kop2024a] V. Koppelmans, M.F.L. Ruitenberg, S.Y. Schaefer, J.B. King, J.M. Jacobo, B.P. Silvester, A.F. Mejia, J. van der Geest, J.M. Hoffman, T. Tasdizen, K. Duff.
**“Classification of Mild Cognitive Impairment and Alzheimer's Disease Using Manual Motor Measures,”** In *Neurodegener Dis*, 2024.

DOI: 10.1159/000539800

PubMed ID: 38865972

[Lan2024a] D. Lange, R. Judson-Torres, T.A. Zangle, A. Lex.
**“Aardvark: Composite Visualizations of Trees, Time-Series, and Images,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2024.

[Lis2024a] M. Lisnic, Z. Cutler, M. Kogan, A. Lex.
**“Visualization Guardrails: Designing Interventions Against Cherry-Picking in Interactive Data Explorers,”** Subtitled **“Preprint,”** 2024.

[Mac2024a] C. Mackenzie, S. Ruckel, A. Morris, S. Elhabian, E. Bieging.
**“Statistical Shape Modeling To Predict Left Atrial Appendage Thrombus,”** In *Journal of Cardiovascular Computed Tomography*, Elsevier, 2024.

DOI: https://doi.org/10.1016/j.jcct.2024.05.195

[Ngu2024a] Q.C. Nguyen, T. Tasdizen, M. Alirezaei, H. Mane, X. Yue, J.S. Merchant, W. Yu, L. Drew, D. Li, T.T. Nguyen.
**“Neighborhood built environment, obesity, and diabetes: A Utah siblings study,”** In *SSM - Population Health*, Vol. 26, 2024.

[Ngu2024b] Q.C. Nguyen, M. Alirezaei, X. Yue, H. Mane, D. Li, L. Zhao, T.T. Nguyen, R. Patel, W. Yu, M. Hu, D. Quistberg, T. Tasdizen.
**“Leveraging computer vision for predicting collision risks: a cross-sectional analysis of 2019–2021 fatal collisions in the USA,”** In *Injury Prevention*, BMJ, 2024.

[Nih2024a] R. Nihalaani, T. Kataria, J. Adams, S.Y. Elhabian.
**“Estimation and Analysis of Slice Propagation Uncertainty in 3D Anatomy Segmentation,”** Subtitled **“arXiv preprint arXiv:2403.12290,”** 2024.

[Par2024a] M. Parashar.
**“Enabling Responsible Artificial Intelligence Research and Development Through the Democratization of Advanced Cyberinfrastructure,”** In *Harvard Data Science Review, Special Issue 4: Democratizing Data*, 2024.

[Par2024b] M. Parashar.
**“Everywhere & Nowhere: Envisioning a Computing Continuum for Science,”** Subtitled **“arXiv:2406.04480v1,”** 2024.

[Pen2024a] M. Penwarden, H. Owhadi, R.M. Kirby.
**“Kolmogorov n-Widths for Multitask Physics-Informed Machine Learning (PIML) Methods: Towards Robust Metrics,”** Subtitled **“arXiv preprint arXiv:2402.11126,”** 2024.

[Scu2024a] C. Scully-Allison, I. Lumsden, K. Williams, J. Bartels, M. Taufer, S. Brink, A. Bhatele, O. Pearce, K. Isaacs.
**“Design Concerns for Integrated Scripting and Interactive Visualization in Notebook Environments,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2024.

DOI: 10.1109/TVCG.2024.3354561

[Shi2024a] N. Shingde, T. Blattner, A. Bardakoff, W. Keyrouz, M. Berzins.
**“An illustration of extending Hedgehog to multi-node GPU architectures using GEMM,”** In *Springer Nature (to appear)*, 2024.

[Sub2024a] S. Subramaniam, M. Miller, several co-authors, Chris R. Johnson, et al..
**“Grand Challenges at the Interface of Engineering and Medicine,”** In *IEEE Open Journal of Engineering in Medicine and Biology*, Vol. 5, IEEE, pp. 1--13. 2024.

DOI: 10.1109/OJEMB.2024.3351717

[Tau2024a] M. Taufer, H. Martinez, J. Luettgau, L. Whitnah, G. Scorzelli, P. Newel, A. Panta, T. Bremer, D. Fils, C.R. Kirkpatrick, N. McCurdy, V. Pascucci.
**“Integrating FAIR Digital Objects (FDOs) into the National Science Data Fabric (NSDF) to Revolutionize Dataflows for Scientific Discovery,”** In *Computing in Science & Engineering*, IEEE, 2024.

[Uke2024a] J. Ukey, T. Kataria, S.Y. Elhabian.
**“MASSM: An End-to-End Deep Learning Framework for Multi-Anatomy Statistical Shape Modeling Directly From Images,”** Subtitled **“arXiv preprint arXiv:2403.11008,”** 2024.

[Wan2024a] S. Wang, H. Yan, K.E. Isaacs, Y. Sun.
**“Visual Exploratory Analysis for Designing Large-Scale Network-on-Chip Architectures: A Domain Expert-Led Design Study,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 30, pp. 1970-1983. 2024.

[Yeh2024a] H.P. Yeh, M. Bayat, A. Arzani, J.H. Hattel.
**“Accelerated process parameter selection of polymer-based selective laser sintering via hybrid physics-informed neural network and finite element surrogate modelling,”** In *Applied Mathematical Modelling*, Vol. 130, pp. 693--712. 2024.

[Zew2024a] H.Y. Zewdie, O.L. Sarmiento, J.D. Pinzón, M.A. Wilches-Mogollon, P. A. Arbelaez, L. Baldovino-Chiquillo, D. Hidalgo, L. Guzman, S.J. Mooney, Q.C. Nguyen, T. Tasdizen, D.A. Quistberg .
**“Road Traffic Injuries and the Built Environment in Bogotá, Colombia, 2015–2019: A Cross-Sectional Analysis,”** In *Journal of Urban Health*, Springer, 2024.

2023

[Ada2023a] J. Adams, S. Elhabian.
**“Fully Bayesian VIB-DeepSSM,”** Subtitled **“arXiv:2305.05797,”** 2023.

[Ada2023b] J. Adams, S. Elhabian.
**“Can point cloud networks learn statistical shape models of anatomies?,”** Subtitled **“arXiv:2305.05610,”** 2023.

[Ada2023c] J. Adams, S. Elhabian.
**“Point2SSM: Learning Morphological Variations of Anatomies from Point Cloud,”** Subtitled **“arXiv:2305.14486,”** 2023.

[Ada2023d] J. Adams, S.Y. Elhabian.
**“Benchmarking Scalable Epistemic Uncertainty Quantification in Organ Segmentation,”** Subtitled **“arXiv:2308.07506,”** 2023.

[Ada2023e] M. Adair, I. Rodero, M. Parashar, D. Melgar.
**“Accelerating Data-Intensive Seismic Research Through Parallel Workflow Optimization and Federated Cyberinfrastructure,”** In *Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis*, ACM, pp. 1970--1977. 2023.

DOI: 10.1145/3624062.3624276

[Akb2023a] D. Akbaba, D. Lange, M. Correll, A. Lex, M. Meyer.
**“Troubling Collaboration: Matters of Care for Visualization Design Study,”** In *Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ’23),*, pp. 23--28. April, 2023.

[Ali2023a] M. Aliakbari, M.S. Sadrabadi, P. Vadasz, A. Arzani.
**“Ensemble physics informed neural networks: A framework to improve inverse transport modeling in heterogeneous domains,”** In *Physics of Fluids*, AIP, 2023.

[Arz2023a] A. Arzani, L. Yuan, P. Newell, B. Wang.
**“Interpreting and generalizing deep learning in physics-based problems with functional linear models,”** Subtitled **“arXiv:2307.04569,”** 2023.

[Ath2023a] T. M. Athawale, C.R. Johnson, S. Sane,, D. Pugmire.
**“Fiber Uncertainty Visualization for Bivariate Data With Parametric and Nonparametric Noise Models,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 29, No. 1, IEEE, pp. 613-23. 2023.

[Azi2023a] A.Z.B. Aziz, J. Adams, S. Elhabian.
**“Progressive DeepSSM: Training Methodology for Image-To-Shape Deep Models,”** Subtitled **“arXiv:2310.01529,”** 2023.

[Bak2023a] J. Baker, E. Cherkaev, A. Narayan, B. Wang.
**“Learning Proper Orthogonal Decomposition of Complex Dynamics Using Heavy-ball Neural ODEs,”** In *Journal of Scientific Computing*, Vol. 95, No. 14, 2023.

[Bei2023a] J.W. Beiriger, W. Tao, M.K. Bruce, E. Anstadt, C. Christiensen, J. Smetona, R. Whitaker, J. Goldstein.
**“CranioRate TM: An Image-Based, Deep-Phenotyping Analysis Toolset and Online Clinician Interface for Metopic Craniosynostosis,”** In *Plastic and Reconstructive Surgery*, 2023.

[Ber2023a] M. Berzins.
**“Error Estimation for the Material Point and Particle in Cell Methods,”** In *admos2023*, 2023.

[Ber2023b] J. A. Bergquist, B. Zenger, L. Rupp, A. Busatto, J. D. Tate, D. H. Brooks, A. Narayan, R. MacLeod.
**“Uncertainty quantification of the effect of cardiac position variability in the inverse problem of electrocardiographic imaging,”** In *Journal of Physiological Measurement*, IOP Science, 2023.

DOI: 10.1088/1361-6579/acfc32

[Bid2023a] T.C. Bidone, D.J. Odde.
**“Multiscale models of integrins and cellular adhesions,”** In *Current Opinion in Structural Biology*, Vol. 80, Elsevier, 2023.

[Bor2023a] B. Borotikar, T.E.M. Mutsvangwa, S..Y Elhabian, E.Audenaert .
**“Editorial: Statistical model-based computational biomechanics: applications in joints and internal organs,”** In *Frontiers in Bioengineering and Biotechnology*, Vol. 11, 2023.

DOI: 10.3389/fbioe.2023.1232464

[Bri2023a] S. Brink, M. McKinsey, D. Boehme, C. Scully-Allison, I. Lumsden, D. Hawkins, T. Burgess, V. Lama, J. Luettgau, K.E. Isaacs, M. Taufer, O. Pearce.
**“Thicket: Seeing the Performance Experiment Forest for the Individual Run Trees,”** In *HPDC ’23*, ACM, 2023.

[Cam2023a] S. Campbell, M. C. Mendoza, A. Rammohan, M. E. McKenzie, T. C. Bidone.
**“Computational model of integrin adhesion elongation under an actin fiber,”** In *PLOS Computatonal Biology*, Vol. 19, No. 7, Public Library of Science, pp. 1-19. 7, 2023.

DOI: 10.1371/journal.pcbi.1011237

[Car2023a] K.R. Carney, A.M. Khan, S. Stam, S.C. Samson, N. Mittal, S. Han, T.C. Bidone, M. Mendoza.
**“Nascent adhesions shorten the period of lamellipodium protrusion through the Brownian ratchet mechanism,”** In *Mol Biol Cell*, 2023.

[Cha2023a] B. Charoenwong, R.M. Kirby, J. Reiter.
**“Computer Science Abstractions To Help Reason About Decentralized Stablecoin Design,”** In *IEEE Access*, IEEE, 2023.

[Csa2023a] H. Csala, A. Mohan, D. Livescu, A. Arzani.
**“Modeling Coupled 1D PDEs of Cardiovascular Flow with Spatial Neural ODEs,”** In *Machine Learning and the Physical Sciences Workshop, NeurIPS 2023*, 2023.

[Dai2023a] H. Dai, M. Penwarden, R.M. Kirby, S. Joshi.
**“Neural Operator Learning for Ultrasound Tomography Inversion,”** Subtitled **“arXiv:2304.03297v1,”** 2023.

[Dai2023b] H. Dai, M. Bauer, P.T. Fletcher, S. Joshi.
**“Modeling the Shape of the Brain Connectome via Deep Neural Networks,”** In *Information Processing in Medical Imaging*, Springer Nature Switzerland, pp. 291--302. 2023.

ISBN: 978-3-031-34048-2

[Dai2023c] D. Dai, Y. Epshteyn, A. Narayan.
**“Energy Stable and Structure-Preserving Schemes for the Stochastic Galerkin Shallow Water Equations,”** Subtitled **“arXiv:2310.06229,”** 2023.

[Dai2023d] H. Dai, V. Sarkar, C. Dial, M.D. Foote, Y. Hitchcock, S. Joshi, B. Salter.
**“High-Fidelity CT on Rails-Based Characterization of Delivered Dose Variation in Conformal Head and Neck Treatments,”** In *Applied Radiation Oncology*, 2023.

DOI: 10.1101/2023.04.07.23288305

[Din2023a] Y. Ding, J. Wilburn, H. Shrestha, A. Ndlovu, K. Gadhave, C. Nobre, A. Lex, L. Harrison.
**“reVISit: Supporting Scalable Evaluation of Interactive Visualizations,”** Subtitled **“OSF Preprints,”** 2023.

[Dub2023a] S. Dubey, T. Kataria, B. Knudsen, S.Y. Elhabian.
**“Structural Cycle GAN for Virtual Immunohistochemistry Staining of Gland Markers in the Colon,”** Subtitled **“arXiv:2308.13182,”** 2023.

[Fal2023a] M. Falk, V. Tobiasson, A. Bock, C. Hansen, A. Ynnerman.
**“A Visual Environment for Data Driven Protein Modeling and Validation,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, pp. 1-11. 2023.

DOI: 10.1109/TVCG.2023.3286582

[Fan2023a] S. Fang, S. Zhe, H.M. Lin, A.A. Azad, H. Fettke, E.M. Kwan, L. Horvath, B. Mak, T. Zheng, P. Du, S. Jia, R.M. Kirby, M. Kohli.
**“Multi-Omic Integration of Blood-Based Tumor-Associated Genomic and Lipidomic Profiles Using Machine Learning Models in Metastatic Prostate Cancer,”** In *Clinical Cancer Informatics*, 2023.

[Fan2023b] S. Fang, X. Yu, S. Li, Z. Wang, R. Kirby, S. Zhe.
**“Streaming Factor Trajectory Learning for Temporal Tensor Decomposition,”** Subtitled **“arxiv.org/abs/2310.17021,”** 2023.

[Fan2023c] S. Fang, M. Cooley, D. Long, S. Li, R. Kirby, S. Zhe.
**“Solving High Frequency and Multi-Scale PDEs with Gaussian Processes,”** Subtitled **“arXiv:2311.04465,”** 2023.

[Hal2023a] M. Hall, G. Gopalakrishnan, E. Eide, J. Cohoon, J. Phillips, M. Zhang, S. Elhabian, A. Bhaskara, H. Dam, A. Yadrov, T. Kataria.
**“An NSF REU Site Based on Trust and Reproducibility of Intelligent Computation: Experience Report,”** In *Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis*, 2023.

[Han2023a] R. Han, A. Narayan, Y. Xu.
**“An approximate control variates approach to multifidelity distribution estimation,”** Subtitled **“arXiv:2303.06422v1,”** 2023.

[Hic2023a] K. G. Hicks, A. A. Cluntun, H. L. Schubert, S. R. Hackett, J. A. Berg, P. G. Leonard, M. A. Ajalla Aleixo, Y. Zhou, A. J. Bott, S. R. Salvatore, F. Chang, A. Blevins, P. Barta, S. Tilley, A. Leifer, A. Guzman, A. Arok, S. Fogarty, J. M. Winter, H. Ahn, K. N. Allen, S. Block, I. A. Cardoso, J. Ding, I. Dreveny, C. Gasper, Q. Ho, A. Matsuura, M. J. Palladino, S. Prajapati, P. Sun, K. Tittmann, D. R. Tolan, J. Unterlass, A. P. VanDemark, M. G. Vander Heiden, B. A. Webb, C. Yun, P. Zhap, B. Wang, F. J. Schopfer, C. P. Hill, M. C. Nonato, F. L. Muller, J. E. Cox, J. Rutter.
**“Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase,”** In *Science*, Vol. 379, No. 6636, pp. 996-1003. 2023.

DOI: 10.1126/science.abm3452

[Hoa2023a] D. Hoang, H. Bhatia, P. Lindstrom, V. Pascucci.
**“Progressive Tree-Based Compression of Large-Scale Particle Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, pp. 1--18. 2023.

DOI: 10.1109/TVCG.2023.3260628

[Hol2023a] J. K. Holmen, V. G. Vergara Larrea, E. W. Draeger, E. T. Phipps, P. J. Smith, M. Berzins, S. T. Smith, J. N. Thornock, S. Parete-Koon.
**“Strengthening the US Department of Energy's Recruitment Pipeline: The DOE/NNSA Predictive Science Academic Alliance Program (PSAAP) Experience,”** In *Practice and Experience in Advanced Research Computing*, ACM, pp. 137--144. 2023.

[Hu2023a] M. Hu, K. Zhang, Q. Nguyen, T. Tasdizen.
**“The effects of passive design on indoor thermal comfort and energy savings for residential buildings in hot climates: A systematic review,”** In *Urban Climate*, Vol. 49, pp. 101466. 2023.

DOI: https://doi.org/10.1016/j.uclim.2023.101466

[Iye2023a] K. Iyer, S. Elhabian.
**“Mesh2SSM: From Surface Meshes to Statistical Shape Models of Anatomy,”** Subtitled **“arXiv:2305.07805,”** 2023.

[Joh2023a] C. R. Johnson, H. Shen.
**“AI for Scientific Visualization,”** In *Artificial Intelligence for Science*, Edited by Alok Choudhary, Geoffrey Fox, and Tony Hey, World Scientific, pp. 535-552. 2023.

DOI: 10.1142/9789811265679_0029

[Joh2023b] S. Johnson, B. Zimmerman, H. Odéen, J. Shea, N. Winkler, R. Factor, S. Joshi, A. Payne.
**“A Non-Contrast Multi-Parametric MRI Biomarker for Assessment of MR-Guided Focused Ultrasound Thermal Therapies,”** In *IEEE Transactions on Biomedical Engineering*, IEEE, pp. 1--12. 2023.

DOI: 10.1109/TBME.2023.3303445

[Kam2023a] R. Kamali, E. Kwan, M. Regouski, T.J. Bunch, D.J. Dosdall, E. Hsu, R. S. Macleod, I. Polejaeva, R. Ranjan.
**“Contribution of atrial myofiber architecture to atrial fibrillation,”** In *PLOS ONE*, Vol. 18, No. 1, Public Library of Science, pp. 1--16. Jan, 2023.

DOI: 10.1371/journal.pone.0279974

[Kar2023a] M.S.T. Karanam, T. Kataria, S. Elhabian.
**“ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images,”** Subtitled **“arXiv:2307.03273v2,”** 2023.

[Kat2023a] T. Kataria, S. Rajamani, A.B. Ayubi, M. Bronner, J. Jedrzkiewicz, B. Knudsen, S. Elhabian.
**“Automating Ground Truth Annotations For Gland Segmentation Through Immunohistochemistry,”** 2023.

[Kat2023b] T. Kataria, B. Knudsen, S. Elhabian.
**“Unsupervised Domain Adaptation for Semantic Segmentation via Feature-space Density Matching,”** Subtitled **“arXiv:2305.05789,”** 2023.

[Kat2023c] T. Kataria, B. Knudsen, S. Elhabian.
**“To pretrain or not to pretrain? A case study of domain-specific pretraining for semantic segmentation in histopathology,”** Subtitled **“arXiv:2307.03275,”** 2023.

[Lev2023a] S. Leventhal, A. Gyulassy, M. Heimann, V. Pascucci.
**“Exploring Classification of Topological Priors with Machine Learning for Feature Extraction,”** In *IEEE Transactions on Visualization and Computer Graphics*, pp. 1--12. 2023.

[Li2023a] J. Li, A. Pepe, C. Gsaxner, G. Luijten, Y. Jin, S. Elhabian, et. al..
**“MedShapeNet - A Large-Scale Dataset of 3D Medical Shapes for Computer Vision,”** Subtitled **“arXiv:2308.16139v3,”** 2023.

[Li2023b] S. Li, X. Yu, W. Xing, R.M. Kirby, A. Narayan, S. Zhe.
**“Multi-Resolution Active Learning of Fourier Neural Operators,”** Subtitled **“arXiv:2309.16971,”** 2023.

[Li2023c] Z. Li, S. Liu, K. Bhavya, T. Bremer, V. Pascucci.
**“Instance-wise Linearization of Neural Network for Model Interpretation,”** Subtitled **“arXiv:2310.16295v1,”** 2023.

[Lin2023a] H. Lin, M. Lisnic, D. Akbaba, M. Meyer, A. Lex.
**“Here’s what you need to know about my data: Exploring Expert Knowledge’s Role in Data Analysis,”** 2023.

[Lis2023a] M. Lisnic, A. Lex, M. Kogan.
**“"Yeah, this graph doesn't show that": Analysis of Online Engagement with Misleading Data Visualizations,”** In *OSF Preprints*, 2023.

[Liu2023a] AVA: Towards Autonomous Visualization Agents through Visual Perception-Driven Decision-Making.
**“S. Liu, H. Miao, Z. Li, M. Olson, V. Pascucci, P.T. Bremer,”** Subtitled **“arXiv preprint arXiv:2312.04494,”** 2023.

[Lon2023a] D. Long, W.W. Xing, A.S. Krishnapriyan, R.M. Kirby, S. Zhe, M.W. Mahoney.
**“Equation Discovery with Bayesian Spike-and-Slab Priors and Efficient Kernels,”** Subtitled **“arXiv:2310.05387v1,”** 2023.

[Lue2023a] J. Luettgau, G. Scorzelli, V. Pascucci, M. Taufer.
**“Development of Large-Scale Scientific Cyberinfrastructure and the Growing Opportunity to Democratize Access to Platforms and Data,”** In *Distributed, Ambient and Pervasive Interactions*, Springer Nature Switzerland, pp. 378--389. 2023.

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[Lue2023b] J. Luettgau, H. Martinez, G. Tarcea, G. Scorzelli, V. Pascucci, M. Taufer.
**“Studying Latency and Throughput Constraints for Geo-Distributed Data in the National Science Data Fabric,”** In *Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing*, ACM, pp. 325–326. 2023.

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[Ly2023a] C. Ly, C. Nizinski, A. Hagen, L. McDonald IV, T. Tasdizen.
**“Improving Robustness for Model Discerning Synthesis Process of Uranium Oxide with Unsupervised Domain Adaptation,”** In *Frontiers in Nuclear Engineering*, 2023.

[Mcd2023a] L.W. McDonald IV, K. Sentz, A. Hagen, B.W. Chung, T. Tasdizen, et. al..
**“Review of Multi-Faceted Morphologic Signatures of Actinide Process Materials for Nuclear Forensic Science,”** In *Journal of Nuclear Materials*, Elsevier, 2023.

[Mor2023a] N. Morrical, S. Zellmann, A. Sahistan, P. Shriwise, V. Pascucci.
**“Attribute-Aware RBFs: Interactive Visualization of Time Series Particle Volumes Using RT Core Range Queries,”** In *IEEE Trans Vis Comput Graph*, IEEE, 2023.

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[Oh2023a] H. Oh, R. Amici, G. Bomarito, S. Zhe, R. Kirby, J. Hochhalter.
**“Genetic Programming Based Symbolic Regression for Analytical Solutions to Differential Equations,”** Subtitled **“arXiv:2302.03175v1,”** 2023.

[Oh2023b] H. Oh, R. Amici, G. Bomarito, S. Zhe, R.M. Kirby, J. Hochhalter.
**“Inherently interpretable machine learning solutions to differential equations,”** In *Engineering with Computers*, 2023.

[Ork2023a] B.A. Orkild, J.A. Bergquist, E.N. Paccione, M. Lange, E. Kwan, B. Hunt, R. MacLeod, A. Narayan, R. Ranjan.
**“A Grid Search of Fibrosis Thresholds for Uncertainty Quantification in Atrial Flutter Simulations,”** In *Computing in Cardiology*, 2023.

[Oue2023a] T. A. J. Ouermi, R. M Kirby, M. Berzins.
**“HiPPIS A High-Order Positivity-Preserving Mapping Software for Structured Meshes,”** In *ACM Trans. Math. Softw*, ACM, Nov, 2023.

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[Par2023a] M. Parashar, T. Kurc, H. Klie, M.F. Wheeler, J.H. Saltz, M. Jammoul, R. Dong.
**“Dynamic Data-Driven Application Systems for Reservoir Simulation-Based Optimization: Lessons Learned and Future Trends,”** In *Handbook of Dynamic Data Driven Applications Systems: Volume 2*, Springer International Publishing, pp. 287--330. 2023.

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[Par2023b] M. Parashar, I. Altintas.
**“Toward Democratizing Access to Science Data: Introducing the National Data Platform,”** In * IEEE 19th International Conference on e-Science*, IEEE, 2023.

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[Par2023c] M. Parashar, T. deBlanc-Knowles, E. Gianchandani, L.E. Parker.
**“Strengthening and Democratizing Artificial Intelligence Research and Development,”** In *Computer*, Vol. 56, No. 11, IEEE, pp. 85-90. 2023.

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[Pen2023a] M. Penwarden, S. Zhe, A. Narayan, R.M. Kirby.
**“A Metalearning Approach for Physics-Informed Neural Networks (PINNs): Application to Parameterized PDEs,”** In *Journal of Computational Physics*, Elsevier, 2023.

DOI: https://doi.org/10.1016/j.jcp.2023.111912

[Pen2023b] M. Penwarden, A.D. Jagtap, S. Zhe, G.E. Karniadakis, R.M. Kirby.
**“A unified scalable framework for causal sweeping strategies for Physics-Informed Neural Networks (PINNs) and their temporal decompositions,”** Subtitled **“arXiv:2302.14227v1,”** 2023.

[Pet2023a] C. Peters, T. Patel, W. Usher, C R. Johnson.
**“Ray Tracing Spherical Harmonics Glyphs,”** In *Vision, Modeling, and Visualization*, The Eurographics Association, 2023.

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[Pet2023b] S. Petruzza, B. Summa, A. Gooch, C.M. Laney, T. Goulden, J. Schreiner, S. Callahan, V. Pascucci.
**“Interactive Visualization and Portable Image Blending of Massive Aerial Image Mosaics,”** In *IEEE International Conference on Big Data*, IEEE, pp. 3365-3370. 2023.

[Pir2023a] S. Pirola, A. Arzani, C. Chiastra, F. Sturla.
**“Editorial: Image-based computational approaches for personalized cardiovascular medicine: improving clinical applicability and reliability through medical imaging and experimental data,”** In *Frontiers in Medical Technology*, Vol. 5, 2023.

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[Sah2023a] S. Saha, W. Gazi, R. Mohammed, T. Rapstine, H. Powers, R. Whitaker.
**“Multi-task Training as Regularization Strategy for Seismic Image Segmentation,”** In *IEEE Geoscience and Remote Sensing Letters*, Vol. 20, IEEE, pp. 1--5. 2023.

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[Sah2023b] S. Saha, S. Joshi, R. Whitaker.
**“Matching aggregate posteriors in the variational autoencoder,”** Subtitled **“arXiv preprint arXiv:2311.07693,”** 2023.

[Sha2023a] M. Shao, T. Tasdizen, S. Joshi.
**“Analyzing the Domain Shift Immunity of Deep Homography Estimation,”** Subtitled **“arXiv:2304.09976v1,”** 2023.

[Shi2023a] N. Shingde, M. Berzins, T. Blattner, W. Keyrouz, A. Bardakoff.
**“Extending Hedgehog’s dataflow graphs to multi-node GPU architectures,”** In *Workshop on Asynchronous Many-Task Systems and Applications (WAMTA23)*, 2023.

[Shu2023a] K. Shukla, V. Oommen, A. Peyvan, M. Penwarden, L. Bravo, A. Ghoshal, R.M. Kirby, G. Karniadakis.
**“Deep neural operators can serve as accurate surrogates for shape optimization: A case study for airfoils,”** Subtitled **“arXiv:2302.00807v1,”** 2023.

[Shu2023b] K. Shukla, V. Oommen, A. Peyvan, M. Penwarden, N. Plewacki, L. Bravo, A. Ghoshal, R.M. Kirby, G. Karniadakis.
**“Deep neural operators as accurate surrogates for shape optimization,”** In *Engineering Applications of Artificial Intelligence*, Vol. 129, pp. 107615. 2023.

ISSN: 0952-1976

[Sic2023a] C. Sicari, A. Catalfamo, L. Carnevale, A. Galletta, D. Balouek-Thomert, M. Parashar, M. Villari.
**“TEMA: Event Driven Serverless Workflows Platform for Natural Disaster Management,”** In *2023 IEEE Symposium on Computers and Communications (ISCC)*, pp. 1-6. 2023.

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[Sic2023b] C. Sicari, D. Balouek, M. Villari, M. Parashar.
**“Event-Driven FaaS Workflows for Enabling IoT Data Processing at the Cloud Edge Continuum,”** In *CC 2023 - International Conference on Utility and Cloud Computing*, 2023.

[Sul2023a] K.M.A. Sultan, B. Orkild, A. Morris, E. Kholmovski, E. Bieging, E. Kwan, R. Ranjan, E. DiBella, s. Elhabian.
**“Two-Stage Deep Learning Framework for Quality Assessment of Left Atrial Late Gadolinium Enhanced MRI Images,”** Subtitled **“arXiv:2310.08805v1,”** 2023.

[Sul2023b] K.M.A.Sultan, B. Orkild, A. Morris, E. Kholmovski, E. Bieging, E. Kwan, R. Ranjan, E. DiBella, S. Elhabian.
**“Two-Stage Deep Learning Framework for Quality Assessment of Left Atrial Late Gadolinium Enhanced MRI Images,”** Subtitled **“arXiv:2310.08805,”** 2023.

[Sun2023a] T. Sun, D. Li, B. Wang.
**“On the Decentralized Stochastic Gradient Descent with Markov Chain Sampling,”** In *IEEE Transactions on Signal Processing*, IEEE, July, 2023.

[Sun2023b] T. Sun, Q. Wang, Y. Lei, D. Li, B. Wang.
**“Pairwise Learning with Adaptive Online Gradient Descent,”** In *Transactions on Machine Learning Research*, 2023.

[Tat2023a] J. Tate, Z. Liu, J.A. Bergquist, S. Rampersad, D. White, C. Charlebois, L. Rupp, D. Brooks, R. MacLeod, A. Narayan.
**“UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines,”** In *Journal of Open Source Software*, Vol. 8, No. 90, 2023.

[Toh2023a] R. Tohid, S. Shirzad, C. Taylor, S.A. Sakin, K.E. Isaacs, H. Kaiser.
**“Halide Code Generation Framework in Phylanx,”** In *Euro-Par 2022: Parallel Processing Workshops*, Springer Nature Switzerland, pp. 32--45. 2023.

ISBN: 978-3-031-31209-0

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[Uke2023a] J Ukey, S Elhabian.
**“Image2SSM: Localization-aware Deep Learning Framework for Statistical Shape Modeling Directly from Images,”** In *Medical Imaging with Deep Learning*, In *Proceedings of Machine Learning Research *, 2023.

[Wan2023a] Z. Wang, T. M. Athawale, K. Moreland, J. Chen, C. R. Johnson, D. Pugmire.
**“FunMC2: A Filter for Uncertainty Visualization of Marching Cubes on Multi-Core Devices,”** In *Eurographics Symposium on Parallel Graphics and Visualization*, 2023.

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[Wil2023a] K. Williams, A. Bigelow, K.E. Isaacs.
**“Data Abstraction Elephants: The Initial Diversity of Data Representations and Mental Models,”** In *Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ’23)*, ACM, 2023.

[Xu2023a] H. Xu, S. Elhabian.
**“Image2SSM: Reimagining Statistical Shape Models from Images with Radial Basis Functions,”** Subtitled **“arXiv:2305.11946,”** 2023.

[Xu2023b] H. Xu, A. Morris, S.Y. Elhabian.
**“Particle-Based Shape Modeling for Arbitrary Regions-of-Interest,”** In *Shape in Medical Imaging, Lecture Notes in Computer Science, vol 14350*, 2023.

[Zha2023a] B. Zhang, P.E. Davis, N. Morales, Z. Zhang, K. Teranishi, M. Parashar.
**“Optimizing Data Movement for GPU-Based In-Situ Workflow Using GPUDirect RDMA,”** In *Euro-Par 2023: Parallel Processing*, Springer Nature Switzerland, pp. 323--338. 2023.

ISBN: 978-3-031-39698-4

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[Zha2023b] B. Zhang, H. Manoochehri, M.M. Ho, F. Fooladgar, Y. Chong, B. Knudsen, D. Sirohi, T. Tasdizen.
**“CLASSMix: Adaptive stain separation-based contrastive learning with pseudo labeling for histopathological image classification,”** Subtitled **“arXiv:2312.06978v2,”** 2023.

[Zho2023a] N. Zhou, G. Scorzelli, J. Luettgau, R.R. Kancharla, J. Kane, R. Wheeler, B. Croom, B. Newell, V. Pascucci, M. Taufer.
**“Orchestration of materials science workflows for heterogeneous resources at large scale,”** In *The International Journal of High Performance Computing Applications*, Sage, 2023.

2022

[Ada2022a] J. Adams, N. Khan, A. Morris, S. Elhabian.
**“Spatiotemporal Cardiac Statistical Shape Modeling: A Data-Driven Approach,”** Subtitled **“arXiv preprint arXiv:2209.02736,”** 2022.

[Ali2022a] M. Alirezaei, T. Tasdizen.
**“Adversarially Robust Classification by Conditional Generative Model Inversion,”** Subtitled **“arXiv preprint arXiv:2201.04733,”** 2022.

[Ali2022b] M. Alirezaei, Q.C. Nguyen, R. Whitaker, T. Tasdizen.
**“Multi-Task Classification for Improved Health Outcome Prediction Based on Environmental Indicators,”** In *IEEE Access*, 2022.

DOI: 10.1109/ACCESS.2023.3295777

[Ans2022a] E.E. Anstadt, W. Tao, E. Guo, L. Dvoracek, M.K. Bruce, P.J. Grosse, L. Wang, L. Kavan, R. Whitaker, J.A. Goldstein.
**“Quantifying the Severity of Metopic Craniosynostosis Using Unsupervised Machine Learning,”** In *Plastic and Reconstructive Surgery*, November, 2022.

[Arz2022a] A. Arzani, K.W. Cassel, R.M. D'Souza.
**“Theory-guided physics-informed neural networks for boundary layer problems with singular perturbation,”** In *Journal of Computational Physics*, 2022.

DOI: https://doi.org/10.1016/j.jcp.2022.111768

[Ath2022a] T. M. Athawale, D. Maljovec. L. Yan, C. R. Johnson, V. Pascucci, B. Wang.
**“Uncertainty Visualization of 2D Morse Complex Ensembles Using Statistical Summary Maps,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 28, No. 4, pp. 1955-1966. April, 2022.

ISSN: 1077-2626

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[Bak2022a] J. Baker, E. Cherkaev, A. Narayan, B. Wang.
**“Learning POD of Complex Dynamics Using Heavy-ball Neural ODEs,”** Subtitled **“arXiv:2202.12373,”** 2022.

[Bak2022b] J. Baker, H. Xia, Y. Wang, E. Cherkaev, A. Narayan, L. Chen, J. Xin, A. L. Bertozzi, S. J. Osher, B. Wang.
**“Proximal Implicit ODE Solvers for Accelerating Learning Neural ODEs,”** Subtitled **“arXiv preprint arXiv:2204.08621,”** 2022.

[Ban2022a] W. Bangerth, C. R. Johnson, D. K. Njeru, B. van Bloemen Waanders.
**“Estimating and using information in inverse problems,”** Subtitled **“arXiv:2208.09095,”** 2022.

[Ber2022a] J. A. Bergquist, J. Coll-Font, B. Zenger, L. C. Rupp, W. W. Good, D. H. Brooks, R. S. MacLeod.
**“Reconstruction of cardiac position using body surface potentials,”** In *Computers in Biology and Medicine*, Vol. 142, pp. 105174. 2022.

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[Ber2022b] M. Berzins.
**“Energy conservation and accuracy of some MPM formulations,”** In *Computational Particle Mechanics*, 2022.

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[Ber2022c] M. Berzins.
**“Computational Error Estimation for The Material Point Method,”** In *Computational Particle Mechanics*, Springer, 2022.

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[Ber2022d] J.A. Bergquist, L.C. Rupp, A. Busatto, B. Orkild, B. Zenger, W. Good, J. Coll-Font, A. Narayan, J. Tate, D. Brooks, R.S. MacLeod.
**“Heart Position Uncertainty Quantification in the Inverse Problem of ECGI,”** In *Computing in Cardiology*, Vol. 49, 2022.

[Blu2022a] J.D. Blum, J. Beiriger, C. Kalmar, R.A. Avery, S. Lang, D.F. Villavisanis, L. Cheung, D.Y. Cho, W. Tao, R. Whitaker, S.P. Bartlett, J.A. Taylor, J.A. Goldstein, J.W. Swanson.
**“Relating Metopic Craniosynostosis Severity to Intracranial Pressure,”** In *The Journal of Craniofacial Surgery*, 2022.

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[Bre2022a] PT. Bremer, G. Tourassi, W. Bethel, K. Gaither, V. Pascucci, W. Xu.
**“Report for the ASCR Workshop on Visualization for Scientific Discovery, Decision-Making, and Communication,”** *DOE*, 2022.

[Bru2022a] M. K. Bruce, W. Tao, J. Beiriger, C. Christensen, M. J. Pfaff, R. Whitaker, J. A. Goldstein.
**“3D Photography to Quantify the Severity of Metopic Craniosynostosis,”** In *The Cleft Palate-Craniofacial Journal*, SAGE Publications, 2022.

[Bus2022a] A. Busatto, J.A. Bergquist, L.C. Rupp, B. Zenger, R.S. MacLeod.
**“Unexpected Errors in the Electrocardiographic Forward Problem,”** In *Computing in Cardiology*, Vol. 49, 2022.

[Che2022a] N. Cheng, O.A. Malik, Y. Xu, S. Becker, A. Doostan, A. Narayan.
**“Quadrature Sampling of Parametric Models with Bi-fidelity Boosting,”** Subtitled **“arXiv:2209.05705v1,”** 2022.

[Csa2022a] H. Csala, S.T.M. Dawson, A. Arzani.
**“Comparing different nonlinear dimensionality reduction techniques for data-driven unsteady fluid flow modeling,”** In *Physics of Fluids*, AIP Publishing, 2022.

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[Dai2022a] H. Dai, M. Bauer, P.T. Fletcher, S.C. Joshi.
**“Deep Learning the Shape of the Brain Connectome,”** Subtitled **“arXiv preprint arXiv:2203.06122, 2022,”** 2022.

[Dor2022a] M. Dorier, Z. Wang, U. Ayachit, S. Snyder, R. Ross, M. Parashar.
**“Colza: Enabling Elastic In Situ Visualization for High-performance Computing Simulations,”** In *2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS)*, IEEE, pp. 538-548. 2022.

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[Fan2022a] S. Fang, A. Narayan, R.M. Kirby, S. Zhe.
**“Bayesian Continuous-Time Tucker Decomposition,”** In *Proceedings of the 39 th International Conference on Machine Learning*, 2022.

[Fau2022a] R. Faust, C. Scheidegger, K. Isaacs, W.Z. Bernstein, M. Sharp, C. North.
**“Interactive Visualization for Data Science Scripts,”** In *2022 IEEE Visualization in Data Science (VDS)*, IEEE, pp. 37-45. 2022.

[Fer2022a] A. Ferrero, B. Knudsen, D. Sirohi, R. Whitaker.
**“A Pathologist-Informed Workflow for Classification of Prostate Glands in Histopathology,”** In *Medical Optical Imaging and Virtual Microscopy Image Analysis*, Springer Nature Switzerland, pp. 53--62. 2022.

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[Gra2022a] M. Grant, M. R. Kunz, K. Iyer, L. I. Held, T. Tasdizen, J. A. Aguiar, P. P. Dholabhai.
**“Integrating atomistic simulations and machine learning to design multi-principal element alloys with superior elastic modulus,”** In *Journal of Materials Research*, Springer International Publishing, pp. 1--16. 2022.

[Gu2022a] J. Gu, P. Davis, G. Eisenhauer, W. Godoy, A. Huebl, S. Klasky, M. Parashar, N. Podhorszki, F. Poeschel, J. Vay, L. Wan, R. Wang, K. Wu.
**“Organizing Large Data Sets for Efficient Analyses on HPC Systems,”** In *Journal of Physics: Conference Series*, Vol. 2224, No. 1, IOP Publishing, pp. 012042. 2022.

[Han2022a] M. Han, S. Sane, C. R. Johnson.
**“Exploratory Lagrangian-Based Particle Tracing Using Deep Learning,”** In *Journal of Flow Visualization and Image Processing*, Begell, 2022.

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[Han2022b] M. Han, T.M. Athawale, D. Pugmire, C.R. Johnson.
**“Accelerated Probabilistic Marching Cubes by Deep Learning for Time-Varying Scalar Ensembles,”** In *2022 IEEE Visualization and Visual Analytics (VIS)*, IEEE, pp. 155-159. 2022.

DOI: 10.1109/VIS54862.2022.00040

[Hog2022a] J.D. Hogue, R.M. Kirby, A. Narayan.
**“Dimensionality Reduction in Deep Learning via Kronecker Multi-layer Architectures,”** Subtitled **“arXiv:2204.04273,”** 2022.

[Hol2022a] John Holmen.
**“Portable, Scalable Approaches For Improving Asynchronous Many-Task Runtime Node Use,”** *School of Computing, University of Utah*, 2022.

[Hol2022b] J.K. Holmen, D. Sahasrabudhe, M. Berzins.
**“Porting Uintah to Heterogeneous Systems,”** In *Proceedings of the Platform for Advanced Scientific Computing Conference (PASC22) Best Paper Award*, ACM, 2022.

[Ish2022a] Y. Ishidoya, E. Kwan, D. J. Dosdall, R. S. Macleod, L. Navaravong, B. A. Steinberg, T. J. Bunch, R. Ranjan.
**“Short-Term Natural Course of Esophageal Thermal Injury After Ablation for Atrial Fibrillation,”** In *Journal of Cardiovascular Electrophysiology*, Wiley, 2022.

DOI: 10.1111/jce.15553

[Ish2022b] Y. Ishidoya, E. Kwan, D. J. Dosdall, R. S. Macleod, L. Navaravong, B. A. Steinberg, T. J. Bunch, R. Ranjan.
**“Shorter Distance Between The Esophagus And The Left Atrium Is Associated With Higher Rates Of Esophageal Thermal Injury After Radiofrequency Ablation,”** In *Journal of Cardiovascular Electrophysiology*, Wiley, 2022.

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[Iye2022a] K. Iyer, A. Morris, B. Zenger, K. Karnath, B.A. Orkild, O. Korshak, S. Elhabian.
**“Statistical Shape Modeling of Biventricular Anatomy with Shared Boundaries,”** Subtitled **“arXiv:2209.02706v1,”** 2022.

[Jen2022a] M.H. Jensen, S. Joshi, S. Sommer.
**“Discrete-Time Observations of Brownian Motion on Lie Groups and Homogeneous Spaces: Sampling and Metric Estimation,”** In *Algorithms*, Vol. 15, No. 8, 2022.

ISSN: 1999-4893

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[Jia2022a] X. Jiang, Z. Li, R. Missel, Md. Zaman, B. Zenger, W. W. Good, R. S. MacLeod, J. L. Sapp, L. Wang.
**“Few-Shot Generation of Personalized Neural Surrogates for Cardiac Simulation via Bayesian Meta-learning,”** In *Medical Image Computing and Computer Assisted Intervention -- MICCAI 2022*, Springer Nature Switzerland, pp. 46--56. 2022.

ISBN: 978-3-031-16452-1

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[Jia2022b] X. Jiang, M. Toloubidokhti, J. Bergquist, B. Zenger, w. Good, R.S. MacLeod, L. Wang.
**“Improving Generalization by Learning Geometry-Dependent and Physics-Based Reconstruction of Image Sequences,”** In *IEEE Transactions on Medical Imaging*, 2022.

DOI: 10.1109/TMI.2022.3218170

[Jia2022c] X. Jiang, J. Tate, J. Bergquist, A. Narayan, R. MacLeod, L. Wang.
**“Uncertainty Quantification of Cardiac Position on Deep Graph Network ECGI,”** In *Computing in Cardiology*, Vol. 49, 2022.

[Kam2022a] R. Kamali, K. Gillete, J. Tate, D. A. Abhyankar, D. J. Dosdall, G. Plank, T. J. Bunch, R. S. Macleod & R. Ranjan .
**“Treatment Planning for Atrial Fibrillation Using Patient-Specific Models Showing the Importance of Fibrillatory-Areas,”** In *Annals of Biomedical Engineering*, Springer, 2022.

DOI: https://doi.org/10.1007/s10439-022-03029-5

[Kes2022a] V. Keshavarzzadeh, R.M. Kirby, A. Narayan.
**“Variational Inference for Nonlinear Inverse Problems via Neural Net Kernels: Comparison to Bayesian Neural Networks, Application to Topology Optimization,”** Subtitled **“arXiv:2205.03681,”** 2022.

[Klo2022a] D. Klotzl, T. Krake, Y. Zhou, I. Hotz, B. Wang, D. Weiskopf.
**“Local Bilinear Computation of Jacobi Sets,”** In *The Visual Computer*, 2022.

[Klo2022b] D. Klötzl, T. Krake, Y. Zhou, J. Stober, K. Schulte, I. Hotz, B. Wang, D. Weiskopf.
**“Reduced Connectivity for Local Bilinear Jacobi Sets,”** Subtitled **“arXiv:2208.07148,”** 2022.

[Lan2022a] R. Lanfredi, J.D. Schroeder, T. Tasdizen.
**“Localization supervision of chest x-ray classifiers using label-specific eye-tracking annotation,”** Subtitled **“arXiv:2207.09771,”** 2022.

[Lan2022b] D. Lange, S. Sahai, J.M. Phillips, A. Lex.
**“Ferret: Reviewing Tabular Datasets for Manipulation,”** Subtitled **“OSF Preprint,”** 2022.

[Li2022a] Z. Li, S. Liu, X. Yu, K. Bhavya, J. Cao, J. Diffenderfer, P.T. Bremer, V. Pascucci.
**““Understanding Robustness Lottery”: A Comparative Visual Analysis of Neural Network Pruning Approaches,”** Subtitled **“arXiv preprint arXiv:2206.07918,”** 2022.

[Li2022b] S. Li, R.M. Kirby, S. Zhe.
**“Decomposing Temporal High-Order Interactions via Latent ODEs,”** In *Proceedings of the 39 th International Conference on Machine Learning*, 2022.

[Li2022c] S. Li, Z Wang, R.M. Kirby, S. Zhe.
**“Infinite-Fidelity Coregionalization for Physical Simulation,”** Subtitled **“arXiv:2207.00678,”** 2022.

[Li2022d] Z. Li, T. Sun, H. Wang, B. Wang.
**“Adaptive and Implicit Regularization for Matrix Completion,”** Subtitled **“arXiv preprint arXiv:2208.05640,”** 2022.

[Li2022e] S. Li, J.M. Phillips, X. Yu, R.M. Kirby, S. Zhe.
**“Batch Multi-Fidelity Active Learning with Budget Constraints,”** Subtitled **“arXiv:2210.12704v1,”** 2022.

[Li2022f] S. Li, M. Penwarden, R.M. Kirby, S. Zhe.
**“Meta Learning of Interface Conditions for Multi-Domain Physics-Informed Neural Networks,”** Subtitled **“arXiv preprint arXiv:2210.12669,”** 2022.

[Li2022g] Z. Li, H. Menon, K. Mohror, S. Liu, L. Guo, P.T. Bremer, V. Pascucci.
**“A Visual Comparison of Silent Error Propagation,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2022.

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[Liu2022a] Z. Liu, A. Narayan.
**“A Stieltjes algorithm for generating multivariate orthogonal polynomials,”** Subtitled **“arXiv preprint arXiv:2202.04843,”** 2022.

[Liv2022a] Y. Livnat, D. Maljovec, A. Gyulassy, B. Mouginot, V. Pascucci.
**“A Novel Tree Visualization to Guide Interactive Exploration of Multi-dimensional Topological Hierarchies,”** Subtitled **“arXiv preprint arXiv:2208.06952,”** 2022.

[Lue2022a] J. Luettgau, C.R. Kirkpatrick, G. Scorzelli, V. Pascucci, G. Tarcea, M. Taufer.
**“NSDF-Catalog: Lightweight Indexing Service for Democratizing Data Delivering,”** 2022.

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**“Fast Algorithms for Monotone Lower Subsets of Kronecker Least Squares Problems,”** Subtitled **“arXiv:2209.05662v1,”** 2022.

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**“Quick Clusters: A GPU-Parallel Partitioning for Efficient Path Tracing of Unstructured Volumetric Grids,”** 2022.

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[Nar2022a] A. Narayan, Z. Liu, J. A. Bergquist, C. Charlebois, S. Rampersad, L. Rupp, D. Brooks, D. White, J. Tate, R. S. MacLeod.
**“UncertainSCI: Uncertainty quantification for computational models in biomedicine and bioengineering,”** In *Computers in Biology and Medicine*, 2022.

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[Ngu2022a] Q. C. Nguyen, T. Belnap, P. Dwivedi, A. Hossein Nazem Deligani, A. Kumar, D. Li, R. Whitaker, J. Keralis, H. Mane, X. Yue, T. T. Nguyen, T. Tasdizen, K. D. Brunisholz.
**“Google Street View Images as Predictors of Patient Health Outcomes, 2017–2019,”** In *Big Data and Cognitive Computing*, Vol. 6, No. 1, Multidisciplinary Digital Publishing Institute, 2022.

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**“Momentum Transformer: Closing the Performance Gap Between Self-attention and Its Linearization,”** Subtitled **“arXiv preprint arXiv:2208.00579,”** 2022.

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**“Characterization of uncertainties and model generalizability for convolutional neural network predictions of uranium ore concentrate morphology,”** In *Chemometrics and Intelligent Laboratory Systems*, Vol. 225, Elsevier, pp. 104556. 2022.

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**“Quantifying and Visualizing Uncertainty for Source Localisation in Electrocardiographic Imaging,”** In *Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization*, Taylor & Francis, pp. 1--11. 2022.

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**“NSDF-FUSE: A Testbed for Studying Object Storage via FUSE File Systems,”** In *Proceedings of the 31st International Symposium on High-Performance Parallel and Distributed Computing*, Association for Computing Machinery, pp. 277–278. 2022.

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**“Accelerating Physics Schemes in Numerical Weather Prediction Codes and Preserving Positivity in the Physics-Dynamics coupling,”** *University of Utah*, 2022.

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**“Scalable CPU Ray Tracing for In Situ Visualization Using OSPRay,”** In *In Situ Visualization for Computational Science*, Springer International Publishing, pp. 353--374. 2022.

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**“Assembling Portable In-Situ Workflow from Heterogeneous Components using Data Reorganization,”** In *22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid)*, pp. 41-50. 2022.

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**“A Review of Three-Dimensional Medical Image Visualization,”** In *Health Data Science*, Vol. 2022, 2022.

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**“Prediction of Femoral Head Coverage from Articulated Statistical Shape Models of Patients with Developmental Dysplasia of the Hip,”** In *Journal of Orthopaedic Research*, Wiley, 2021.

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**“Integrated Construction of Multimodal Atlases with Structural Connectomes in the Space of Riemannian Metrics,”** Subtitled **“arXiv preprint arXiv:2109.09808,”** 2021.

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**“Uintah+Hedgehog: Combining Parallelism Models for End-to-End Large-Scale Simulation Performance,”** *Scientific Computing and Imaging Institute*, 2021.

[Hou2021a] Z. Houmani, D. Balouek-Thomert, E. Caron, M. Parashar.
**“Enabling microservices management for Deep Learning applications across the Edge-Cloud Continuum,”** In *SBAC-PAD 2021 - IEEE 33rd International Symposium on Computer Architecture and High Performance Computing*, October, 2021.

[Hua2021a] X. Huang, P. Klacansky, S. Petruzza, A. Gyulassy, P.T. Bremer, V. Pascucci.
**“Distributed merge forest: a new fast and scalable approach for topological analysis at scale,”** In *Proceedings of the ACM International Conference on Supercomputing*, pp. 367-377. 2021.

[Jen2021a] M. H. Jensen, S. Joshi, S. Sommer.
**“Bridge Simulation and Metric Estimation on Lie Groups,”** Subtitled **“arXiv preprint arXiv:2106.03431,”** 2021.

[Jen2021b] M. Højgaard Jensen, L. Hilgendorf, S. Joshi, S. Sommer.
**“Bridge Simulation on Lie Groups and Homogeneous Spaces with Application to Parameter Estimation,”** Subtitled **“arXiv:2112.00866,”** 2021.

[Jia2021a] X. Jiang, J. C. Font, J. A. Bergquist, B. Zenger, W. W. Good, D. H. Brooks, R. S. MacLeod, L. Wang.
**“Deep Adaptive Electrocardiographic Imaging with Generative Forward Model for Error Reduction,”** In *Functional Imaging and Modeling of the Heart: 11th International Conference*, In *Functional Imaging and Modeling of the Heart: 11th International Conference*, Vol. 12738, Springer Nature, pp. 471. 2021.

[Joh2021a] C. R. Johnson.
**“Translational computer science at the scientific computing and imaging institute,”** In *Journal of Computational Science*, Vol. 52, pp. 101217. 2021.

ISSN: 1877-7503

DOI: https://doi.org/10.1016/j.jocs.2020.101217

[Jun2021a] A. Junn, J. Dinis, S. C. Hauc, M. K. Bruce, K. E. Park, W. Tao, C. Christensen, R. Whitaker, J. A. Goldstein, M. Alperovich.
**“Validation of Artificial Intelligence Severity Assessment in Metopic Craniosynostosis,”** In *The Cleft Palate-Craniofacial Journal*, SAGE Publications, 2021.

DOI: https://doi.org/10.1177/10.1177/10556656211061021

[Kam2021a] R. Kamali, J. Kump, E. Ghafoori, M. Lange, N. Hu, T. J. Bunch, D. J. Dosdall, R. S. Macleod, R. Ranjan.
**“Area Available for Atrial Fibrillation to Propagate Is an Important Determinant of Recurrence After Ablation,”** In *JACC: Clinical Electrophysiology*, Elsevier, 2021.

[Kes2021a] V. Keshavarzzadeh, M. Alirezaei, T. Tasdizen, R. M. Kirby.
**“Image-Based Multiresolution Topology Optimization Using Deep Disjunctive Normal Shape Model,”** In *Computer-Aided Design*, Vol. 130, Elsevier, pp. 102947. 2021.

[Kes2021b] V. Keshavarzzadeh, R. M. Kirby, A. Narayan.
**“Multilevel Designed Quadrature for Partial Differential Equations with Random Inputs,”** In *SIAM Journal on Scientific Computing*, Vol. 43, No. 2, Society for Industrial and Applied Mathematics, pp. A1412-A1440. 2021.

[Kes2021c] V. Keshavarzzadeh, R. M. Kirby, A. Narayan.
**“Robust topology optimization with low rank approximation using artificial neural networks,”** In *Computational Mechanics*, 2021.

DOI: 10.1007/s00466-021-02069-3

[Kes2021d] V. Keshavarzzadeh, S. Zhe, R.M. Kirby, A. Narayan.
**“GP-HMAT: Scalable, $O(n\log (n)) $ Gaussian Process Regression with Hierarchical Low-Rank Matrices,”** Subtitled **“arXiv preprint arXiv:2201.00888,”** 2021.

[Kir2021a] R. Kirby, K. Nottingham, R. Roy, S. Godil, B. Catanzaro.
**“Guiding Global Placement With Reinforcement Learning,”** Subtitled **“arXiv preprint arXiv:2109.02631,”** 2021.

[Kou2021a] D Kouřil, T Isenberg, B Kozlíková, M Meyer, E Gröller, I Viola.
**“HyperLabels---Browsing of Dense and Hierarchical Molecular 3D Models,”** In *IEEE transactions on visualization and computer graphics*, IEEE, 2021.

DOI: 10.1109/TVCG.2020.2975583

[Kri2021a] A.S. Krishnapriyan, A. Gholami, S. Zhe, R.M. Kirby, M.W. Mahoney.
**“Characterizing possible failure modes in physics-informed neural networks,”** Subtitled **“arXiv preprint arXiv:2109.01050,”** 2021.

[Kuh2021a] L. Kühnel, T. Fletcher, S. Joshi, S. Sommer.
**“Latent Space Geometric Statistics,”** In *Pattern Recognition. ICPR International Workshops and Challenges: Virtual Event, January 10–15, 2021, Proceedings, Part VI*, Springer International Publishing, pp. 163-178. 2021.

[Lan2021a] D. Lange, E. Polanco, R. Judson-Torres, T. Zangle, A. Lex.
**“Loon: Using Exemplars to Visualize Large Scale Microscopy Data,”** In *OSF Preprints*, 2021.

[Lan2021b] R. B. Lanfredi, M. Zhang, W. F. Auffermann, J. Chan, P. T. Duong, V. Srikumar, T. Drew, J. D. Schroeder, T. Tasdizen.
**“REFLACX, a dataset of reports and eye-tracking data for localization of abnormalities in chest x-rays,”** Subtitled **“arXiv:2109.14187,”** 2021.

[Lan2021c] R.B. Lanfredi, A. Arora, T. Drew, J.D. Schroeder, T. Tasdizen.
**“Comparing radiologists’ gaze and saliency maps generated by interpretability methods for chest x-rays,”** Subtitled **“arXiv:2112.11716v1,”** 2021.

[Lau2021a] E. Laughton, V. Zala, A. Narayan, R. M. Kirby, D. Moxey.
**“Fast Barycentric-Based Evaluation Over Spectral/hp Elements,”** Subtitled **“arXiv preprint arXiv:2103.03594,”** 2021.

[Li2021a] Z. Li, H. Menon, K. Mohror, P. T. Bremer, Y. Livant, V. Pascucci.
**“Understanding a program's resiliency through error propagation,”** In *Proceedings of the 26th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming*, ACM, pp. 362-373. 2021.

[Li2021b] S. Li, Z. Wang, A. Narayan, R. Kirby, S. Zhe.
**“Meta-Learning with Adjoint Methods,”** Subtitled **“arXiv preprint arXiv:2110.08432,”** 2021.

[Liu2021a] Z. Liu, A. Narayan.
**“On the computation of recurrence coefficients for univariate orthogonal polynomials,”** Subtitled **“arXiv preprint arXiv:2101.11963,”** 2021.

[Ly2021a] C. Ly, C. Nizinski, C. Vachet, L. McDonald, T. Tasdizen.
**“Learning to Estimate the Composition of a Mixture with Synthetic Data,”** In *Microscopy and Microanalysis*, 2021.

[Ly2021b] C. Ly, C. A. Nizinski, A. Toydemir, C. Vachet, L. W. McDonald, T. Tasdizen.
**“Determining the Composition of a Mixed Material with Synthetic Data,”** In *Microscopy and Microanalysis*, Cambridge University Press, pp. 1--11. 2021.

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[Mar2021a] N. Marshak, P. Grosset, A. Knoll, J. P. Ahrens, C. R. Johnson.
**“Evaluation of GPU Volume Rendering in PyTorch Using Data-Parallel Primitives,”** In *Eurographics Symposium on Parallel Graphics and Visualization (EGPGV)*, 2021.

[Mcd2021a] T. McDonald, R. Shrestha, X. Yi, H. Bhatia, D. Chen, D. Goswami, V. Pascucci, T. Turbyville, P‐T Bremer.
**“Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion,”** In *Computer Graphics Forum*, Vol. 40, No. 3, pp. 251-262. 2021.

[Moo2021a] R. A. Moore, A. Narayan.
**“Adaptive Density Tracking by Quadrature for Stochastic Differential Equations,”** Subtitled **“arXiv preprint arXiv:2105.08148,”** 2021.

[Mor2021a] N. Morrical, J. Tremblay, Y. Lin, S. Tyree, S. Birchfield, V. Pascucci, I. Wald.
**“NViSII: A Scriptable Tool for Photorealistic Image Generation,”** Subtitled **“arXiv preprint arXiv:2105.13962,”** 2021.

[Nar2021a] A. Narayan, L. Yan, T. Zhou.
**“Optimal design for kernel interpolation: Applications to uncertainty quantification,”** In *Journal of Computational Physics*, Vol. 430, Academic Press, pp. 110094. 2021.

[Ngu2021a] Q. C Nguyen, J. M. Keralis, P. Dwivedi, A. E. Ng, M. Javanmardi, S. Khanna, Y. Huang, K. D. Brunisholz, A. Kumar, T. Tasdizen.
**“Leveraging 31 Million Google Street View Images to Characterize Built Environments and Examine County Health Outcomes ,”** In *Public Health Reports*, Vol. 136, No. 2, SAGE Publications, pp. 201-211. 2021.

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**“Computational Image Techniques for Analyzing Lanthanide and Actinide Morphology,”** In *Rare Earth Elements and Actinides: Progress in Computational Science Applications*, Ch. 6, pp. 133-155. 2021.

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[Nob2021a] C. Nobre, D. Wootton, Z. T. Cutler, L. Harrison, H. Pfister, A. Lex.
**“reVISit: Looking Under the Hood of Interactive Visualization Studies,”** In *SIGCHI Conference on Human Factors in Computing Systems (CHI)*, ACM, pp. 1--12. 2021.

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[Nou2021a] A. Nouri, P.E. Davis, P. Subedi, M. Parashar.
**“Scalable Graph Embedding LearningOn A Single GPU,”** Subtitled **“arXiv preprint arXiv:2110.06991,”** 2021.

[Nou2021b] A. Nouri, P.E. Davis, P. Subedi, M. Parashar.
**“Exploring the Role of Machine Learning in Scientific Workflows: Opportunities and Challenges,”** Subtitled **“arXiv preprint arXiv:2110.13999,”** 2021.

[Pen2021a] M. Penwarden, S. Zhe, A. Narayan, R. M. Kirby.
**“Multifidelity Modeling for Physics-Informed Neural Networks (PINNs),”** Subtitled **“arXiv preprint arXiv:2106.13361,”** 2021.

[Pen2021b] M. Penwarden, S. Zhe, A. Narayan, R. M. Kirby.
**“Physics-Informed Neural Networks (PINNs) for Parameterized PDEs: A Metalearning Approach,”** Subtitled **“arXiv preprint arXiv:2110.13361,”** 2021.

[Pul2021a] R. Pulch, A. Narayan, T. Stykel.
**“Sensitivity analysis of random linear differential–algebraic equations using system norms,”** In *Journal of Computational and Applied Mathematics*, North-Holland, pp. 113666. 2021.

[Qia2021a] E. Qian, J.M. Tabeart, C. Beattie, S. Gugercin, J. Jiang, P. Kramer, A. Narayan.
**“Model Reduction of Linear Dynamical Systems via Balancing for Bayesian Inference,”** Subtitled **“arXiv preprint arXiv:2111.13246,”** 2021.

[Qin2021a] Y. Qin, A. Narayan, K. Cheng, P. Wang.
**“An efficient method of calculating composition-dependent inter-diffusion coefficients based on compressed sensing method,”** In *Computational Materials Science*, Vol. 188, Elsevier, pp. 110145. 2021.

[Qin2021b] Y. Qin, I. Rodero, A. Simonet, C. Meertens, D. Reiner, J. Riley, M. Parashar.
**“Leveraging user access patterns and advanced cyberinfrastructure to accelerate data delivery from shared-use scientific observatories,”** In *Future Generation Computer Systems*, North-Holland, pp. 14-27. 2021.

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**“Facilitating Data Discovery for Large-scale Science Facilities using Knowledge Networks,”** In *2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS)*, IEEE, pp. 651-660. 2021.

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[Qin2021d] Y. Qin, I. Rodero, M. Parashar.
**“Toward Democratizing Access to Facilities Data: A Framework for Intelligent Data Discovery and Delivery,”** Subtitled **“arXiv:2112.06479,”** 2021.

[Rab2021a] A.S. Rababah, L.R. Bear, Y.S. Dogrusoz, W. Good, J. Bergquist, J. Stoks, R. MacLeod, K. Rjoob, M. Jennings, J. Mclaughlin, D. D. Finlay.
**“Reducing Line-of-block Artifacts in Cardiac Activation Maps Estimated Using ECG Imaging: A Comparison of Source Models and Estimation Methods,”** In *Computers in Biology and Medicine*, Vol. 136, pp. 104666. 2021.

[Ram2021a] N. Ramesh, T. Tasdizen.
**“Detection and segmentation in microscopy images,”** In *Computer Vision for Microscopy Image Analysis*, Academic Press, pp. 43-71. 2021.

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[Ras2021a] M. Rasouli, R. M. Kirby, H. Sundar.
**“A Compressed, Divide and Conquer Algorithm for Scalable Distributed Matrix-Matrix Multiplication,”** In *The International Conference on High Performance Computing in Asia-Pacific Region*, pp. 110-119. 2021.

[Rat2021a] A. Rathore, N. Chalapathi, S. Palande, Bei Wang.
**“TopoAct: Visually Exploring the Shape of Activations in Deep Learning,”** In *Computer Graphics Forum*, Vol. 40, No. 1, pp. 382-397. 2021.

[Rau2021a] A. Rauff, L.H. Timmins, R.T. Whitaker, J.A. Weiss.
**“A Nonparametric Approach for Estimating Three-Dimensional Fiber Orientation Distribution Functions (ODFs) in Fibrous Materials,”** In *IEEE Transactions on Medical Imaging*, 2021.

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[Raz2021a] M. Razi, M. Kirby, A. Narayan.
**“Kernel optimization for Low-Rank Multi-Fidelity Algorithms,”** In *International Journal for Uncertainty Quantification*, Begel House Inc., pp. 31-54. 2021.

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**“Using Contour Trees in the Analysis and Visualization of Radio Astronomy Data Cubes,”** In *Topological Methods in Data Analysis and Visualization VI*, Springer-Verlag, pp. 87--108. 2021.

[Roy2021a] R. Roy, J. Raiman, N. Kant, I. Elkin, R. Kirby, M. Siu, S. Oberman, S. Godil, B. Catanzaro.
**“PrefixRL: Optimization of Parallel Prefix Circuits using Deep Reinforcement Learning,”** In *2021 58th ACM/IEEE Design Automation Conference (DAC)*, IEEE, pp. 853-858. 2021.

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[Sah2021a] Damodar Sahasrabudhe.
**“Enhancing Asynchronous Many-Task Runtime Systems for Next-Generation Architectures and Exascale Supercomputers,”** *School of Computing, University of Utah, Salt Lake City, UT, USA*, 2021.

[Sal2021a] J. Salinet, R. Molero, F. S. Schlindwein, J. Karel, M. Rodrigo, J. L. Rojo-Álvarez, O. Berenfeld, A. M. Climent, B. Zenger, F. Vanheusden, J. G. S. Paredes, R. MacLeod, F. Atienza, M. S. Guillem, M. Cluitmans, P. Bonizzi.
**“Electrocardiographic imaging for atrial fibrillation: a perspective from computer models and animal experiments to clinical value,”** In *Frontiers in Physiology*, Vol. 12, Frontiers Media, April, 2021.

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**“Prestin Generates Instantaneous Force in Outer Hair Cell Membranes,”** In *Biophysical Journal*, Vol. 120, No. 3, 2021.

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**“Visualization of Uncertain Multivariate Data via Feature Confidence Level-Sets,”** In *EuroVis 2021*, 2021.

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**“Scalable In Situ Computation of Lagrangian Representations via Local Flow Maps,”** In *Eurographics Symposium on Parallel Graphics and Visualization*, The Eurographics Association, 2021.

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[San2021e] S. Sane, C. R. Johnson, H. Childs.
**“Investigating In Situ Reduction via Lagrangian Representations for Cosmology and Seismology Applications,”** In *Computational Science -- ICCS 2021*, Springer International Publishing, pp. 436--450. 2021.

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[Sin2021a] A. Singh, M. Bauer, S. Joshi.
**“Physics Informed Convex Artificial Neural Networks (PICANNs) for Optimal Transport based Density Estimation,”** Subtitled **“arXiv,”** 2021.

[Sol2021a] W. T. Sołowski, M. Berzins, W. Coombs, J. Guilkey, M. Möller, Q. A. Tran, T. Adibaskoro, S. Seyedan, R. Tielen, K. Soga.
**“Material point method: Overview and challenges ahead (with videos),”** In *Advances in Applied Mechanics*, 1, Vol. 14, Ch. 2, Elsevier, pp. 113-204. 2021.

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**“Material point method: Overview and challenges ahead (without videos),”** In *Advances in Applied Mechanics*, 1, Vol. 14, Ch. 2, Elsevier, pp. 113-204. 2021.

[Sub2021a] P. Subedi, P.E .Davis, M. Parashar.
**“RISE: Reducing I/O Contention in Staging-based Extreme-Scale In-situ Workflows,”** In *2021 IEEE International Conference on Cluster Computing (CLUSTER)*, pp. 146--156. 2021.

[Suc2021a] E. Suchyta, S. Klasky, N. Podhorszki, M. Wolf, A. Adesoji, C.S. Chang, J. Choi, P. E. Davis, J. Dominski, S. Ethier, I. Foster, K. Germaschewski, B. Geveci, C. Harris, K. A. Huck, Q. Liu, J. Logan, K. Mehta, G. Merlo, S. V. Moore, T. Munson, M. Parashar, D. Pugmire, M. S. Shephard, C. W. Smith, P. Subedi, L. Wan, R. Wang, S. Zhang.
**“The Exascale Framework for High Fidelity coupled Simulations (EFFIS): Enabling whole device modeling in fusion science,”** In *The International Journal of High Performance Computing Applications*, SAGE Publications, pp. 10943420211019119. 2021.

[Sun2021a] T. Sun, D. Li, B. Wang.
**“Decentralized Federated Averaging,”** Subtitled **“arXiv preprint arXiv:2104.11375,”** 2021.

[Sun2021b] T. Sun, D. Li, B. Wang.
**“Stability and Generalization of the Decentralized Stochastic Gradient Descent,”** Subtitled **“arXiv preprint arXiv:2102.01302,”** 2021.

[Tao2021a] W. Tao, R. Bhalodia, R. Whitaker.
**“A Gaussian Process Model for Unsupervised Analysis of High Dimensional Shape Data,”** In *Machine Learning in Medical Imaging*, Springer International Publishing, pp. 356--365. 2021.

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[Tat2021a] J. D. Tate, W. W. Good, N. Zemzemi, M. Boonstra, P. van Dam, D. H. Brooks, A. Narayan, R. S. MacLeod.
**“Uncertainty Quantification of the Effects of Segmentation Variability in ECGI,”** In *Functional Imaging and Modeling of the Heart*, Springer International Publishing, pp. 515--522. 2021.

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[Tat2021b] J. Tate, S. Rampersad, C. Charlebois, Z. Liu, J. Bergquist, D. White, L. Rupp, D. Brooks, A. Narayan, R. MacLeod.
**“Uncertainty Quantification in Brain Stimulation using UncertainSCI,”** In *Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation*, Vol. 14, No. 6, Elsevier, pp. 1659-1660. 2021.

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**“Robust Certification for Laplace Learning on Geometric Graphs,”** Subtitled **“arXiv preprint arXiv:2104.10837,”** 2021.

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**“Small-molecule mimicry hunting strategy in the imperial cone snail, Conus imperialis,”** In *Science Advances*, Vol. 7, No. 11, American Association for the Advancement of Science, 2021.

[Tru2021a] N. Truong, C. Yuksel, C. Watcharopas, J. A. Levine, R. M. Kirby.
**“Particle Merging-and-Splitting,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2021.

[Ush2021a] W. Usher, X. Huang, S. Petruzza, S. Kumar, S. R. Slattery, S. T. Reeve, F. Wang, C. R. Johnson,, V. Pascucci.
**“Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts,”** In *IPDPS*, 2021.

[Ved2021a] V. Vedam-Mai, K. Deisseroth, J. Giordano, G. Lazaro-Munoz, W. Chiong, N. Suthana, J. Langevin, J. Gill, W. Goodman, N. R. Provenza, C. H. Halpern, R. S. Shivacharan, T. N. Cunningham, S. A. Sheth, N. Pouratian, K. W. Scangos, H. S. Mayberg, A. Horn, K. A. Johnson, C. R. Butson, R. Gilron, C. de Hemptinne, R. Wilt, M. Yaroshinsky, S. Little, P. Starr, G. Worrell, P. Shirvalkar, E. Chang, J. Volkmann, M. Muthuraman, S. Groppa, A. A. Kühn, L. Li, M. Johnson, K. J. Otto, R. Raike, S. Goetz, C. Wu, P. Silburn, B. Cheeran, Y. J. Pathak, M. Malekmohammadi, A. Gunduz, J. K. Wong, S. Cernera, A. W. Shukla, A. Ramirez-Zamora, W. Deeb, A. Patterson, K. D. Foote, M. S. Okun.
**“Proceedings of the Eighth Annual Deep Brain Stimulation Think Tank: Advances in Optogenetics, Ethical Issues Affecting DBS Research, Neuromodulatory Approaches for Depression, Adaptive Neurostimulation, and Emerging DBS Technologies,”** In *Frontiers in Human Neuroscience*, Vol. 15, pp. 169. 2021.

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[Ven2021a] A. Venkat, A. Gyulassy, G. Kosiba, A. Maiti, H. Reinstein, R. Gee, P.-T. Bremer, V. Pascucci.
**“Towards replacing physical testing of granular materials with a Topology-based Model,”** Subtitled **“arXiv preprint arXiv:2109.08777,”** 2021.

[Wan2021a] B. Wang, D. Zou, Q. Gu, S. J. Osher.
**“Laplacian smoothing stochastic gradient markov chain monte carlo,”** In *SIAM Journal on Scientific Computing*, Vol. 43, No. 1, SIAM, pp. A26-A53. 2021.

[Wan2021b] Z. Wang, W. Xing, R. Kirby, S. Zhe.
**“Multi-Fidelity High-Order Gaussian Processes for Physical Simulation,”** In *International Conference on Artificial Intelligence and Statistics*, PMLR, pp. 847-855. 2021.

[Wan2021c] Y. Wan, H.A. Holman, C. Hansen.
**“Interactive Analysis for Large Volume Data from Fluorescence Microscopy at Cellular Precision,”** In *Computers & Graphics*, Vol. 98, Pergamon, pp. 138-149. 2021.

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**“Facilitating Staging-based Unstructured Mesh Processing to Support Hybrid In-Situ Workflows,”** In *2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)*, pp. 960-964. 2021.

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**“An Adaptive Elasticity Policy For Staging Based In-Situ Processing,”** In *IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)*, pp. 33-41. 2021.

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**“Adaptive Placement of Data Analysis Tasks For Staging Based In-Situ Processing,”** In *2021 IEEE 28th International Conference on High Performance Computing, Data, and Analytics (HiPC)*, pp. 242-251. 2021.

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[Xin2021a] W. W. Xing, A. A. Shah, P. Wang, S. Zhe, Q. Fu, R. M. Kirby.
**“Residual Gaussian process: A tractable nonparametric Bayesian emulator for multi-fidelity simulations,”** In *Applied Mathematical Modelling*, Vol. 97, Elsevier, pp. 36-56. 2021.

[Xin2021b] W. W. Xing, R. M. Kirby, S. Zhe.
**“Deep coregionalization for the emulation of simulation-based spatial-temporal fields,”** In *Journal of Computational Physics*, Academic Press, pp. 109984. 2021.

[Xu2021a] Y. Xu, V. Keshavarzzadeh, R. M. Kirby, A. Narayan.
**“A bandit-learning approach to multifidelity approximation,”** Subtitled **“arXiv preprint arXiv:2103.15342,”** 2021.

[Xu2021b] Y. Xu, A. Narayan.
**“Randomized weakly admissible meshes,”** Subtitled **“arXiv preprint arXiv:2101.04043,”** 2021.

[Xu2021c] Y. Xu, A. Narayan.
**“Budget-limited distribution learning in multifidelity problems,”** Subtitled **“arXiv preprint arXiv:2105.04599,”** 2021.

[Zal2021a] V. Zala, R. M. Kirby, A. Narayan.
**“Structure-preserving Nonlinear Filtering for Continuous and Discontinuous Galerkin Spectral/hp Element Methods,”** Subtitled **“arXiv preprint arXiv:2106.08316,”** 2021.

[Zam2021a] R. Zambre, D. Sahasrabudhe, H. Zhou, M. Berzins, A. Chandramowlishwaran, P. Balaji.
**“Logically Parallel Communication for Fast MPI+Threads Communication,”** In *Proceedings of the Transactions on Parallel and Distributed Computing*, IEEE, April, 2021.

[Zen2021a] B. Zenger, W. W. Good, J. A. Bergquist, L. C. Rupp, M. Perez, G. J. Stoddard, V. Sharma, R. S. MacLeod.
**“Transient recovery of epicardial and torso ST-segment ischemic signals during cardiac stress tests: A possible physiological mechanism,”** In *Journal of Electrocardiology*, Churchill Livingstone, 2021.

[Zho2021a] L. Zhou, C. R. Johnson, D. Weiskopf.
**“Data-Driven Space-Filling Curves,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 27, No. 2, IEEE, pp. 1591-1600. 2021.

DOI: 10.1109/TVCG.2020.3030473

[Zho2021b] Y. Zhou, N. Chalapathi, A. Rathore, Y. Zhao, Bei Wang.
**“Mapper Interactive: A Scalable, Extendable, and Interactive Toolbox for the Visual Exploration of High-Dimensional Data.,”** In *IEEE Pacific Visualization Symposium*, 2021.

2020

[Ath2020a] T. M. Athawale, D. Maljovec, L. Yan, C. R. Johnson, V. Pascucci,, B. Wang.
**“Uncertainty Visualization of 2D Morse Complex Ensembles using Statistical Summary Maps,”** In *IEEE Transactions on Visualization and Computer Graphics*, 2020.

DOI: 10.1109/TVCG.2020.3022359

[Chi2020a] H. Childs, S. D. Ahern, J. Ahrens, A. C. Bauer, J. Bennett, E. W. Bethel, P. Bremer, E. Brugger, J. Cottam, M. Dorier, S. Dutta, J. M. Favre, T. Fogal, S. Frey, C. Garth, B. Geveci, W. F. Godoy, C. D. Hansen, C. Harrison, B. Hentschel, J. Insley, C. R. Johnson, S. Klasky, A. Knoll, J. Kress, M. Larsen, J. Lofstead, K. Ma, P. Malakar, J. Meredith, K. Moreland, P. Navratil, P. O’Leary, M. Parashar, V. Pascucci, J. Patchett, T. Peterka, S. Petruzza, N. Podhorszki, D. Pugmire, M. Rasquin, S. Rizzi, D. H. Rogers, S. Sane, F. Sauer, R. Sisneros, H. Shen, W. Usher, R. Vickery, V. Vishwanath, I. Wald, R. Wang, G. H. Weber, B. Whitlock, M. Wolf, H. Yu, S. B. Ziegeler.
**“A Terminology for In Situ Visualization and Analysis Systems,”** In *International Journal of High Performance Computing Applications*, Vol. 34, No. 6, pp. 676–691. 2020.

DOI: 10.1177/1094342020935991

[Cin2020a] L. Cinquini, S. Petruzza, Jason J. Boutte, S. Ames, G. Abdulla, V. Balaji, R. Ferraro, A. Radhakrishnan, L. Carriere, T. Maxwell, G. Scorzelli, V. Pascucci.
**“Distributed Resources for the Earth System Grid Advanced Management (DREAM), Final Report,”** 2020.

[Han2020a] M. Han, I. Wald, W. Usher, N. Morrical, A. Knoll, V. Pascucci, C.R. Johnson.
**“A virtual frame buffer abstraction for parallel rendering of large tiled display walls,”** In *2020 IEEE Visualization Conference (VIS)*, pp. 11--15. 2020.

DOI: 10.1109/VIS47514.2020.00009

[Jan2020a] A. P. Janson, D. N. Anderson, C. R. Butson.
**“Activation robustness with directional leads and multi-lead configurations in deep brain stimulation,”** In *Journal of Neural Engineering*, Vol. 17, No. 2, IOP Publishing, pp. 026012. March, 2020.

DOI: 10.1088/1741-2552/ab7b1d

[Joh2020a] C. R. Johnson, T. Kapur, W. Schroeder,, T. Yoo.
**“Remembering Bill Lorensen: The Man, the Myth, and Marching Cubes,”** In *IEEE Computer Graphics and Applications*, Vol. 40, No. 2, pp. 112-118. March, 2020.

DOI: 10.1109/MCG.2020.2971168

[Joh2020b] K. A. Johnson, G. Duffley, D. Nesterovich Anderson, J. L. Ostrem, M. Welter, J. C. Baldermann, J. Kuhn, D. Huys, V. Visser-Vandewalle, T. Foltynie, L. Zrinzo, M. Hariz, A. F. G. Leentjens, A. Y. Mogilner, M. H. Pourfar, L. Almeida, A. Gunduz, K. D. Foote, M. S. Okun, C. R. Butson.
**“Structural connectivity predicts clinical outcomes of deep brain stimulation for Tourette syndrome,”** In *Brain*, July, 2020.

ISSN: 0006-8950

DOI: 10.1093/brain/awaa188

[Kun2020a] B. Kundu, T. S. Davis, B. Philip, E. H. Smith, A. Arain, A. Peters, B. Newman, C. R. Butson, J. D. Rolston.
**“A systematic exploration of parameters affecting evoked intracranial potentials in patients with epilepsy,”** In *Brain Stimulation*, Vol. 13, No. 5, pp. 1232-1244. 2020.

[Ly2020a] C. Ly, C. Vachet, I. Schwerdt, E. Abbott, A. Brenkmann, L.W. McDonald, T. Tasdizen.
**“Determining uranium ore concentrates and their calcination products via image classification of multiple magnifications,”** In *Journal of Nuclear Materials*, 2020.

[Mar2020a] S. Zellmann, M. Aumüller, N. Marshak, I. Wald.
**“High-Quality Rendering of Glyphs Using Hardware-Accelerated Ray Tracing,”** In *Eurographics Symposium on Parallel Graphics and Visualization (EGPGV)*, The Eurographics Association, 2020.

DOI: 10.2312/pgv.20201076

[Oue2020a] T. A. J. Ouermi, R. M. Kirby, M. Berzins.
**“Numerical Testing of a New Positivity-Preserving Interpolation Algorithm,”** Subtitled **“arXiv,”** 2020.

[Pas2020a] V. Pascucci, I. Altintas, J. Fortes, I. Foster, H. Gu, S. Hariri, D. Stanzione, M. Taufer, X. Zhao.
**“Report from the NSF Workshop on Smart Cyberinfrastructure 2020,”** *NSF*, 2020.

[Pon2020a] S. P. Ponnapalli, M. W. Bradley, K. Devine, J. Bowen, S. E. Coppens, K. M. Leraas, B. A. Milash, F. Li, H. Luo, S. Qiu, K. Wu, H. Yang, C. T. Wittwer, C. A. Palmer, R. L. Jensen, J. M. Gastier-Foster, H. A. Hanson, J. S. Barnholtz-Sloan, O. Alter.
**“Retrospective clinical trial experimentally validates glioblastoma genome-wide pattern of DNA copy-number alterations predictor of survival,”** In *Applied Physics Letters (APL) Bioengineering*, Vol. 4, No. 2, May, 2020.

[Sah2020a] D. Sahasrabudhe, M. Berzins.
**“Improving Performance of the Hypre Iterative Solver for Uintah Combustion Codes on Manycore Architectures Using MPI Endpoints and Kernel Consolidation,”** In *Computational Science -- ICCS 2020, 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part I*, Springer International Publishing, pp. 175--190. 2020.

ISBN: 978-3-030-50371-0

[Sah2020b] D. Sahasrabudhe, R. Zambre, A. Chandramowlishwaran, M. Berzins.
**“Optimizing the Hypre solver for manycore and GPU architectures,”** In *Journal of Computational Science*, Springer International Publishing, pp. 101279. 2020.

ISBN: 978-3-030-50371-0

ISSN: 1877-7503

DOI: https://doi.org/10.1016/j.jocs.2020.101279

[Wan2020a] F. Wang, N. Marshak, W. Usher, C. Burstedde, A. Knoll, T. Heister, C. R. Johnson.
**“CPU Ray Tracing of Tree-Based Adaptive Mesh Refinement Data,”** In *Eurographics Conference on Visualization (EuroVis) 2020*, Vol. 39, No. 3, 2020.

[Zho2020a] L. Zhou, M. Rivinius, C. R. Johnson,, D. Weiskopf.
**“Photographic High-Dynamic-Range Scalar Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 26, No. 6, IEEE, pp. 2156-2167. 2020.

2019

[And2019a] D.N. Anderson, G. Duffley, J. Vorwerk, A.D. Dorval, C.R. Butson.
**“Anodic stimulation misunderstood: preferential activation of fiber orientations with anodic waveforms in deep brain stimulation,”** In *Journal of Neural Engineering*, Vol. 16, No. 1, IOP Publishing, pp. 016026. Jan, 2019.

DOI: 10.1088/1741-2552/aae590

[And2019b] C.J. Anderson, D.N. Anderson, S.M. Pulst, C.R. Butson, A.D. Dorval.
**“Neural Selectivity, Efficiency, and Dose Equivalence in Deep Brain Stimulation through Pulse Width Tuning and Segmented Electrodes,”** In *bioRxiv*, Cold Spring Harbor Laboratory, April, 2019.

DOI: 10.1101/613133

[And2019c] D. N. Anderson, C. Anderson, N. Lanka, R. Sharma, C. R. Butson, B. W. Baker, A. D. Dorval.
**“The μDBS: Multiresolution, Directional Deep Brain Stimulation for Improved Targeting of Small Diameter Fibers,”** In *Frontiers in Neuroscience*, Vol. 13, October, 2019.

DOI: 10.3389/fnins.2019.01152

[Aqu2019a] C. C. Aquino, G. Duffley, D. M. Hedges, J. Vorwerk, P. A. House, H. B. Ferraz, J. D. Rolston, C. R. Butson, L. E. Schrock.
**“Interleaved deep brain stimulation for dyskinesia management in Parkinson's disease,”** In *Movement Disorders*, 2019.

DOI: 10.1002/mds.27839

[Ath2019a] T. Athawale, C. R. Johnson.
**“Probabilistic Asymptotic Decider for Topological Ambiguity Resolution in Level-Set Extraction for Uncertain 2D Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 25, No. 1, IEEE, pp. 1163-1172. Jan, 2019.

DOI: 10.1109/TVCG.2018.2864505

[Ath2019b] T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson.
**“A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,”** In *Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization*, Vol. 7, No. 4, Taylor & Francis, pp. 438-449. 2019.

DOI: 10.1080/21681163.2018.1523750

[Atk2019a] P. R. Atkins, Y. Shin, P. Agrawal, S. Y. Elhabian, R. T. Whitaker, J. A. Weiss, S. K. Aoki, C. L. Peters, A. E. Anderson.
**“Which Two-dimensional Radiographic Measurements of Cam Femoroacetabular Impingement Best Describe the Three-dimensional Shape of the Proximal Femur?,”** In *Clinical Orthopaedics and Related Research*, Vol. 477, No. 1, 2019.

[Ber2019a] M. Berzins.
**“Time Integration Errors and Energy Conservation Properties of the Stormer Verlet Method Applied to MPM,”** In *Proceedings of VI International Conference on Particle-based Methods – Fundamentals and Applications*, Barcelona, Edited by E. O ̃ nate, M. Bischoff, D.R.J. Owen, P. Wriggers & T. Zohdi, *PARTICLES 2019*, pp. 555-566. October, 2019.

ISBN: 978-84-121101-1-1

[Bha2019a] R. Bhalodia, S. Y. Elhabian, L. Kavan, R. T. Whitaker.
**“A Cooperative Autoencoder for Population-Based Regularization of CNN Image Registration,”** In *Medical Image Computing and Computer Assisted Intervention – MICCAI 2019*, In *Medical Image Computing and Computer Assisted Intervention -- MICCAI 2019*, Springer International Publishing, pp. 391--400. 2019.

[Cla2019a] D. Clark, K. Johnson, C. Butson, C. Lebel, D. Gobbi, R. Ramasubbu, Z. Kiss.
**“White matter tracts activated by successful subgenual cingulate deep brain stimulation,”** In *European Neuropsychopharmacology*, Vol. 29, Elsevier, pp. S532--S533. 2019.

DOI: 10.1016/j.euroneuro.2018.11.789

[Duf2019a] G. Duffley, D. N. Anderson, J. Vorwerk, A. C. Dorval, C. R. Butson.
**“Evaluation of methodologies for computing the deep brain stimulation volume of tissue activated,”** In *Journal of Neural Engineering*, Aug, 2019.

DOI: 10.1088/1741-2552/ab3c95

[Gop2019a] Anupama Goparaju.
**“Evaluation and validation of off-the-shelf statistical shape modeling tools in clinical applications,”** *School of Computing, University of Utah*, 2019.

[Gyu2019a] A. Gyulassy, P.-T. Bremer, V. Pascucci.
**“Shared-Memory Parallel Computation of Morse-Smale Complexes with Improved Accuracy,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 25, No. 1, IEEE, pp. 1183--1192. Jan, 2019.

DOI: 10.1109/tvcg.2018.2864848

[Han2019a] M. Han, I. Wald, W. Usher, Q. Wu, F. Wang, V. Pascicci, C. D. Hansen, C. R. Johnson.
**“Ray Tracing Generalized Tube Primitives: Method and Applications,”** In *Computer Graphics Forum*, Vol. 38, No. 3, John Wiley & Sons Ltd., 2019.

[Han2019b] A. B. Hanson, R. N. Lee, C. Vachet, I. J. Schwerdt, T. Tasdizen, L. W. McDonald IV.
**“Quantifying Impurity Effects on the Surface Morphology of α-U3O8,”** In *Analytical Chemistry*, 2019.

DOI: doi:10.1021/acs.analchem.9b02013

[Hef2019a] S. T. Heffernan, N. Ly, B. J. Mower, C. Vachet, I. J. Schwerdt, T. Tasdizen, L. W. McDonald IV.
**“Identifying surface morphological characteristics to differentiate between mixtures of U3O8 synthesized from ammonium diuranate and uranyl peroxide,”** In *Radiochimica Acta*, 2019.

[Hoa2019a] D. Hoang, P. Klacansky, H. Bhatia, P.-T. Bremer, P. Lindstrom, V. Pascucci.
**“A Study of the Trade-off Between Reducing Precision and Reducing Resolution for Data Analysis and Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 25, No. 1, IEEE, pp. 1193--1203. Jan, 2019.

DOI: 10.1109/tvcg.2018.2864853

[Hol2019a] J. K. Holmen, B. Peterson, A. Humphrey, D. Sunderland, O. H. Diaz-Ibarra, J. N. Thornock, M. Berzins.
**“Portably Improving Uintah's Readiness for Exascale Systems Through the Use of Kokkos,”** *SCI Institute*, 2019.

[Hol2019b] J. K. Holmen, B. Peterson, M. Berzins.
**“An Approach for Indirectly Adopting a Performance Portability Layer in Large Legacy Codes,”** In *2nd International Workshop on Performance, Portability, and Productivity in HPC (P3HPC)*, *In conjunction with SC19*, 2019.

[Hum2019a] Alan Humphrey.
**“Scalable Asynchronous Many-Task Runtime Solutions to Globally Coupled Problems,”** *School of Computing, University of Utah*, 2019.

[Hum2019b] A. Humphrey, M. Berzins.
**“An Evaluation of An Asynchronous Task Based Dataflow Approach For Uintah,”** In *2019 IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC)*, Vol. 2, pp. 652-657. July, 2019.

ISSN: 0730-3157

DOI: 10.1109/COMPSAC.2019.10282

[Joh2019a] K. A. Johnson, P. T. Fletcher, D. Servello, A. Bona, M. Porta, J. L. Ostrem, E. Bardinet, M. Welter, A. M. Lozano, J. C. Baldermann, J. Kuhn, D. Huys, T. Foltynie, M. Hariz, E. M. Joyce, L. Zrinzo, Z. Kefalopoulou, J. Zhang, F. Meng, C. Zhang, Z. Ling, X. Xu, X. Yu, A. YJM Smeets, L. Ackermans, V. Visser-Vandewalle, A. Y. Mogilner, M. H. Pourfar, L. Almeida, A. Gunduz, W. Hu, K. D. Foote, M. S. Okun, C. R. Butson.
**“Image-based analysis and long-term clinical outcomes of deep brain stimulation for Tourette syndrome: a multisite study,”** In *Journal of Neurology, Neurosurgery & Psychiatry*, BMJ Publishing Group, 2019.

DOI: 10.1136/jnnp-2019-320379

[Lan2019a] R.B. Lanfredi, J.D. Schroeder, C. Vachet, T. Tasdizen.
**“Adversarial regression training for visualizing the progression of chronic obstructive pulmonary disease with chest x-rays,”** In *Arxiv*, In *International Conference on Medical Image Computing and Computer-Assisted Intervention*, 2019.

[Pet2019a] B. Peterson.
**“Portable and Performant GPU/Heterogeneous Asynchronous Many-task Runtime System,”** Subtitled **“Ph.D. Dissertation,”** *University of Utah, School of Computing*, Dec, 2019.

[Pra2019a] A. Prakosa, H.J. Arevalo, D. Deng, P.M. Boyle, P.P. Nikolov, H. Ashikaga, J.E. Blauer, E. Ghafoori, C.J. Park, R.C. Blake III, F.T. Han, R.S. MacLeod, H.R. Halperin, D.J. Callans, R. Ranjan, J. Chrispin, S. Nazarian,, N.A. Trayanova.
**“Personalized Virtual-heart Technology for Guiding the Ablation of Infarct-related Ventricular Tachycardia,”** In *Nature Biomedical Engineering*, Vol. 2, pp. 732–740. 2019.

DOI: doi.org/10.1038/s41551-018-0282-2

[Sah2019a] D. Sahasrabudhe, M. Berzins, J. Schmidt.
**“Node failure resiliency for Uintah without checkpointing,”** In *Concurrency and Computation: Practice and Experience*, pp. e5340. 2019.

DOI: doi:10.1002/cpe.5340

[Sah2019b] D. Sahasrabudhe, E. T. Phipps, S. Rajamanickam, M. Berzins.
**“A Portable SIMD Primitive using Kokkos for Heterogeneous Architectures,”** In *Sixth Workshop on Accelerator Programming Using Directives (WACCPD)*, 2019.

[San2019a] A. Sanderson, A. Humphrey, J. Schmidt, R. Sisneros,, M. Papka.
**“ In situ visualization of performance metrics in multiple domains,”** In *2019 IEEE/ACM International Workshop on Programming and Performance Visualization Tools (ProTools)*, IEEE, Nov, 2019.

DOI: 10.1109/protools49597.2019.00014

[Smi2019a] G. S. Smith, K. A. Mills, G. M. Pontone, W. S. Anderson, K. M. Perepezko, J. Brasic, Y. Zhou, J. Brandt, C. R. Butson, D. P. Holt, W. B. Mathews, R. F. Dannals, D. F. Wong, Z. Mari.
**“Effect of STN DBS on vesicular monoamine transporter 2 and glucose metabolism in Parkinson's disease,”** In *Parkinsonism and Related Disorders*, Elsevier, 2019.

[Tra2019a] Q. Tran, M. Berzins, W. Solowski.
**“An improved moving least squares method for the Material Point Method,”** In *Proceedings of the 2nd International Conference on the Material Point Method for Modelling Soil-Water-Structure Interaction (MPM 2019)*, 2019.

[Tra2019b] Q. A. Tran, W. Sołowski, M. Berzins, J. Guilkey.
**“A convected particle least square interpolation material point method,”** In *International Journal for Numerical Methods in Engineering*, Wiley, October, 2019.

[Ush2019a] W. Usher, I. Wald, J. Amstutz, J. Gunther, C. Brownlee, V. Pascucci.
**“Scalable Ray Tracing Using the Distributed FrameBuffer,”** In *Eurographics Conference on Visualization (EuroVis) 2019*, Vol. 38, No. 3, 2019.

[Vor2019a] J. Vorwerk, A. Brock, D.N. Anderson, J.D. Rolston, C.R. Butson.
**“A Retrospective Evaluation of Automated Optimization of Deep Brain Stimulation Settings,”** In *Brain Stimulation*, Vol. 12, No. 2, Elsevier, pp. e54--e55. March, 2019.

DOI: 10.1016/j.brs.2018.12.167

[Vor2019b] J. Vorwerk, Ü. Aydin, C.H. Wolters, C.R. Butson.
**“Influence of head tissue conductivity uncertainties on EEG dipole reconstruction,”** In *Frontiers in Neuroscience*, 2019.

DOI: 10.3389/fnins.2019.00531

[Vor2019c] J. Vorwerk, A. Brock, D.N. Anderson, J.D. Rolston, C.R. Butson.
**“A retrospective evaluation of automated optimization of deep brain stimulation parameters,”** In *Journal of Neural Engineering*, 2019.

DOI: 10.1088/1741-2552/ab35b1

[Vor2019d] J. Vorwerk, D. McCann, J. Krüger, C.R. Butson.
**“Interactive computation and visualization of deep brain stimulation effects using Duality,”** In *Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization*, Taylor & Francis, 2019.

[Wan2019a] F. Wang, I. Wald, Q. Wu, W. Usher, C. R. Johnson.
**“CPU Isosurface Ray Tracing of Adaptive Mesh Refinement Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 25, No. 1, IEEE, pp. 1142-1151. Jan, 2019.

DOI: 10.1109/TVCG.2018.2864850

[Wan2019b] F. Wang, I. Wald,, C.R. Johnson.
**“Interactive Rendering of Large-Scale Volumes on Multi-Core CPUs ,”** In *2019 IEEE 9th Symposium on Large Data Analysis and Visualization (LDAV)*, pp. 27--36. 2019.

DOI: 10.1109/LDAV48142.2019.8944267

[War2019a] A. Warner, J. Tate, B. Burton,, C.R. Johnson.
**“A High-Resolution Head and Brain Computer Model for Forward and Inverse EEG Simulation,”** In *bioRxiv*, Cold Spring Harbor Laboratory, Feb, 2019.

DOI: 10.1101/552190

[Zho2019a] L. Zhou, D. Weiskopf, C. R. Johnson.
**“Perceptually guided contrast enhancement based on viewing distance,”** In *Journal of Computer Languages*, Vol. 55, Elsevier, pp. 100911. 2019.

ISSN: 2590-1184

DOI: https://doi.org/10.1016/j.cola.2019.100911

[Zho2019b] L. Zhou, R. Netzel, D. Weiskopf,, C. R. Johnson.
**“Spectral Visualization Sharpening,”** In *ACM Symposium on Applied Perception 2019*, No. 18, Association for Computing Machinery, pp. 1--9. 2019.

DOI: https://doi.org/10.1145/3343036.3343133

2018

[Abd2018a] O. Abdullah, L. Dai, J. Tippetts, B. Zimmerman, A. Van Hoek, S. Joshi, E. Hsu.
**“High resolution and high field diffusion MRI in the visual system of primates (P3.086),”** In *Neurology*, Vol. 90, No. 15 Supplement, Wolters Kluwer Health, Inc, 2018.

ISSN: 0028-3878

[Aie2018a] K. A. Aiello, S. P. Ponnapalli, O. Alter.
**“Mathematically universal and biologically consistent astrocytoma genotype encodes for transformation and predicts survival phenotype,”** In *APL Bioengineering*, Vol. 2, No. 3, AIP Publishing, pp. 031909. September, 2018.

DOI: 10.1063/1.5037882

[And2018a] D. N. Anderson, B. Osting, J. Vorwerk, A. D Dorval, C. R Butson.
**“Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes,”** In *Journal of Neural Engineering*, Vol. 15, No. 2, pp. 026005. 2018.

[And2018b] D. N. Anderson, G. Duffley, J. Vorwerk, A. Dorval, C. R. Butson.
**“Anodic Stimulation Misunderstood: Preferential Activation of Fiber Orientations with Anodic Waveforms in Deep Brain Stimulation,”** In *Journal of Neural Engineering*, IOP Publishing, Oct, 2018.

DOI: 10.1088/1741-2552/aae590

[Ate2018a] G.A. Ateshian, J.J. Shim, S.A. Maas, J.A. Weiss.
**“Finite Element Framework for Computational Fluid Dynamics in FEBio,”** In *Journal of Biomechanical Engineering*, Vol. 140, No. 2, ASME International, pp. 021001. Jan, 2018.

DOI: 10.1115/1.4038716

[Ayy2018a] D. Ayyagari, N. Ramesh, D. Yatsenko, T. Tasdizen, C. Atria.
**“Image reconstruction using priors from deep learning,”** In *Medical Imaging 2018: Image Processing*, SPIE, March, 2018.

[Ber2018a] M. Berzins.
**“Nonlinear stability and time step selection for the MPM method,”** In *Computational Particle Mechanics*, Jan, 2018.

ISSN: 2196-4386

DOI: 10.1007/s40571-018-0182-y

[Bha2018a] H. Bhatia, A.G. Gyulassy, V. Lordi, J.E. Pask, V. Pascucci, P.T. Bremer.
**“TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems,”** In *Journal of Computational Chemistry*, Vol. 39, No. 16, Wiley, pp. 936--952. March, 2018.

DOI: 10.1002/jcc.25181

[Boc2018a] A. Bock, E. Axelsson, C. Emmart, M. Kuznetsova, C. Hansen, A. Ynnerman.
**“OpenSpace: Changing the Narrative of Public Dissemination in Astronomical Visualization from What to How,”** In *IEEE Computer Graphics and Applications*, Vol. 38, No. 3, IEEE, pp. 44--57. May, 2018.

DOI: 10.1109/mcg.2018.032421653

[Bur2018a] B.M. Burton, K.K. Aras, W.W. Good, J.D. Tate, B. Zenger, R.S. MacLeod.
**“A Framework for Image-Based Modeling of Acute Myocardial Ischemia Using Intramurally Recorded Extracellular Potentials,”** In *Annals of Biomedical Engineering*, Springer Nature, May, 2018.

DOI: 10.1007/s10439-018-2048-0

[Bur2018b] B.M. Burton, K.K. Aras, W.W. Good, J.D. Tate, B. Zenger, R.S. MacLeod.
**“Image-Based Modeling of Acute Myocardial Ischemia Using Experimentally Derived Ischemic Zone Source Representations,”** In *Journal of Electrocardiology*, Vol. 51, No. 4, Elsevier BV, pp. 725--733. July, 2018.

DOI: 10.1016/j.jelectrocard.2018.05.005

[Clu2018a] M.J.M. Cluitmans, S. Ghimire, J. Dhamala, J. Coll-Font, J.D. Tate, S. Giffard-Roisin, J. Svehlikova, O. Doessel, M.S. Guillem, D.H. Brooks, R.S. Macleod, L. Wang.
**“P1125 Noninvasive localization of premature ventricular complexes: a research-community-based approach,”** In *EP Europace*, Vol. 20, No. Supplement, Oxford University Press, March, 2018.

DOI: 10.1093/europace/euy015.611

[Clu2018b] M. Cluitmans, D. H. Brooks, R. MacLeod, O. Dössel, M. S. Guillem, P. M. van Dam, J. Svehlikova, B. He, J. Sapp, L. Wang, L. Bear.
**“Validation and Opportunities of Electrocardiographic Imaging: From Technical Achievements to Clinical Applications,”** In *Frontiers in Physiology*, Vol. 9, Frontiers Media SA, pp. 1305. 2018.

ISSN: 1664-042X

DOI: 10.3389/fphys.2018.01305

[Erd2018a] A. Erdemir, P.J. Hunter, G.A. Holzapfel, L.M. Loew, J. Middleton, C.R. Jacobs, P. Nithiarasu, R. Löhner, G. Wei, B.A. Winkelstein, V.H. Barocas, F. Guilak, J.P. Ku, J.L. Hicks, S.L. Delp, M.S. Sacks, J.A. Weiss, G.A. Ateshian, S.A. Maas, A.D. McCulloch, G.C.Y. Peng.
**“Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research,”** In *Journal of Biomechanical Engineering*, Vol. 140, No. 2, ASME International, pp. 024701. Jan, 2018.

DOI: 10.1115/1.4038768

[Foo2018a] M.D. Foote, B. Zimmerman, A. Sawant, S. Joshi.
**“Real-Time Patient-Specific Lung Radiotherapy Targeting using Deep Learning,”** In *1st Conference on Medical Imaging with Deep Learning (MIDL 2018)*, Amsterdam, The Netherlands, 2018.

[Gul2018a] S. Guler, M. Dannhauer, B. Roig-Solvas, A. Gkogkidis, R. Macleod, T. Ball, J. G. Ojemann, D. H. Brooks.
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**“Uncertainty quantification guided robust design for nanoparticles' morphology,”** In *Computer Methods in Applied Mechanics and Engineering*, Elsevier BV, pp. 578--593. July, 2018.

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**“Numerical integration in multiple dimensions with designed quadrature,”** In *CoRR*, 2018.

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**“Scalable Data Management of the Uintah Simulation Framework for Next-Generation Engineering Problems with Radiation,”** In *Supercomputing Frontiers*, Springer International Publishing, pp. 219--240. 2018.

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**“Visual Exploration of Semantic Relationships in Neural Word Embeddings,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 24, No. 1, IEEE, pp. 553--562. Jan, 2018.

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**“Neighbourhood looking glass: 360º automated characterisation of the built environment for neighbourhood effects research,”** In *Journal of Epidemiology and Community Health*, BMJ, Jan, 2018.

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**“Performance Optimization Strategies for WRF Physics Schemes Used in Weather Modeling,”** In *International Journal of Networking and Computing*, Vol. 8, No. 2, IJNC , pp. 301--327. 2018.

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**“Demonstrating GPU Code Portability and Scalability for Radiative Heat Transfer Computations,”** In *Journal of Computational Science*, Elsevier BV, June, 2018.

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**“Personalized virtual-heart technology for guiding the ablation of infarct-related ventricular tachycardia,”** In *Nature Biomedical Engineering*, Springer Nature America, Inc, September, 2018.

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**“Fast predictive models based on multi-fidelity sampling of properties in molecular dynamics simulations,”** In *Computational Materials Science*, Vol. 152, Elsevier BV, pp. 125--133. September, 2018.

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**“Outcomes of an electronic social network intervention with neuro-oncology patient family caregivers,”** In *Journal of Neuro-Oncology*, Springer Nature, pp. 1--7. May, 2018.

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**“PFEIFER: Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings,”** In *The Journal of Open Source Software*, Vol. 3, No. 21, The Open Journal, pp. 472. Jan, 2018.

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**“Research and Education in Computational Science and Engineering,”** In *SIAM Review*, Vol. 60, No. 3, SIAM, pp. 707--754. Jan, 2018.

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**“Nuclear proliferomics: A new field of study to identify signatures of nuclear materials as demonstrated on alpha-UO3,”** In *Talanta*, Vol. 186, Elsevier BV, pp. 433--444. Aug, 2018.

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**“Flexible Live‐Wire: Image Segmentation with Floating Anchors,”** In *Computer Graphics Forum*, Vol. 37, No. 2, Wiley, pp. 321-328. May, 2018.

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**“Improving the robustness of convolutional networks to appearance variability in biomedical images,”** In *2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)*, IEEE, April, 2018.

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[Tho2018a] S. Thomas, J. Silvernagel, N. Angel, E. Kholmovski, E. Ghafoori, N. Hu, J. Ashton, D.J. Dosdall, R.S. MacLeod, R. Ranjan.
**“Higher contact force during radiofrequency ablation leads to a much larger increase in edema as compared to chronic lesion size,”** In *Journal of Cardiovascular Electrophysiology*, Wiley, June, 2018.

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[Tod2018a] J.N. Todd, T.G. Maak, G.A. Ateshian, S.A. Maas, J.A. Weiss.
**“Hip chondrolabral mechanics during activities of daily living: Role of the labrum and interstitial fluid pressurization,”** In *Journal of Biomechanics*, Vol. 69, Elsevier BV, pp. 113--120. March, 2018.

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[Tu2018a] L. Tu, M. Styner, J. Vicory, S. Elhabian, R. Wang, J. Hong, B. Paniagua, J.C. Prieto, D. Yang, R. Whitaker, M. Pizer.
**“Skeletal Shape Correspondence through Entropy,”** In *IEEE Transactions on Medical Imaging*, Vol. 37, No. 1, IEEE, pp. 1--11. Jan, 2018.

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**“A virtual reality visualization tool for neuron tracing,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 24, No. 1, IEEE, pp. 994--1003. Jan, 2018.

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**“libIS: A Lightweight Library for Flexible In Transit Visualization,”** In *Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization*, ACM Press, 2018.

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**“Association Rules-Based Multivariate Analysis and Visualization of Spatiotemporal Climate Data,”** In *ISPRS International Journal of Geo-Information*, Vol. 7, No. 7, MDPI AG, pp. 266. July, 2018.

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**“Fully Automatic Left Atrium Segmentation from Late Gadolinium Enhanced Magnetic Resonance Imaging Using a Dual Fully Convolutional Neural Network,”** In *IEEE Transactions on Medical Imaging*, IEEE, pp. 1--1. 2018.

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[Yan2018a] Z. Yang, D. Sahasrabudhe, A. Humphrey, M. Berzins.
**“A Preliminary Port and Evaluation of the Uintah AMT Runtime on Sunway TaihuLight,”** In *9th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018)*, IEEE, May, 2018.

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**“Clustering With Pairwise Relationships: A Generative Approach,”** In *CoRR*, 2018.

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**“Curvilinear Mesh Adaptation Using Radial Basis Function Interpolation and Smoothing,”** In *Journal of Scientific Computing*, Springer Nature, pp. 1--22. April, 2018.

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**“Fabrication of dense anisotropic collagen scaffolds using biaxial compression,”** In *Acta Biomaterialia*, Vol. 65, Elsevier BV, pp. 76--87. Jan, 2018.

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**“Vietoris-Rips and Cech Complexes of Metric Gluings,”** In *CoRR*, 2017.

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**“Massively Parallel Simulations of Spread of Infectious Diseases over Realistic Social Networks,”** In *2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID)*, May, 2017.

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**“Shape analysis of the basioccipital bone in Pax7-deficient mice,”** In *Scientific Reports*, Vol. 7, No. 1, Springer Nature, Dec, 2017.

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[Doc2017a] J. Docampo-Sánchez, J.K. Ryan, M. Mirzargar, R.M. Kirby.
**“Multi-Dimensional Filtering: Reducing the Dimension Through Rotation Read More: https://epubs.siam.org/doi/abs/10.1137/16M1097845,”** In *SIAM Journal on Scientific Computing*, Vol. 39, No. 5, SIAM, pp. A2179--A2200. Jan, 2017.

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**“Nonparametric joint shape and feature priors for image segmentation,”** In *IEEE Transactions on Image Processing*, Vol. 26, No. 11, IEEE, pp. 5312--5323. Nov, 2017.

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**“Numerical Computation of Weil-Peterson Geodesics in the Universal Teichmueller Space,”** In *SIAM Journal on Imaging Sciences*, Vol. 10, No. 3, SIAM, pp. 1322--1345. Jan, 2017.

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**“Rank Constrained Diffeomorphic Density Motion Estimation for Respiratory Correlated Computed Tomography,”** In *Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics*, Springer International Publishing, pp. 177--185. 2017.

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**“Taggle: Scalable Visualization of Tabular Data through Aggregation,”** In *CoRR*, 2017.

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**“Characterization of Gadolinium Contrast Enhancement of Radiofrequency Ablation Lesions in Predicting Edema and Chronic Lesion Size,”** In *Circulation: Arrhythmia and Electrophysiology*, Vol. 10, No. 11, Ovid Technologies (Wolters Kluwer Health), pp. e005599. Oct, 2017.

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**“Detecting Ischemic Stress to the Myocardium Using Laplacian Eigenmaps and Changes to Conduction Velocity,”** In *Computing in Cardiology*, Vol. 44, IEEE, 2017.

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**“Using the material point method to model chemical/mechanical coupling in the deformation of a silicon anode,”** In *Modelling and Simulation in Materials Science and Engineering*, Vol. 25, No. 4, pp. 045005. 2017.

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**“Stochastic Collocation Methods via L1 Minimization Using Randomized Quadratures,”** In *SIAM Journal on Scientific Computing*, Vol. 39, No. 1, pp. A333--A359. Jan, 2017.

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**“Improving Uintah's Scalability Through the Use of Portable Kokkos-Based Data Parallel Tasks,”** In *Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact*, PEARC17, No. 27, pp. 27:1--27:8. 2017.

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**“A Generalized Sampling and Preconditioning Scheme for Sparse Approximation of Polynomial Chaos Expansions,”** In *SIAM Journal on Scientific Computing*, Vol. 39, No. 3, SIAM, pp. A1114--A1144. Jan, 2017.

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**“Offline-Enhanced Reduced Basis Method Through Adaptive Construction of the Surrogate Training Set,”** In *Journal of Scientific Computing*, Vol. 73, No. 2-3, Springer Nature, pp. 853--875. September, 2017.

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**“Reducing Network Congestion and Synchronization Overhead During Aggregation of Hierarchical Data,”** In *2017 IEEE 24th International Conference on High Performance Computing (HiPC)*, pp. 223-232. Dec, 2017.

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**“Reducing network congestion and synchronization overhead during aggregation of hierarchical data,”** In *2017 IEEE 24th International Conference on High Performance Computing (HiPC)*, IEEE, Dec, 2017.

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**“Worksheets for Guiding Novices through the Visualization Design Process,”** In *CoRR*, 2017.

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**“Hexagonal Smoothness-Increasing Accuracy-Conserving Filtering,”** In *Journal of Scientific Computing*, Vol. 73, No. 2-3, Springer Nature, pp. 1072--1093. Aug, 2017.

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[Mir2017b] M. Mirzargar, R.T. Whitaker, R.M. Kirby.
**“Exploration of Heterogeneous Data Using Robust Similarity,”** In *CoRR*, 2017.

[Nar2017a] A. Narayan, J. Jakeman, T. Zhou.
**“A Christoffel function weighted least squares algorithm for collocation approximations,”** In *Mathematics of Computation*, Vol. 86, No. 306, pp. 1913--1947. 2017.

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[Oue2017b] T.A.J. Ouermi, A. Knoll, R.M. Kirby, M. Berzins.
**“OpenMP 4 Fortran Modernization of WSM6 for KNL,”** In *Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact*, PEARC17, No. 12, ACM, pp. 12:1--12:8. 2017.

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[Oue2017c] T.A.J. Ouermi, A. Knoll, R.M. Kirby, M. Berzins.
**“Optimization Strategies for WRF Single-Moment 6-Class Microphysics Scheme (WSM6) on Intel Microarchitectures,”** In *Proceedings of the fifth international symposium on computing and networking (CANDAR 17). Awarded Best Paper *, IEEE, 2017.

[Pal2017a] S. Palande, V. Jose, B. Zielinski, J. Anderson, P.T. Fletcher, B. Wang.
**“Revisiting Abnormalities in Brain Network Architecture Underlying Autism Using Topology-Inspired Statistical Inference,”** In *Connectomics in NeuroImaging*, Springer International Publishing, pp. 98--107. 2017.

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[Pet2017a] B. Peterson, A. Humphrey, J. Schmidt, M. Berzins.
**“Addressing Global Data Dependencies in Heterogeneous Asynchronous Runtime Systems on GPUs. Awarded Best Paper,”** In *Proceedings of the Third International Workshop on Extreme Scale Programming Models and Middleware - ESPM2'17*, ACM, 2017.

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[Pet2017b] S. Petruzza, A. Venkat, A. Gyulassy, G. Scorzelli, F. Federer, A. Angelucci, V. Pascucci, P. T. Bremer.
**“ISAVS: Interactive Scalable Analysis and Visualization System,”** In *ACM SIGGRAPH Asia 2017 Symposium on Visualization*, ACM Press, 2017.

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[Rau2017a] M. Rautenhaus, M. Böttinger, S. Siemen, R. Hoffman, R.M. Kirby, M. Mirzargar, N. Rober, R. Westermann.
**“Visualization in Meteorology---A Survey of Techniques and Tools for Data Analysis Tasks,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, pp. 1--1. 2017.

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[Ses2017a] P. Seshadri, A. Narayan, S. Mahadevan.
**“Effectively Subsampled Quadratures for Least Squares Polynomial Approximations,”** In *SIAM/ASA Journal on Uncertainty Quantification*, pp. 1003--1023. Jan, 2017.

[Sod2017a] T. Sodergren, J. Hair, J.M. Phillips, B. Wang.
**“Visualizing Sensor Network Coverage with Location Uncertainty,”** In *CoRR*, Vol. abs/1710.06925, 2017.

[Suh2017a] A. Suh, M. Hajij, B. Wang, C. Scheidegger, P. Rosen.
**“Driving Interactive Graph Exploration Using 0-Dimensional Persistent Homology Features,”** In *CoRR*, 2017.

[Tat2017a] J. Tate, K. Gillette, B. Burton, W. Good, J. Coll-Font, D. Brooks, R. MacLeod.
**“Analyzing Source Sampling to Reduce Error in ECG Forward Simulations,”** In *Computing in Cardiology*, Vol. 44, 2017.

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**“Pedunculopontine nucleus deep brain stimulation in Parkinson's disease: A clinical review,”** In *Movement Disorders*, Vol. 33, No. 1, pp. 10--20. 2017.

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[Ush2017b] W. Usher, J. Amstutz, C. Brownlee, A. Knoll, I. Wald .
**“Progressive CPU Volume Rendering with Sample Accumulation,”** In *Eurographics Symposium on Parallel Graphics and Visualization*, Edited by Alexandru Telea and Janine Bennett, The Eurographics Association, 2017.

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[Ush2017c] W. Usher, P. Klacansky, F. Federer, P. T. Bremer, A. Knoll, J. Yarch, A. Angelucci, V. Pascucci.
**“A Virtual Reality Visualization Tool for Neuron Tracing,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, 2017.

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[Var2017a] A. Vardhan, J. Fishbaugh, C. Vachet, G. Gerig.
**“Longitudinal Modeling of Multi-modal Image Contrast Reveals Patterns of Early Brain Growth,”** In *Medical Image Computing and Computer Assisted Intervention - MICCAI 2017*, Springer International Publishing, pp. 75--83. 2017.

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[Wal2017a] I. Wald, C. Brownlee, W. Usher, A. Knoll.
**“CPU Volume Rendering of Adaptive Mesh Refinement Data,”** In *ACM SIGGRAPH Asia 2017 Symposium on Visualization*, ACM Press, 2017.

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[Wan2017d] Y. Wan, C. Hansen.
**“Uncertainty Footprint: Visualization of Nonuniform Behavior of Iterative Algorithms Applied to 4D Cell Tracking,”** In *Computer Graphics Forum*, Wiley, 2017.

[Wan2017e] Y. Wan, H. Otsuna, H. A. Holman, B. Bagley, M. Ito, A. K. Lewis, M. Colasanto, G. Kardon, K. Ito, C. Hansen.
**“FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis,”** In *BMC Bioinformatics*, Vol. 18, No. 1, Springer Nature, May, 2017.

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[Wol2017a] J. J. Wolff, M. R. Swanson, J. T. Elison, G. Gerig, J. R. Pruett, M. A. Styner, C. Vachet, K. N. Botteron, S. R. Dager, A. M. Estes, H. C. Hazlett, R. T. Schultz, M. D. Shen, L. Zwaigenbaum, J. Piven.
**“Neural circuitry at age 6~months associated with later repetitive behavior and sensory responsiveness in autism,”** In *Molecular Autism*, Vol. 8, No. 1, Springer Nature, March, 2017.

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**“Sequential data assimilation with multiple nonlinear models and applications to subsurface flow,”** In *Journal of Computational Physics*, Vol. 346, pp. 356--368. Oct, 2017.

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2016

[Ara2016a] K. Aras B. Burton, D. Swenson, R.S. MacLeod.
**“Spatial organization of acute myocardial ischemia,”** In *Journal of Electrocardiology*, Vol. 49, No. 3, Elsevier, pp. 323–336. May, 2016.

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**“Quantitative comparison of cortical bone thickness using correspondence-based shape modeling in patients with cam femoroacetabular impingement,”** In *Journal of Orthopaedic Research*, Wiley-Blackwell, Nov, 2016.

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**“Robust modulation of arousal regulation, performance, and frontostriatal activity through central thalamic deep brain stimulation in healthy nonhuman primates,”** In *Journal of Neurophysiology*, Vol. 116, No. 5, American Physiological Society, pp. 2383--2404. Aug, 2016.

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[Bar2016a] M. Barjatia, T. Tasdizen, B. Song, K.M. Golden.
**“Network modeling of Arctic melt ponds,”** In *Cold Regions Science and Technology*, Vol. 124, Elsevier BV, pp. 40--53. April, 2016.

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**“Packing Configurations of PBX-9501 Cylinders to Reduce the Probability of a Deflagration to Detonation Transition (DDT),”** In *Propellants, Explosives, Pyrotechnics*, 2016.

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**“Resonant Laboratory and Candela: Spreading Your Visualization Ideas to the Masses,”** In *Proceedings of Workshop on Visualization in Practice (VIP '16)*, Note: *Best Paper Award *, 2016.

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**“Proceedings of the Fourth Annual Deep Brain Stimulation Think Tank: A Review of Emerging Issues and Technologies,”** In *Frontiers in Integrative Neuroscience*, Vol. 10, pp. 38. 2016.

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**“Disjunctive Normal Unsupervised LDA for P300-based Brain-Computer Interfaces,”** In *2016 24th Signal Processing and Communication Application Conference (SIU)*, IEEE, May, 2016.

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**“MCMC Shape Sampling for Image Segmentation with Nonparametric Shape Priors,”** In *2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)*, IEEE, June, 2016.

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**“Nonparametric joint shape and feature priors for segmentation of dendritic spines,”** In *2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2016.

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**“Extensions to a manifold learning framework for time-series analysis on dynamic manifolds in bioelectric signals,”** In *Physical Review E*, Vol. 93, No. 4, American Physical Society, apr, 2016.

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**“The role of blood vessels in high-resolution volume conductor head modeling of EEG,”** In *NeuroImage*, Vol. 128, Elsevier, pp. 193--208. March, 2016.

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**“Alternating Current Stimulation for Vision Restoration after Optic Nerve Damage: A Randomized Clinical Trial,”** In *PLOS ONE*, Vol. 11, No. 6, Public Library of Science, pp. e0156134. June, 2016.

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**“Dendritic Spine Shape Analysis: A Clustering Perspective,”** In *Lecture Notes in Computer Science*, Springer International Publishing, pp. 256--273. 2016.

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**“On comparison of manifold learning techniques for dendritic spine classification,”** In *2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2016.

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**“Dendritic spine shape analysis using disjunctive normal shape models,”** In *2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2016.

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[Gra2016a] Samuel Gratzl, Alexander Lex, Nils Gehlenborg, Nicola Cosgrove, Marc Streit .
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**“Improving accuracy in the MPM method using a null space filter,”** In *Computational Particle Mechanics*, pp. 1--12. 2016.

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[Gro2016a] A.V. P. Grosset, A. Knoll, C.D. Hansen.
**“Dynamically Scheduled Region-Based Image Compositing,”** In *Eurographics Symposium on Parallel Graphics and Visualization*, June, 2016.

[Gro2016b] A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen.
**“TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism and GPUs,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE, pp. 1--1. 2016.

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**“Optimization of focality and direction in dense electrode array transcranial direct currentstimulation (tDCS),”** In *Journal of Neural Engineering*, Vol. 13, No. 3, IOP Publishing, pp. 036020. May, 2016.

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[Hol2016a] B. Hollister, G. Duffley, C. Butson,, C.R. Johnson.
**“Visualization for Understanding Uncertainty in Activation Volumes for Deep Brain Stimulation,”** In *Eurographics Conference on Visualization*, Edited by K.L. Ma G. Santucci, and J. van Wijk, 2016.

[Hum2016a] A. Humphrey, D. Sunderland, T. Harman, M. Berzins.
**“Radiative Heat Transfer Calculation on 16384 GPUs Using a Reverse Monte Carlo Ray Tracing Approach with Adaptive Mesh Refinement,”** In *2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)*, pp. 1222-1231. May, 2016.

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[Iye2016a] S.K. Iyer, T. Tasdizen, D. Likhite, E.V.R. DiBella.
**“Split Bregman multicoil accelerated reconstruction technique: A new framework for rapid reconstruction of cardiac perfusion MRI,”** In *Medical Physics*, Vol. 43, No. 4, Wiley-Blackwell, pp. 1969--1981. March, 2016.

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**“Compressed sending for rapid late gadolinium enhanced imaging of the left atrium: A preliminary study, Magnetic Resonance Imaging,”** In *Magnetic Resonance Imaging*, Vol. 34, No. 7, Elsevier BV, pp. 846--854. September, 2016.

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**“Development of Cortical Shape in the Human Brain from 6 to 24 Months of Age via a Novel Measure of Shape Complexity,”** In *NeuroImage*, Vol. 135, Elsevier, pp. 163--176. July, 2016.

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[Lar2016a] M. Larsen, K. Moreland, C.R. Johnson,, H. Childs.
**“Optimizing Multi-Image Sort-Last Parallel Rendering,”** In *Symposium on Large Data Analysis and Visualization*, IEEE, 2016.

[Liu2016a] T. Liu, S.M. Seyedhosseini, T. Tasdizen.
**“Image Segmentation Using Hierarchical Merge Tree,”** In *IEEE Transactions on Image Processing*, Vol. 25, No. 10, IEEE, pp. 4596--4607. Oct, 2016.

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[Liu2016b] T. Liu, M. Zhang, M. Javanmardi , N. Ramesh, T. Tasdizen.
**“SSHMT: Semi-supervised Hierarchical Merge Tree for Electron Microscopy Image Segmentation,”** In *Lecture Notes in Computer Science*, Vol. 9905, Springer International Publishing, pp. 144--159. 2016.

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[Lju2016a] P. Ljung, J. Krüger, E. Gröller, M. Hadwiger, C. D. Hansen,, A. Ynnerman.
**“State of the Art in Transfer Functions for Direct Volume Rendering,”** In *Computer Graphics Forum*, Vol. 35, No. 3, Wiley-Blackwell, pp. 669--691. June, 2016.

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[Mal2016a] D. Maljovec, S. Liu, Bei Wang, V. Pascucci, P. T. Bremer, D. Mandelli, C. Smith..
**“Analyzing Simulation-Based PRA Data Through Traditional and Topological Clustering: A BWR Station Blackout Case Study,”** In *Reliability Engineering & System Safety*, Vol. 145, Elsevier, pp. 262--276. January, 2016.

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[Mes2016a] F. Mesadi, M. Cetin, T. Tasdizen.
**“Disjunctive normal level set: An efficient parametric implicit method,”** In *2016 IEEE International Conference on Image Processing (ICIP)*, IEEE, September, 2016.

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**“VTK-m: Accelerating the Visualization Toolkit for Massively Threaded Architectures,”** In *IEEE Computer Graphics and Applications*, Vol. 36, No. 3, pp. 48--58. May, 2016.

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[Mur2016a] P. Muralidharan, J. Fishbaugh, E. Y. Kim, H. J. Johnson, J. S. Paulsen, G. Gerig, P. T. Fletcher.
**“Bayesian Covariate Selection in Mixed Effects Models for Longitudinal Shape Analysis,”** In *International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2016.

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[Par2016a] C. Partl, S. Gratzl, M. Streit, A. Wassermann, H. Pfister, D. Schmalstieg, A. Lex.
**“Pathfinder: Visual Analysis of Paths in Graphs,”** In *Computer Graphics Forum (EuroVis '16)*, Vol. 35, No. 3, pp. 71-80. jun, 2016.

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[Pat2016a] Y. Pathak, O. Salami, S. Baillet, Z. Li, C.R. Butson.
**“Longitudinal Changes in Depressive Circuitry in Response to Neuromodulation Therapy,”** In *Frontiers in Neural Circuits*, Vol. 10, rontiers Media SA, July, 2016.

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[Pol2016a] I.A. Polejaeva, R. Ranjan, C.J. Davies, M. Regouski, J. Hall, A.L. Olsen, Q. Meng, H.M. Rutigliano, D.J. Dosdall, N.A. Angel, F.B. Sachse, T. Seidel, A.J. Thomas, R. Stott, K.E. Panter, P.M. Lee, A.J. Van Wettere, J.R. Stevens, Z. Wang, R.S. Macleod, N.F. Marrouche, K.L. White.
**“Increased Susceptibility to Atrial Fibrillation Secondary to Atrial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-β1,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 27, No. 10, Wiley-Blackwell, pp. 1220--1229. Aug, 2016.

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[Raj2016a] M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston.
**“Evaluating Shape Alignment via Ensemble Visualization,”** In *IEEE Computer Graphics and Applications*, Vol. 36, No. 3, IEEE, pp. 60--71. May, 2016.

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[Rod2016a] I. Rodero, M. Parashar, A.G. Landge, S. Kumar, V. Pascucci,, P.T. Bremer.
**“Evaluation of in-situ analysis strategies at scale for power efficiency and scalability,”** In *Cluster, Cloud and Grid Computing (CCGrid), 2016 16th IEEE/ACM International Symposium on*, IEEE, pp. 156--164. 2016.

[Ros2016a] P. Rosen, B. Burton, K. Potter, C.R. Johnson.
**“muView: A Visual Analysis System for Exploring Uncertainty in Myocardial Ischemia Simulations,”** In *Visualization in Medicine and Life Sciences III*, Springer Nature, pp. 49--69. 2016.

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[Rud2016a] U. Rüde, K. Willcox, L. C. McInnes, H. De Sterck, G. Biros, H. Bungartz, J. Corones, E. Cramer, J. Crowley, O. Ghattas, M. Gunzburger, M. Hanke, R. Harrison, M. Heroux, J. Hesthaven, P. Jimack, C. Johnson, K. E. Jordan, D. E. Keyes, R. Krause, V. Kumar, S. Mayer, J. Meza, K. M. Mørken, J. T. Oden, L. Petzold, P. Raghavan, S. M. Shontz, A. Trefethen, P. Turner, V. Voevodin, B. Wohlmuth, C. S. Woodward.
**“Research and Education in Computational Science and Engineering,”** Subtitled **“Report from a workshop sponsored by the Society for Industrial and Applied Mathematics (SIAM) and the European Exascale Software Initiative (EESI-2),”** Aug, 2016.

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**“Disjunctive Normal Networks,”** In *Neurocomputing*, Vol. 218, Elsevier BV, pp. 276--285. Dec, 2016.

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**“Regularization With Stochastic Transformations and Perturbations for Deep Semi-Supervised Learning,”** In *CoRR*, Vol. abs/1606.04586, 2016.

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**“Special Section on Two Themes: CSE Software and Big Data in CSE,”** In *SIAM J. Sci. Comput*, Vol. 38, No. 5, SIAM, pp. S1--S2. 2016.

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**“An Overview of Performance Portability in the Uintah Runtime System Through the Use of Kokkos,”** In *Proceedings of the Second Internationsl Workshop on Extreme Scale Programming Models and Middleware*, Salt Lake City, Utah, ESPM2, IEEE Press, Piscataway, NJ, USA pp. 44--47. 2016.

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[Sun2016c] D. Sunderland, B. Peterson, J. Schmidt, A. Humphrey, J. Thornock, M. Berzins.
**“An Overview of Performance Portability in the Uintah Runtime System through the Use of Kokkos,”** In *2016 Second International Workshop on Extreme Scale Programming Models and Middlewar (ESPM2)*, IEEE, Nov, 2016.

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[Ton2016a] X. Tong, J. Edwards, C. Chen, H. Shen, C. R. Johnson, P. Wong.
**“View-Dependent Streamline Deformation and Exploration,”** In *Transactions on Visualization and Computer Graphics*, Vol. 22, No. 7, IEEE, pp. 1788--1801. July, 2016.

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[Ush2016b] W. Usher, I. Wald, A. Knoll, M. Papka, V. Pascucci.
**“In Situ Exploration of Particle Simulations with CPU Ray Tracing,”** In *Supercomputing Frontiers and Innovations*, Vol. 3, No. 4, 2016.

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**“Kernel Partial Least Squares Regression for Relating Functional Brain Network Topology to Clinical Measures of Behavior,”** In *2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2016.

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2015

[Ara2015a] K.K. Aras, W. Good, J. Tate, B.M. Burton, D.H. Brooks, J. Coll-Font, O. Doessel, W. Schulze, D. Patyogaylo, L. Wang, P. Van Dam,, R.S. MacLeod.
**“Experimental Data and Geometric Analysis Repository: EDGAR,”** In *Journal of Electrocardiology*, 2015.

[Bar2015a] I. Arganda-Carreras, S.C. Turaga, D.R. Berger, D. Ciresan, A. Giusti, L.M. Gambardella, J. Schmidhuber, D. Laptev, S. Dwivedi, J. Buhmann, T. Liu, M. Seyedhosseini, T. Tasdizen, L. Kamentsky, R. Burget, V. Uher, X. Tan, C. Sun, T.D. Pham, E. Bas, M.G. Uzunbas, A. Cardona, J. Schindelin, H.S. Seung.
**“Crowdsourcing the creation of image segmentation algorithms for connectomics,”** In *Frontiers in Neuroanatomy*, Vol. 9, Frontiers Media SA, Nov, 2015.

DOI: 10.3389/fnana.2015.00142

[Ben2015a] J. Bennett, F. Vivodtzev, V. Pascucci (Eds.).
**“Topological and Statistical Methods for Complex Data,”** Subtitled **“Tackling Large-Scale, High-Dimensional, and Multivariate Data Spaces,”** Mathematics and Visualization, Springer Berlin Heidelberg, 2015.

ISBN: 978-3-662-44899-1

[Ben2015b] J. Bennett, R. Clay, G. Baker, M. Gamell, D. Hollman, S. Knight, H. Kolla, G. Sjaardema, N. Slattengren, K. Teranishi, J. Wilke, M. Bettencourt, S. Bova, K. Franko, P. Lin, R. Grant, S. Hammond, S. Olivier.
**“ASC ATDM Level 2 Milestone #5325,”** Subtitled **“Asynchronous Many-Task Runtime System Analysis and Assessment for Next Generation Platforms,”** Note: *Sandia Report*, 2015.

[Ben2015c] J. Bennett, R. Clay, G. Baker, M. Gamell, D. Hollman, S. Knight, H. Kolla, G. Sjaardema, N. Slattengren, K. Teranishi, J. Wilke, M. Bettencourt, S. Bova, K. Franko, P. Lin, R. Grant, S. Hammond, S. Olivier, L. Kale, N. Jain, E. Mikida, A. Aiken, M. Bauer, W. Lee, E. Slaughter, S. Treichler, M. Berzins, T. Harman, A. Humphrey, J. Schmidt, D. Sunderland, P. McCormick, S. Gutierrez, M. Schulz, A. Bhatele, D. Boehme, P. Bremer, T. Gamblin.
**“ASC ATDM level 2 milestone #5325: Asynchronous many-task runtime system analysis and assessment for next generation platforms,”** *Sandia National Laboratories*, 2015.

[Bha2015a] H. Bhatia, Bei Wang, G. Norgard, V. Pascucci, P. T. Bremer.
**“Local, Smooth, and Consistent Jacobi Set Simplification,”** In *Computational Geometry*, Vol. 48, No. 4, Elsevier, pp. 311-332. May, 2015.

DOI: 10.1016/j.comgeo.2014.10.009

[Bre2015a] P. T. Bremer, D. Maljovec, A. Saha, Bei Wang, J. Gaffney, B. K. Spears, V. Pascucci.
**“ND2AV: N-Dimensional Data Analysis and Visualization -- Analysis for the National Ignition Campaign,”** In *Computing and Visualization in Science*, 2015.

[Bre2015b] T. Bregman, R. Reznikov, M. Diwan, R. Raymond, C. R.Butson, J. N.Nobrega, C. Hamani.
**“Antidepressant-like Effects of Medial Forebrain Bundle Deep Brain Stimulation in Rats are not Associated With Accumbens Dopamine Release,”** In *Brain Stimulation*, Vol. 8, No. 4, pp. 708--713. 2015.

[But2015a] C. R. Butson, C. C. McIntyre.
**“The use of stimulation field models for deep brain stimulation programming,”** In *Brain Stimulation*, Vol. 8, No. 5, Elsevier BV, pp. 976--978. September, 2015.

DOI: 10.1016/j.brs.2015.06.005

[Car2015a] H. Carr, Z. Geng, J. Tierny, A. Chattophadhyay,, A. Knoll.
**“Fiber Surfaces: Generalizing Isosurfaces to Bivariate Data,”** In *Computer Graphics Forum*, Vol. 34, No. 3, pp. 241-250. 2015.

[CIBCData] CIBC.
Note: *Data Sets: NCRR Center for Integrative Biomedical Computing (CIBC) data set archive. Download from: http://www.sci.utah.edu/cibc/software.html*, 2015.

[Cleaver] CIBC.
Note: *Cleaver: A MultiMaterial Tetrahedral Meshing Library and Application. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/cibc/software.html*, 2015.

[Con2015a] C.C. Conlin, J.L. Zhang, F. Rousset, C. Vachet, Y. Zhao, K.A. Morton, K. Carlston, G. Gerig, V.S. Lee.
**“Performance of an Efficient Image-registration Algorithm in Processing MR Renography Data,”** In *J Magnetic Resonance Imaging*, July, 2015.

DOI: 10.1002/jmri.25000

[Dur2015a] S. Durrleman, T.P. Fletcher, G. Gerig, M. Niethammer, X. Pennec (Eds.).
**“Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data,”** In *Proceedings of the Third International Workshop, STIA 2014*, Image Processing, Computer Vision, Pattern Recognition, and Graphics, Vol. 8682, *Springer LNCS*, 2015.

ISBN: 978-3-319-14905-9

[Edw2015a] J. Edwards, S. Kumar, V. Pascucci.
**“Big data from scientific simulations,”** In *Big Data and High Performance Computing*, Vol. 26, IOS Press, pp. 32. 2015.

[Edw2015b] J. Edwards, E. Daniel, V. Pascucci, C. Bajaj.
**“Approximating the Generalized Voronoi Diagram of Closely Spaced Objects,”** In *Computer Graphics Forum*, Vol. 34, No. 2, Wiley-Blackwell, pp. 299-309. May, 2015.

DOI: 10.1111/cgf.12561

[Erd2015a] E. Erdil, A.O. Argunsah, T. Tasdizen, D. Unay, M. Cetin.
**“A joint classification and segmentation approach for dendritic spine segmentation in 2-photon microscopy images,”** In *2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2015.

DOI: 10.1109/isbi.2015.7163992

[Eti2015b] T. Etiene, R.M. Kirby, C. Silva.
**“An Introduction to Verification of Visualization Techniques,”** Morgan & Claypool Publishers, 2015.

[FluoRender] SCI Institute.
Note: *FluoRender: An interactive rendering tool for confocal microscopy data visualization. Scientific Computing and Imaging Institute (SCI) Download from: http://www.fluorender.org*, 2015.

[Fusion] Note: *FusionView: Problem Solving Environment for MHD Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org*, 2015.

[Gao2015a] Y. Gao, L. Zhu, J. Cates, R. S. MacLeod, S. Bouix,, A. Tannenbaum.
**“A Kalman Filtering Perspective for Multiatlas Segmentation,”** In *SIAM J. Imaging Sciences*, Vol. 8, No. 2, pp. 1007-1029. 2015.

DOI: 10.1137/130933423

[Gha2015a] M.U. Ghani, S.D. Kanik, A.O. Argunsah, T. Tasdizen, D. Unay, M. Cetin.
**“Dendritic spine shape classification from two-photon microscopy images,”** In *2015 23nd Signal Processing and Communications Applications Conference (SIU)*, IEEE, May, 2015.

DOI: 10.1109/siu.2015.7129985

[Gil2015a] K. Gillette, J.D. Tate, B. Kindall, P. Van Dam, E. Kholmovski, R.S. MacLeod.
**“Generation of Combined-Modality Tetrahedral Meshes,”** In *Computing in Cardiology*, 2015.

[Goo2015a] B. D. Goodwin, C. R. Butson.
**“Subject-Specific Multiscale Modeling to Investigate Effects of Transcranial Magnetic Stimulation,”** In *Neuromodulation: Technology at the Neural Interface*, Vol. 18, No. 8, Wiley-Blackwell, pp. 694--704. May, 2015.

DOI: 10.1111/ner.12296

[Gri2015a] C. Gritton, M. Berzins, R. M. Kirby.
**“Improving Accuracy In Particle Methods Using Null Spaces and Filters,”** In *Proceedings of the IV International Conference on Particle-Based Methods - Fundamentals and Applications*, Barcelona, Spain, Edited by E. Onate and M. Bischoff and D.R.J. Owen and P. Wriggers and T. Zohdi, CIMNE, pp. 202-213. September, 2015.

ISBN: 978-84-944244-7-2

[Gro2015a] A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen.
**“TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism,”** In *Eurographics Symposium on Parallel Graphics and Visualization (2015)*, Edited by C. Dachsbacher, P. Navrátil, 2015.

[Gun2015a] A. Gunduz, H. Morita, P. J. Rossi, W. L. Allen, R. L. Alterman, H. Bronte-Stewart, C. R. Butson, D. Charles, S. Deckers, C. de Hemptinne, M. DeLong, D. Dougherty, J. Ellrich, K. D. Foote, J. Giordano, W. Goodman, B. D. Greenberg, D. Greene, R. Gross, J. W. Judy, E. Karst, A. Kent, B. Kopell, A. Lang, A. Lozano, C. Lungu, K. E. Lyons, A. Machado, H. Martens, C. McIntyre, H. Min, J. Neimat, J. Ostrem, S. Pannu, F. Ponce, N. Pouratian, D. Reymers, L. Schrock, S. Sheth, L. Shih, S. Stanslaski, G. K. Steinke, P. Stypulkowski, A. I. Tröster, L. Verhagen, H. Walker, M. S. Okun.
**“Proceedings of the Second Annual Deep Brain Stimulation Think Tank: What's in the Pipeline,”** In *International Journal of Neuroscience*, Vol. 125, No. 7, Taylor & Francis, pp. 475-485. 2015.

DOI: 10.3109/00207454.2014.999268

PubMed ID: 25526555

[Gyu2015a] A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, P. T. Bremer, M. E. Papka, L. A. Curtiss, V. Pascucci.
**“Morse-Smale Analysis of Ion Diffusion for DFT Battery Materials Simulations,”** In *Topology-Based Methods in Visualization (TopoInVis)*, 2015.

[Gyu2015b] A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, PT. Bremer, M.l E. Papka, L. A. Curtiss, V. Pascucci.
**“Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials,”** In *Proceedings IEEE Visualization Conference*, 2015.

[Hol2015a] J. K. Holmen, A. Humphrey, M. Berzins.
**“Exploring Use of the Reserved Core,”** In *High Performance Parallelism Pearls*, Edited by J. Reinders and J. Jeffers, Elsevier, pp. 229-242. 2015.

DOI: 10.1016/b978-0-12-803819-2.00010-0

[Hum2015a] A. Humphrey, T. Harman, M. Berzins, P. Smith.
**“A Scalable Algorithm for Radiative Heat Transfer Using Reverse Monte Carlo Ray Tracing,”** In *High Performance Computing*, Lecture Notes in Computer Science, Vol. 9137, Edited by Kunkel, Julian M. and Ludwig, Thomas, Springer International Publishing, pp. 212-230. 2015.

ISBN: 978-3-319-20118-4

DOI: 10.1007/978-3-319-20119-1_16

[ImageVis3D] CIBC.
Note: *ImageVis3D: An interactive visualization software system for large-scale volume data. Scientific Computing and Imaging Institute (SCI), Download from: http://www.imagevis3d.org*, 2015.

[Joh2015a] C.R. Johnson, K. Potter.
**“Visualization,”** In *The Princeton Companion to Applied Mathematics*, Edited by Nicholas J. Higham, Princeton University Press, pp. 843-846. September, 2015.

ISBN: 9780691150390

[Joh2015b] H. De Sterck, C.R. Johnson.
**“Data Science: What Is It and How Is It Taught?,”** In *SIAM News*, SIAM, July, 2015.

[Joh2015c] C.R. Johnson.
**“Computational Methods and Software for Bioelectric Field Problems,”** In *Biomedical Engineering Handbook*, 4, Vol. 1, Ch. 43, Edited by J.D. Bronzino and D.R. Peterson, CRC Press, pp. 1--28. 2015.

[Joh2015d] C.R. Johnson.
**“Visualization,”** In *Encyclopedia of Applied and Computational Mathematics*, Edited by Björn Engquist, Springer, pp. 1537-1546. 2015.

ISBN: 978-3-540-70528-4

DOI: 10.1007/978-3-540-70529-1_368

[Jon2015a] C. Jones, T. Liu, N.W. Cohan, M. Ellisman, T. Tasdizen.
**“Efficient semi-automatic 3D segmentation for neuron tracing in electron microscopy images,”** In *Journal of Neuroscience Methods*, Vol. 246, Elsevier BV, pp. 13--21. May, 2015.

DOI: 10.1016/j.jneumeth.2015.03.005

[Kim2015a] M. Kim, C.D. Hansen.
**“Surface Flow Visualization using the Closest Point Embedding,”** In *2015 IEEE Pacific Visualization Symposium*, April, 2015.

[Kim2015b] M. Kim, C.D. Hansen.
**“GPU Surface Extraction with the Closest Point Embedding,”** In *Proceedings of IS&T/SPIE Visualization and Data Analysis, 2015*, February, 2015.

[Kir2015c] R.M. Kirby, M. Berzins, J.S. Hesthaven (Editors).
**“Spectral and High Order Methods for Partial Differential Equations,”** Subtitled **“Selected Papers from the ICOSAHOM'14 Conference, June 23-27, 2014, Salt Lake City, UT, USA.,”** In *Lecture Notes in Computational Science and Engineering*, Springer, 2015.

[Lil2015a] O. A. von Lilienfeld, R. Ramakrishanan, M., A. Knoll.
**“Fourier Series of Atomic Radial Distribution Functions: A Molecular Fingerprint for Machine Learning Models of Quantum Chemical Properties,”** In *International Journal of Quantum Chemistry*, Wiley Online Library, 2015.

[Liu2015a] S. Liu, D. Maljovec, Bei Wang, P. T. Bremer, V. Pascucci.
**“Visualizing High-Dimensional Data: Advances in the Past Decade,”** In *State of The Art Report*, *Eurographics Conference on Visualization (EuroVis)*, 2015.

[Liu2015b] S. Liu, Bei Wang, J. J. Thiagarajan, P. T. Bremer, V. Pascucci.
**“Visual Exploration of High-Dimensional Data through Subspace Analysis and Dynamic Projections,”** In *Computer Graphics Forum*, Vol. 34, No. 3, Wiley-Blackwell, pp. 271--280. June, 2015.

DOI: 10.1111/cgf.12639

[Map3d] CIBC.
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*, 2015.

[Mcd2015a] K.S. McDowell, S. Zahid, F. Vadakkumpadan, J.J. Blauer, R.S. MacLeod, N.A. Trayanova.
**“Virtual Electrophysiological Study of Atrial Fibrillation in Fibrotic Remodeling,”** In *PLoS ONE*, Vol. 10, No. 2, pp. e0117110. February, 2015.

DOI: 10.1371/journal.pone.0117110

[Mcd2015b] K. S. McDowell, S. Zahid, F. Vadakkumpadan, J. Blauer, R. S. MacLeod, N. A. Trayanova.
**“Virtual Electrophysiological Study of Atrial Fibrillation in Fibrotic Remodeling,”** In *PLoS ONE*, Vol. 10, No. 2, Public Library of Science, pp. 1-16. May, 2015.

DOI: doi.org/10.1371/journal.pone.0117110

[Mck2015a] S. McKenna, M. Meyer, C. Gregg, S. Gerber.
**“s-CorrPlot: An Interactive Scatterplot for Exploring Correlation,”** In *Journal of Computational and Graphical Statistics*, 2015.

DOI: 10.1080/10618600.2015.1021926

[Mes2015a] F. Mesadi, M. Cetin, T. Tasdizen.
**“Disjunctive Normal Shape and Appearance Priors with Applications to Image Segmentation,”** In *Lecture Notes in Computer Science*, Springer International Publishing, pp. 703--710. 2015.

ISBN: 978-3-319-24574-4

DOI: 10.1007/978-3-319-24574-4_84

[NCRTools] SCI Institute.
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*, 2015.

[Nob2015a] C. Nobre, A. Lex.
**“OceanPaths: Visualizing Multivariate Oceanography Data,”** In *Eurographics Conference on Visualization (EuroVis) - Short Papers*, Edited by E. Bertini, J. Kennedy, E. Puppo, The Eurographics Association, 2015.

DOI: 10.2312/eurovisshort.20151124

[Ogu2015a] I. OguzI, J. Cates, M. Datar, B. Paniagua, T. Fletcher, C. Vachet, M. Styner, R. Whitaker.
**“Entropy-based particle correspondence for shape populations,”** In *International Journal of Computer Assisted Radiology and Surgery*, Springer, pp. 1-12. December, 2015.

[Par2015a] B.R. Parmar, T.R. Jarrett, E.G. Kholmovski, N. Hu, D. Parker, R.S. MacLeod, N.F. Marrouche, R. Ranjan.
**“Poor scar formation after ablation is associated with atrial fibrillation recurrence,”** In *Journal of Interventional Cardiac Electrophysiology*, Vol. 44, No. 3, pp. 247-256. December, 2015.

[Pet2015f] B. Peterson, N. Xiao, J. Holmen, S. Chaganti, A. Pakki, J. Schmidt, D. Sunderland, A. Humphrey, M. Berzins.
**“Developing Uintah’s Runtime System For Forthcoming Architectures,”** Subtitled **“Refereed paper presented at the RESPA 15 Workshop at SuperComputing 2015 Austin Texas,”** *SCI Institute*, 2015.

[Pet2015g] B. Peterson, H. K. Dasari, A. Humphrey, J.C. Sutherland, T. Saad, M. Berzins.
**“Reducing overhead in the Uintah framework to support short-lived tasks on GPU-heterogeneous architectures,”** In *Proceedings of the 5th International Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing (WOLFHPC'15)*, ACM, pp. 4:1-4:8. 2015.

DOI: 10.1145/2830018.2830023

[Phi2015a] J. M. Phillips, Bei Wang, Y. Zheng.
**“Geometric Inference on Kernel Density Estimates,”** In *CoRR*, Vol. abs/1307.7760, 2015.

[Pru2015a] J.R. Pruett Jr., S. Kandala, S. Hoertel, A.Z. Snyder, J.T. Elison, T. Nishino, E. Feczko, N.U.F. Dosenbach, B. Nardos, J.D. Power, B. Adeyemo, K.N. Botteron, R.C. McKinstry, A.C. Evans, H.C. Hazlett, S.R. Dager, S. Paterson, R.T. Schultz, D.L. Collins, V.S. Fonov, M. Styner, G. Gerig, S. Das, P. Kostopoulos, J.N. Constantino, A.M. Estes, The IBIS Network, S.E. Petersen, B.L. Schlaggar, J. Piven.
**“Accurate age classification of 6 and 12 month-old infants based on resting-state functional connectivity magnetic resonance imaging data,”** In *Developmental Cognitive Neuroscience*, Vol. 12, pp. 123--133. April, 2015.

DOI: 10.1016/j.dcn.2015.01.003

[Puj2015a] S. Pujol, W. Wells, C. Pierpaoli, C. Brun, J. Gee, G. Cheng, B. Vemuri, O. Commowick, S. Prima, A. Stamm, M. Goubran, A. Khan, T. Peters, P. Neher, K. H. Maier-Hein, Y. Shi, A. Tristan-Vega, G. Veni, R. Whitaker, M. Styner, C.F. Westin, S. Gouttard, I. Norton, L. Chauvin, H. Mamata, G. Gerig, A. Nabavi, A. Golby,, R. Kikinis.
**“The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery,”** In *Journal of Neuroimaging*, Wiley, August, 2015.

DOI: 10.1111/jon.12283

[Raj2015a] M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston.
**“Evaluating Alignment of Shapes by Ensemble Visualization,”** In *IEEE Computer Graphics and Applications*, IEEE, 2015.

[Ram2015a] N. Ramesh, F. Mesadi, M. Cetin, T. Tasdizen.
**“Disjunctive normal shape models,”** In *2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)*, IEEE, April, 2015.

DOI: 10.1109/isbi.2015.7164170

[Ree2015a] D. Reed, M. Berzins, R. Lucas, S. Matsuoka, R. Pennington, V. Sarkar, V. Taylor.
**“DOE Advanced Scientific Computing Advisory Committee (ASCAC) Report: Exascale Computing Initiative Review,”** Note: *DOE Report*, 2015.

DOI: DOI 10.2172/1222712

[Rut2015a] H. J.V. Rutherford, G. Gerig, S. Gouttard, M. N. Potenza, L. C. Mayes.
**“Investigating maternal brain structure and its relationship to substance use and motivational systems,”** In *Yale Journal of Biology and Medicine, in print*, 2015.

[Sad2015a] N. Sadeghi, J. H. Gilmore , G. Gerig.
**“Modeling Brain Growth and Development,”** In *Brain*, Vol. 1, pp. 429-436. 2015.

DOI: 10.1016/B978-0-12-397025-1.00314-6

[Saj2015a] M. Sajjadi, M. Seyedhosseini,, T. Tasdizen.
**“Nonlinear Regression with Logistic Product Basis Networks,”** In *IEEE Signal Processing Letters*, Vol. 22, No. 8, IEEE, pp. 1011--1015. Aug, 2015.

DOI: 10.1109/lsp.2014.2380791

[Sal2015b] A. P. Salzwedel, K. M. Grewen, C. Vachet, G. Gerig, W. Lin,, W. Gao.
**“Prenatal Drug Exposure Affects Neonatal Brain Functional Connectivity,”** In *The Journal of Neuroscience*, Vol. 35, No. 14, pp. 5860-5869. April, 2015.

DOI: 10.1523/JNEUROSCI.4333-14.2015

[San2015a] S. Sankaranarayanan, T.E. Schomay, K.A. Aiello, O. Alter.
**“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,”** In *PLoS ONE*, Vol. 10, No. e121396, 2015.

DOI: 10.1371/journal.pone.0121396

[SciInst] Note: *Scientific Computing and Imaging Institute (SCI), University of Utah, www.sci.utah.edu*, 2015.

[SCIRun] SCI Institute.
Note: *SCIRun: A Scientific Computing Problem Solving Environment, Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org*, 2015.

[Seg3D] CIBC.
Note: *Seg3D: Volumetric Image Segmentation and Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.seg3d.org*, 2015.

[Sey2015a] M. Seyedhosseini , T. Tasdizen.
**“Disjunctive normal random forests,”** In *Pattern Recognition*, Vol. 48, No. 3, Elsevier BV, pp. 976--983. March, 2015.

DOI: 10.1016/j.patcog.2014.08.023

[Sey2015b] S.M. Seyedhosseini, S. Shushruth, T. Davis, J.M. Ichida, P.A. House, B. Greger, A. Angelucci, T. Tasdizen.
**“Informative features of local field potential signals in primary visual cortex during natural image stimulation,”** In *Journal of Neurophysiology*, Vol. 113, No. 5, American Physiological Society, pp. 1520--1532. March, 2015.

DOI: 10.1152/jn.00278.2014

[ShapeWorks] SCI Institute.
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*, 2015.

[Skr2015a] P. Skraba, Bei Wang, G. Chen, P. Rosen.
**“Robustness-Based Simplification of 2D Steady and Unsteady Vector Fields,”** In *IEEE Transactions on Visualization and Computer Graphics (to appear)*, 2015.

[SLASH] SLASH.
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.*, 2015.

[Str2015a] H. Strobelt, B. Alsallakh, J. Botros, B. Peterson, M. Borowsky, H. Pfister,, A. Lex.
**“Vials: Visualizing Alternative Splicing of Genes,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '15)*, Vol. 22, No. 1, pp. 399-408. 2015.

[Sum2015a] B. Summa, A. A. Gooch, G. Scorzelli, V. Pascucci.
**“Paint and Click: Unified Interactions for Image Boundaries,”** In *Computer Graphics Forum*, Vol. 34, No. 2, Wiley-Blackwell, pp. 385--393. May, 2015.

DOI: 10.1111/cgf.12568

[Swa2015a] M. R. Swanson, J. J. Wolff, J. T. Elison, H. Gu, H. C. Hazlett, K. Botteron, M. Styner, S. Paterson, G. Gerig, J. Constantino, S. Dager, A. Estes, C. Vachet, J. Piven.
**“Splenium development and early spoken language in human infants,”** In *Developmental Science*, Wiley Online Library, 2015.

ISSN: 1467-7687

DOI: 10.1111/desc.12360

[VisTrails] Note: *VisTrails: A scientific workflow management system. Scientific Computing and Imaging Institute (SCI), Download from: http://www.vistrails.org*, 2015.

[Wal2015a] I. Wald, A. Knoll, G. P. Johnson, W. Usher, V. Pascucci, M. E. Papka.
**“CPU Ray Tracing Large Particle Data with Balanced P-k-d Trees,”** In *2015 IEEE Scientific Visualization Conference*, IEEE, Oct, 2015.

DOI: 10.1109/scivis.2015.7429492

[Whi2015a] R. Whitaker, W. Thompson, J. Berger, B. Fischhof, M. Goodchild, M. Hegarty, C. Jermaine, K. S. McKinley, A. Pang, J. Wendelberger.
**“Workshop on Quantification, Communication, and Interpretation of Uncertainty in Simulation and Data Science,”** Note: *Computing Community Consortium*, 2015.

[Wol2015b] J. J. Wolff, G. Gerig, J. D. Lewis, T. Soda, M. A. Styner, C. Vachet, K. N. Botteron, J. T. Elison, S. R. Dager, A. M. Estes, H. C. Hazlett, R. T. Schultz, L. Zwaigenbaum, J. Piven.
**“Altered corpus callosum morphology associated with autism over the first 2 years of life,”** In *Brain*, 2015.

DOI: 10.1093/brain/awv118

[Zha2015a] M. Zhang, P. T. Fletcher.
**“Finite-Dimensional Lie Algebras for Fast Diffeomorphic Image Registration,”** In *Information Processing in Medical Imaging (IPMI)*, 2015.

[Zha2015b] M. Zhang, P. T. Fletcher.
**“Bayesian Principal Geodesic Analysis for Estimating Intrinsic Diffeomorphic Image Variability,”** In *Medical Image Analysis (accepted)*, 2015.

[Zha2015c] M. Zhang, H. Shao, P. T. Fletcher.
**“A Mixture Model for Automatic Diffeomorphic Multi-Atlas Building,”** In *MICCAI Workshop*, Springer, 2015.

2014

[Adl2014a] G. Adluru, Y. Gur, J. Anderson, L. Richards, N. Adluru, E. DiBella.
**“Assessment of white matter microstructure in stroke patients using NODDI,”** In *Proceedings of the 2014 IEEE Int. Conf. Engineering and Biology Society (EMBC)*, 2014.

[Awa2014a] S.P. Awate, R.T. Whitaker.
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[Awa2014b] S.P. Awate, Y.-Y. Yu, R.T. Whitaker.
**“Kernel Principal Geodesic Analysis,”** In *Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD)*, Springer LNAI, 2014.

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**“Extracting Features from Time-Dependent Vector Fields Using Internal Reference Frames,”** In *Computer Graphics Forum*, Vol. 33, No. 3, pp. 21--30. June, 2014.

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[Bha2014b] H. Bhatia, A. Gyulassy, H. Wang, P.-T. Bremer, V. Pascucci .
**“Robust Detection of Singularities in Vector Fields,”** In *Topological Methods in Data Analysis and Visualization III*, Mathematics and Visualization, Springer International Publishing, pp. 3--18. March, 2014.

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[Bha2014c] H. Bhatia, V. Pascucci, P.-T. Bremer.
**“The Natural Helmholtz-Hodge Decomposition For Open-Boundary Flow Analysis,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 99, pp. 1566--1578. 2014.

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[Big2014a] A. Bigelow, S. Drucker, D. Fisher, M.D. Meyer.
**“Reflections on How Designers Design With Data,”** In *Proceedings of the ACM International Conference on Advanced Visual Interfaces (AVI)*, Note: *Awarded Best Paper!*, 2014.

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**“Sensitivity and Specificity of Substrate Mapping: An In Silico Framework for the Evaluation of Electroanatomical Substrate Mapping Strategies,”** In *Journal of Cardiovascular Electrophysiology*, In *Journal of Cardiovascular Electrophysiology*, Vol. 25, No. 7, Note: *Featured on journal cover.*, pp. 774--780. May, 2014.

[Bon2014a] G.P. Bonneau, H.C. Hege, C.R. Johnson, M.M. Oliveira, K. Potter, P. Rheingans, T. Schultz.
**“Overview and State-of-the-Art of Uncertainty Visualization,”** In *Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization*, Edited by M. Chen and H. Hagen and C.D. Hansen and C.R. Johnson and A. Kauffman, Springer-Verlag, pp. 3--27. 2014.

ISBN: 978-1-4471-6496-8

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[Bre2014a] **“Topological Methods in Data Analysis and Visualization III,”** Edited by Peer-Timo Bremer and Ingrid Hotz and Valerio Pascucci and Ronald Peikert, Springer International Publishing, 2014.

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**“Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guarantees,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, pp. 223--237. 2014.

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**“Acute and Chronic Mood and Apathy Outcomes from a Randomized Study of Unilateral STN and GPi DBS,”** In *PLoS ONE*, Vol. 9, No. 12, pp. e114140. December, 2014.

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**“ASCAC Workforce Subcommittee Letter,”** Note: *Office of Scientific and Technical Information*, DOE ASCAC Committee Report, July, 2014.

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**“Anatomical targets associated with abrupt versus gradual washout of subthalamic deep brain stimulation effects on bradykinesia,”** In *PloS One*, Vol. 9, No. 8, pp. e99663. January, 2014.

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**“A survey of high level frameworks in block-structured adaptive mesh refinement packages,”** In *Journal of Parallel and Distributed Computing*, 2014.

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[Edg2014a] L.T. Edgar, C.J. Underwood, J.E. Guilkey, J.B. Hoying, J.A. Weiss.
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**“A Preliminary Study on the Effect of Motion Correction On HARDI Reconstruction,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

[Elh2014b] S. Elhabian, Y. Gur, J. Piven, M. Styner, I. Leppert, G.B. Pike, G. Gerig.
**“Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences,”** In *Proceeding of the 2014 Joint Annual Meeting ISMRM-ESMRMB*, pp. (accepted). 2014.

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**“Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences,”** In *Frontiers in Neurology - Brain Imaging Methods*, 2014.

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**“Verifying Volume Rendering Using Discretization Error Analysis,”** In *IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS*, Vol. 20, No. 1, IEEE, pp. 140-154. January, 2014.

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**“Computational Determination of the Modified Vortex Shedding Frequency for a Rigid, Truncated, Wall-Mounted Cylinder in Cross Flow,”** In *Volume 10: Micro- and Nano-Systems Engineering and Packaging*, Montreal, ASME International Mechanical Engineering Congress and Exposition (IMECE), *International Conference on Computational Science*, November, 2014.

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**“Geodesic Regression of Image and Shape Data for Improved Modeling of 4D Trajectories,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

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**“Freeprocessing: Transparent in situ visualization via data interception,”** In *Proceedings of the 14th Eurographics Conference on Parallel Graphics and Visualization*, EGPGV, Eurographics Association, 2014.

[Fu2014a] Z. Fu, H.K. Dasari, M. Berzins, B. Thompson.
**“Parallel Breadth First Search on GPU Clusters,”** SCI Technical Report, No. UUSCI-2014-002, *SCI Institute, University of Utah*, 2014.

[Fu2014b] Z. Fu, H.K. Dasari, M. Berzins, B. Thompson.
**“Parallel Breadth First Search on GPU Clusters,”** In *Proceedings of the IEEE BigData 2014 Conference*, Washington DC, October, 2014.

[Gao2014a] Y. Gao, M. Prastawa, M. Styner, J. Piven, G. Gerig.
**“A Joint Framework for 4D Segmentation and Estimation of Smooth Temporal Appearance Changes,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

[Gen2014a] M.G. Genton, C.R. Johnson, K. Potter, G. Stenchikov, Y. Sun.
**“Surface boxplots,”** In *Stat Journal*, Vol. 3, No. 1, pp. 1--11. 2014.

[Gey2014a] T. Geymayer, M. Steinberger, A. Lex, M. Streit,, D. Schmalstieg.
**“Show me the Invisible: Visualizing Hidden Content,”** In *Proceedings of the ACM SIGCHI Conference on Human Factors in Computing Systems (CHI '14)*, CHI '14, ACM, pp. 3705--3714. 2014.

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[Gra2014a] S. Gratzl, N. Gehlenborg, A. Lex, H. Pfister, M. Streit.
**“Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '14)*, Vol. 20, No. 12, pp. 2023--2032. 2014.

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[Gre2014a] K. Grewen, M. Burchinal, C. Vachet, S. Gouttard, J.H. Gilmore, W. Lin, J. Johns, M. Elam, G. Gerig.
**“Prenatal cocaine effects on brain structure in early infancy,”** In *NeuroImage*, Vol. 101, pp. 114--123. November, 2014.

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[Gri2014a] C.E. Gritton.
**“Ringing Instabilities in Particle Methods,”** Note: *M.S. in Computational Engineering and Science, advisor Martin Berzins*, *School of Computing, University of Utah*, August, 2014.

[Gur2014a] Y. Gur, C.R. Johnson.
**“Generalized HARDI Invariants by Method of Tensor Contraction,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 718--721. April, 2014.

[Ham2014a] C. Hamani, B.O. Amorim, A.L. Wheeler, M. Diwan, K. Driesslein, L. Covolan, C.R. Butson, J.N. Nobrega.
**“Deep brain stimulation in rats: Different targets induce similar antidepressant-like effects but influence different circuits,”** In *Neurobiology of Disease*, Vol. 71, Elsevier Inc., pp. 205--214. August, 2014.

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[Han2014a] C.D. Hansen, M. Chen, C.R. Johnson, A.E. Kaufman, H. Hagen (Eds.).
**“Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization,”** Mathematics and Visualization, Springer, 2014.

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[Hao2014a] X. Hao, K. Zygmunt, R.T. Whitaker, P.T. Fletcher.
**“Improved Segmentation of White Matter Tracts with Adaptive Riemannian Metrics,”** In *Medical Image Analysis*, Vol. 18, No. 1, pp. 161--175. Jan, 2014.

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[Hin2014a] J. Hinkle, P.T. Fletcher, S. Joshi .
**“Intrinsic Polynomials for Regression on Riemannian Manifolds,”** In *Journal of Mathematical Imaging and Vision*, pp. 1-21. 2014.

[Hol2014a] T. Hollt, A. Magdy, P. Zhan, G. Chen, G. Gopalakrishnan, I. Hoteit, C.D. Hansen, M. Hadwiger.
**“Ovis: A Framework for Visual Analysis of Ocean Forecast Ensembles,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. PP, No. 99, pp. 1. 2014.

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[Hoy2014a] J.B. Hoying, U. Utzinger, J.A. Weiss.
**“Formation of microvascular networks: role of stromal interactions directing angiogenic growth,”** In *Microcirculation*, Vol. 21, No. 4, pp. 278--289. May, 2014.

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PubMed ID: 24447042

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[Hum2014a] A. Humphrey, Q. Meng, M. Berzins, D. Caminha B.de Oliveira, Z. Rakamaric, G. Gopalakrishnan.
**“Systematic Debugging Methods for Large-Scale HPC Computational Frameworks,”** In *Computing in Science Engineering*, Vol. 16, No. 3, pp. 48--56. May, 2014.

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**“Geometric constraints on quadratic Bézier curves using minimal length and energy,”** In *Journal of Computational and Applied Mathematics*, Vol. 255, pp. 887--897. 2014.

[Kno2014a] A. Knoll, I. Wald, P. Navratil, A. Bowen, K. Reda, M. E. Papka, K. Gaither.
**“RBF Volume Ray Casting on Multicore and Manycore CPUs,”** In *Computer Graphics Forum*, Vol. 33, No. 3, Edited by H. Carr and P. Rheingans and H. Schumann, Wiley-Blackwell, pp. 71--80. June, 2014.

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[Kum2014a] S. Kumar, C. Christensen, P.-T. Bremer, E. Brugger, V. Pascucci, J. Schmidt, M. Berzins, H. Kolla, J. Chen, V. Vishwanath, P. Carns, R. Grout.
**“Fast Multi-Resolution Reads of Massive Simulation Datasets,”** In *Proceedings of the International Supercomputing Conference ISC'14*, Leipzig, Germany, June, 2014.

[Kum2014b] S. Kumar, J. Edwards, P.-T. Bremer, A. Knoll, C. Christensen, V. Vishwanath, P. Carns, J.A. Schmidt, V. Pascucci.
**“Efficient I/O and storage of adaptive-resolution data,”** In *Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis*, IEEE Press, pp. 413--423. 2014.

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[Lan2014a] A.G. Landge, V. Pascucci, A. Gyulassy, J.C. Bennett, H. Kolla, J. Chen, P.-T. Bremer.
**“In-situ feature extraction of large scale combustion simulations using segmented merge trees,”** In *Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2014)*, New Orleans, Louisana, IEEE Press, Piscataway, NJ, USA pp. 1020--1031. 2014.

ISBN: 978-1-4799-5500-8

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[Lew2014a] J.D. Lewis, A.C. Evans, J.R. Pruett, K. Botteron, L. Zwaigenbaum, A. Estes, G. Gerig, L. Collins, P. Kostopoulos, R. McKinstry, S. Dager, S. Paterson, R. Schultz, M. Styner, H. Hazlett, J. Piven, IBIS network.
**“Network inefficiencies in autism spectrum disorder at 24 months,”** In *Translational Psychiatry*, Vol. 4, No. 5, Nature Publishing Group, pp. e388. May, 2014.

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[Lex2014a] A. Lex, N. Gehlenborg, H. Strobelt, R. Vuillemot,, H. Pfister.
**“UpSet: Visualization of Intersecting Sets,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '14)*, Vol. 20, No. 12, pp. 1983--1992. 2014.

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[Liu2014a] W. Liu, S.P. Awate, J.S. Anderson, P.T. Fletcher.
**“A functional network estimation method of resting-state fMRI using a hierarchical Markov random field,”** In *NeuroImage*, Vol. 100, pp. 520--534. 2014.

ISSN: 1053-8119

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[Liu2014b] Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci.
**“Visual Exploration of High-Dimensional Data: Subspace Analysis through Dynamic Projections,”** SCI Technical Report, No. UUSCI-2014-003, *SCI Institute, University of Utah*, 2014.

[Liu2014c] S. Liu, Bei Wang, P.-T. Bremer, V. Pascucci.
**“Distortion-Guided Structure-Driven Interactive Exploration of High-Dimensional Data,”** In *Computer Graphics Forum*, Vol. 33, No. 3, Wiley-Blackwell, pp. 101--110. June, 2014.

[Liu2014d] Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci.
**“Multivariate Volume Visualization through Dynamic Projections,”** In *Proceedings of the IEEE Symposium on Large Data Analysis and Visualization (LDAV)*, 2014.

[Liu2014e] T. Liu, C. Jones, M. Seyedhosseini, T. Tasdizen.
**“A modular hierarchical approach to 3D electron microscopy image segmentation,”** In *Journal of Neuroscience Methods*, Vol. 226, No. 15, pp. 88--102. April, 2014.

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[Mal2014a] D. Maljovec, Bei Wang, J. Moeller, V. Pascucci.
**“Topology-Based Active Learning,”** SCI Technical Report, No. UUSCI-2014-001, *SCI Institute, University of Utah*, 2014.

[Mal2014b] D. Maljovec, S. Liu, Bei Wang, V. Pascucci, P.-T. Bremer, D. Mandelli, C. Smith.
**“Analyzing Simulation-Based PRA Data Through Clustering: a BWR Station Blackout Case Study,”** In *Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM)*, 2014.

[Man2014a] D. Mandelli, C. Smith, T. Riley, J. Nielsen, J. Schroeder, C. Rabiti, A. Alfonsi, J. Cogliati, R. Kinoshita, V. Pascucci, Bei Wang, D. Maljovec.
**“Overview of New Tools to Perform Safety Analysis: BWR Station Black Out Test Case,”** In *Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM)*, 2014.

[Mcg2014a] C. McGann, N. Akoum, A. Patel, E. Kholmovski, P. Revelo, K. Damal, B. Wilson, J. Cates, A. Harrison, R. Ranjan, N.S. Burgon, T. Greene, D. Kim, E.V. Dibella, D. Parker, R.S. MacLeod, N.F. Marrouche.
**“Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI,”** In *Circ Arrhythm Electrophysiol*, Vol. 7, No. 1, pp. 23--30. 2014.

DOI: 10.1161/CIRCEP.113.000689

PubMed ID: 24363354

[Mci2014a] G. McInerny, M. Chen, R. Freeman, D. Gavaghan, M.D. Meyer, F. Rowland, D. Spiegelhalter, M. Steganer, G. Tessarolo, J. Hortal.
**“Information Visualization for Science and Policy: Engaging Users and Avoiding Bias,”** In *Trends in Ecology & Evolution*, Vol. 29, No. 3, pp. 148--157. 2014.

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**“Design Activity Framework for Visualization Design,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, 2014.

[Men2014b] Q. Meng, M. Berzins.
**“Scalable large-scale fluid-structure interaction solvers in the Uintah framework via hybrid task-based parallelism algorithms,”** In *Concurrency and Computation: Practice and Experience*, Vol. 26, No. 7, pp. 1388--1407. May, 2014.

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[Men2014c] Qingyu Meng.
**“Large-Scale Distributed Runtime System for DAG-Based Computational Framework,”** Note: *Ph.D. in Computer Science, advisor Martin Berzins*, *School of Computing, University of Utah*, August, 2014.

[Mer2014a] J. Mercer, B. Pandian, A. Lex, N. Bonneel,, H. Pfister.
**“Mu-8: Visualizing Differences between Proteins and their Families ,”** In *BMC Proceedings*, Vol. 8, No. Suppl 2, pp. S5. Aug, 2014.

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**“The Nested Blocks and Guidelines Model,”** In *Journal of Information Visualization, Special Issue on Evaluation (BELIV)*, 2014.

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**“Assessment of regularization techniques for electrocardiographic imaging,”** In *Journal of electrocardiology*, Vol. 47, No. 1, pp. 20--28. 2014.

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**“Curve Boxplot: Generalization of Boxplot for Ensembles of Curves,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 20, No. 12, IEEE, pp. 2654-63. December, 2014.

[Mur2014a] P. Muralidharan, J. Fishbaugh, H.J. Johnson, S. Durrleman, J.S. Paulsen, G. Gerig, P.T. Fletcher.
**“Diffeomorphic Shape Trajectories for Improved Longitudinal Segmentation and Statistics,”** In *Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)*, 2014.

[Nei2014a] J.A. Nielsen, B.A. Zielinski, P.T. Fletcher, A.L. Alexander, N. Lange, E.D. Bigler, J.E. Lainhart, J.S. Anderson.
**“Abnormal lateralization of functional connectivity between language and default mode regions in autism,”** In *Molecular Autism*, Vol. 5, No. 1, pp. 8. 2014.

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[Nes2014a] K.A. Nestor, J.D. Jones, C.R. Butson, T. Morishita, C.E. Jacobson, D.A. Peace, D. Chen, K.D. Foote, M.S. Okun.
**“Coordinate-based lead location does not predict Parkinson's disease deep brain stimulation outcome,”** In *PloS One*, Vol. 9, No. 4, pp. e93524. January, 2014.

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**“DTIPrep: Quality Control of Diffusion-Weighted Images,”** In *Frontiers in Neuroinformatics*, Vol. 8, No. 4, 2014.

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[Oli2014a] D.C.B. de Oliveira, A. Humphrey, Q. Meng, Z. Rakamaric, M. Berzins, G. Gopalakrishnan.
**“Systematic Debugging of Concurrent Systems Using Coalesced Stack Trace Graphs,”** In *Proceedings of the 27th International Workshop on Languages and Compilers for Parallel Computing (LCPC)*, September, 2014.

[Par2014a] B.R. Parmar, T.R. Jarrett, N.S. Burgon, E.G. Kholmovski, N.W. Akoum, N. Hu, R.S. Macleod, N.F. Marrouche, R. Ranjan.
**“Comparison of Left Atrial Area Marked Ablated in Electroanatomical Maps with Scar in MRI,”** In *Journal of Cardiovascular Electrophysiology*, 2014.

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[Par2014b] Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wasserman, Hanspeter Pfister,, Dieter Schmalstieg.
**“ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery,”** In *IEEE Transactions on Visualization and Computer Graphics (VAST '14)*, Vol. 20, No. 12, pp. 1883--1892. 2014.

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**“A workflow for the automatic segmentation of organelles in electron microscopy image stacks,”** In *Frontiers in Neuroanatomy*, Vol. 8, No. 126, 2014.

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**“Automated workflows for the morphological characterization of organelles in electron microscopy image stacks (LB72),”** In *The FASEB Journal*, Vol. 28, No. 1 Supplement LB72, April, 2014.

[Ram2014a] N. Ramesh, T. Tasdizen.
**“Cell tracking using particle filters with implicit convex shape model in 4D confocal microscopy images,”** In *2014 IEEE International Conference on Image Processing (ICIP)*, IEEE, Oct, 2014.

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[Rou2014a] F. Rousset, C. Vachet, C. Conlin, M. Heilbrun, J.L. Zhang, V.S. Lee, G. Gerig.
**“Semi-automated application for kidney motion correction and filtration analysis in MR renography,”** In *Proceeding of the 2014 Joint Annual Meeting ISMRM-ESMRMB*, pp. (accepted). 2014.

[Sad2014a] N. Sadeghi, J.H. Gilmore, W. Lin, G. Gerig.
**“Normative Modeling of Early Brain Maturation from Longitudinal DTI Reveals Twin-Singleton Differences,”** In *Proceeding of the 2014 Joint Annual Meeting ISMRM-ESMRMB*, pp. (accepted). 2014.

[Sad2014b] N. Sadeghi, P.T. Fletcher, M. Prastawa, J.H. Gilmore, G. Gerig.
**“Subject-specific prediction using nonlinear population modeling: Application to early brain maturation from DTI,”** In *Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2014)*, 2014.

[San2014a] A.R. Sanderson.
**“An Alternative Formulation of Lyapunov Exponents for Computing Lagrangian Coherent Structures,”** In *Proceedings of the 2014 IEEE Pacific Visualization Symposium (PacificVis)*, Yokahama Japan, 2014.

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**“Disjunctive normal random forests,”** In *Pattern Recognition*, September, 2014.

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[Sha2014a] A. Sharma, P.T. Fletcher, J.H. Gilmore, M.L. Escolar, A. Gupta, M. Styner, G. Gerig.
**“Parametric Regression Scheme for Distributions: Analysis of DTI Fiber Tract Diffusion Changes in Early Brain Development,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

[Sin2014a] N.P. Singh, J. Hinkle, S. Joshi, P.T. Fletcher.
**“An Efficient Parallel Algorithm for Hierarchical Geodesic Models in Diffeomorphisms,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

[Skr2014a] P. Skraba, Bei Wang, G. Chen, P. Rosen.
**“2D Vector Field Simplification Based on Robustness,”** In *Proceedings of the 2014 IEEE Pacific Visualization Symposium*, PacificVis, Note: *Awarded Best Paper!*, 2014.

[Skr2014b] P. Skraba, Bei Wang.
**“Interpreting Feature Tracking Through the Lens of Robustness,”** In *Mathematics and Visualization*, Springer, pp. 19-37. 2014.

DOI: 10.1007/978-3-319-04099-8_2

[Skr2014c] P. Skraba, Bei Wang.
**“Approximating Local Homology from Samples,”** In *Proceedings 25th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)*, pp. 174-192. 2014.

[Sto2014a] R. Stoll, E. Pardyjak, J.J. Kim, T. Harman, A.N. Hayati.
**“An inter-model comparison of three computation fluid dynamics techniques for step-up and step-down street canyon flows,”** In *ASME FEDSM/ICNMM symposium on urban fluid mechanics*, August, 2014.

[Str2014a] M. Streit, A. Lex, S. Gratzl, C. Partl, D. Schmalstieg, H. Pfister, P. J. Park,, N. Gehlenborg.
**“Guided visual exploration of genomic stratifications in cancer,”** In *Nature Methods*, Vol. 11, No. 9, pp. 884--885. Sep, 2014.

ISSN: 1548-7091

DOI: 10.1038/nmeth.3088

[Sum2014a] B. Summa, A.A. Gooch, G. Scorzelli, V. Pascucci.
**“Towards Paint and Click: Unified Interactions for Image Boundaries,”** SCI Technical Report, No. UUSCI-2014-004, *SCI Institute, University of Utah*, December, 2014.

[Tas2014a] T. Tasdizen, M. Seyedhosseini, T. Liu, C. Jones, E. Jurrus.
**“Image Segmentation for Connectomics Using Machine Learning,”** In *Computational Intelligence in Biomedical Imaging*, Edited by Suzuki, Kenji, Springer New York, pp. 237--278. 2014.

ISBN: 978-1-4614-7244-5

DOI: 10.1007/978-1-4614-7245-2_10

[Tur2014a] C. Turkay, A. Lex, M. Streit, H. Pfister,, H. Hauser.
**“Characterizing Cancer Subtypes using Dual Analysis in Caleydo,”** In *IEEE Computer Graphics and Applications*, Vol. 34, No. 2, pp. 38--47. March, 2014.

ISSN: 0272-1716

DOI: 10.1109/MCG.2014.1

[Und2014a] C.J. Underwood, L.T. Edgar, J.B. Hoying, J.A. Weiss.
**“Cell-generated traction forces and the resulting matrix deformation modulate microvascular alignment and growth during angiogenesis,”** In *American Journal of Physiology: Heart and Circulatory Physiology*, Vol. 307, No. H152-H164, 2014.

DOI: 10.1152/ajpheart.00995.2013

PubMed ID: 24816262

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[Vac2014a] C. Vachet, H.C. Hazlett, J. Piven, G. Gerig.
**“4D Modeling of Infant Brain Growth in Down's Syndrome and Controls from longitudinal MRI,”** In *Proceeding of the 2014 Joint Annual Meeting ISMRM-ESMRMB*, pp. (accepted). 2014.

[Var2014a] A. Vardhan, M. Prastawa, C. Vachet, J. Piven, G. Gerig.
**“Characterizing growth patterns in longitudinal MRI using image contrast,”** In *Proceedings of Medical Imaging 2014: Image Processing*, 2014.

[Var2014b] A. Vardhan, N. Sadeghi, C. Vachet, J. Piven, G. Gerig.
**“Joint Longitudinal Modeling of Brain Appearance in Multimodal MRI for the Characterization of Early Brain Developmental Processes,”** In *Spatiotemporal Image Analysis for Longitudinal and Time-Series Image Data (STIA'14) , LNCS. MICCAI'14*, Springer Verlag, June, 2014.

[Ver2014a] A.R. Verde, F. Budin, J.-B. Berger, A. Gupta, M. Farzinfar, A. Kaiser, M. Ahn, H. Johnson, J. Matsui, H.C. Hazlett, A. Sharma, C. Goodlett, Y. Shi, S. Gouttard, C. Vachet, J. Piven, H. Zhu, G. Gerig, M. Styner.
**“UNC-Utah NA-MIC framework for DTI fiber tract analysis,”** In *Frontiers in Neuroinformatics*, Vol. 7, No. 51, January, 2014.

DOI: 10.3389/fninf.2013.00051

[Wan2014a] Bo Wang, W. Liu, M. Prastawa, A. Irimia, P.M. Vespa, J.D. van Horn, P.T. Fletcher, G. Gerig.
**“4D Active Cut: An Interactive Tool for Pathological Anatomy Modeling,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. (accepted). 2014.

[Wan2014b] J. Wang, C. Vachet, A. Rumple, S. Gouttard, C. Ouzie, E. Perrot, G. Du, X. Huang, G. Gerig, M.A. Styner.
**“Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline,”** In *Frontiers in Neuroinformatics*, Vol. 8, No. 7, 2014.

DOI: 10.3389/fninf.2014.00007

[Wan2014c] Y. Wan, H. Otsuna, K. Kwan, C.D. Hansen.
**“Real-Time Dense Nucleus Selection from Confocal Data,”** In *Proceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine*, 2014.

[Wid2014a] W. Widanagamaachchi, P.-T. Bremer, C. Sewell, L.-T. Lo; J. Ahrens, V. Pascucci.
**“Data-Parallel Halo Finding with Variable Linking Lengths,”** In *Proceedings of the 2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV)*, pp. 27--34. November, 2014.

[Yu2014a] Y.-Y. Yu, P.T. Fletcher, S.P. Awate.
**“Hierarchical Bayesian Modeling, Estimation, and Sampling for Multigroup Shape Analysis,”** In *Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)*, 2014.

[Zha2014a] M. Zhang, P.T. Fletcher.
**“Bayesian Principal Geodesic Analysis in Diffeomorphic Image Registration,”** In *Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)*, 2014.

[Zho2014a] L. Zhou, C.D. Hansen.
**“GuideME: Slice-guided Semiautomatic Multivariate Exploration of Volumes,”** In *Computer Graphics Forum*, Vol. 33, No. 3, Wiley-Blackwell, pp. 151--160. jun, 2014.

DOI: 10.1111/cgf.12371

[Zie2014a] B.A. Zielinski, M.B.D. Prigge, J.A. Nielsen, A.L. Froehlich, T.J. Abildskov, J.S. Anderson, P.T. Fletcher, K.M. Zygmunt, B.G. Travers, N. Lange, A.L. Alexander, E.D. Bigler, J.E. Lainhart.
**“Longitudinal changes in cortical thickness in autism and typical development,”** In *Brain*, Vol. 137, No. 6, Edited by Dimitri M. Kullmann, pp. 1799--1812. 2014.

DOI: 10.1093/brain/awu083

2013

[Abd2013a] A. Abdul-Rahman, J. Lein, K. Coles, E. Maguire, M.D. Meyer, M. Wynne, C.R. Johnson, A. Trefethen, M. Chen.
**“Rule-based Visual Mappings - with a Case Study on Poetry Visualization,”** In *Proceedings of the 2013 Eurographics Conference on Visualization (EuroVis)*, Vol. 32, No. 3, pp. 381--390. June, 2013.

[Abr2013a] C.L. Abraham, S.A. Maas, J.A. Weiss, B.J. Ellis, C.L. Peters, A.E. Anderson.
**“A new discrete element analysis method for predicting hip joint contact stresses,”** In *Journal of Biomechanics*, Vol. 46, No. 6, pp. 1121--1127. 2013.

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[And2013a] E.W. Anderson, C. Chong, G.A. Preston, C.T. Silva.
**“Discovering and Visualizing Patterns in EEG Data,”** In *Proceedings of the 2013 IEEE Pacific Visualization Symposium (PacificVis)*, pp. 105--112. 2013.

[And2013b] J.S. Anderson, J.A. Nielsen, M.A. Ferguson, M.C. Burback, E.T. Cox, L. Dai, G. Gerig, J.O. Edgin, J.R. Korenberg.
**“Abnormal brain synchrony in Down Syndrome,”** In *NeuroImage: Clinical*, Vol. 2, pp. 703--715. 2013.

ISSN: 2213-1582

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[Bec2013a] J. Beckvermit, J. Peterson, T. Harman, S. Bardenhagen, C. Wight, Q. Meng, M. Berzins.
**“Multiscale Modeling of Accidental Explosions and Detonations,”** In *Computing in Science and Engineering*, Vol. 15, No. 4, pp. 76--86. 2013.

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[Ber2013a] M. Berzins, J. Schmidt, Q. Meng, A. Humphrey.
**“Past, Present, and Future Scalability of the Uintah Software,”** In *Proceedings of the Blue Waters Extreme Scaling Workshop 2012*, pp. Article No.: 6. 2013.

[Ber2013b] M. Berzins.
**“Data and Range-Bounded Polynomials in ENO Methods,”** In *Journal of Computational Science*, Vol. 4, No. 1-2, pp. 62--70. 2013.

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[Ber2013c] N.M. Bertagnolli, J.A. Drake, J.M. Tennessen, O. Alter.
**“SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism,”** In *Public Library of Science (PLoS) One*, Vol. 8, No. 11, pp. article e78913. November, 2013.

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[Bha2013a] H. Bhatia, G. Norgard, V. Pascucci, P.-T. Bremer.
**“The Helmholtz-Hodge Decomposition - A Survey,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 19, No. 8, Note: *Selected as Spotlight paper for August 2013 issue*, pp. 1386--1404. 2013.

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[Bha2013c] H. Bhatia, G. Norgard, V. Pascucci, P.-T. Bremer.
**“Comments on the “Meshless Helmholtz-Hodge decomposition”,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 19, No. 3, pp. 527--528. 2013.

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[Bro2013a] C. Brownlee, T. Ize, C.D. Hansen.
**“Image-parallel Ray Tracing using OpenGL Interception,”** In *Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (EGPGV 2013)*, pp. 65--72. 2013.

[Bur2013a] B. Burton, B. Erem, K. Potter, P. Rosen, C.R. Johnson, D. Brooks, R.S. Macleod.
**“Uncertainty Visualization in Forward and Inverse Cardiac Models,”** In *Computing in Cardiology CinC*, pp. 57--60. 2013.

ISSN: 2325-8861

[But2013a] C. Butson, G. Tamm, S. Jain, T. Fogal, J. Krüger.
**“Evaluation of Interactive Visualization on Mobile Computing Platforms for Selection of Deep Brain Stimulation Parameters,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 19, No. 1, pp. 108--117. January, 2013.

DOI: 10.1109/TVCG.2012.92

PubMed ID: 22450824

[Che2013a] J. Chen, A. Choudhary, S. Feldman, B. Hendrickson, C.R. Johnson, R. Mount, V. Sarkar, V. White, D. Williams.
**“Synergistic Challenges in Data-Intensive Science and Exascale Computing,”** Note: *Summary Report of the Advanced Scientific Computing Advisory Committee (ASCAC) Subcommittee*, March, 2013.

[Che2013b] F. Chen, H. Obermaier, H. Hagen, B. Hamann, J. Tierny, V. Pascucci.
**“Topology analysis of time-dependent multi-fluid data using the Reeb graph,”** In *Computer Aided Geometric Design*, Vol. 30, No. 6, pp. 557--566. 2013.

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[Dad2013a] A. Daducci, E.J. Canales-Rodriguez, M. Descoteaux, E. Garyfallidis, Y. Gur, Y.-C Lin, M. Mani, S. Merlet, M. Paquette, A. Ramirez-Manzanares, M. Reisert, P.R. Rodrigues, F. Sepehrband, E. Caruyer, J. Choupan, R. Deriche, M. Jacob, G. Menegaz, V. Prckovska, M. Rivera, Y. Wiaux, J.-P. Thiran.
**“Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI,”** In *IEEE Transactions on Medical Imaging*, Vol. 33, No. 2, pp. 384--399. 2013.

ISSN: 0278-0062

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[Dat2013a] M. Datar, I. Lyu, S. Kim, J. Cates, M.A. Styner, R.T. Whitaker.
**“Geodesic distances to landmarks for dense correspondence on ensembles of complex shapes,”** In *Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011)*, Vol. 16(Pt. 2), pp. 19--26. 2013.

PubMed ID: 24579119

[Dos2013a] D.J. Dosdall, R. Ranjan, K. Higuchi, E. Kholmovski, N. Angel, L. Li, R.S. Macleod, L. Norlund, A. Olsen, C.J. Davies, N.F. Marrouche.
**“Chronic atrial fibrillation causes left ventricular dysfunction in dogs but not goats: experience with dogs, goats, and pigs,”** In *American Journal of Physiology: Heart and Circulatory Physiology*, Vol. 305, No. 5, pp. H725--H731. September, 2013.

DOI: 10.1152/ajpheart.00440.2013

PubMed ID: 23812387

PubMed Central ID: PMC4116536

[Dur2013a] S. Durrleman, X. Pennec, A. Trouvé, J. Braga, G. Gerig, N. Ayache.
**“Toward a comprehensive framework for the spatiotemporal statistical analysis of longitudinal shape data,”** In *International Journal of Computer Vision (IJCV)*, Vol. 103, No. 1, pp. 22--59. September, 2013.

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[Dur2013b] S. Durrleman, S. Allassonnière, S. Joshi.
**“Sparse adaptive parameterization of variability in image ensembles,”** In *International Journal of Computer Vision (IJCV)*, Vol. 101, No. 1, pp. 161--183. 2013.

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[Edg2013a] L.T. Edgar, S.C. Sibole, C.J. Underwood, J.E. Guilkey, J.A. Weiss.
**“A computational model of in vitro angiogenesis based on extracellular matrix fiber orientation,”** In *Computer Methods in Biomechanical and Biomedical Engineering*, Vol. 16, No. 7, pp. 790--801. 2013.

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[Elh2013a] S. Elhabian, A. Farag, D. Tasman, W. Aboelmaaty, A. Farman.
**“Clinical Crowns Shape Reconstruction - An Image-based Approach,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 93--96. 2013.

DOI: 10.1109/ISBI.2013.6556420

[Eli2013a] J.T. Elison, J.J. Wolff, D.C. Heimer, S.J. Paterson, H. Gu, M. Styner, G. Gerig, J. Piven, the IBIS Network.
**“Frontolimbic neural circuitry at 6 months predicts individual differences in joint attention at 9 months,”** In *Developmental Science*, Vol. 16, No. 2, Wiley-Blackwell, pp. 186--197. 2013.

DOI: 10.1111/desc.12015

PubMed Central ID: PMC3582040

[Eli2013b] J.T. Elison, S.J. Paterson, J.J. Wolff, J.S. Reznick, N.J. Sasson, H. Gu, K.N. Botteron, S.R. Dager, A.M. Estes, A.C. Evans, G. Gerig, H.C. Hazlett, R.T. Schultz, M. Styner, L. Zwaigenbaum, J. Piven for the IBIS Network.
**“White Matter Microstructure and Atypical Visual Orienting in 7 Month-Olds at Risk for Autism,”** In *American Journal of Psychiatry*, Vol. AJP-12-09-1150.R2, March, 2013.

DOI: 10.1176/appi.ajp.2012.12091150

PubMed ID: 23511344

[Ere2013a] B. Erem, J. Coll-Font, R.M. Orellana, P. Stovicek, D.H. Brooks, R.S. MacLeod.
**“Noninvasive reconstruction of potentials on endocardial surface from body surface potentials and CT imaging of partial torso,”** In *Journal of Electrocardiology*, Vol. 46, No. 4, pp. e28. 2013.

DOI: 10.1016/j.jelectrocard.2013.05.104

[Ere2013b] B. Erem, R.M. Orellana, P. Stovicek, D.H. Brooks, R.S. MacLeod.
**“Improved averaging of multi-lead ECGs and electrograms,”** In *Journal of Electrocardiology*, Vol. 46, No. 4, Elsevier, pp. e28. July, 2013.

DOI: 10.1016/j.jelectrocard.2013.05.103

[Eti2013a] T. Etiene, D. Jonsson, T. Ropinski, C. Scheidegger, J. Comba, L. Gustavo Nonato, R.M. Kirby, A. Ynnerman, C.T. Silva.
**“Verifying Volume Rendering Using Discretization Error Analysis,”** SCI Technical Report, No. UUSCI-2013-001, *SCI Institute, University of Utah*, 2013.

[Fak2013a] K. Fakhar, E. Hastings, C.R. Butson, K.D. Foote, P. Zeilman, M.S. Okun.
**“Management of deep brain stimulator battery failure: battery estimators, charge density, and importance of clinical symptoms,”** In *PloS One*, Vol. 8, No. 3, pp. e58665. January, 2013.

ISSN: 1932-6203

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PubMed ID: 23536810

[Far2013a] M. Farzinfar, Y. Li, A.R. Verde, I. Oguz, G. Gerig, M.A. Styner.
**“DTI Quality Control Assessment via Error Estimation From Monte Carlo Simulations,”** In *Proceedings of SPIE 8669, Medical Imaging 2013: Image Processing*, Vol. 8669, 2013.

DOI: 10.1117/12.2006925

PubMed ID: 23833547

PubMed Central ID: PMC3702180

[Far2013b] M. Farzinfar, I. Oguz, R.G. Smith, A.R. Verde, C. Dietrich, A. Gupta, M.L. Escolar, J. Piven, S. Pujol, C. Vachet, S. Gouttard, G. Gerig, S. Dager, R.C. McKinstry, S. Paterson, A.C. Evans, M.A. Styner.
**“Diffusion imaging quality control via entropy of principal direction distribution,”** In *NeuroImage*, Vol. 82, pp. 1--12. 2013.

ISSN: 1053-8119

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[Far2013c] N. Farah, A. Zoubi, S. Matar, L. Golan, A. Marom, C.R. Butson, I. Brosh, S. Shoham.
**“Holographically patterned activation using photo-absorber induced neural-thermal stimulation,”** In *Journal of Neural Engineering*, Vol. 10, No. 5, pp. 056004. October, 2013.

ISSN: 1741-2560

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[Fis2013a] J. Fishbaugh, M.W. Prastawa, G. Gerig, S. Durrleman.
**“Geodesic Shape Regression in the Framework of Currents,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Vol. 23, pp. 718--729. 2013.

PubMed ID: 24684012

PubMed Central ID: PMC4127488

[Fis2013b] J. Fishbaugh, M. Prastawa, G. Gerig, S. Durrleman.
**“Geodesic image regression with a sparse parameterization of diffeomorphisms,”** In *Geometric Science of Information Lecture Notes in Computer Science (LNCS)*, In *Proceedings of the Geometric Science of Information Conference (GSI)*, Vol. 8085, pp. 95--102. 2013.

[Fog2013a] T. Fogal, A. Schiewe, J. Krüger.
**“An Analysis of Scalable GPU-Based Ray-Guided Volume Rendering,”** In *2013 IEEE Symposium on Large Data Analysis and Visualization (LDAV)*, 2013.

[Fu2013a] Z. Fu, R.M. Kirby, R.T. Whitaker.
**“A Fast Iterative Method for Solving the Eikonal Equation on Tetrahedral Domains,”** In *SIAM Journal on Scientific Computing*, Vol. 35, No. 5, pp. C473--C494. 2013.

[Gam2013a] M. Gamell, I. Rodero, M. Parashar, J.C. Bennett, H. Kolla, J.H. Chen, P.-T. Bremer, A. Landge, A. Gyulassy, P. McCormick, Scott Pakin, Valerio Pascucci, Scott Klasky.
**“Exploring Power Behaviors and Trade-offs of In-situ Data Analytics,”** In *Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis*, Association for Computing Machinery, 2013.

ISBN: 978-1-4503-2378-9

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[Gar2013a] G. Gardner, A. Morris, K. Higuchi, R.S. MacLeod, J. Cates.
**“A Point-Correspondence Approach to Describing the Distribution of Image Features on Anatomical Surfaces, with Application to Atrial Fibrillation,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 226--229. 2013.

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[Ger2013a] S. Gerber, O. Reubel, P.-T. Bremer, V. Pascucci, R.T. Whitaker.
**“Morse-Smale Regression,”** In *Journal of Computational and Graphical Statistics*, Vol. 22, No. 1, pp. 193--214. 2013.

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[Gil2013a] J.M. Gililland, L.A. Anderson, H.B. Henninger, E.N. Kubiak, C.L. Peters.
**“Biomechanical analysis of acetabular revision constructs: is pelvic discontinuity best treated with bicolumnar or traditional unicolumnar fixation?,”** In *Journal of Arthoplasty*, Vol. 28, No. 1, pp. 178--186. 2013.

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[Gra2013a] S. Gratzl, A. Lex, N. Gehlenborg, H. Pfister,, M. Streit.
**“LineUp: Visual Analysis of Multi-Attribute Rankings,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '13)*, Vol. 19, No. 12, pp. 2277--2286. 2013.

ISSN: 1077-2626

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[Gro2013a] A. Grosset, M. Schott, G.-P. Bonneau, C.D. Hansen.
**“Evaluation of Depth of Field for Depth Perception in DVR,”** In *Proceedings of the 2013 IEEE Pacific Visualization Symposium (PacificVis)*, pp. 81--88. 2013.

[Ha2013a] L.K. Ha, J. King, Z. Fu, R.M. Kirby.
**“A High-Performance Multi-Element Processing Framework on GPUs,”** SCI Technical Report, No. UUSCI-2013-005, *SCI Institute, University of Utah*, 2013.

[Hal2013a] M. Hall, R.M. Kirby, F. Li, M.D. Meyer, V. Pascucci, J.M. Phillips, R. Ricci, J. Van der Merwe, S. Venkatasubramanian.
**“Rethinking Abstractions for Big Data: Why, Where, How, and What,”** In *Cornell University Library*, 2013.

[Hal2013b] M. Hall, J.C. Beckvermit, C.A. Wight, T. Harman, M. Berzins.
**“The influence of an applied heat flux on the violence of reaction of an explosive device,”** In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery*, San Diego, California, XSEDE '13, pp. 11:1--11:8. 2013.

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[Ham2013a] D.K. Hammond, Y. Gur, C.R. Johnson.
**“Graph Diffusion Distance: A Difference Measure for Weighted Graphs Based on the Graph Laplacian Exponential Kernel,”** In *Proceedings of the IEEE global conference on information and signal processing (GlobalSIP'13)*, Austin, Texas, pp. 419--422. 2013.

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[Hao2013a] X. Hao, P.T. Fletcher.
**“Joint Fractional Segmentation and Multi-Tensor Estimation in Diffusion MRI,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), pp. (accepted). 2013.

[Har2013a] M.D. Harris, S.P. Reese, C.L. Peters, J.A. Weiss, A.E. Anderson.
**“Three-dimensional Quantification of Femoral Head Shape in Controls and Patients with Cam-type Femoroacetabular Impingement,”** In *Annals of Biomedical Engineering*, Vol. 41, No. 6, pp. 1162--1171. 2013.

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[Har2013b] M.D. Harris, M. Datar, R.T. Whitaker, E.R. Jurrus, C.L. Peters, A.E. Anderson.
**“Statistical Shape Modeling of Cam Femoroacetabular Impingement,”** In *Journal of Orthopaedic Research*, Vol. 31, No. 10, pp. 1620--1626. 2013.

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[Har2013c] M.D. Harris.
**“The geometry and biomechanics of normal and pathomorphologic human hips,”** Note: *Ph.D. Thesis*, *Department of Bioengineering, University of Utah*, 2013.

[Hen2013a] C.R. Henak, A.E. Anderson, J.A. Weiss.
**“Subject-specific analysis of joint contact mechanics: application to the study of osteoarthritis and surgical planning,”** In *Journal of Biomechanical Engineering*, Vol. 135, No. 2, 2013.

DOI: 10.1115/1.4023386

PubMed ID: 23445048

[Hen2013b] H.B. Henninger, C.J. Underwood, S.J. Romney, G.L. Davis, J.A. Weiss.
**“Effect of Elastin Digestion on the Quasi-Static Tensile Response of Medial Collateral Ligament,”** In *Journal of Orthopaedic Research*, pp. (published online). 2013.

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[Hen2013c] C.R. Henak, Carruth E, A.E. Anderson, M.D. Harris, B.J. Ellis, C.L. Peters, J.A. Weiss.
**“Finite element predictions of cartilage contact mechanics in hips with retroverted acetabula,”** In *Osteoarthritis and Cartilage*, Vol. 21, pp. 1522-1529. 2013.

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[Hen2013d] C.R. Henak, A.K. Kapron, B.J. Ellis, S.A. Maas, A.E. Anderson, J.A. Weiss.
**“Specimen-specific predictions of contact stress under physiological loading in the human hip: validation and sensitivity studies,”** In *Biomechanics and Modeling in Mechanobiology*, pp. 1-14. 2013.

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[Hen2013e] C.R. Henak.
**“Cartilage and labrum mechanics in the normal and pathomorphologic human hip,”** Note: *Ph.D. Thesis*, *Department of Bioengineering, University of Utah*, 2013.

[Her2013a] H. Hernandez, J. Knezevic, T. Fogal, T. Sherman, T. Jevremovic.
**“Visual numerical steering in 3D AGENT code system for advanced nuclear reactor modeling and design,”** In *Annals of Nuclear Energy*, Vol. 55, pp. 248--257. 2013.

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**“The Effect of Fat Pad Modification during Ablation of Atrial Fibrillation: Late Gadolinium Enhancement MRI Analysis,”** In *Pacing and Clinical Electrophysiology (PACE)*, Vol. 36, No. 4, pp. 467--476. April, 2013.

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[Hin2013a] J. Hinkle, S. Joshi.
**“PDiff: Irrotational Diffeomorphisms for Computational Anatomy,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), pp. (accepted). 2013.

[Hol2013a] T. Höllt, A. Magdy, G. Chen, G. Gopalakrishnan, I. Hoteit, C.D. Hansen, M. Hadwiger.
**“Visual Analysis of Uncertainties in Ocean Forecasts for Planning and Operation of Off-Shore Structures,”** In *Proceedings of 2013 IEEE Pacific Visualization Symposium (PacificVis)*, Note: *Received Honerable Mention*, pp. 185--192. 2013.

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**“Uncertainty Visualization in HARDI based on Ensembles of ODFs,”** In *Proceedings of 2013 IEEE Pacific Visualization Symposium*, pp. 193--200. 2013.

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[Joh2013a] C.R. Johnson, A. Pang (Eds.).
**“International Journal for Uncertainty Quantification,”** Subtitled **“Special Issue on Working with Uncertainty: Representation, Quantification, Propagation, Visualization, and Communication of Uncertainty,”** In *Int. J. Uncertainty Quantification*, Vol. 3, No. 2, Begell House, Inc., pp. vii--viii. 2013.

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[Joh2013b] C.R. Johnson, A. Pang (Eds.).
**“International Journal for Uncertainty Quantification,”** Subtitled **“Special Issue on Working with Uncertainty: Representation, Quantification, Propagation, Visualization, and Communication of Uncertainty,”** In *Int. J. Uncertainty Quantification*, Vol. 3, No. 3, Begell House, Inc., 2013.

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**“Semi-Automatic Neuron Segmentation in Electron Microscopy Images Via Sparse Labeling,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1304--1307. April, 2013.

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[Jon2013b] C. Jones, M. Seyedhosseini, M. Ellisman, T. Tasdizen.
**“Neuron Segmentation in Electron Microscopy Images Using Partial Differential Equations,”** In *Proceedings of 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1457--1460. April, 2013.

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**“Toward an Understanding of the Short Bone Phenotype Associated with Multiple Osteochondromas,”** In *Journal of Orthopaedic Research*, Vol. 31, No. 4, pp. 651--657. 2013.

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**“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,”** In *Journal of Cardiovascular Magnetic Resonance*, Vol. 15, No. 105, 2013.

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**“Adaptive prior probability and spatial temporal intensity change estimation for segmentation of the one-year-old human brain,”** In *Journal of Neuroscience Methods*, Vol. 212, No. 1, Note: *Published online Sept. 29*, pp. 43--55. January, 2013.

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[Kir2013a] R.M. Kirby, M.D. Meyer.
**“Visualization Collaborations: What Works and Why,”** In *IEEE Computer Graphics and Applications: Visualization Viewpoints*, Vol. 33, No. 6, pp. 82--88. 2013.

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**“Ray Tracing and Volume Rendering Large Molecular Data on Multi-core and Many-core Architectures.,”** In *Proc. 8th International Workshop on Ultrascale Visualization at SC13 (Ultravis), 2013*, 2013.

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**“Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '13)*, Vol. 19, No. 12, pp. 2536--2545. 2013.

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**“Watershed Merge Forest Classification for Electron Microscopy Image Stack Segmentation,”** In *Proceedings of the 2013 International Conference on Image Processing*, 2013.

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**“The CommonGround visual paradigm for biosurveillance,”** In *Proceedings of the 2013 IEEE International Conference on Intelligence and Security Informatics (ISI)*, pp. 352--357. 2013.

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[Mal2013a] D. Maljovec, Bei Wang, V. Pascucci, P.-T. Bremer, M.Pernice, D. Mandelli, R. Nourgaliev.
**“Exploration of High-Dimensional Scalar Function for Nuclear Reactor Safety Analysis and Visualization,”** In *Proceedings of the 2013 International Conference on Mathematics and Computational Methods Applied to Nuclear Science & Engineering (M&C)*, pp. 712-723. 2013.

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**“Adaptive Sampling Algorithms for Probabilistic Risk Assessment of Nuclear Simulations,”** In *Proceedings of the 2013 International Topical Meeting on Probabilistic Safety Assessment and Analysis (PSA 2013)*, Note: *First runner-up for Best Student Paper Award*, 2013.

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[Mal2013d] D. Maljovec, Bei Wang, A. Kupresanin, G. Johannesson, V. Pascucci, P.-T. Bremer.
**“Adaptive Sampling with Topological Scores,”** In *Int. J. Uncertainty Quantification*, Vol. 3, No. 2, Begell House, pp. 119--141. 2013.

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**“Localized differences in caudate and hippocampal shape associated with schizophrenia but not antipsychotic type,”** In *Psychiatry Research: Neuroimaging*, Vol. 211, No. 1, pp. 1--10. January, 2013.

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**“Mechanistic Inquiry into the Role of Tissue Remodeling in Fibrotic Lesions in Human Atrial Fibrillation,”** In *Biophysical Journal*, Vol. 104, pp. 2764--2773. 2013.

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**“Atrial Fibrillation Ablation Outcome is Predicted by Left Atrial Remodeling on MRI,”** In *Circulation: Arrhythmia and Electrophysiology*, Note: *Published online before print.*, December, 2013.

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**“Similarity Measures for Enhancing Interactive Streamline Seeding,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 19, No. 8, pp. 1342--1353. 2013.

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[Men2013a] Q. Meng, A. Humphrey, J. Schmidt, M. Berzins.
**“Preliminary Experiences with the Uintah Framework on Intel Xeon Phi and Stampede,”** SCI Technical Report, No. UUSCI-2013-002, *SCI Institute, University of Utah*, 2013.

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**“Investigating Applications Portability with the Uintah DAG-based Runtime System on PetaScale Supercomputers,”** SCI Technical Report, No. UUSCI-2013-003, *SCI Institute, University of Utah*, 2013.

[Men2013d] Q. Meng, A. Humphrey, J. Schmidt, M. Berzins.
**“Investigating Applications Portability with the Uintah DAG-based Runtime System on PetaScale Supercomputers,”** In *Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis*, pp. 96:1--96:12. 2013.

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**“Preliminary Experiences with the Uintah Framework on Intel Xeon Phi and Stampede,”** In *Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE 2013)*, San Diego, California, pp. 48:1--48:8. 2013.

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**“Crash Early, Crash Often, Explain Well: Practical Formal Correctness Checking of Million-core Problem Solving Environments for HPC,”** In *Proceedings of the 35th International Conference on Software Engineering (ICSE 2013)*, pp. (accepted). 2013.

[Pan2013a] B. Paniagua, O. Emodi, J. Hill, J. Fishbaugh, L.A. Pimenta, S.R. Aylward, E. Andinet, G. Gerig, J. Gilmore, J.A. van Aalst, M. Styner.
**“3D of brain shape and volume after cranial vault remodeling surgery for craniosynostosis correction in infants,”** In *Proceedings of SPIE 8672, Medical Imaging 2013: Biomedical Applications in Molecular, Structural, and Functional Imaging, 86720V*, 2013.

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**“Lateral ventricle morphology analysis via mean latitude axis,”** In *Proceedings of SPIE 8672, Biomedical Applications in Molecular, Structural, and Functional Imaging, 86720M*, 2013.

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[Par2013a] C. Partl, A. Lex, M. Streit, D. Kalkofen, K. Kashofer, D. Schmalstieg.
**“enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets,”** In *BMC Bioinformatics*, Vol. 14, No. Suppl 19, Nov, 2013.

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[Pas2013a] V. Pascucci, P.-T. Bremer, A. Gyulassy, G. Scorzelli, C. Christensen, B. Summa, S. Kumar.
**“Scalable Visualization and Interactive Analysis Using Massive Data Streams,”** In *Cloud Computing and Big Data*, Advances in Parallel Computing, Vol. 23, IOS Press, pp. 212--230. 2013.

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**“The role of electrode location and stimulation polarity in patient response to cortical stimulation for major depressive disorder,”** In *Brain Stimulation*, Vol. 6, No. 3, Elsevier Ltd., pp. 254--260. July, 2013.

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**“Applying high-performance computing to petascale explosive simulations,”** In *Procedia Computer Science*, 2013.

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**“Scalable Seams for Gigapixel Panoramas,”** In *Proceedings of the 2013 Eurographics Symposium on Parallel Graphics and Visualization*, Note: *Awarded Best Paper!*, pp. 25--32. 2013.

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**“Visualization of Uncertainty without a Mean,”** In *IEEE Computer Graphics and Applications*, Visualization Viewpoints, Vol. 33, No. 1, pp. 75--79. 2013.

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**“Three-dimensional alignment and merging of confocal microscopy stacks,”** In *2013 IEEE International Conference on Image Processing*, IEEE, September, 2013.

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[Ree2013a] S.P. Reese, C.J. Underwood, J.A. Weiss.
**“Effects of decorin proteoglycan on fibrillogenesis, ultrastructure, and mechanics of type I collagen gels,”** In *Matrix Biology*, pp. (in press). 2013.

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**“Micromechanical model of a surrogate for collagenous soft tissues: development, validation, and analysis of mesoscale size effects,”** In *Biomechanics and Modeling in Mechanobiology*, pp. (in press). 2013.

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[Ros2013a] P. Rosen, B. Burton, K. Potter, C.R. Johnson.
**“Visualization for understanding uncertainty in the simulation of myocardial ischemia,”** In *Proceedings of the 2013 Workshop on Visualization in Medicine and Life Sciences*, 2013.

[Ros2013b] P. Rosen.
**“A Visual Approach to Investigating Shared and Global Memory Behavior of CUDA Kernels,”** In *Computer Graphics Forum*, Vol. 32, No. 3, Wiley-Blackwell, pp. 161--170. June, 2013.

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**“ManyVis: Multiple Applications in an Integrated Visualization Environment,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 19, No. 12, pp. 2878--2885. December, 2013.

[Sad2013a] N. Sadeghi, M.W. Prastawa, P.T. Fletcher, C. Vachet, Bo Wang, J.H. Gilmore, G. Gerig.
**“Multivariate Modeling of Longitudinal MRI in Early Brain Development with Confidence Measures,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1400--1403. 2013.

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**“Regional characterization of longitudinal DT-MRI to study white matter maturation of the early developing brain,”** In *NeuroImage*, Vol. 68, pp. 236--247. March, 2013.

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**“Analysis of Diffusion Tensor Imaging for Subjects with Down Syndrome,”** In *Proceedings of the 19th Annual Meeting of the Organization for Human Brain Mapping OHBM*, pp. (in print). 2013.

[Sad2013d] N. Sadeghi.
**“Modeling and Analysis of Longitudinal Multimodal Magnetic Resonance Imaging: Application to Early Brain Development,”** Note: *Ph.D. Thesis*, *Department of Bioengineering, University of Utah*, December, 2013.

[Saq2013a] Nazmus Saquib.
**“Visualizing Intrinsic Isosurface Variation due to Uncertainty Through Heat Kernel Signatures,”** Note: *Master of Science Thesis, Computational Engineering and Science (CES) Program*, *University of Utah School of Computing*, 2013.

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**“Ambient Occlusion Effects for Combined Volumes and Tubular Geometry,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 19, No. 6, Note: *Selected as Spotlight paper for June 2013 issue*, pp. 913--926. 2013.

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**“Relationship of the intercondylar roof and the tibial footprint of the ACL: implications for ACL reconstruction,”** In *American Journal of Sports Medicine*, Vol. 41, No. 2, pp. 396--401. 2013.

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**“Large Scale Parallel Solution of Incompressible Flow Problems using Uintah and hypre,”** In *2013 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)*, pp. 458--465. 2013.

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**“Segmentation of Mitochondria in Electron Microscopy Images using Algebraic Curves,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 860--863. 2013.

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**“Multi-class Multi-scale Series Contextual Model for Image Segmentation,”** In *IEEE Transactions on Image Processing*, Vol. PP, No. 99, 2013.

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**“Image Segmentation with Cascaded Hierarchical Models and Logistic Disjunctive Normal Networks,”** In *Proceedings of the IEEE International Conference on Computer Vison (ICCV 2013)*, pp. (accepted). 2013.

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**“Spatiotemporal Modeling of Discrete-Time Distribution-Valued Data Applied to DTI Tract Evolution in Infant Neurodevelopment,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 684--687. 2013.

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[Shi2013a] Y. Shi, G. Roger, C. Vachet, F. Budin, E. Maltbie, A. Verde, M. Hoogstoel, J.-B. Berger, M. Styner.
**“Software-based diffusion MR human brain phantom for evaluating fiber-tracking algorithms,”** In *Proceedings of SPIE 8669, Medical Imaging 2013: Image Processing, 86692A*, 2013.

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**“Associations Between White Matter Microstructure and Infants' Working Memory,”** In *Neuroimage*, Vol. 64, No. 1, Elsvier, pp. 156--166. January, 2013.

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[Sib2013a] S.C. Sibole, S.A. Maas, J.P. Halloran, J.A. Weiss, A. Erdemir.
**“Evaluation of a post-processing approach for multiscale analysis of biphasic mechanics of chondrocytes,”** In *Computer Methods in Biomechanical and Biomedical Engineering*, Vol. 16, No. 10, pp. 1112--1126. 2013.

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[Sin2013a] N.P. Singh, J. Hinkle, S. Joshi, P.T. Fletcher.
**“A Vector Momenta Formulation of Diffeomorphisms for Improved Geodesic Regression and Atlas Construction,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, Note: *Received Best Student Paper Award*, pp. 1219--1222. 2013.

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[Sin2013b] N.P. Singh, J. Hinkle, S. Joshi, P.T. Fletcher.
**“A Hierarchical Geodesic Model for Diffeomorphic Longitudinal Shape Analysis,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), pp. (accepted). 2013.

[Skr2013a] P. Skraba, Bei Wang, G. Chen, P. Rosen.
**“2D Vector Field Simplification Based on Robustness,”** SCI Technical Report, No. UUSCI-2013-004, *SCI Institute, University of Utah*, 2013.

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**“Potential for unreliable interpretation of EEG recorded with microelectrodes,”** In *Epilepsia*, May, 2013.

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[Sut2013a] T. Suter, A. Barg, M. Knupp, H.B. Henninger, B. Hintermann.
**“Surgical technique: talar neck osteotomy to lengthen the medial column after a malunited talar neck fracture,”** In *Clinical Orthopaedics & Related research*, Vol. 471, No. 4, pp. 1356--1364. 2013.

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[Sze2013a] M. Szegedi, J. Hinkle, P. Rassiah, V. Sarkar, B. Wang, S. Joshi, B. Salter.
**“Four‐dimensional tissue deformation reconstruction (4D TDR) validation using a real tissue phantom,”** In *Journal of Applied Clinical Medical Physics*, Vol. 14, No. 1, pp. 115-132. 2013.

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[Tas2013a] R.Z. Tashjian, H.B. Henninger.
**“Biomechanical evaluation of subpectoral biceps tenodesis: dual suture anchor versus interference screw fixation,”** In *Journal of Shoulder and Elbow Surgery*, Vol. 22, No. 10, pp. 1408–-1412. 2013.

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**“Modeling Longitudinal MRI Changes in Populations Using a Localized, Information-Theoretic Measure of Contrast,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1396--1399. 2013.

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[Var2013b] A. Vardhan, J. Piven, M. Prastawa, G. Gerig.
**“A longitudinal structural MRI study of change in regional contrast in Autism Spectrum Disorder,”** In *Proceedings of the 19th Annual Meeting of the Organization for Human Brain Mapping OHBM*, pp. (in print). 2013.

[Ven2013a] G. Veni, Z. Fu, S.P. Awate, R.T. Whitaker.
**“Proper Ordered Meshing of Complex Shapes and Optimal Graph Cuts Applied to Atrial-Wall Segmentation from DE-MRI,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1296--1299. 2013.

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[Ven2013b] G. Veni, S. Awate, Z. Fu, R.T. Whittaker.
**“Bayesian Segmentation of Atrium Wall using Globally-Optimal Graph Cuts on 3D Meshes,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), Vol. 23, pp. 656--677. 2013.

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[Ver2013a] A.R. Verde, J.-B. Berger, A. Gupta, M. Farzinfar, A. Kaiser, V.W. Chanon, C. Boettiger, H. Johnson, J. Matsui, A. Sharma, C. Goodlett, Y. Shi, H. Zhu, G. Gerig, S. Gouttard, C. Vachet, M. Styner.
**“UNC-Utah NA-MIC DTI framework: atlas based fiber tract analysis with application to a study of nicotine smoking addiction,”** In *Proc. SPIE 8669, Medical Imaging 2013: Image Processing, 86692D*, Vol. 8669, pp. 86692D-86692D-8. 2013.

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[Wan2013a] Bo Wang, M.W. Prastawa, A. Irimia, M.C. Chambers, N. Sadeghi, P.M. Vespa, J.D. van Horn, G. Gerig.
**“Analyzing Imaging Biomarkers for Traumatic Brain Injury Using 4D Modeling of Longitudinal MRI,”** In *2013 IEEE Proceedings of 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1392 - 1395. 2013.

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[Wan2013b] D. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson.
**“Inverse Electrocardiographic Source Localization of Ischemia: An Optimization Framework and Finite Element Solution,”** In *Journal of Computational Physics*, Vol. 250, Academic Press, pp. 403--424. 2013.

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[Wan2013c] Bei Wang, P. Rosen, P. Skraba, H. Bhatia, V. Pascucci.
**“Visualizing Robustness of Critical Points for 2D Time-Varying Vector Fields,”** In *Computer Graphics Forum*, Vol. 32, No. 3, Wiley-Blackwell, pp. 221--230. jun, 2013.

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[Wan2013d] Y. Wan, H. Otsuna, C.D. Hansen.
**“Synthetic Brainbows,”** In *Computer Graphics Forum*, Vol. 32, No. 3pt4, Wiley-Blackwell, pp. 471--480. jun, 2013.

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[Wan2013e] Bo Wang, M. Prastawa, A. Saha, S.P. Awate, A. Irimia, M.C. Chambers, P.M. Vespa, J.D. Van Horn, V. Pascucci, G. Gerig.
**“Modeling 4D changes in pathological anatomy using domain adaptation: analysis of TBI imaging using a tumor database,”** In *Proceedings of the 2013 MICCAI-MBIA Workshop*, Lecture Notes in Computer Science (LNCS), Vol. 8159, Note: *Awarded Best Paper!*, pp. 31--39. 2013.

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[Wan2013f] Y. Wan.
**“Fluorender, An Interactive Tool for Confocal Microscopy Data Visualization and Analysis,”** Note: *Ph.D. Thesis*, *School of Computing, University of Utah*, June, 2013.

[Web2013a] G.H. Weber, K. Beketayev, P.-T. Bremer, B. Hamann, M. Haranczyk, M. Hlawitschka, V. Pascucci.
**“Comprehensible Presentation of Topological Information,”** No. LBNL-5693E, *Lawrence Berkeley National Laboratory*, 2013.

[Whi2013a] R.T. Whitaker, M. Mirzargar, R.M. Kirby.
**“Contour Boxplots: A Method for Characterizing Uncertainty in Feature Sets from Simulation Ensembles,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 19, No. 12, pp. 2713--2722. December, 2013.

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**“A Flexible Framework for Fusing Image Collections into Panoramas,”** In *Proceedings of the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images*, Note: *Awarded Best Paper.*, pp. 195-202. 2013.

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**“Bayesian Estimation of Regularization and Atlas Building in Diffeomorphic Image Registration,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), pp. (accepted). 2013.

[Zha2013b] M. Zhang, P.T. Fletcher.
**“Probabilistic Principal Geodesic Analysis,”** In *Proceedings of the 2013 Conference on Neural Information Processing Systems (NIPS)*, pp. (accepted). 2013.

[Zho2013a] L. Zhou, C.D. Hansen.
**“Transfer Function Design based on User Selected Samples for Intuitive Multivariate Volume Exploration,”** In *Proceedings of the 2013 IEEE Pacific Visualization Symposium (PacificVis)*, pp. 73--80. 2013.

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**“Interactive rendering and efficient querying for large multivariate seismic volumes on consumer level PCs,”** In *Proceedings of the 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV)*, pp. 117--118. 2013.

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**“Model Selection and Estimation of Multi-Compartment Models in Diffusion MRI with a Rician Noise Model,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), Vol. 23, pp. 644--655. 2013.

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**“Differences in subcortical structures in young adolescents at familial risk for schizophrenia: A preliminary study,”** In *Psychiatry Res.*, pp. (Epub ahead of print. Nov. 9, 2012.

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**“Topology Preserving Atlas Construction from Shape Data without Correspondence using Sparse Parameters,”** In *Proceedings of MICCAI 2012*, Lecture Notes in Computer Science (LNCS), pp. 223--230. October, 2012.

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**“Quantitative Tract-Based White Matter Development from Birth to Age Two Years,”** In *NeuroImage*, pp. 1-44. March, 2012.

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**“The EpiCanvas infectious disease weather map: an interactive visual exploration of temporal and spatial correlations,”** In *J. Amer. Med. Inform. Assoc.*, Vol. 19, Note: *Awarded 1st place for Outstanding Research Article at ISDS 2012 and the Homer R. Warner Award at the AMIA Annual Symposium 2012*, pp. 954--959. 2012.

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**“Multiscale mechanics of articular cartilage: potentials and challenges of coupling musculoskeletal, joint, and microscale computational models,”** In *Annals of Biomedical Engineering*, Vol. 40, No. 11, pp. 2456--2474. 2012.

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**“Correlation between radiographic measures of acetabular morphology with 3D femoral head coverage in patients with acetabular retroversion,”** In *Acta Orthopaedica*, Vol. 83, No. 3, pp. 233--239. 2012.

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**“Finite element prediction of cartilage contact stresses in normal human hips,”** In *Journal of Orthopaedic Research*, Vol. 30, No. 7, pp. 1133--1139. 2012.

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**“Brain Volume Findings in Six Month Old Infants at High Familial Risk for Autism,”** In *American Journal of Psychiatry (AJP)*, pp. (in print). 2012.

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**“Serial section registration of axonal confocal microscopy datasets for long-range neural circuit reconstruction,”** In *Journal of Neuroscience Methods*, Vol. 207, No. 2, pp. 200--210. 2012.

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**“Output-Coherent Image-Space LIC for Surface Flow Visualization,”** In *Proceedings of the IEEE Pacific Visualization Symposium 2012*, Korea, pp. 137--144. 2012.

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**“Sliding Contact Loading Enhances The Tensile Properties Of Mesenchymal Stem Cell-Seeded Hydrogels,”** In *European Cells and Materials*, Vol. 24, pp. 29--45. 2012.

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[Hum2012a] A. Humphrey, Q. Meng, M. Berzins, T. Harman.
**“Radiation Modeling Using the Uintah Heterogeneous CPU/GPU Runtime System,”** SCI Technical Report, No. UUSCI-2012-003, *SCI Institute, University of Utah*, 2012.

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**“Radiation Modeling Using the Uintah Heterogeneous CPU/GPU Runtime System,”** In *Proceedings of the first conference of the Extreme Science and Engineering Discovery Environment (XSEDE'12)*, Association for Computing Machinery, 2012.

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[Iri2012a] A. Irimia, M.C. Chambers, C.M. Torgerson, M. Filippou, D.A. Hovda, J.R. Alger, G. Gerig, A.W. Toga, P.M. Vespa, R. Kikinis, J.D. Van Horn.
**“Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury,”** In *Frontiers in Neurotrauma*, Note: *http://www.frontiersin.org/neurotrauma/10.3389/fneur.2012.00010/abstract*, 2012.

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[Iri2012b] A. Irimia, Bo Wang, S.R. Aylward, M.W. Prastawa, D.F. Pace, G. Gerig, D.A. Hovda, R.Kikinis, P.M. Vespa, J.D. Van Horn.
**“Neuroimaging of Structural Pathology and Connectomics in Traumatic Brain Injury: Toward Personalized Outcome Prediction,”** In *NeuroImage: Clinical*, Vol. 1, No. 1, Elsvier, pp. 1--17. 2012.

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[Iye2012a] S.K. Iyer, T. Tasdizen, E.V.R. DiBella.
**“Edge Enhanced Spatio-Temporal Constrained Reconstruction of Undersampled Dynamic Contrast Enhanced Radial MRI,”** In *Magnetic Resonance Imaging*, Vol. 30, No. 5, pp. 610--619. 2012.

[Joh2012a] C.R. Johnson.
**“Biomedical Visual Computing: Case Studies and Challenges,”** In *IEEE Computing in Science and Engineering*, Vol. 14, No. 1, pp. 12--21. 2012.

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[Jur2012a] E. Jurrus, S. Watanabe, R.J. Giuly, A.R.C. Paiva, M.H. Ellisman, E.M. Jorgensen, T. Tasdizen.
**“Semi-Automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images,”** In *Neuroinformatics*, pp. (published online). 2012.

[Kap2012a] T. Kapur, S. Pieper, R.T. Whitaker, S. Aylward, M. Jakab, W. Schroeder, R. Kikinis.
**“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,”** In *Journal of the American Medical Informatics Association*, In *Journal of the American Medical Informatics Association*, Vol. 19, No. 2, pp. 176--180. 2012.

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[Kim2012a] M. Kim, G. Chen, C.D. Hansen.
**“Dynamic particle system for mesh extraction on the GPU,”** In *Proceedings of the 5th Annual Workshop on General Purpose Processing with Graphics Processing Units*, London, England, GPGPU-5, ACM, New York, NY, USA pp. 38--46. 2012.

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**“A Multiscale Approach to Network Event Identification using Geolocated Twitter Data,”** In *First IMC Workshop on Internet Visualization (WIV 2012)*, pp. (accepted). 2012.

[Zho2012a] L. Zhou, M. Schott, C.D. Hansen.
**“Transfer Function Combinations,”** In *Computers and Graphics*, Vol. 36, No. 6, pp. 596--606. October, 2012.

DOI: 10.1016/j.cag.2012.02.007

[Zhu2012a] L. Zhu, Y. Gao, A. Yezzi, R.S. MacLeod, J. Cates, A. Tannenbaum.
**“Automatic Segmentation of the Left Atrium from MRI Images using Salient Feature and Contour Evolution,”** In *Proceedings of the 34th Annual International Conference of the IEEE EMBS*, pp. 3211--214. 2012.

DOI: 10.1109/EMBC.2012.6346648

PubMed ID: 23366609

PubMed Central ID: PMC3652873

[Zie2012a] T. Ziemek, S. Creem-Regehr, W. Thompson, R.T. Whitaker.
**“Evaluating the effectiveness of orientation indicators with an awareness of individual differences,”** In *ACM Transactions on Applied Perception (TAP)*, Vol. 9, No. 2, pp. Article 7. 2012.

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[Zie2012b] B.A. Zielinski, J.S. Anderson, A.L. Froehlich, M.B.D. Prigge, J.A. Nielsen, J.R. Cooperrider, A.N. Cariello, P.T. Fletcher, A.L. Alexander, Nicholas Lange, Erin D Bigler, Janet E Lainhart.
**“scMRI Reveals Large-Scale Brain Network Abnormalities in Autism,”** In *PloS one*, Vol. 7, No. 11, pp. e49172. 2012.

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2011

[Ahe2011a] S. Ahern, A. Shoshani, K.L. Ma, A. Choudhary, T. Critchlow, S. Klasky, V. Pascucci.
**“Scientific Discovery at the Exascale: Report from the (DOE) (ASCR) 2011 Workshop on Exascale Data Management, Analysis, and Visualization,”** Note: *Office of Scientific and Technical Information (OSTI)*, January, 2011.

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[Ako2011a] N. Akoum, M. Daccarett, C. McGann, N. Segerson, G. Vergara, S. Kuppahally, T. Badger, N. Burgon, T. Haslam, E. Kholmovski, R.S. MacLeod, N.F. Marrouche.
**“Atrial fibrosis helps select the appropriate patient and strategy in catheter ablation of atrial fibrillation: a DE-MRI guided approach,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 22, No. 1, pp. 16--22. 2011.

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PubMed ID: 20807271

[Alt2011a] I. Altrogge, T. Preusser, T. Kroeger, S. Haase, T. Paetz, R.M. Kirby.
**“Sensitivity Analysis for the Optimization of Radiofrequency Ablation in the Presence of Material Parameter Uncertainty,”** In *International Journal for Uncertainty Quantification*, 2011.

[And2011a] J.R. Anderson, B.W. Jones, C.B. Watt, M.V. Shaw, J.-H. Yang, D. DeMill, J.S. Lauritzen, Y. Lin, K.D. Rapp, D. Mastronarde, P. Koshevoy, B. Grimm, T. Tasdizen, R.T. Whitaker, R.E. Marc.
**“Exploring the Retinal Connectome,”** In *Molecular Vision*, Vol. 17, pp. 355--379. 2011.

PubMed ID: 21311605

[And2011b] E.W. Anderson, K.C. Potter, L.E. Matzen, J.F. Shepherd, G.A. Preston, C.T. Silva.
**“A User Study of Visualization Effectiveness Using EEG and Cognitive Load,”** In *Computer Graphics Forum*, Vol. 30, No. 3, Note: *Awarded 2nd Best Paper!*, Edited by H. Hauser and H. Pfister and J.J. van Wijk, pp. 791--800. June, 2011.

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[And2011c] N. Andrysco, P. Rosen, V. Popescu, B. Benes, K.R. Gurney.
**“Experiences in Disseminating Educational Visualizations,”** In *Lecture Notes in Computer Science (7th International Symposium on Visual Computing)*, Vol. 2, pp. 239--248. September, 2011.

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[And2011d] J.S. Anderson, J.A. Nielsen, A.L. Froehlich, M.B. DuBray, T.J. Druzgal, A.N. Cariello, J.R. Cooperrider, B.A. Zielinski, C. Ravichandran, P.T. Fletcher, A.L. Alexander, E.D. Bigler, N. Lange, J.E. Lainhart.
**“Functional connectivity magnetic resonance imaging classification of autism,”** In *Brain*, pp. (published online). 2011.

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[And2011e] J.R. Anderson, S. Mohammed, B.C. Grimm, B.W. Jones, P. Koshevoy, T. Tasdizen, R.T. Whitaker, R.E. Marc.
**“The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets,”** In *Journal of Microscopy*, Vol. 241, No. 1, pp. 13--28. 2011.

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[Ate2011a] G.A. Ateshian, M.B. Albro, S.A. Maas, J.A. Weiss.
**“Finite element implementation of mechanochemical phenomena in neutral deformable porous media under finite deformation,”** In *Journal of Biomechanical Engineering*, Vol. 133, No. 8, 2011.

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[Ben2011a] J.C. Bennett, V. Krishnamoorthy, S. Liu, R.W. Grout, E.R. Hawkes, J.H. Chen, J. Shepherd, V. Pascucci, P.-T. Bremer.
**“Feature-Based Statistical Analysis of Combustion Simulation Data,”** In *IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2011 IEEE Visualization Conference*, Vol. 17, No. 12, pp. 1822--1831. 2011.

[Ber2011a] M. Berger, J.A. Levine, L.G. Nonato, G. Taubin, C.T. Silva.
**“An End-to-End Framework for Evaluating Surface Reconstruction,”** SCI Technical Report, No. UUSCI-2011-001, *SCI Institute, University of Utah*, 2011.

[Ber2011c] M.L. Berlanga, S. Phan, E.A. Bushong, S. Lamont, S. Wu, O. Kwon, B.S. Phung, M. Terada, T. Tasdizen, E. Martone, M.H. Ellisman.
**“Three-dimensional reconstruction of serial mouse brain sections using high-resolution large-scale mosaics,”** In *Frontiers in Neuroscience Methods*, Vol. 5, pp. (published online). March, 2011.

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[Bha2011a] H. Bhatia, S. Jadhav, P.-T. Bremer, G. Chen, J.A. Levine, L.G. Nonato, V. Pascucci.
**“Edge Maps: Representing Flow with Bounded Error,”** In *Proceedings of IEEE Pacific Visualization Symposium 2011*, Hong Kong, China, Note: *Won Best Paper Award!*, pp. 75--82. March, 2011.

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[Bha2011b] H. Bhatia, S. Jadhav, P.-T. Bremer, G. Chen, J.A. Levine, L.G. Nonato, V. Pascucci.
**“Flow Visualization with Quantified Spatial and Temporal Errors using Edge Maps,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 18, No. 9, IEEE Society, pp. 1383--1396. 2011.

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**“Physically-Based Interactive Flow Visualization Based on Schlieren and Interferometry Experimental Techniques,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 17, No. 11, pp. 1574--1586. 2011.

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**“Physically-Based Interactive Flow Visualization Based on Schlieren and Interferometry Experimental Techniques,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE Transactions on Visualization and Computer Graphics, Vol. 17, No. 11, IEEE, pp. 1574--1586. November, 2011.

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[Bur2011a] B.M. Burton, J.D. Tate, B. Erem, D.J. Swenson, D.F. Wang, D.H. Brooks, P.M. van Dam, R.S. MacLeod.
**“A Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment,”** In *Proceedings of the 2011 IEEE Int. Conf. Engineering and Biology Society (EMBC)*, pp. 267--270. 2011.

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[But2011a] C.R. Butson, S.E. Cooper, J.M. Henderson, B. Wolgamuth, C.C. McIntyre.
**“Probabilistic Analysis of Activation Volumes Generated During Deep Brain Stimulation,”** In *NeuroImage*, Vol. 54, pp. 2096--2104. 2011.

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**“Selective neural activation in a histologically derived model of peripheral nerve,”** In *Journal of Neural Engineering*, Vol. 8, No. 3, pp. 036009. June, 2011.

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[Buz2011a] G.T. Buzzard, D. Xiu.
**“Variance-based Global Sensitivity Analysis via Sparse-grid Interpolation and Cubature,”** In *Communications in Computational Physics*, Vol. 9, No. 3, pp. 542--567. 2011.

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[Can2011a] C.D. Cantwell, S.J. Sherwin, R.M. Kirby, P.H.J. Kelly.
**“From h to p Efficiently: Strategy Selection for Operator Evaluation on Hexahedral and Tetrahedral Elements,”** In *Computers and Fluids*, Vol. 43, No. 1, pp. 23--28. 2011.

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[Can2011b] C.D. Cantwell, S.J. Sherwin, R.M. Kirby, P.H.J. Kelly.
**“From h to p Efficiently: Selecting the Optimal Spectral/hp Discretisation in Three Dimensions,”** In *Mathematical Modelling of Natural Phenomena*, Vol. 6, No. 3, pp. 84--96. 2011.

[Che2011b] G. Chen, D. Palke, Z. Lin, H. Yeh, P. Vincent, R.S. Laramee, E. Zhang.
**“Asymmetric Tensor Field Visualization for Surfaces,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 17, No. 12, IEEE, pp. 1979-1988. Dec, 2011.

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[Che2011c] Guoning Chen, Qingqing Deng, Andrzej Szymczak, Robert S. Laramee, and Eugene Zhang.
**“Morse Set Classification and Hierarchical Refinement using Conley Index,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 18, No. 5, pp. 767--782. June, 2011.

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[Cho2011a] A.N.M. Imroz Choudhury, P. Rosen.
**“Abstract Visualization of Runtime Memory Behavior,”** In *6th IEEE International Workshop on Visualizing Software for Understanding and Analysis (VISSOFT 2011)*, pp. 22--29. 2011.

[Cua2011a] A. Cuadros-Vargas, L.G. Nonato, V. Pascucci.
**“Combinatorial Laplacian Image Cloning,”** In *Proceedings of XXIV Sibgrapi – Conference on Graphics, Patterns and Images*, pp. 236--241. 2011.

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[Dac2011a] M. Daccarett, T.J. Badger, N. Akoum, N.S. Burgon, C. Mahnkopf, G.R. Vergara, E.G. Kholmovski, C.J. McGann, D.L. Parker, J. Brachmann, R.S. Macleod, N.F. Marrouche.
**“Association of left atrial fibrosis detected by delayed-enhancement magnetic resonance imaging and the risk of stroke in patients with atrial fibrillation,”** In *Journal of the American College of Cardiology*, Vol. 57, No. 7, pp. 831--838. 2011.

PubMed ID: 21310320

[Dac2011b] M. Daccarett, C.J. McGann, N.W. Akoum, R.S. MacLeod, N.F. Marrouche.
**“MRI of the left atrium: predicting clinical outcomes in patients with atrial fibrillation,”** In *Expert Review of Cardiovascular Therapy*, Vol. 9, No. 1, pp. 105--111. 2011.

PubMed ID: 21166532

[Dat2011a] M. Datar, Y. Gur, B. Paniagua, M. Styner, R.T. Whitaker.
**“Geometric Correspondence for Ensembles of Nonregular Shapes,”** In *Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011)*, Lecture Notes in Computer Science (LNCS), Vol. 6892, pp. 368--375. 2011.

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PubMed ID: 21995050

PubMed Central ID: PMC3346950

[Dru2011a] N.J. Drury, B.J. Ellis, J.A. Weiss, P.J. McMahon, R.E. Debski.
**“Finding consistent strain distributions in the glenohumeral capsule between two subjects: Implications for development of physical examinations,”** In *Journal of Biomechanics*, Vol. 44, No. 4, pp. 607-613. February, 2011.

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[Dur2011a] S. Durrleman, M.W. Prastawa, G. Gerig, S. Joshi.
**“Optimal data-driven sparse parameterization of diffeomorphisms for population analysis,”** In *Proceedings of the IPMI 2011 conference*, Springer LNCS, Vol. 6801/2011, pp. 123--134. July, 2011.

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PubMed ID: 20516153

[Dur2011b] S. Durrleman, X. Pennec, A. Trouvé, N. Ayache, J. Braga.
**“Comparison of the endocranial ontogenies between chimpanzees and bonobos via temporal regression and spatiotemporal registration,”** In *Journal of Human Evolution*, pp. 74--88. January, 2011.

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[Edm2011a] M. Edmunds, T. McLoughlin, R.S. Laramee, G. Chen, E. Zhang, N. Max.
**“Automatic Stream Surface Seeding,”** In *EUROGRAPHICS 2011 Short Papers*, pp. 53--56. 2011.

[Elk2011a] J.M. Elkins, J.S. Stroud, M.J. Rudert, Y. Tochigi, D.R. Pedersen, B.J. Ellis, J.J. Callaghan, J.A. Weiss, T.D. Brown.
**“The capsule's contribution to total hip construct stability - a finite element analysis,”** In *Journal of Orthopedic Research*, Vol. 29, No. 11, Note: *William Harris, MD Award*, pp. 1642--1648. November, 2011.

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[Ell2011a] B.J. Ellis.
**“Finite element modeling of knee and shoulder ligaments,”** Note: *Ph.D. Thesis*, *Department of Bioengineering, University of Utah*, 2011.

[Ere2011a] B. Erem, D.H. Brooks, P.M. van Dam, J.G. Stinstra, R.S. MacLeod.
**“Spatiotemporal Estimation of Activation Times of Fractionated ECGs on Complex Heart Surfaces,”** In *Proceedings of the International Coference of the IEEE Engineering in Medicine and Biology Society (EMBS)*, pp. 5884--5887. 2011.

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PubMed ID: 22255678

PubMed Central ID: PMC3345888

[Eti2011b] T. Etiene, L.G. Nonato, C. Scheidegger, J. Tierny, T.J. Peters, V. Pascucci, R.M. Kirby, C.T. Silva.
**“Topology Verfication for Isosurface Extraction,”** In *IEEE Transactions on Visualization and Computer Graphics*, pp. (accepted). 2011.

[Fis2011a] J. Fishbaugh, S. Durrleman, G. Gerig.
**“Estimation of Smooth Growth Trajectories with Controlled Acceleration from Time Series Shape Data,”** In *Lecture Notes in Computer Science*, LNCS 6892, Springer, pp. 401--408. 2011.

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[Fle2011a] P.T. Fletcher.
**“Geodesic Regression on Riemannian Manifolds,”** In *Proceedings of the Third MICCIA International Workshop on Mathematical Foundations of Computational Anatomy (MFCA)*, Toronto, Canada, pp. 75--86. 2011.

[Fle2011b] P.T. Fletcher, J. Moeller, J. Phillips, S. Venkatasubramanian.
**“Horoball hulls and extents in positive definite space,”** In *Algorithms and Data Structures*, Lecture Notes in Computer Science (LNCS), Vol. 6844/2011, pp. 386--398. 2011.

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[Fog2011a] T. Fogal, J. Krüger.
**“Efficient I/O for Parallel Visualization,”** In *Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (2011)*, Edited by T. Kuhlen and R. Pajarola and K. Zhou, pp. 81--90. 2011.

[Fow2011a] C. Fowlkes, K. Eckenrode, M. Bragdon, M.D. Meyer, Z. Wunderlich, L. Simirenko, C. Luengo, S. Keranen, C. Henriquez, D. Knowles, M. Biggin, M. Eisen, A. DePace.
**“A Conservered Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila,”** In *PLoS Genetics*, Vol. 7, No. 10:e1002346, pp. 17 pages. October, 2011.

[Fu2011a] Z. Fu, W.-K. Jeong, Y. Pan, R.M. Kirby, R.T. Whitaker.
**“A fast iterative method for solving the Eikonal equation on triangulated surfaces,”** In *SIAM Journal of Scientific Computing*, Vol. 33, No. 5, pp. 2468--2488. 2011.

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[Gen2011a] S.E. Geneser, J.D. Hinkle, R.M. Kirby, Bo Wang, B. Salter, S. Joshi.
**“Quantifying variability in radiation dose due to respiratory-induced tumor motion,”** In *Medical Image Analysis*, Vol. 15, No. 4, pp. 640--649. 2011.

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[Ger2011c] G. Gerig, I. Oguz, S. Gouttard, J. Lee, H. An, W. Lin, M. McMurray, K. Grewen, J. Johns, M.A. Styner.
**“Synergy of image analysis for animal and human neuroimaging supports translational research on drug abuse,”** In *Frontiers in Child and Neurodevelopmental Psychiatry*, Vol. 2, Edited by Linda Mayes, pp. 9 pages. 2011.

ISSN: 1664-0640

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[Ger2011d] G. Gerig, J.H. Gilmore, W. Lin.
**“Brain Maturation of Newborns and Infants,”** *Encyclopedia on Early Childhood Development (online): Brain Development in Children - According to Experts*, Montreal, Quebec, Centre of Excellence for Early Childhood Development and Strategic Knowledge Cluster on Early Child Development, pp. 1--6. 2011.

[Gey2011a] T. Geymayer, A. Lex, M. Streit, D. Schmalstieg.
**“Visualizing the Effects of Logically Combined Filters,”** In *Proceedings of the Conference on Information Visualisation (IV '11)*, IEEE, pp. 47--52. 2011.

[Gop2011a] G. Gopalakrishnan, R.M. Kirby, S. Siegel, R. Thakur, W. Gropp, E. Lusk, B.R. de Supinski, M. Schultz, G. Bronevetsky.
**“Formal Analysis of MPI-Based Parallel Programs: Present and Future,”** In *Communications of the ACM*, pp. (accepted). 2011.

[Gru2011a] J. Grueninger, H. Hoffman, U. Kloos, J. Krüger.
**“Multi-Resolution-Display System for Virtual Reality Setups,”** In *Proceedings of the 14th International Conference on Human-Computer Interaction, HCI International*, Lecture Notes in Computer Science, Vol. 6779/2011, pp. 180--189. 2011.

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[Gyu2011a] Attila Gyulassy, J.A. Levine, V. Pascucci.
**“Visualization of Discrete Gradient Construction (Multimedia submission),”** In *Proceedings of the 27th Symposium on Computational Geometry*, Paris, France, ACM, pp. 289--290. June, 2011.

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[Ha2011a] L.K. Ha, J. Krüger, J. Comba, S. Joshi, C.T. Silva.
**“Optimal Multi-Image Processing Streaming Framework on Parallel Heterogeneous Systems,”** In *Proceedings of Eurographics Symposium on Parallel Graphics and Visualization 2011*, Note: *Awarded Best Paper!*, pp. 1--10. 2011.

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[Ha2011b] L.K. Ha, M.W. Prastawa, G. Gerig, J.H. Gilmore, C.T. Silva.
**“Efficient Probabilistic and Geometric Anatomical Mapping Using Particle Mesh Approximation on GPUs,”** In *International Journal of Biomedical Imaging, Special Issue in Parallel Computation in Medical Imaging Applications*, Vol. 2011, Note: *Article ID 572187*, pp. 16 pages. 2011.

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[Ha2011c] L.K. Ha, J. Krüger, S. Joshi, C.T. Silva.
**“Multi-scale Unbiased Diffeomorphic Atlas Construction on Multi-GPUs,”** Vol. 1, Ch. 10, Morgan Kaufmann, pp. 42. 2011.

[Hao2011b] X. Hao, R.T. Whitaker, P.T. Fletcher.
**“Adaptive Riemannian Metrics for Improved Geodesic Tracking of White Matter,”** In *Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), Vol. 6801/2011, pp. 13--24. 2011.

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[Har2011a] D.E. Hart, M. Berzins, C.E. Goodyer, P.K. Jimack.
**“Using Adjoint Error Estimation Techniques for Elastohydrodynamic Lubrication Line Contact Problems,”** In *International Journal for Numerical Methods in Fluids*, Vol. 67, Note: *Published online 29 October*, pp. 1559--1570. 2011.

[Haz2011a] H.C. Hazlett, M. Poe, G. Gerig, M. Styner, C. Chappell, R.G. Smith, C. Vachet, J. Piven.
**“Early Brain Overgrowth in Autism Associated with an Increase in Cortical Surface Area Before Age 2,”** In *Arch of Gen Psych*, Vol. 68, No. 5, pp. 467--476. 2011.

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[Hen2011a] C.R. Henak, B.J. Ellis, M.D. Harris, A.E. Anderson, C.L. Peters, J.A. Weiss.
**“Role of the acetabular labrum in load support across the hip joint,”** In *Journal of Biomechanics*, Vol. 44, No. 12, pp. 2201-2206. 2011.

[Hog2011a] L. Hogrebe, A. Paiva, E. Jurrus, C. Christensen, M. Bridge, J.R. Korenberg, T. Tasdizen.
**“Trace Driven Registration of Neuron Confocal Microscopy Stacks,”** In *IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 1345--1348. 2011.

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[Iri2011a] A. Irimia, M.C. Chambers, J.R. Alger, M. Filippou, M.W. Prastawa, Bo Wang, D. Hovda, G. Gerig, A.W. Toga, R. Kikinis, P.M. Vespa, J.D. Van Horn.
**“Comparison of acute and chronic traumatic brain injury using semi-automatic multimodal segmentation of MR volumes,”** In *Journal of Neurotrauma*, Vol. 28, No. 11, pp. 2287--2306. November, 2011.

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[Isa2011a] B.M. Isaacson, J.G. Stinstra, R.D. Bloebaum, COL P.F. Pasquina, R.S. MacLeod.
**“Establishing Multiscale Models for Simulating Whole Limb Estimates of Electric Fields for Osseointegrated Implants,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 58, No. 10, pp. 2991--2994. 2011.

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[Isa2011b] S.A. Isaacson, R.M. Kirby.
**“Numerical Solution of Linear Volterra Integral Equations of the Second Kind with Sharp Gradients,”** In *Journal of Computational and Applied Mathematics*, Vol. 235, No. 14, pp. 4283--4301. 2011.

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**“RTSAH Traversal Order for Occlusion Rays,”** In *Computer Graphics Forum*, Vol. 30, No. 2, Wiley-Blackwell, pp. 297--305. April, 2011.

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[Ize2011b] T. Ize, C. Brownlee, C.D. Hansen.
**“Real-Time Ray Tracer for Visualizing Massive Models on a Cluster,”** In *Proceedings of the 2011 Eurographics Symposium on Parallel Graphics and Visualization*, pp. 61--69. 2011.

[Jad2011a] S. Jadhav, H. Bhatia, P.-T. Bremer, J.A. Levine, L.G. Nonato, V. Pascucci.
**“Consistent Approximation of Local Flow Behavior for 2D Vector Fields,”** In *Mathematics and Visualization*, Springer, pp. 141--159. Nov, 2011.

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**“Characterization of Discontinuities in High-dimensional Stochastic Problmes on Adaptive Sparse Grids,”** In *Journal of Computational Physics*, Vol. 230, No. 10, pp. 3977--3997. 2011.

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**“Detection of crossing white matter fibers with high-order tensors and rank-k decompositions,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI 2011)*, Lecture Notes in Computer Science (LNCS), Vol. 6801, pp. 538--549. 2011.

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[Jim2011a] P.K. Jimack, R.M. Kirby.
**“Towards the Development on an h-p-Refinement Strategy Based Upon Error Estimate Sensitivity,”** In *Computers and Fluids*, Vol. 46, No. 1, pp. 277--281. 2011.

[Jur2011a] E. Jurrus, S. Watanabe, R. Guily, A.R.C. Paiva, M.H. Ellisman, E.M. Jorgensen, T. Tasdizen.
**“Semi-automated Neuron Boundary Detection and Slice Traversal Algorithm for Segmentation of Neurons from Electron Microscopy Images,”** In *Microscopic Image Analysis with Applications in Biology (MIAAB) Workshop*, 2011.

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**“A Diffusion Approach to Network Localization,”** In *IEEE Transactions on Signal Processing*, Vol. 59, No. 6, pp. 2642--2654. 2011.

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**“Advisory Committee for CyberInfrastructure Task Force on Software for Science and Engineering,”** Note: *NSF Report*, 2011.

[Kim2011a] S.H. Kim, V. Fonov, J. Piven, J. Gilmore, C. Vachet, G. Gerig, D.L. Collins, M. Styner.
**“Spatial Intensity Prior Correction for Tissue Segmentation in the Developing human Brain,”** In *Proceedings of IEEE ISBI 2011*, pp. 2049--2052. 2011.

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[Kir2011a] R.M. Kirby, B. Cockburn, S.J. Sherwin.
**“To CG or to HDG: A Comparative Study,”** In *Journal of Scientific Computing*, Note: *published online*, 2011.

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[Kni2011a] R.C. Knickmeyer, C. Kang, S. Woolson, K.J. Smith, R.M. Hamer, W. Lin, G. Gerig, M. Styner, J.H. Gilmore.
**“Twin-Singleton Differences in Neonatal Brain Structure,”** In *Twin Research and Human Genetics*, Vol. 14, No. 3, pp. 268--276. 2011.

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**“Full-Resolution Interactive CPU Volume Rendering with Coherent BVH Traversal,”** In *Proceedings of IEEE Pacific Visualization 2011*, pp. 3--10. 2011.

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**“Epidural cortical stimulation of the left dorsolateral prefrontal cortex for refractory major depressive disorder,”** In *Neurosurgery*, Vol. 69, No. 5, pp. 1015--1029. November, 2011.

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[Kum2011a] S. Kumar, V. Vishwanath, P. Carns, B. Summa, G. Scorzelli, V. Pascucci, R. Ross, J. Chen, H. Kolla, R. Grout.
**“PIDX: Efficient Parallel I/O for Multi-resolution Multi-dimensional Scientific Datasets,”** In *Proceedings of The IEEE International Conference on Cluster Computing*, pp. 103--111. September, 2011.

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**“A rapid 2-D centerline extraction method based on tensor voting,”** In *2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro*, pp. 1000--1003. 2011.

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[Lex2011a] A. Lex, H. Schulz, M. Streit, C. Partl, D. Schmalstieg.
**“VisBricks: Multiform Visualization of Large, Inhomogeneous Data,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '11)*, Vol. 17, No. 12, 2011.

[Li2011a] G. Li, R. Palmer, M. DeLisi, G. Gopalakrishnan, R.M. Kirby.
**“Formal Specification of MPI 2.0: Case Study in Specifying a Practical Concurrent Programming API,”** In *Science of Computer Programming*, Vol. 76, pp. 65--81. 2011.

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[Li2011b] J. Li, J. Li, D. Xiu.
**“An Efficient Surrogate-based Method for Computing Rare Failure Probability,”** In *Journal of Computational Physics*, Vol. 230, No. 24, pp. 8683--8697. 2011.

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**“DEFOG: A System for Data-Backed Visual Composition,”** SCI Technical Report, No. UUSCI-2011-003, *SCI Institute, University of Utah*, 2011.

[Liu2011a] W. Liu, S. Awate, J. Anderson, D. Yurgelun-Todd, P.T. Fletcher.
**“Monte Carlo expectation maximization with hidden Markov models to detect functional networks in resting-state fMRI,”** In *Machine Learning in Medical Imaging*, Lecture Notes in Computer Science (LNCS), Vol. 7009/2011, pp. 59--66. 2011.

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[Lui2011a] J. Luitjens, M. Berzins.
**“Scalable parallel regridding algorithms for block-structured adaptive mesh renement,”** In *Concurrency And Computation: Practice And Experience*, Vol. 23, No. 13, John Wiley & Sons, Ltd., pp. 1522--1537. 2011.

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[Lui2011b] J.P. Luitjens.
**“The Scalability of Parallel Adaptive Mesh Refinement Within Uintah,”** Note: *Advisor: Martin Berzins*, *School of Computing, University of Utah*, 2011.

[Lui2011c] J. Luitjens, M. Berzins.
**“Scalable parallel regridding algorithms for block-structured adaptive mesh refinement,”** In *Concurrency and Computation: Practice and Experience*, Vol. 23, No. 13, pp. 1522--1537. September, 2011.

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[Maa2011a] S.A. Maas, B.J. Ellis, D.S. Rawlins, L.T. Edgar, C.R. Henak, J.A. Weiss.
**“Implementation and Verification of a Nodally-Integrated Tetrahedral Element in FEBio,”** SCI Technical Report, No. UUSCI-2011-007, *SCI Institute, University of Utah*, 2011.

[Mac2011a] R.S. MacLeod, J.J.E. Blauer.
**“Atrial Fibrillation,”** In *Multimodal Cardiovascular Imaging: Principles and Clinical Applications*, Ch. 25, Edited by O. Pahlm and G. Wagner, McGraw Hill, 2011.

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[Man2011a] J. Mandel, J.D. Beezley, A. Kochanski, V.Y. Kondratenko, L. Zhang, E. Anderson, J. Daniels II, C.T. Silva, C.R. Johnson.
**“A wildland fire modeling and visualization environment,”** In *Proceedings of the Ninth Symposium on Fire and Forest Meteorology*, pp. (published online). 2011.

[Mar2011a] T. Martin, E. Cohen, R.M. Kirby.
**“Direct Isosurface Visualization of Hex-Based High-Order Geometry and Attribute Representations,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. PP, No. 99, pp. 1--14. 2011.

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[Mcg2011a] C.J. McGann, E.G. Kholmovski, J.J. Blauer, S. Vijayakumar, T.S. Haslam, J.E. Cates, E.V. DiBella, N.S. Burgon, B. Wilson, A.J. Alexander, M.W. Prastawa, M. Daccarett, G. Vergara, N.W. Akoum, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“Dark Regions of No-Reflow on Late Gadolinium Enhancement Magnetic Resonance Imaging Result in Scar Formation After Atrial Fibrillation Ablation,”** In *Journal of the American College of Cardiology*, Vol. 58, No. 2, pp. 177--185. 2011.

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**“Using Hybrid Parallelism to improve memory use in Uintah,”** In *Proceedings of the TeraGrid 2011 Conference*, Salt Lake City, Utah, ACM, July, 2011.

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**“Smoothness-Increasing Accuracy-Conserving (SIAC) Postprocessing for Discontinuous Galerkin Solutions Over Structured Triangular Meshes,”** In *SIAM Journal of Numerical Analysis*, Vol. 49, No. 5, pp. 1899--1920. 2011.

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**“Efficient Implementation of Smoothness-Increasing Accuracy-Conserving (SIAC) Filters for Discontinuous Galerkin Solutions,”** In *Journal of Scientific Computing*, pp. (in press). 2011.

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**“Sample drift correction in 3D fluorescence photoactivation localization microscopy,”** In *Optics Express*, Vol. 19, No. 16, pp. 15009--15019. 2011.

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**“Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA,”** In *PLoS ONE*, Vol. 6, No. 4, Public Library of Science, pp. e18768. April, 2011.

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**“Distributional Sensitivity for Uncertainty Quantification,”** In *Communications in Computational Physics*, Vol. 10, No. 1, pp. 140--160. 2011.

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**“GPU-Based Interactive Cut-Surface Extraction From High-0rder Finite Element Fields,”** In *IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue)*, Vol. 17, No. 12, pp. 1803--1811. 2011.

[Ode2011a] J.T. Oden, O. Ghattas, J.L. King, B.I. Schneider, K. Bartschat, F. Darema, J. Drake, T. Dunning, D. Estep, S. Glotzer, M. Gurnis, C.R. Johnson, D.S. Katz, D. Keyes, S. Kiesler, S. Kim, J. Kinter, G. Klimeck, C.W. McCurdy, R. Moser, C. Ott, A. Patra, L. Petzold, T. Schlick, K. Schulten, V. Stodden, J. Tromp, M. Wheeler, S.J. Winter, C. Wu, K. Yelick.
**“Cyber Science and Engineering: A Report of the National Science Foundation Advisory Committee for Cyberinfrastructure Task Force on Grand Challenges,”** Note: *NSF Report*, 2011.

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**“Markov surfaces: A probabilistic framework for user-assisted three-dimensional image segmentation,”** In *Computer Vision and Image Understanding*, Vol. 115, No. 10, pp. 1375--1383. 2011.

[Pas2011a] Valerio Pascucci, Xavier Tricoche, Hans Hagen, Julien Tierny.
**“Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications (Mathematics and Visualization),”** Springer, 2011.

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[Pet2011a] T. Peterka, R. Ross, A. Gyulassy, V. Pascucci, W. Kendall, H.-W. Shen, T.-Y. Lee, A. Chaudhuri.
**“Scalable Parallel Building Blocks for Custom Data Analysis,”** In *Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV)*, pp. 105--112. October, 2011.

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[Phi2011a] S. Philip, B. Summa, P.-T. Bremer, and V. Pascucci.
**“Parallel Gradient Domain Processing of Massive Images,”** In *Proceedings of the 2011 Eurographics Symposium on Parallel Graphics and Visualization*, pp. 11--19. 2011.

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**“Hybrid CPU-GPU Solver for Gradient Domain Processing of Massive Images,”** In *Proceedings of 2011 International Conference on Parallel and Distributed Systems (ICPADS)*, pp. 244--251. 2011.

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**“Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing,”** In *Progress in Biophysics and Molecular Biology*, Vol. 107, No. 1, Elsevier, pp. 4--10. October, 2011.

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[Rei2011a] W. Reich, Dominic Schneider, Christian Heine, Alexander Wiebel, Guoning Chen, Gerik Scheuermann.
**“Combinatorial Vector Field Topology in 3 Dimensions,”** In *Mathematical Methods in Biomedical Image Analysis (MMBIA) Proceedings IEEE MMBIA 2012*, pp. 47--59. November, 2011.

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[Ros2011a] P. Rosen, V. Popescu, K. Hayward, C. Wyman.
**“Non-Pinhole Approximations for Interactive Rendering,”** In *IEEE Computer Graphics and Applications*, Vol. 99, 2011.

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**“An Evaluation of 3-D Scene Exploration Using a Multiperspective Image Framework,”** In *The Visual Computer*, Vol. 27, No. 6-8, Springer-Verlag New York, Inc., pp. 623--632. 2011.

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[Sad2011a] N. Sadeghi, M.W. Prastawa, P.T. Fletcher, J.H. Gilmore, W. Lin, G. Gerig.
**“Statistical Growth Modeling of Longitudinal DT-MRI for Regional Characterization of Early Brain Development,”** In *Proceedings of the Medical Image Computing and Computer Assisted Intervention (MICCAI) 2011 Workshop on Image Analysis of Human Brain Development*, pp. 1507--1510. 2011.

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[Sal2011a] B. Salter, B. Wang, M. Sadinski, S. Ruhnau, V. Sarkar, J. Hinkle, Y. Hitchcock, K. Kokeny, S. Joshi.
**“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,”** In *Medical Physics*, Vol. 38, No. 6, pp. 3820. 2011.

[Sam2011a] R. Samuel, H.J. Sant, F. Jiao, C.R. Johnson, B.K. Gale.
**“Microfluidic laminate-based phantom for diffusion tensor-magnetic resonance imaging,”** In *Journal of Micromech. Microeng.*, Vol. 21, pp. 095027--095038. 2011.

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[Sch2011a] M. Schott, A.V.P. Grosset, T. Martin, V. Pegoraro, S.T. Smith, C.D. Hansen.
**“Depth of Field Effects for Interactive Direct Volume Rendering,”** In *Computer Graphics Forum*, Vol. 30, No. 3, Edited by H. Hauser and H. Pfister and J.J. van Wijk, Wiley-Blackwell, pp. 941--950. jun, 2011.

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[Sch2011b] M. Schulz, J.A. Levine, P.-T. Bremer, T. Gamblin, V. Pascucci.
**“Interpreting Performance Data Across Intuitive Domains,”** In *International Conference on Parallel Processing*, Taipei, Taiwan, IEEE, pp. 206--215. 2011.

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[Sey2011a] M. Seyedhosseini, A.R.C. Paiva, T. Tasdizen.
**“Multi-scale Series Contextual Model for Image Parsing,”** SCI Technical Report, No. UUSCI-2011-004, *SCI Institute, University of Utah*, 2011.

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**“Fast AdaBoost training using weighted novelty selection,”** In *Proc. IEEE Intl. Joint Conf. on Neural Networks*, San Jose, CA, USA pp. 1245--1250. August, 2011.

[Sey2011c] M. Seyedhosseini, R. Kumar, E. Jurrus, R. Guily, M. Ellisman, H. Pfister, T. Tasdizen.
**“Detection of Neuron Membranes in Electron Microscopy Images using Multi-scale Context and Radon-like Features,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011*, Lecture Notes in Computer Science (LNCS), Vol. 6891, pp. 670--677. 2011.

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[Shi2011a] F. Shi, D. Shen, P.-T. Yap, Y. Fan, J.-Z. Cheng, H. An, L.L. Wald, G. Gerig, J.H. Gilmore, W. Lin.
**“CENTS: Cortical Enhanced Neonatal Tissue Segmentation,”** In *Human Brain Mapping HBM*, Vol. 32, No. 3, Note: *ePub 5 Aug 2010*, pp. 382--396. March, 2011.

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[Ste2011a] M. Steinberger, M. Waldner, M. Streit, A. Lex, D. Schmalstieg.
**“Context-Preserving Visual Links,”** In *IEEE Transactions on Visualization and Computer Graphics (InfoVis '11)*, Vol. 17, No. 12, 2011.

[Sum2011a] B. Summa, G. Scorzelli, M. Jiang, P.-T. Bremer, V. Pascucci.
**“Interactive Editing of Massive Imagery Made Simple: Turning Atlanta into Atlantis,”** In *ACM Transactions on Graphics*, Vol. 30, No. 2, pp. 7:1--7:13. April, 2011.

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[Swe2011a] D.J. Swenson, S.E. Geneser, J.G. Stinstra, R.M. Kirby, R.S. MacLeod.
**“Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods,”** In *Annals of Biomedical Engineering*, Vol. 39, No. 12, pp. 2900--2910. 2011.

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[Sze2011a] M. Szegedi, J. Hinkle, S. Joshi, V. Sarkar, P. Rassiah-Szegedi, B. Wang, B. Salter.
**“WE-E-BRC-05: Voxel Based Four Dimensional Tissue Deformation Reconstruction (4DTDR) Validation Using a Real Tissue Phantom,”** In *Medical Physics*, Vol. 38, pp. 3819. 2011.

[Tam2011a] G. Tamm, A. Schiewe, J. Krüger.
**“ZAPP – A management framework for distributed visualization systems,”** In *Proceedings of CGVCVIP 2011 : IADIS International Conference on Computer Graphics, Visualization, Computer Vision And Image Processing*, pp. (accepted). 2011.

[Tat2011a] J.D. Tate, J.G. Stinstra, T. Pilcher, A. Poursaid, E. Saarel, R.S. MacLeod.
**“Measuring Defibrillator Surface Potentials for Simulation Verification,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society EMBS 33rd Annual International Conference*, pp. 239 - 242. 2011.

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[Tat2011g] J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod.
**“Measurement of Defibrillator Surface Potentials for Simulation Verification,”** In *Computing in Cardiology*, In *2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, IEEE, pp. 853--856. Aug, 2011.

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[Tho2011a] D. Thompson, J.A. Levine, J.C. Bennett, P.-T. Bremer, A. Gyulassy, V. Pascucci, P.P. Pebay.
**“Analysis of Large-Scale Scalar Data Using Hixels,”** In *Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV)*, Providence, RI, pp. 23--30. 2011.

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[Tra2011a] L.T. Tran, M. Berzins.
**“IMPICE Method for Compressible Flow Problems in Uintah,”** In *International Journal For Numerical Methods In Fluids*, Note: *Published online 20 July*, 2011.

[Tra2011b] L.T. Tran, M. Berzins.
**“Defect Sampling in Global Error Estimation for ODEs and Method-Of-Lines PDEs Using Adjoint Methods,”** SCI Technical Report, No. UUSCI-2011-006, *SCI Institute, University of Utah*, 2011.

[Tri2011a] X. Tricoche, C. Garth, A. Sanderson.
**“Visualization of topological structures in area-preserving maps,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 17, No. 12, pp. 1765--1774. Dec, 2011.

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[Tsu2011a] P. Tsuji, D. Xiu, L. Ying.
**“A Fast Method for High-frequency Acoustic Scattering from Random Scatterers,”** In *International Journal for Uncertainty Quantification*, Vol. 1, No. 2, pp. 99--117. 2011.

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[Tus2011a] N.J. Tustison, S.P. Awate, G. Song, T.S. Cook, J.C. Gee.
**“Point Set Registration Using Havrda–Charvat–Tsallis Entropy Measures,”** In *IEEE Transactions on Medical Imaging*, Vol. 30, No. 2, pp. 451--460. 2011.

[Ver2011a] G.R. Vergara, S. Vijayakumar, E.G. Kholmovski, J.J. Blauer, M.A. Guttman, C. Gloschat, G. Payne, K. Vij, N.W. Akoum, M. Daccarett, C.J. McGann, R.S. Macleod, N.F. Marrouche.
**“Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla,”** In *Heart Rhythm*, Vol. 8, No. 2, pp. 295--303. 2011.

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[Vo2011a] H.T. Vo, J. Bronson, B. Summa, J.L.D. Comba, J. Freire, B. Howe, V. Pascucci, C.T. Silva.
**“Parallel Visualization on Large Clusters using MapReduce,”** SCI Technical Report, No. UUSCI-2011-002, *SCI Institute, University of Utah*, 2011.

[Vo2011b] H.T. Vo, J. Bronson, B. Summa, J.L.D. Comba, J. Freire, B. Howe, V. Pascucci, C.T. Silva.
**“Parallel Visualization on Large Clusters using MapReduce,”** In *Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV)*, pp. 81--88. 2011.

[Vo2011c] H.T. Vo, C.T. Silva, L.F. Scheidegger, V. Pascucci.
**“Simple and Efficient Mesh Layout with Space-Filling Curves,”** In *Journal of Graphics, GPU, and Game Tools*, pp. 25--39. 2011.

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[Wan2011a] Y. Wang, A. Gupta, Z. Liu, H. Zhang, M.L. Escolar, J.H. Gilmore, S. Gouttard, P. Fillard, E. Maltbie, G. Gerig, M. Styner.
**“DTI registration in atlas based fiber analysis of infantile Krabbe disease,”** In *Neuroimage*, pp. (in print). 2011.

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[Wan2011b] D. Wang, R.M. Kirby, C.R. Johnson.
**“Finite Element Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography,”** In *IEEE Transactions for Biomedical Engineering*, Vol. 58, No. 6, pp. 1827--1838. 2011.

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[Wan2011c] Bei Wang, B. Summa, V. Pascucci, M. Vejdemo-Johansson.
**“Branching and Circular Features in High Dimensional Data,”** SCI Technical Report, No. UUSCI-2011-005, *SCI Institute, University of Utah*, 2011.

[Wan2011d] Bei Wang, B. Summa, V. Pascucci, M. Vejdemo-Johansson.
**“Branching and Circular Features in High Dimensional Data,”** In *IEEE Transactions of Visualization and Computer Graphics (TVCG)*, Vol. 17, No. 12, pp. 1902--1911. 2011.

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[Wan2011e] D. Wang, R.M. Kirby, R.S. Macleod, C.R. Johnson.
**“An optimization framework for inversely estimating myocardial transmembrane potentials and localizing ischemia,”** In *Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS)*, pp. 1680--1683. 2011.

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[Wil2011a] S. Williams, M. Petersen, P.-T. Bremer, M. Hecht, V. Pascucci, J. Ahrens, M. Hlawitschka, B. Hamann.
**“Adaptive Extraction and Quantification of Geophysical Vortices,”** In *IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2011 IEEE Visualization Conference*, Vol. 17, No. 12, pp. 2088--2095. 2011.

[Yan2011a] C. Yang, D. Xiu, R.M. Kirby.
**“Visualization of Covariance and Cross-covariance Field,”** In *International Journal for Uncertainty Quantification*, Vol. 3, No. 1, pp. 25--38. 2011.

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[Zhu2011a] H. Zhu, L. Kong, R. Li, M.S. Styner, G. Gerig, W. Lin, J.H. Gilmore.
**“FADTTS: Functional Analysis of Diffusion Tensor Tract Statistics,”** In *NeuroImage*, Vol. 56, No. 3, pp. 1412--1425. 2011.

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2010

[Adl2010a] G. Adluru, T. Tasdizen, M.C. Schabel, E.V.R. DiBella.
**“Reconstruction of 3D Dynamic Contrast-Enhanced Magnetic Resonance Imaging Using Nonlocal Means,”** In *Journal of Magnetic Resonance Imaging*, Vol. 32, pp. 1217--1227. 2010.

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**“Improving Undersampled MRI Reconstruction Using Non-Local Means,”** In *Proceedings of the 2010 International Conference on Pattern Recognition*, pp. 4000--4003. 2010.

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**“Evaluation of left atrial lesions after initial and repeat atrial fibrillation ablation: lessons learned from delayed-enhancement MRI in repeat ablation procedures,”** In *Circulation. Arrhythmia and Electrophysiology*, Vol. 3, No. 3, pp. 249--259. 2010.

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[Ber2010a] M. Berger, L.G. Nonato, V. Pascucci, C.T. Silva.
**“Fiedler Trees for Multiscale Surface Analysis,”** In *Computer & Graphics*, Vol. 34, No. 3, Note: *Special Issue of Sha*, pp. 272--281. June, 2010.

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**“MRI Based Injury Characterization Immediately Following Ablation of Atrial Fibrillation,”** In *Computing in Cardiology*, Vol. 37, pp. 165--168. 2010.

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**“Patient-specific models of deep brain stimulation: influence of field model complexity on neural activation predictions,”** In *Brain Stimulation*, Vol. 3, No. 2, Elsevier Inc., pp. 65--67. April, 2010.

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**“Registration, Atlas Estimation and Variability Analysis of White Matter Fiber Bundles Modeled as Currents,”** In *NeuroImage*, Vol. 55, No. 3, pp. 1073--1090. 2010.

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[Els2010a] M. El-Sayed, R.G. Steen, M.D. Poe, T.C. Bethea, G. Gerig, J. Lieberman, L. Sikich.
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**“Microstructural connectivity of the arcuate fasciculus in adolescents with high-functioning autism,”** In *NeuroImage*, Vol. 51, No. 3, Note: *Epub Feb 2 2010*, pp. 1117--1125. July, 2010.

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**“Tuvok, an Architecture for Large Scale Volume Rendering,”** In *Proceedings of the 15th International Workshop on Vision, Modeling, and Visualization*, pp. 139--146. November, 2010.

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**“Quantifying Variability in Radiation Dose Due to Respiratory-Induced Tumor Motion,”** In *Medical Image Analysis*, Vol. 15, No. 4, pp. 640--649. 2010.

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**“Manifold modeling for brain population analysis,”** In *Medical Image Analysis*, Special Issue on the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2009, Vol. 14, No. 5, Note: *Awarded MICCAI 2010, Best of the Journal Issue Award*, pp. 643--653. 2010.

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**“Prenatal and Neonatal Brain Structure and White Matter Maturation in Children at High Risk for Schizophrenia,”** In *American Journal of Psychiatry*, Vol. 167, No. 9, Note: *Epub 2010 Jun 1*, pp. 1083--1091. September, 2010.

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**“Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context,”** In *Proceeding of the IEEE Symposium on Pacific Visualization (PacificVis '10)*, pp. 57--64. 2010.

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**“A Novel Workbench for Epidemic investigation and Analysis of Search Strategies in public health practice,”** In *Proceedings of AMIA 2010 Annual Symposium*, pp. 647--651. 2010.

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**“Improving the Performance of Uintah: A Large-Scale Adaptive Meshing Computational Framework,”** In *Proceedings of the 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS10)*, Atlanta, GA, pp. 1--10. 2010.

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**“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,”** In *Heart Rhythm*, Vol. 7, No. 10, pp. 1475--1481. 2010.

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**“Using Sequential Context for Image Analysis,”** In *Proc. IEEE Intl. Conference on Pattern Recognition*, Istanbul, Turkey, pp. 2800--2803. 2010.

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[Pan2010a] Y. Pan, R.T. Whitaker, A. Cheryauka, D. Ferguson.
**“Regularized 3D Iterative Reconstruction on a Mobile C-ARM CT,”** In *Proceedings of The First CT Meeting*, Salt Lake City, UT, pp. (accepted). 2010.

[Pan2010b] Y. Pan, R.T. Whitaker, A. Cheryauka, D. Ferguson.
**“TV-regularized Iterative Image Reconstruction on a Mobile C-ARM CT,”** In *Proceedings of SPIE Medical Imaging 2010*, San Diego, CA, Vol. 7622, pp. (published online). 2010.

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[Pau2010a] F.V. Paulovich, C.T. Silva, L.G. Nonato.
**“Two-Phase Mapping for Projecting Massive Data Sets,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, In *IEEE Tr*, Vol. 16, No. 6, pp. 1281--1290. Nov, 2010.

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[Peg2010a] V. Pegoraro, M. Schott, S.G. Parker.
**“A Closed-Form Solution to Single Scattering for General Phase Functions and Light Distributions,”** In *Computer Graphics Forum*, Vol. 29, No. 4, Wiley-Blackwell, pp. 1365--1374. Aug, 2010.

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[Pil2010a] T.A. Pilcher, J.D. Tate, J.G. Stinstra, E.V. Saarel, M.D. Puchalski, and R.S. MacLeod.
**“Partially extracted defibrillator coils and pacing leads alter defibrillation thresholds,”** In *Proceedings of the 15th International Academy of Cardiology World Congress of Cardiology*, 2010.

[Pot2010a] K. Potter, J.M. Kniss, R. Riesenfeld, C.R. Johnson.
**“Visualizing Summary Statistics and Uncertainty,”** In *Computer Graphics Forum*, Vol. 29, No. 3, Wiley-Blackwell, pp. 823--831. Aug, 2010.

[Pra2010a] M.W. Prastawa, N. Sadeghi, J.H. Gilmore, W. Lin, G. Gerig.
**“A new framework for analyzing white matter maturation in early brain development,”** In *Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro*, pp. 97--100. April, 2010.

ISBN: 978-1-4244-4125-9

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[Ree2010a] S.P. Reese, S.A. Maas, J.A. Weiss.
**“Micromechanical models of helical superstructures in ligament and tendon fibers predict large poisson's ratios,”** In *Journal of Biomechanics*, Vol. 43, No. 7, pp. 1394--1400. 2010.

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**“Spatio-Temporal Analysis of Early Brain Development,”** In *Proceedings IEEE Asilomar Conference on Signals, Systems and Computers*, pp. 777--781. 2010.

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[Sad2010b] N. Sadeghi, M.W. Prastawa, J.H. Gilmore, W. Lin, G. Gerig.
**“Towards Analysis of Growth Trajectory through Multi-modal Longitudinal MR Imaging,”** In *SPIE Medical Imaging 2010: Image Processing*, Vol. 7623, 76232U, Edited by Benoit M. Dawant and David R. Haynor, pp. (published online). March, 2010.

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[Sam2010a] A.A. Samsonov, J.V. Velikina, Y.K. Jung, E.G. Kholmovski, C.R. Johnson, W.F. Block.
**“POCS-enhanced correction of motion artifacts in parallel MRI,”** In *Magnetic Resonance in Medicine*, Vol. 63, No. 4, pp. 1104--1110. May, 2010.

[San2010a] Allen R. Sanderson, Scott Kruger, and Stephane Either.
**“Visualization and Analysis Tools for Assisting in Evaluating Fusion Simulations,”** In *Proceedings of the Sherwood Fusion Theory Conference*, 2010.

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**“Analysis of Recurrent Patterns in Toroidal Magnetic Fields,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 16, No. 6, IEEE, pp. 1431-1440. Nov, 2010.

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[Sch2010a] J. Schmidt, M. Berzins.
**“Development of the Uintah Gateway for Fluid-Structure-Interaction Problems,”** In *Proceedings of the Teragrid 2010 Conference*, ACM, 2010.

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[Sch2010b] C.E. Scheidegger, T. Etiene, L.G. Nonato, C.T. Silva.
**“Edge Flows: Stratified Morse Theory for Simple, Correct Isosurface Extraction,”** SCI Technical Report, No. UUSCI-2010-002, *SCI Institute, University of Utah*, 2010.

[Sch2010c] M. Schott, P. Grosset, T. Martin, V. Pegoraro, C.D. Hansen.
**“Depth of Field Effects for Interactive Direct Volume Rendering,”** SCI Technical Report, No. UUSCI-2010-005, *SCI Institute, University of Utah*, 2010.

[Sch2010d] C. Schlimper, O. Nemitz, U. Dorenbeck, J. Scorzin, R.T. Whitaker, T. Tasdizen, M. Rumpf, K. Schaller.
**“Restoring three-dimensional magnetic resonance angiography images with mean curvature motion,”** In *Neurological Research*, Vol. 32, No. 1, Note: *Epub 2009 Nov 26*, pp. 87--93. February, 2010.

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[Seg2010a] N.M. Segerson, M. Daccarett, T.J. Badger, A. Shabaan, N. Akoum, E.N. Fish, S. Rao, N.S. Burgon, Y. Adjei-Poku, E. Kholmovski, S. Vijayakumar, E.V. DiBella, R.S. MacLeod, N.F. Marrouche.
**“Magnetic resonance imaging-confirmed ablative debulking of the left atrial posterior wall and septum for treatment of persistent atrial fibrillation: rationale and initial experience,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 21, No. 2, pp. 126--132. 2010.

PubMed ID: 19804549

[Sey2010a] M. Seyedhosseini, A.R.C. Paiva, T. Tasdizen.
**“Image Parsing with a Three-State Series Neural Network Classifier,”** In *Proc. IEEE Intl. Conference on Pattern Recognition*, Istanbul, Turkey, pp. 4508--4511. 2010.

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[Sil2010a] C. Silva, E. Anderson, E. Santos, J. Freire.
**“Using VisTrails and Provenance for Teaching Scientific Visualization,”** In *EUROGRAPHICS 2010 Educator Program*, Note: *Awarded Best Paper!*, 2010.

[Sin2010a] N.P. Singh, P.T. Fletcher, J.S. Preston, L. Ha, R. King, J.S. Marron, M. Wiener, S. Joshi.
**“Multivariate Statistical Analysis of Deformation Momenta Relating Anatomical Shape to Neuropsychological Measures,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2010, Lecture Notes in Computer Science (LCNS)*, Vol. 6363/2010, pp. 529-537. 2010.

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PubMed ID: 20879441

[Ste2010a] M. Steffen, R.M. Kirby, M. Berzins.
**“Decoupling and Balancing of Space and Time Errors in the Material Point Method (MPM),”** In *International Journal for Numerical Methods in Engineering*, Vol. 82, No. 10, pp. 1207--1243. 2010.

[Sti2010a] J.G. Stinstra, R.S. MacLeod, C.S. Henriquez.
**“Incorporating Histology into a 3D Microscopic Computer Model of Myocardium to Study Propagation at a Cellular Level,”** In *Annals of Biomedical Engineering (ABME)*, Vol. 38, No. 4, pp. 3399--1414. 2010.

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[Swe2010a] D. Swenson, J.A. Levine, Z. Fu, J.D. Tate, R.S. MacLeod.
**“The Effect of Non-Conformal Finite Element Boundaries on Electrical Monodomain and Bidomain Simulations,”** In *Computing in Cardiology*, Vol. 37, IEEE, pp. 97--100. 2010.

ISSN: 0276-6547

[Tas2010a] T. Tasdizen, P. Koshevoy, B.C. Grimm, J.R. Anderson, B.W. Jones, C.B. Watt, R.T. Whitaker, R.E. Marc.
**“Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy,”** In *Journal of Neuroscience Methods*, Vol. 193, No. 1, pp. 132--144. 2010.

PubMed ID: 20713087

[Tat2010b] J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod.
**“Implantable Cardioverter Defibrillator Predictive Simulation Validation,”** In *Computing in Cardiology*, pp. 853-–856. September, 2010.

[Tch2010a] R. Tchoua, S. Klasky, N. Podhorszki, B. Grimm, A. Khan, E. Santos, C.T. Silva, P. Mouallem, M. Vouk.
**“Collaborative Monitoring and Analysis for Simulation Scientists,”** In *Proceedings of The 2010 International Symposium on Collaborative Technologies and Systems (CTS 2010)*, pp. 235--244. 2010.

DOI: 10.1109/CTS.2010.5478506

[Tie2010a] J. Tierny, J. Daniels II, L.G. Nonato, V. Pascucci, C.T. Silva.
**“Interactive Quadrangulation with Reeb Atlases and Connectivity Textures,”** SCI Technical Report, No. UUSCI-2010-006, *SCI Institute, University of Utah*, 2010.

[Tus2010a] N.J. Tustison, S.P. Awate, J. Cai, T.A. Altes, G.W. Miller, E.E. de Lange, J.P. Mugler 3rd, J.C. Gee.
**“Pulmonary kinematics from tagged hyperpolarized helium-3 MRI,”** In *Journal of Magnetic Resonance Imaging, JMRI*, Vol. 31, No. 5, pp. 1236--1241. 2010.

PubMed ID: 20432362

[Tut2010a] C. Tuttle, L.G. Nonato, C.T. Silva.
**“PedVis: A Structured, Space-Efficient Technique for Pedigree Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 16, No. 6, pp. 1063--1072. Nov, 2010.

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[Van2010a] A. van Dam, J. Foley, J. Guttag, P. Hanrahan, C.R. Johnson, R. Katz, H. Kelly, P. Lee, D.E. Shaw.
**“CRA-E White Paper: Creating Environments for Computational Researcher Education,”** Note: *Computing Research Association (CRA)*, August, 2010.

[Vo2010a] H.T. Vo, D.K. Osmari, B. Summa, J.L.D. Comba, V. Pascucci, C.T. Silva.
**“Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems,”** In *Computer Graphics Forum*, Vol. 29, No. 3, pp. 1073--1082. 2010.

[Vo2010b] H.T. Vo, D.K. Osmari, B. Summa, J.L.D. Comba, V. Pascucci, C.T. Silva.
**“Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems,”** In *Computer Graphics Forum*, Vol. 29, No. 3, Wiley-Blackwell, pp. 1073--1082. Aug, 2010.

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[Vos2010a] P.E.J. Vos, S.J. Sherwin, R.M. Kirby.
**“h-p Efficiently: Implementing Finite and Spectral/hp Element Methods to Achieve Optimal Performance for Low- and High-Order Discretisations,”** In *Journal of Computational Physics*, Vol. 229, No. 13, pp. 5161--5181. 2010.

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**“Visual Links across Applications,”** In *Proceedings of the Conference on Graphics Interface (GI '10)*, Canadian Human-Computer Communications Society, pp. 129--136. 2010.

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[Wan2010a] D.F. Wang, R.M. Kirby, C.R. Johnson.
**“Resolution Strategies for the Finite-Element-Based Solution of the ECG Inverse Problem,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 57, No. 2, pp. 220--237. February, 2010.

[Wan2010b] Y. Wan, C.D. Hansen.
**“Fast Volumetric Data Exploration with Importance-Based Accumulated Transparency Modulation,”** In *Proceedings of IEEE/EG International Symposium on Volume Graphics 2010*, pp. 61--68. 2010.

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[Wan2010c] D.F. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson.
**“A New Family of Variational-Form-Based Regularizers for Reconstructing Epicardial Potentials from Body-Surface Mapping,”** In *Computing in Cardiology, 2010*, pp. 93--96. 2010.

[Wol2010a] C.H. Wolters, S. Lew, R.S. MacLeod, M.S. Hämäläinen.
**“Combined EEG/MEG source analysis using calibrated finite element head models,”** In *Proc. of the 44th Annual Meeting, DGBMT*, Note: *to appear, http://conference.vde.com/bmt-2010*, Rostock-Warnemünde, Germany, Oct.5-8, 2010 2010.

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**“A tract-specific framework for white matter morphometry combining macroscopic and microscopic tract features,”** In *Medical Image Analysis*, Vol. 14, No. 5, pp. 666--673. 2010.

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2009

[And2009a] J.R. Anderson, B.W. Jones, J.-H. Yang, M.V. Shaw, C.B. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U.V., R.T. Whitaker, D. Mastronarde, T. Tasdizen, R.E. Marc.
**“A Computational Framework for Ultrastructural Mapping of Neural Circuitry,”** In *PLoS Biology*, Vol. 7, No. 3, pp. e74. 2009.

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**“Ultra Structural Mapping of Neural Circuitry: A Computational Framework,”** In *IEEE International Symposium on Biomedical Engineering (ISBI 2009)*, pp. 1135--1137. 2009.

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[Arc2009a] R. Archibald, A. Gelb, R. Saxena, D. Xiu.
**“Discontinuity Detection in Multivariate Space for Stochastic Simulations,”** In *Journal of Computational Physics*, Vol. 228, No. 7, pp. 2676--2689. 2009.

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**“Temporal Left Atrial Lesion Formation After Ablation of Atrial Fibrillation,”** In *Heart Rhythm*, Vol. 6, No. 2, pp. 161--168. February, 2009.

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**“Initial Experience of Assessing Esophageal Tissue Injury and Recovery Using Delayed-Enhancement MRI After Atrial Fibrillation Ablation,”** In *Circulation: Arrhythmia and Electrophysiology*, Vol. 2, pp. 620--625. 2009.

[Ber2009a] M. Berzins.
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**“Occam's Razor and Petascale Visual Data Analysis,”** In *Journal of Physics: Conference Series*, Journal of Physics: Conference Series, Vol. 180, No. 012084, pp. (published online). 2009.

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**“A Bayesian Monte Carlo Approach to Global Illumination,”** In *Computer Graphics Forum Journal, Early View*, Vol. 28, No. 8, pp. 2315--2329. October, 2009.

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**“A Meshing Pipeline for Biomedical Models,”** In *Engineering with Computers*, Vol. 25, No. 1, SpringerLink, pp. 115-130. 2009.

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**“Ray Tracing NPR-Style Feature Lines,”** In *Proceedings of the 7th International Symposium on Non-Photorealistic Animation and Rendering (NPAR) 2009*, pp. 5--14. 2009.

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**“Semi-Regular Quadrilateral-only Remeshing from Simplified Base Domains,”** In *Computer Graphics Forum*, Computer Graphics Forum, Vol. 28, No. 5, Wiley-Blackwell, pp. 1427--1435. July, 2009.

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**“Localized Quadrilateral Coarsening,”** In *Computer Graphics Forum*, Vol. 28, No. 5, Wiley-Blackwell, pp. 1437--1444. July, 2009.

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[Dat2009a] M. Datar, J. Cates, P.T. Fletcher, S. Gouttard, G. Gerig, R.T. Whitaker.
**“Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009*, Lecture Notes in Computer Science LNCS, Vol. 5762, pp. 167--174. 2009.

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**“Edge Transformations for Improving Mesh Quality of Marching Cubes,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 15, No. 1, pp. 150--159. Sept/Oct, 2009.

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**“Spatiotemporal atlas estimation for developmental delay detection in longitudinal datasets,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009*, Lecture Notes in Computer Science LNCS, Vol. 5761, pp. 297--304. 2009.

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**“A First Study on Strategies for Generating Workflow Snippets,”** In *Proceedings of the ACM SIGMOD Intenational Workshop on Keyword Search on Structured Data (KEYS)*, pp. 15--20. 2009.

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**“Using Mediation to Achieve Provenance Interoperability,”** In *Proceedings of the IEEE International Workshop on Scientific Workflows, 2009*, pp. 291--298. 2009.

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**“Scientific Grand Challenges: Opportunities in biology at the Extreme Scale of Computing,”** Note: *DOE Office of Advanced Scientific Computing Research*, August, 2009.

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**“Verifiable Visualization for Isosurface Extraction,”** In *IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2009 IEEE Visualization Conference*, Vol. 15, No. 6, pp. 1227--1234. Sept/Oct, 2009.

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**“The geometric median on Riemannian manifolds with application to robust atlas estimation,”** In *Neuroimage*, Vol. 45, No. 1, pp. S143--S152. March, 2009.

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**“Size Matters - Revealing Small Scale Structures in Large Datasets,”** In *Proceedings of the World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany*, IFMBE Proceedings, Vol. 25/13, Springer Berlin Heidelberg, pp. 41--44. 2009.

[Fre2009a] J. Freire.
**“Provenance Management: Challenges and Opportunities,”** In *Datenbanksysteme in Business, Technologie und Web (BTW)*, pp. 4. 2009.

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**“Temporal and Spatial Development of Axonal Maturation and Myelination of White Matter in the Developing Brain,”** In *American Journal of Neuroradiology (AJNR)*, Vol. 30, pp. 290--296. 2009.

PubMed ID: 19001533

[Gen2009a] S.E. Geneser, R.M. Kirby, Brian Wang, B. Salter, S. Joshi.
**“Incorporating patient breathing variability into a stochastic model of dose deposition for stereotactic body radiation therapy,”** In *Information Processing in Medical Imaging*, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 688--700. 2009.

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[Ger2009a] S. Gerber, T. Tasdizen, S. Joshi, R.T. Whitaker.
**“On the Manifold Structure of the Space of Brain Images,”** In *Medical Image Computing and Computer-Assisted Intervention (MICCAI 2009)*, Springer, pp. 305--312. 2009.

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[Ger2009b] S. Gerber, T. Tasdizen, R.T. Whitaker.
**“Dimensionality Reduction and Principal Surfaces via Kernel Map Manifolds,”** In *Proceedings of the 2009 International Conference on Computer Vison (ICCV 2009)*, pp. 529--536. September, 2009.

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**“Group analysis of DTI fiber tract statistics with application to neurodevelopment,”** In *Neuroimage*, Vol. 45, No. 1 (suppl 1), pp. S133--S142. 2009.

PubMed ID: 19059345

[Goo2009b] C. Goodlett, P.T. Fletcher, J.H. Gilmore, G. Gerig.
**“Group Analysis of DTI Fiber Tract Statistics with Application to Neurodevelopment,”** In *NeuroImage*, Vol. 45, pp. S133--S142. December, 2009.

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[Gou2009a] S. Gouttard, M.W. Prastawa, E. Bullitt, W. Lin, C. Goodlett, G. Gerig.
**“Constrained Data Decomposition and Regression for Analyzing Healthy Aging from Fiber Tract Diffusion Properties,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009*, Lecture Notes in Computer Science LNCS, Vol. 5761, pp. 321--328. 2009.

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[Gui2009a] J. Guilkey, T. Harman, J. Luitjens, J. Schmidt, J. Thornock, J.D. de St. Germain, S. Shankar, J. Peterson, C. Brownlee.
**“Uintah User Guide Version 1.1,”** SCI Technical Report, No. UUSCI-2009-007, *SCI Institute, University of Utah*, 2009.

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**“Fast Parallel Unbiased Diffeomorphic Atlas Construction on Multi-Graphics Processing Units,”** In *Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization 2009*, 2009.

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**“Fast 4-way parallel radix sorting on GPUs,”** In *Computer Graphic Forum*, 2009.

[Han2009a] C.D. Hansen, C.R. Johnson, V. Pascucci, C.T. Silva.
**“Visualization for Data-Intensive Science,”** In *The Fourth Paradigm: Data-Intensive Science*, Edited by S. Tansley and T. Hey and K. Tolle, Microsoft Research, pp. 153--164. 2009.

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**“Teasing apart the heterogeneity of autism: Same behavior, different brains in toddlers with fragile X syndrome and autism,”** In *Journal of Neurodevelopmental Disorders*, Vol. 1, No. 1, pp. 81--90. 2009.

PubMed ID: 20700390

[Hen2009a] H.B. Henninger, S.A. Maas, J.H. Shepherd, S. Joshi, J.A. Weiss.
**“Transversely Isotropic Distribution of Sulfated Glycosaminoglycans in Human Medial Collateral Ligament: A Quantitative Analysis,”** In *Journal of Structural Biology*, Vol. 165, pp. 176-183. 2009.

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**“Validation of computational models in biomechanics,”** In *Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine*, Vol. 224, No. 7, SAGE Publications, pp. 801--812. 2009.

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**“4D MAP image reconstruction incorporating organ motion,”** In *Information Processing in Medical Imaging*, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 676--687. 2009.

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**“Bioelectric Analyses of an Osseointegrated Intelligent Implant Design System for Amputees,”** In *JoVE*, Vol. 29, 2009.

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**“Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets,”** In *IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2009 IEEE Visualization Conference*, Vol. 15, No. 6, pp. 1505--1514. Sept/Oct, 2009.

[Jur2009a] E. Jurrus, M. Hardy, T. Tasdizen, P.T. Fletcher, P. Koshevoy, C.-B. Chien, W. Denk, R.T. Whitaker.
**“Axon Tracking in Serial Block-Face Scanning Electron Microscopy,”** In *Medical Image Analysis (MEDIA)*, Vol. 13, No. 1, Elsevier, pp. 180--188. February, 2009.

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[Jur2009b] E. Jurrus, A.R.C. Paiva, S. Watanabe, R.T. Whitaker, E.M. Jorgensen, T. Tasdizen.
**“Serial Neural Network Classifier for Membrane Detection using a Filter Bank.,”** SCI Technical Report, No. UUSCI-2009-006, *SCI Institute, University of Utah*, 2009.

[Jur2009c] E. Jurrus, A.R.C. Paiva, S. Watanabe, R. Whitaker, E.M. Jorgensen, T. Tasdizen.
**“Serial Neural Network Classifier for Membrane Detection using a Filter Bank,”** In *Proc. Workshop on Microscopic Image Analysis with Applications in Biology*, Bethesda, MD, USA, 2009.

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**“Coherent Multiresolution Isosurface Ray Tracing,”** In *The Visual Computer*, Vol. 25, No. 3, pp. 209--225. 2009.

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**“Fast Ray Tracing of Arbitrary Implicit Surfaces with Interval and Affine Arithmetic,”** In *Computer Graphics Forum*, Vol. 28, No. 1, pp. 26--40. 2009.

[Kno2009c] A. Knoll, Y. Hijazi, R. Westerteiger, M. Schott, C.D. Hansen, H. Hagen.
**“Volume Ray Casting with Peak Finding and Differential Sampling,”** In *IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2009 IEEE Visualization Conference*, Vol. 15, No. 6, pp. 1571--1578. Sept/Oct, 2009.

[Kno2009d] A. Knoll, Y. Hijazi, R. Westerteiger, M. Schott, C.D. Hansen, Hans Hagen.
**“Volume Ray Casting with Peak Finding and Differential Sampling,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 15, No. 6, pp. 1571-1578. 2009.

[Kru2009a] J. Krüger, T. Fogal.
**“Focus and Context - Visualization without the Complexity,”** In *Proceedings of the World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany*, IFMBE Proceedings, Vol. 25/13, Springer Berlin Heidelberg, pp. 44--48. 2009.

[Lew2009a] S. Lew, C.H. Wolters, T. Dierkes, C. Röer, R.S. MacLeod.
**“Accuracy and run-time comparison for different potential approaches and iterative solvers in finite element method based EEG source analysis,”** In *Applied Numerical Mathematics*, Vol. 59, pp. 1970--1988. 2009.

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**“Improved EEG Source Analysis Using Low-Resolution Conductivity Estimation in a Four-Compartment Finite Element Head Model,”** In *Human Brain Mapping*, Vol. 30, pp. 2862--2878. 2009.

[Li2009a] J. Li, D. Xiu.
**“A Generalized Polynomial Chaos Based Ensemble Kalman Filter with High Accuracy,”** In *Journal of Computational Physics*, Vol. 228, No. 15, pp. 5454--5469. 2009.

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**“Voxel-wise group analysis of DTI,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009*, pp. 807--810. 2009.

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**“A Comparison of FEBio, ABAQUS, and NIKE3D Results for a Suite of Verification Problems,”** SCI Technical Report, No. UUSCI-2009-009, *SCI Institute, University of Utah*, 2009.

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**“Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples,”** In *Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences*, Vol. 367, No. 1896, pp. 2293--2310. 2009.

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**“Deep brain stimulation activation volumes and their association with neurophysiological mapping and therapeutic outcomes,”** In *Journal of Neurology, Neurosurgery, and Psychiatry*, Vol. 80, No. 6, pp. 659--666. June, 2009.

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[Mar2009a] H.G. Martinez, S.I. Prajapati, C.A. Estrada, F. Jimenez, M.P. Quinones, I. Wu, A. Bahadur, A. Sanderson, C.R. Johnson, M. Shim, C. Keller, S.S. Ahuja.
**“Microscopic Computed Tomography Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice,”** In *Circulation: Journal of the American Heart Association*, Vol. 120, No. 9, pp. 821--822. 2009.

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**“Microscopic Computed Tomography–Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice,”** In *Circulation*, Vol. 120, No. 821--822, 2009.

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**“A Stochastic Collocation Approach to Bayesian Inference in Inverse Problems,”** In *Communications in Computational Physics*, Vol. 6, No. 4, pp. 826--847. 2009.

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[Mey2009a] M.D. Meyer, T. Munzner, H. Pfister.
**“MizBee: A Multiscale Synteny Browser,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis 2009)*, Vol. 15, No. 6, Note: *Honorable Mention for Best Paper Award*, pp. 897--904. 2009.

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**“Evaluation of Approaches of Solving Electrocardiographic Imaging Problem,”** In *Proceeding of Computers in Cardiology 2010*, Park City, Utah, September, 2009.

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**“Experimental and theoretical characterization of the voltage distribution generated by deep brain stimulation,”** In *Experimental Neurology*, Vol. 216, No. 1, Elsevier Inc., pp. 166--176. March, 2009.

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[Mir2009a] H. Mirzaee, C. Eskilsson, S.J. Sherwin, R.M. Kirby.
**“Comparison of Consistent Integration Versus Adaptive Quadrature for Taming Aliasing Errors,”** SCI Technical Report, No. UUSCI-2009-008, *SCI Institute, University of Utah*, 2009.

[Moo2009a] S.M. Moore, B.J. Ellis, J.A. Weiss, P.J. McMahon, R.E. Debski.
**“The Glenohumeral Capsule Should be Evaluated as a Sheet of Fibrous Tissue: A Validated Finite Element Model,”** In *Annals of Biomedical Engineering*, Vol. 38, No. 1, pp. 66--76. 2009.

[Mos2009a] M.W. Mosconi, H. Cody-Hazlett, M.D. Poe, G. Gerig, R. Gimpel-Smith, J. Piven.
**“Longitudinal study of amygdala volume and joint attention in 2- to 4-year-old children with autism,”** In *Arch Gen Psychiatry*, Vol. 66, No. 5, pp. 509--516. 2009.

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[Muk2009a] N. Mukherjee, C. Kang, H.M. Wolfe, B.S. Hertzberg, J.K. Smith, W. Lin, G. Gerig, R.M. Hamer, J.H. Gilmore.
**“Discordance of Prenatal and Neonatal Brain Development in Twins,”** In *Early Human Development*, Vol. 85, No. 3, pp. 171--175. 2009.

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[Mul2009a] H Müller, R Reihs, S Sauer, K Zatloukal, M Streit, A Lex, B Schlegl, D Schmalstieg.
**“Connecting Genes with Diseases,”** In *Information Visualisation, 2009 13th International Conference*, pp. 323--330. July, 2009.

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[Oak2009a] R.S. Oakes, T.J. Badger, E.G. Kholmovski, N. Akoum, N.S. Burgon, E.N. Fish, J.J. Blauer, S.N. Rao, E.V. DiBella, N.M. Segerson, M. Daccarett, J. Windfelder, C.J. McGann, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“Detection and quantification of left atrial structural remodeling with delayed-enhancement magnetic resonance imaging in patients with atrial fibrillation,”** In *Circulation*, Vol. 119, No. 13, pp. 1758--1767. 2009.

[Ogu2009a] I. Oguz, M. Niethammer, J. Cates, R.T. Whitaker, P.T. Fletcher, C. Vachet, M. Styner.
**“Cortical Correspondence with Probabilistic Fiber Connectivity,”** In *Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LCNS), Vol. 5636, pp. 651--663. 2009.

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[Omb2009a] L. Omberg, J.R. Meyerson, K. Kobayashi, L.S. Drury, J.F.X. Diffley, O. Alter.
**“Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression,”** In *Nature Molecular Systems Biology*, Vol. 5, No. 312, pp. (published online). October, 2009.

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[Pai2009a] A.R.C. Paiva, I. Park, J.C. Principe.
**“A Reproducing Kernel Hilbert Space Framework for Spike Train Signal Processing,”** In *Neural Computation*, Vol. 21, No. 2, pp. 424--449. 2009.

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**“Feasibility of GPU-Assisted Iterative Image Reconstruction for Mobile C-ARM CT,”** In *Progress in biomedical optics and imaging*, In *Proceedings of SPIE Medical Imaging 2009*, Vol. 10, No. 3, 2009.

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[Pan2009b] Y. Pan, W.-K. Jeong, R.T. Whitaker.
**“Markov Surfaces: A Probabilistic Framework for User-Assisted Three Dimensional Image Segmentation,”** In *Proceedings of MICCAI 2009 workshop on Probabilistic Models for Medical Image Analysis*, London, UK, 2009.

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**“The SCIJump Framework for Parallel and Distributed Scientific Computing,”** In *Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications*, Edited by Manish Parashar and Xiaolin Li and Sumir Chandra, Wiley-Blackwell, pp. 149--170. 2009.

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[Peg2009a] V. Pegoraro, S.G. Parker.
**“An Analytical Solution to Single Scattering in Homogeneous Participating Media,”** In *Computer Graphics Forum (Proceedings of the 30th Eurographics Conference)*, Vol. 28, No. 2, pp. 329--335. 2009.

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**“An Analytical Approach to Single Scattering for Anisotropic Media and Light Distributions,”** In *Proceedings of the 35th Graphics Interface Conference*, pp. 71--77. 2009.

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**“Strain Measurement in the Left Ventricle During Systole with Deformable Image Registration,”** In *Medical Image Analysi*, Vol. 13, No. 2, pp. 354--361. 2009.

[Pot2009a] K. Potter, A. Wilson, P.-T. Bremer, D. Williams, C. Doutriaux, V. Pascucci, C.R. Johhson.
**“Visualization of Uncertainty and Ensemble Data: Exploration of Climate Modeling and Weather Forecast Data with Integrated ViSUS-CDAT Systems,”** In *J. Phys.: Conf. Ser.*, Vol. 180, No. 012089, IOP Publishing, pp. 012089. July, 2009.

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**“Ensemble-Vis: A Framework for the Statistical Visualization of Ensemble Data,”** In *Proceedings of the 2009 IEEE International Conference on Data Mining Workshops*, pp. 233--240. 2009.

[Pra2009a] M.W. Prastawa, E. Bullitt, G. Gerig.
**“Simulation of brain tumors in MR images for evaluation of segmentation efficacy,”** In *Med Image Anal*, Vol. 13, No. 2, pp. 297--311. 2009.

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[Pre2009a] J.S. Preston, T. Tasdizen, C.M. Terry, A.K. Cheung, R.M. Kirby.
**“Using the stochastic collocation method for the uncertainty quantification of drug concentration due to depot shape variability,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 56, No. 3, Note: *Epub 2008 Dec 2*, pp. 609--620. 2009.

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[Rai2009a] E.J. Rainis, S.A. Maas, H.B. Henninger, P.J. McMahon, J.A. Weiss, R.E. Debski.
**“Material properties of the axillary pouch of the glenohumeral capsule: Is isotropic material symmetry appropriate?,”** In *Journal of Biomechanical Engineering*, Vol. 131, No. 13, pp. (7 pages). 2009.

[San2009a] E. Santos, D. Koop, H.T. Vo, E. Anderson, J. Freire, C.T. Silva.
**“Using Workflow Medleys to Streamline Exploratory Tasks,”** In *21st International Conference on Scientific and Statistical Database Management (SSDBM)*, pp. 292--301. 2009.

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[San2009c] A.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson.
**“A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach,”** In *Journal of Computing and Visualization in Science*, Vol. 12, pp. 155--170. 2009.

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[Sat2009a] D. Sato, Y. Xie, J.N. Weiss, Z. Qu, A. Garfinkel, A.R. Sanderson.
**“Acceleration of Cardiac Tissue Simulation with Graphic Processing Units,”** In *Medical and Biological Engineering and Computing*, Note: *Published online Aug 5, 2009*, 2009.

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[Sch2009a] M. Schott, V. Pegoraro, C.D. Hansen, K. Boulanger, K. Bouatouch.
**“A Directional Occlusion Shading Model for Interactive Direct Volume Rendering,”** In *Computer Graphics Forum*, Vol. 28, No. 3, Wiley-Blackwell, pp. 855--862. jun, 2009.

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[Sch2009b] J.M. Schreiner.
**“Uniform and Adaptive (Re)meshing of Surfaces,”** Note: *Ph.D. Thesis*, *School of Computing, University of Utah*, June, 2009.

[Seg2009a] N.M. Segerson, M. Daccarett, T.J. Badger, A. Shabaan, N. Akoum, E.N. Fish, S. Rao, N.S. Burgon, Y. Adjei-Poku, E.G. Kholmovski, S. Vijayakumar, E.V.R. Dibella, R.S. Macleod, N.F. Marrouche.
**“Magnetic Resonance Imaging-Confirmed Ablative Debulking of the Left Atrial Posterior Wall and Septum for Treatment of Persistent Atrial Fibrillation: Rationale and Initial Experience,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 21, No. 2, pp. 126--132. 2009.

[She2009a] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation for Biomedical Models in SCIRun,”** In *Engineering with Computers*, Vol. 25, No. 1, pp. 97--114. 2009.

[Shi2009a] F. Shi, P.T. Yap, Y. Fan, J.Z. Cheng, L.L. Wald, G. Gerig, W. Lin, D. Shen.
**“Cortical Enhanced Tissue Segmentation of Neonatal Brain MR Images Acquired by a Dedicated Phased Array Coil,”** In *Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition*, pp. 39--45. 2009.

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[Ste2009a] M. Steffen.
**“Analysis-Guided Improvements of the Material Point Method,”** *School of Computing, University of Utah*, 2009.

[Str2009a] M. Streit, A. Lex, H. Müller, D. Schmalstieg.
**“Gaze-Based Focus Adaption in an Information Visualization System,”** In *Proceedings of the Conference on Computer Graphics and Visualization and Image Processing (CGVCVIP '09)*, 2009.

[Str2009b] M. Streit, A. Lex, M. Kalkusch, K. Zatloukal, D. Schmalstieg.
**“Caleydo: Connecting Pathways with Gene Expression,”** In *Bioinformatics*, Vol. 25, No. 20, pp. 2760--2761. 2009.

[Tao2009a] R. Tao, P.T. Fletcher, R.T. Whitaker.
**“A Variational Image-Based Approach to the Correction of Susceptibility Artifacts in the Alignment of Diffusion Weighted and Structural MRI,”** In *Lecture Notes in Computer Science*, Springer, pp. 664--675. 2009.

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[Tas2009a] T. Tasdizen.
**“Principal neighborhood dictionaries for nonlocal means image denoising,”** In *IEEE Transactions on Image Processing*, Vol. 18, No. 12, Note: *Epub 2009 Jul 24*, pp. 2649--2660. 2009.

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[Tat2009a] J.D. Tate, J.G. Stinstra, T. Pilcher, and R.S. MacLeod.
**“Measuring Implantable Cardioverter Defibrillators (ICDs) During Implantation Surgery: Verification of a Simulation,”** In *Computers in Cardiology*, pp. 473--476. 2009.

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[Tie2009a] J. Tierny, A. Gyulassy, E. Simon, V. Pascucci.
**“Loop Surgery for Volumetric Meshes: Reeb Graphs Reduced to Contour Trees,”** In

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[Tra2009a] L.T. Tran, J. Kim, M. Berzins.
**“Solving Time-Dependent PDEs using the Material Point Method, A Case Study from Gas Dynamics,”** In *International Journal for Numerical Methods in Fluids*, Vol. 62, No. 7, pp. 709--732. 2009.

[Uv2009a] Kannan U.V., A.R.C. Paiva, E. Jurrus, T. Tasdizen.
**“Automatic Markup of Neural Cell Membranes Using Boosted Decision Stumps,”** In *Proceedings of the IEEE International Symposium on Biomedical Engineering (ISBI 2009)*, Boston, MA, pp. 1039--1042. 2009.

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[Uv2009b] Kannan UV, M. Kim, D. Gerszewski, J.R. Anderson, M. Hall.
**“Assembling Large Mosaics of Electron Microscope Images using GPU,”** In *Proceedings of the 2009 Symposium on Application Accelerators in High Performance Computing (SAAHPC'09)*, 2009.

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[Vo2009a] A. Vo, S. Vakkalanka, M. Delisi, G. Gopalakrishnan, R.M. Kirby, R. Thakur.
**“Formal Verification of Practical MPI Programs,”** In *Proceedings of 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP)*, Raleigh, NC, pp. 261--270. February 14-18, 2009.

[Vo2009b] H.T. Vo, D.K. Osmari, B. Summa, J.L.D. Comba, V. Pascucci, C.T. Silva.
**“Parallel Dataflow Scheme for Streaming (Un)Structured Data,”** SCI Technical Report, No. UUSCI-2009-004, *SCI Institute, University of Utah*, 2009.

[Vo2009c] H.T. Vo, C.T. Silva.
**“Multi-Threaded Streaming Pipeline For VTK,”** SCI Technical Report, No. UUSCI-2009-005, *SCI Institute, University of Utah*, 2009.

[Wal2009a] I. Wald, W.R. Mark, J. Günther, S. Boulos, T. Ize, W. Hunt, S.G. Parker, P. Shirley.
**“State of the Art in Ray Tracing Animated Scenes,”** In *Computer Graphics Forum*, Vol. 28, No. 6, pp. 1691--1722. 2009.

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**“Design Considerations for Collaborative Information Workspaces in Multi-Display Environments,”** In *Proceedings of the Workshop on Collaborative Visualization on Interactive Surfaces (VisWeek '09)*, pp. 36--39. 2009.

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[Wan2009a] Y. Wan, H. Otsuna, C.-B. Chien, C.D. Hansen.
**“An Interactive Visualization Tool for Multi-channel Confocal Microscopy Data in Neurobiology Research,”** SCI Technical Report, No. UUSCI-2009-001, *SCI Institute, University of Utah*, 2009.

[Wan2009b] Y. Wan, H. Otsuna, C.-B. Chien, C.D. Hansen.
**“An Interactive Visualization Tool for Multi-Channel Confocal Microscopy Data in Neurobiology Research,”** In

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**“Finite Element Discretization Strategies for the Inverse Electrocardiographic (ECG) Problem,”** In *Proceedings of the 11th World Congress on Medical Physics and Biomedical Engineering*, Munich, Germany, Vol. 25/2, pp. 729-732. September, 2009.

[Wan2009d] D.F. Wang, R.M. Kirby, C.R. Johnson.
**“Finite Element Refinements for Inverse Electrocardiography: Hybrid-Shaped Elements, High-Order Element Truncation and Variational Gradient Operator,”** In *Proceeding of Computers in Cardiology 2009*, Park City, September, 2009.

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**“Sequential Monte Carlo Point Process Estimation of Kinematics from Neural Spiking Activity for Brain Machine Interfaces,”** In *Neural Computation*, Vol. 21, No. 10, pp. 2894--2930. 2009.

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**“Efficient Stochastic Galerkin Methods for Random Diffusion Equations,”** In *Journal of Computational Physics*, Vol. 228, No. 2, pp. 266--281. 2009.

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**“Fast Numerical Methods for Stochastic Computations: a Review,”** In *Communications in Computational Physics*, Vol. 5, No. 2-4, pp. 242--272. 2009.

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**“Probabilistic White Matter Fiber Tracking using, Particle Filtering and von Mises-Fisher Sampling,”** In *Medical Image Analysis*, Vol. 13, No. 1, pp. 5--18. 2009.

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2008

[Adl2008a] G. Adluru, E.V.R. DiBella, C.J. McGann.
**“Data Acquisition and Reconstruction of Undersampled Radial MR Myocardial Perfusion,”** In *Proceedings of the 11th Annual Scientific Sessions of the Society for Cardiovascular Magnetic Resonance (SCMR) 2008*, pp. 215. 2008.

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**“A Comparison of L1 and L2 Norms as Temporal Constraints for Reconstruction of Undersampled Dynamic Contrast Enhanced Cardiac Scans with Respiratory Motion,”** In *Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008*, pp. 340. 2008.

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**“Data Reordering for Improved Constrained Reconstruction from Undersampled k-space Data,”** In *Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008*, pp. 3153. 2008.

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**“Cartilage Thickness: Factors Influencing Multidetector CT Measurements in a Phantom Study,”** In *Radiology*, Vol. 246, No. 1, pp. 133-141. 2008.

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**“Validation of Finite Element Predictions of Cartilage Contact Pressure in the Human Hip Joint,”** In *ASME Journal of Biomechanical Engineering*, Vol. 130, No. 3, pp. 051008-1--10. May, 2008.

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**“Provenance in Comparative Analysis: A Study in Cosmology,”** In *Computing in Science and Engineering*, Vol. 10, No. 3, pp. 30--37. 2008.

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**“Factors Influencing Cartilage Thickness Measurements with Multi-Detector CT: A Phantom Study,”** In *Radiology*, Vol. 246, No. 1, pp. 144-141. 2008.

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**“Scientific Exploration in the Era of Ocean Observatories,”** In *Computing in Science and Engineering*, Vol. 10, No. 3, pp. 53--58. 2008.

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**“A Physical Model for the Polarized Scattering of Light,”** In *Proceedings of The sixth Theory and Practice of Computer Graphics 2008 Conference (TPCG08)*, University of Manchester, UK, Note: *Best Paper Award*, June, 2008.

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**“Importance-Driven Particle Techniques for Flow Visualization,”** In *Proceedings of IEEE VGTC PacificVis 2008*, pp. 71--78. 2008.

[But2008a] C.R. Butson, G.A. Clark.
**“Mechanisms of noise-induced improvement in light-intensity encoding in Hermissenda photoreceptor network,”** In *Journal of Neurophysiology*, Vol. 99, No. 1, pp. 155--165. January, 2008.

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[But2008b] C.R. Butson, G.A. Clark.
**“Random noise paradoxically improves light-intensity encoding in Hermissenda photoreceptor network,”** In *Journal of Neurophysiology*, Vol. 99, No. 1, pp. 146--154. January, 2008.

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[But2008c] C.R. Butson, C.C. McIntyre.
**“Current Steering to Control the Volume of Tissue Activated During Deep Brain Stimulation,”** In *Brain Stimulation*, Vol. 1, No. 1, pp. 7--15. January, 2008.

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[Cal2008a] S.P. Callahan, J.H. Callahan, C.E. Scheidegger, C.T. Silva.
**“Direct Volume Rendering: A 3D Plotting Technique for Scientific Data,”** In *Computing in Science and Engineering*, Vol. 10, No. 1, pp. 88--92. 2008.

[Cal2008b] S.P. Callahan.
**“Adaptive Visualization of Dynamic Unstructured Meshes,”** SCI Technical Report, No. UUSCI-2008-003, Note: *Ph.D. Thesis*, *University of Utah School of Computing*, 2008.

[Cal2008c] S.P. Callahan, C.T. Silva.
**“Image-Space Acceleration for Direct Volume Rendering of Unstructured Grids using Joint Bilateral Upsampling,”** SCI Technical Report, No. UUSCI-2008-002, *University of Utah*, 2008.

[Cal2008d] S.P. Callahan, J. Freire, C.E. Scheidegger, C.T. Silva, and H.T. Vo.
**“Towards a Provenance-Enabling ParaView,”** In *Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008)*, pp. 120--127. 2008.

[Cat2008a] J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker.
**“A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11,”** In *Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08)*, pp. 512--516. 2008.

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[Cat2008b] J. Cates, P.T. Fletcher, M. Styner, H. Hazlett, R.T. Whitaker.
**“Particle-Based Shape Analysis of Multi-Object Complexes,”** In *Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08)*, Lecture Notes In Computer Science (LCNS), pp. 477--485. 2008.

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[Cho2008a] A.N.M. Imroz Choudhury, K. Potter, S.G. Parker.
**“Interactive Visualization for Memory Reference Traces,”** In *Computer Graphics Forum*, In *Proceedings of EuroVis 2008*, Vol. 27, No. 3, pp. 815--822. May, 2008.

[Dan2008a] J.D. Daniels, T. Ochotta, L. Ha, C.T. Silva.
**“Spline-Based Feature Curves from Point-Sampled Geometry,”** In *The Visual Computer*, Vol. 24, No. 6, pp. 449--462. 2008.

[Dan2008b] J.D. Daniels, C.T. Silva, J. Shepherd, E. Cohen.
**“Quadrilateral Mesh Simplification,”** In *ACM Transactions on Graphics - Proceedings of ACM SIGGRAPH Asia 2008*, Vol. 27, No. 5, 2008.

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[Dav2008b] S.B. Davidson, J. Freire.
**“Provenance and Scientific Workflows: Challenges and Opportunities,”** In *Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data*, pp. 1345--1350. 2008.

ISBN: 978-1-60558-102-6

[Die2008b] C. Dietrich, J. Comba, L. Nedel, C.E. Scheidegger, C.T. Silva.
**“Edge Groups: A New Approach to Understanding the Mesh Quality of Marching Methods,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008)*, Vol. 14, No. 6, pp. 1651 - 1666. 2008.

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[Dra2008a] G. Draper, R. Riesenfeld.
**“Who Votes For What? A Visual Query Language for Opinion Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 6, IEEE, pp. 1197--1204. Nov, 2008.

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[Dra2008b] G. Draper, Y. Livnat, R. Riesenfeld.
**“A Visual Query Language for Correlation Discovery and Management,”** In *Proceedings of Visual and Iconic Language Conference (VaIL 2008)*, pp. 14--23. 2008.

[Ell2008a] T. Ellkvist, D. Koop, E.W. Anderson, J. Freire, C.T. Silva.
**“Using Provenance to Support Real-Time Collaborative Design of Workflows,”** In *Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008)*, pp. 266--279. 2008.

[Ell2008b] T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback.
**“Using Mediation to Achieve Provenance Interoperability,”** In *Proceedings of the 2008 Fourth IEEE International Conference on eScience*, pp. 398--399. 2008.

[Fed2008a] A. Fedorov, E. Billet, M.W. Prastawa, G. Gerig, A. Radmanesh, S.K. Warfield, R. Kikinis, N. Chrisochoides.
**“Evaluation of Brain MRI Alignment with the Robust Hausdorff Distance Measures,”** In *Lecture Notes in Computer Science*, Vol. 5358, Springer, pp. 594--603. 2008.

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[Fle2008a] P.T. Fletcher, S. Venkatasubramanian, S. Joshi.
**“Robust Statistics on Riemannian Manifolds via the Geometric Median,”** In *IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2008)*, pp. 1--8. 2008.

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[Fos2008a] N.L. Foster, A.Y. Wang, T. Tasdizen, P.T. Fletcher, J.M. Hoffman, R.A. Koeppe.
**“Realizing the Potential of Positron Emission Tomography with 18F-Fluorodeoxyglucose to Improve the Treatment of Alzheimer,”** In *Journal of the Alzheimer*, Vol. 4, No. 1, Suppl. 1, pp. S29--36. 2008.

PubMed ID: 18631997

[Fos2008b] N. L. Foster, A.Y. Wang, T. Tasdizen, K. Chen, W. Jagust, R.A. Koeppe, E. Reiman, M.W. Weiner, S. Minoshima.
**“Cerebral Hypometabolism Suggesting Frototemporal Dementia in an Alzheimer’s Disease Clinical Trial,”** In *Neurology*, Vol. 70, No. 11, pp. A103. 2008.

[Fre2008a] J. Freire, C.T. Silva.
**“Towards Enabling Social Analysis of Scientific Data,”** In *Proceedings of CHI Social Data Analysis Workshop 2008*, 2008.

[Fre2008b] J. Freire, D. Koop, C.T. Silva.
**“Provenance for Computational Tasks: A Survey,”** In *Computing in Science and Engineering*, Vol. 10, No. 3, pp. 11--21. 2008.

[Fuc2008a] M. Fuchs, S. Gerber.
**“Variational Shape Detection in Microscope Images Based on Joint Shape and Image Feature Statistics,”** In *Proceedings of the IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2008)*, pp. 1--8. 2008.

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[Gao2008a] W. Gao, Y. Chen, G. Gerig, J.K. Smith, V. Jewells, J.H. Gilmore, W. Lin.
**“Temporal and Spatial Development of Axonal Maturation and Myelination of White Matter in the Developing Brain,”** In *American Journal of Neuroradiology*, pp. (published online). Nov 11, 2008.

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[Gen2008a] S.E. Geneser, R.M. Kirby, R.S. MacLeod.
**“Application of Stochastic Finite Element Methods to Study the Sensitivity of ECG Forward Modeling to Organ Conductivity,”** In *IEEE Transations on Biomedical Engineering*, Vol. 55, No. 1, pp. 31--40. January, 2008.

[Gil2008a] J.H. Gilmore, L. Smith, H. Wolfe, B. Hertzberg, J.K. Smith, N. Chescheir, D. Evans, C. Kang, R.M. Hamer, W. Lin, G. Gerig.
**“Prenatal Mild Ventriculomegaly Predicts Abnormal Development of the Neonatal Brain,”** In *Biological Psychiatry*, Vol. 64, No. 12, pp. 1069-1076. Dec, 2008.

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[Goo2008a] C. Goodlett, P.T. Fletcher, J. Gilmore, G. Gerig.
**“Group Statistics of DTI Fiber Bundles Using Spatial Functions of Tensor Measures,”** In *Medical Image Computing and Computer-Assisted Intervention (MICCAI 2008)*, Springer Verlag, pp. 1068--1075. 2008.

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[Goo2008c] C.E. Goodyer, J. Wood, M. Berzins.
**“Mathematical modeling of chemical diffusion through skin using Grid-based PSEs,”** In *Modeling, Simulation and Optimization of Complex Processes: Proceedings of the Third International Conference on High Performance Scientific Computing*, Edited by H.G. Bock and E. Kostina and H.X. Phu and R. Rannacher, Springer, pp. 249--258. 2008.

[Got2008a] D. Gottlieb, D. Xiu.
**“Galerkin Method for Wave Equations with Uncertain Coefficients,”** In *Communications in Computational Physics*, Vol. 3, No. 2, pp. 505--518. 2008.

[Gou2008a] S. Gouttard, M. Styner, M.W. Prastawa, J. Piven, G. Gerig.
**“Assessment of Reliability of Multi-site Neuroimaging via Traveling Phantom Study,”** In *Proceedings of Medical Image Computing and Computer Assisted Intervention 2008, Lecture Notes in Computer Science LNCS*, Vol. 5242, pp. 263--270. September, 2008.

[Gri2008a] C. Gribble, C. Brownlee, S.G. Parker.
**“Practical Global Illumination for Interactive Particle Visualization,”** In *Computers and Graphics*, Vol. 32, No. 1, pp. 14--24. February, 2008.

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[Ham2008a] C.W. Hamman, J.C. Klewicki, R.M. Kirby.
**“On the Lamb Vector Divergence in Navier-Stokes Flows,”** In *Journal of Fluid Mechanics*, Vol. 610, pp. 261--284. 2008.

[Har2008a] D.E. Hart.
**“Adjoint Error Estimation for Elastohydrodynamic Lubrication,”** Note: *Advisor: Martin Berzins*, *School of Computing, University of Leeds*, January, 2008.

[Hes2008a] J.S. Hesthaven, R.M. Kirby.
**“Filtering in Legendre Spectral Methods,”** In *Mathematics of Computation*, Vol. 77, No. 263, pp. 1425--1452. 2008.

[Hij2008a] Y. Hijazi, A. Knoll, M. Schott, A. Kensler, C.D. Hansen, H. Hagen.
**“CSG Operations of Arbitrary Primitives with Interval Arithmetic and Real-Time Ray Tracing,”** SCI Technical Report, No. UUSCI-2008-008, *University of Utah School of Computing*, 2008.

[How2008a] B. Howe, P. Lawson, R. Bellinger, J. Freire, E. Anderson, E. Santos, C.E. Scheidegger, A. Baptista, C.T. Silva.
**“End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory,”** In *Proceedings of the 2008 Fourth IEEE International Conference on eScience*, pp. 127--134. 2008.

[Ize2008a] T. Ize, I. Wald, S.G. Parker.
**“Ray Tracing with the BSP Tree,”** In *Proceedings of the IEEE Symposium on Interactive Ray Tracing, 2008*, pp. 159--166. 2008.

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[Jeo2008a] W.-K. Jeong, R.T. Whitaker.
**“A Fast Iterative Method for Eikonal Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 30, No. 5, pp. 2512-2534. 2008.

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[Joh2008a] C.R. Johnson, X. Tricoche.
**“Biomedical Visualization,”** In *Advances in Biomedical Engineering*, Ch. 6, Edited by Pascal Verdonck, Elsvier Science, pp. 209--272. 2008.

[Jol2008a] M. Jolley, J.G. Stinstra, S. Pieper, R.S. MacLeod, D.H. Brooks, F. Cecchin, J.K. Triedman.
**“A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults,”** In *Heart Rhythm*, Vol. 5, No. 4, pp. 565--572. April, 2008.

PubMed ID: 18362024

[Jur2008b] E. Jurrus, R.T. Whitaker, B. Jones, R. Marc, T. Tasdizen.
**“An Optimal-Path Approach for Neural Circuit Reconstruction,”** In *Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro*, pp. 1609--1612. 2008.

PubMed ID: 19172170

[Kas2008a] R. Kashani, M. Hub, J.M. Balter, M.L. Kessler, L. Dong, L. Zhang, L. Xing, Y. Xie, D. Hawkes, J.A. Schnabel, J. McClelland, S. Joshi, Q. Chen, W. Lu.
**“Objective assessment of deformable image registration in radiotherapy: a multi-institution study,”** In *Medical Physics*, Vol. 35, No. 12, pp. 5944--5953. 2008.

PubMed ID: 19175149

[Ken2008a] A. Kensler, A. Knoll, P. Shirley.
**“Better Gradient Noise,”** SCI Institute Technical Report, No. UUSCI-2008-001, *University of Utah*, 2008.

[Ken2008b] A. Kensler.
**“Tree Rotations for Improving Bounding Volume Heirarchies,”** In *Proceedings of the 2008 IEEE Symposium on Interactive Ray Tracing*, pp. 73--76. 2008.

[Kir2008a] R.M. Kirby, C.T. Silva.
**“The Need For Verifiable Visualization,”** In *IEEE Computer Graphics and Applications*, Vol. 28, No. 5, pp. 78--83. 2008.

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[Kla2008a] S. Klasky, M. Vouk, M. Parashar, A. Khan, N. Podhorszki, R. Barreto, D. Silver, S.G. Parker.
**“Collaborative Visualization Spaces for Petascale Simulations,”** In *Proceedings of 2008 International Symposium on Collaborative Technologies and Systems (CTS 2008)*, pp. 203--211. 2008.

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[Kni2008a] R.C. Knickmeyer, S. Gouttard, C. Kang, D. Evans, K. Wilber, K.J. Smith, R.M. Hamer, W. Lin, G. Gerig, J.H. Gilmore.
**“A Structural MRI Study of Human Brain Development from Birth to Two Years,”** In *The Journal of Neuroscience*, Vol. 28, No. 47, pp. 12176--12182. Nov, 2008.

PubMed ID: 19020011

[Koo2008a] D. Koop, C.E. Scheidegger, S.P. Callahan, J. Freire, C.T. Silva.
**“VisComplete: Automating Suggestions for Visualization Systems,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008)*, Vol. 14, No. 6, pp. 1691--1698. 2008.

[Kri2008a] L. Krishnan, C.J. Underwood, S.A. Maas, B.J. Ellis, T.C. Kode, J.B. Hoying, J.A. Weiss.
**“Effect of Mechanical Boundary Conditions on Orientation of Angiogenic Microvessels,”** In *Cardiovascular Research*, Vol. 78, No. 2, pp. 324--332. 2008.

[Kru2008a] J. Krüger.
**“A GPU Framework for Interactive Simulation and Rendering of Fluid Effects,”** In *IT - Information Technology*, Vol. 4, pp. 265--268. 2008.

[Kru2008b] J. Krüger, K. Potter, R.S. MacLeod, C.R. Johnson.
**“Unified Volume Format: A General System For Efficient Handling Of Large Volumetric Datasets,”** In *Proceedings of IADIS Computer Graphics and Visualization 2008 (CGV 2008)*, pp. 19--26. 2008.

PubMed ID: 20953270

[Kub2008a] M. Kubicki, M. Styner, S. Bouix, G. Gerig, D. Markant, K. Smith, R. Kikinis, R.W. McCarley, M.E. Shenton.
**“Reduced Interhemispheric Connectivity in Schizophrenia- Tractography Based Segmentation of the Corpus Callosum,”** In *Schizophrenia Research*, Vol. 106, No. 2-3, pp. 125--131. December, 2008.

[Led2008a] C. Ledergerber, G. Guennebaud, M.D. Meyer, M. Bacher, H. Pfister.
**“Volume MLS Ray Casting,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of Visualization 2008)*, Vol. 14, No. 6, pp. 1539--1546. 2008.

[Lew2008a] S. Lew, C.H. Wolters, A. Anwander, S. Makeig, R.S. Macleod.
**“Improved EEG Source Analysis Using Low-Resolution Conductivity Estimation in a Four-Compartment Finite Element Head Model,”** In *Human Brain Mapping*, Vol. 31, December, 2008.

[Li2008a] G.-S. Li, X. Tricoche, D. Weiskopf, C.D. Hansen.
**“Flow Charts: Visualization of Vector Fields on Arbitrary Surfaces,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 5, pp. 1--14. September/October, 2008.

[Li2008b] G.-S. Li, X. Tricoche, C.D. Hansen.
**“Physically-based Dye Advection for Flow Visualization,”** In *Computer Graphics Forum*, Vol. 27, No. 3, Edited by A. Vilanova and A. Telea and G. Scheuermann and T. Moeller, Wiley-Blackwell, pp. 727--734. May, 2008.

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[Li2008c] J. Li, D. Xiu.
**“On Numerical Properties of the Ensemble Kalman Filter for Data Assimilation,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 197, No. 43--44, pp. 3574--3583. 2008.

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[Lin2008a] L. Lins, D. Koop, E.W. Anderson, S.P. Callahan, E. Santos, C.E. Scheidegger, J. Freire, C.T. Silva.
**“Examining Statistics of Workflow Evolution Provenance: A First Study,”** In *Proceedings of the 20th International Conference on Scientific and Statistical Database Management (SSDBM)*, pp. 573--579. 2008.

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[Lin2008b] W. Lin, Q. Zhu, W. Gao, Y. Chen, C.-H. Toh, M. Styner, G. Gerig, J.K. Smith, B. Biswal, J. Gilmore.
**“Functional Connectivity Magnetic Resonance Imaging Reveals Cortical Functional Connectivity in the Developing Brain,”** In *American Journal of Neuroradiology*, Vol. 29, pp. 1883--1889. Fall, 2008.

[Liv2008a] Y. Livnat, S.G. Parker, C.R. Johnson.
**“Fast Isosurface Extraction Methods for Large Image Data Sets,”** In *Handbook of Medical Image Processing and Analysis*, 2nd edition, Ch. 47, Note: *(to appear)*, Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.

[Liz2008a] M. Lizier, J.F. Shepherd, L.G. Nonato, J. Comba, C.T. Silva.
**“Comparing Techniques for Tetrahedral Mesh Generation,”** In *Proceedings of the Inaugural International Conference of the Engineering Mechanics Institute (EM 2008)*, pp. (accepted). 2008.

[Lui2008a] J. Luitjens, Q. Meng, M. Berzins, T. Henderson.
**“Improving the Load Balance of Parallel Adaptive Mesh Refined Simulations,”** SCI Technical Report, No. UUSCI-2008-007, *University of Utah School of Computing*, 2008.

[Lui2008b] J. Luitjens, B. Worthen, M. Berzins, T. Henderson.
**“Scalable Parallel AMR for the Uintah Multiphysics Code,”** In *Petascale Computing Algorithms and Applications*, Ch. 4, CRC Press LLC., pp. 67--82. 2008.

[Luj2008a] T.J. Lujan, C.J. Underwood, N.T. Jacobs, J.A. Weiss.
**“Contribution of Glycosaminoglycans to Viscoelastic Tensile Behavior of Human Ligament,”** In *Journal of Applied Physiology*, Vol. 106, No. 2, pp. 423--431. 2008.

[Mar2008a] T. Martin, E. Cohen, R.M. Kirby.
**“Volumetric Parameterization and Trivariate B-spline Fitting using Harmonic Functions,”** In *Proceedings of ACM Solid and Physical Modeling*, Stony Brook, NY, Note: *Awarded Best Paper*, pp. 269-280. 2008.

[Mcg2008a] C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,”** In *Journal of the American College of Cardiology*, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008.

[Men2008a] Q. Meng, J. Luitjens, M. Berzins.
**“A Comparison of Load Balancing Algorithms for AMR in Uintah,”** SCI Technical Report, No. UUSCI-2008-006, *University of Utah*, 2008.

[Mer2008a] S. Mergen, C. Heuser, J. Freire.
**“Querying Structured Information Sources on the Web,”** In *Proceedings of the 10th International Conference on Information Integration and Web-based Applications and Services*, pp. 470--476. 2008.

[Mer2008b] D. Merck, G. Tracton, R. Saboo, J. Levy, E. Chaney, S. Pizer, S. Joshi.
**“Training models of anatomic shape variability,”** In *Medical Physics*, Vol. 35, No. 8, pp. 3584--3596. 2008.

PubMed ID: 18777919

[Mey2008a] M.D. Meyer, R.T. Whitaker, R.M. Kirby, C. Ledergerber, H. Pﬁster.
**“Particle-based Sampling and Meshing of Surfaces in Multimaterial Volumes,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 6, pp. 1539--1546. 2008.

[Mey2008b] M.D. Meyer.
**“Dynamic Particle Systems for Adaptive Sampling of Implicit Surfaces,”** *School of Computing, University of Utah*, 2008.

[Mor2008a] L. Moreau, B. Ludäscher, I. Altintas, R. Barga, S. Bowers, S.P. Callahan, G. Chin Jr., B. Clifford, S. Cohen, S. Cohen-Boulakia, S. Davidson, E. Deelman, L. Digiampietri, I. Foster, J. Freire, J. Frew, J. Futrelle, T. Gibson, Y. Gil, C. Goble, J. Golbeck, P. Groth, D. A. Holland, S. Jiang, J. Kim, D. Koop, A. Krenek, T. McPhillips, G. Mehta, S. Miles, D. Metzger, S. Munroe, J. Myers, B. Plale, N. Podhorszki, V. Ratnakar, E. Santos, C.E. Scheidegger, K. Schuchardt, M. Seltzer, Y. L. Simmhan, C.T. Silva, P. Slaughter, E. Stephan, R. Stevens, D. Turi, H.T. Vo, M. Wilde, J. Zhao, Y. Zhao.
**“The First Provenance Challenge,”** In *Concurrency and Computation: Practice and Experience*, Vol. 20, No. 5, pp. 409--418. April, 2008.

[Mor2008b] L. Moreau, J. Freire, J. Futrelle, R.E. McGrath, J. Myers, P. Paulson.
**“The Open Provenance Model: An Overview,”** In *Provenance and Annotation of Data and Processes*, Lecture Notes in Computer Science (LNCS), pp. 323--326. 2008.

ISBN: 978-3-540-89964-8

[Muk2008a] N. Mukherjee, C. Kang, H.M. Wolfe, B.S. Hertzberg, J.K. Smith, W. Lin, G. Gerig, R.M. Hamer, J.H. Gilmore.
**“Discordance of Prenatal and Neonatal Brain Development in Twins,”** In *Early Human Development*, pp. (in press). August, 2008.

[New2008a] E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby.
**“A Comparison of Implicit Solvers for the Immersed Boundary Equations,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 197, No. 25--28, pp. 2290--2304. 2008.

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[Ngu2008a] H. Nguyen, T. Nguyen, J. Freire.
**“Learning to Extract Form Labels,”** In *Proceedings of the VLDB Endowment*, Vol. 1, No. 1, VLDB Endowment, pp. 684--694. Aug, 2008.

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[Ngu2008b] H. Nguyen, E.Y. Kang, J. Freire.
**“Automatically Extracting Form Labels,”** In *Proceedings of the 2008 IEEE 24th International Conference on Data Engineering*, pp. 1498--1500. 2008.

[Och2008a] T. Ochotta, D. Saupe.
**“Image-Based Surface Compression,”** In *Computer Graphics Forum*, Vol. 27, No. 6, pp. 1647--1663. 2008.

[Ogu2008a] I. Oguz, J. Cates, P.T. Fletcher, R.T. Whitaker, D. Cool, S. Aylward, M. Styner.
**“Cortical Correspondence using Entropy-Based Particle Systems and Local Features,”** In *5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008. (ISBI 2008)*, pp. 1637--1640. 2008.

[Pal2008a] R. Palmer, M. DeLisi, G. Gopalakrishnan, R.M. Kirby.
**“An Approach to Formalization and Analysis of Message Passing Libraries,”** In *Proceedings of the 12th International Workshop on Formal Methods for Industrial Critical Systems (FMICS 2007)*, Berlin, Germany, Vol. 4916/2008, Note: *Awarded Best Paper.*, pp. 164--181. 2008.

[Peg2008a] V. Pegoraro, I. Wald, S.G. Parker.
**“Sequential Monte Carlo Adaptation in Low-Anisotropy Participating Media,”** In *Proceedings of the 19th Eurographics Symposium on Rendering*, pp. 1097--1104. 2008.

[Peg2008b] V. Pegoraro, C. Brownlee, P.S. Shirley, S.G. Parker.
**“Towards Interactive Global Illumination Effects via Sequential Monte Carlo Adaptation,”** In *Proceedings of the 3rd IEEE Symposium on Interactive Ray Tracing*, pp. 107--114. 2008.

[Pha2008a] N.S. Phatak, S.A. Maas, A.I. Veress, N.A. Pack, E.V.R. Di Bella, J.A. Weiss.
**“Strain measurement in the left ventricle during systole with deformable image registration,”** In *Medical Image Analysis*, pp. (in press). 2008.

[Piz2008g] S. Pizer, M. Styner, T. Terriberry, R. Broadhurst, S. Joshi, E. Chaney, P.T. Fletcher.
**“Statistical Applications with Deformable M-Reps,”** In *Computational Imaging and Vision*, Springer, pp. 269--308. 2008.

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[Pot2008a] K. Potter, J. Krüger, C.R. Johnson.
**“Towards the Visualization of Multi-Dimentional Stochastic Distribution Data,”** In *Proceedings of The International Conference on Computer Graphics and Visualization (IADIS) 2008*, pp. 191--196. 2008.

[Pra2008b] M.W. Prastawa, G. Gerig.
**“Brain Lesion Segmentation Through Physical Model Estimation,”** In *Lecture Notes in Computer Science*, Vol. 5358, pp. 562--571. 2008.

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[Pre2008a] T. Preusser, H. Scharr, K. Krajsek, R.M. Kirby.
**“Building Blocks for Computer Vision with Stochastic Partial Differential Equations,”** In *International Journal of Computer Vision*, Vol. 80, No. 3, Springer, pp. 375--405. July, 2008.

DOI: 10.1007/s11263-008-0145-5

[Pri2008g] J.C. Principe, J. Xu, R. Jenssen, A.R.C. Paiva, I. Park.
**“A Reproducing Kernel Hilbert Space framework for Information-Theoretic Learning,”** In *IEEE Transactions on Signal Processing*, Vol. 56, No. 12, Edited by J.C. Principe, IEEE, pp. 5891--5902. Dec, 2008.

ISBN: 978-1-4419-1569-6

DOI: 10.1109/tsp.2008.2005085

[Rul2008a] M. Rullmann, A. Anwander, M. Dannhauer, S.K. Warfield, F.H. Duffy, C.H. Wolters.
**“EEG Source Analysis of Epileptiform Activity Using a 1mm Anisotropic Hexahedra Finite Element Head Model.,”** In *NeuroImage*, Vol. 44, No. 2, pp. 399--410. 2008.

DOI: 10.1016/j.neuroimage.2008.09.009

[Sad2008a] N. Sadeghi, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman, T. Tasdizen.
**“Automatic Classification of Alzheimer,”** In *Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2008): From Nano to Macro*, pp. 408--411. 2008.

DOI: 10.1109/ISBI.2008.4541019

[San2008b] E. Santos, L. Lins, J.P. Ahrens, J. Freire, C.T. Silva.
**“A First Study on Clustering Collections of Workflow Graphs,”** In *Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008)*, pp. 160--173. 2008.

[Sch2008a] C.E. Scheidegger, D. Koop, E. Santos, H.T. Vo, S.P. Callahan, J. Freire, C.T. Silva..
**“Tackling the Provenance Challenge One Layer at a Time,”** In *Concurrency Computat.: Pract. Exper.*, Vol. 20, No. 5, pp. 473--483. 2008.

[Sch2008b] C.E. Scheidegger, H.T. Vo, D. Koop, J. Freire, C.T. Silva.
**“Querying and Re-Using Workflows with VisTrails,”** In *Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data*, pp. 1251--1254. 2008.

DOI: 10.1145/1376616.1376747

[Sch2008c] J.A. Schmidt.
**“Uintah Application Development,”** SCI Technical Report, No. UUSCI-2008-005, *University of Utah*, 2008.

[Sch2008d] M. Schott, V. Pegoraro, C.D. Hansen, K. Boulanger, J. Stratton, K. Bouatouch.
**“A Directional Occlusion Shading Model for Interactive Direct Volume Rendering,”** SCI Technical Report, No. UUSCI-2008-009, *University of Utah Scientific Computing and Imaging Institute*, 2008.

[Sch2008e] C.E. Scheidegger, J. Schreiner, B. Duffy, H. Carr, C.T. Silva.
**“Revisiting Histograms and Isosurface Statistics,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008)*, Vol. 14, No. 6, pp. 1659--1666. 2008.

DOI: 10.1109/TVCG.2008.160

[Sha2008a] S. Sharma, S. Vakkalanka, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp.
**“A Formal Approach to Detect Functionally Irrelevant Barriers in MPI Programs,”** In *Proceedings of EuroPVM-MPI 2008*, Dublin, Ireland, Vol. 5205, pp. 265--273. September, 2008.

DOI: 10.1007/978-3-540-87475-1_36

[She2008a] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation Constraints,”** In *Journal of Engineering with Computers*, Vol. 24, No. 3, pp. 195--213. 2008.

[Shv2008a] A.G. Shvedko, M.D. Warren, S. Shome, J.G. Stinstra, A.V. Zaitsev.
**“Influence of the Skeletal Muscle Activity on Time and Frequency Domain Properties of the Body Surface ECG During Evolving Ventricular Fibrillation in the Pig,”** In *Resuscitation*, Vol. 78, No. 2, pp. 215--223. May 24, 2008.

DOI: 10.1016/j.resuscitation.2008.03.010

[Sil2008a] C.T. Silva, J. Tohline.
**“Guest Editorial: Special Issue on Computational Provenance,”** In *Computing in Science and Engineering*, Vol. 10, No. 3, pp. 9--10. 2008.

[Sil2008b] C.T. Silva, J. Freire.
**“Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present and Future,”** In *Journal of Physics: Conference Series (SciDAC 2008 Conference)*, Vol. 125, 2008.

[Spj2008a] J. Spjut, D. Kopta, S. Kellis, S. Boulos, E. Brunvand.
**“TRaX: A Multi-Threaded Architecture for Real-Time Ray Tracing,”** In *Proceedings of the IEEE Symposium on Application Specific Processors, SASP 2008*, Note: *Awarded Best Paper*, pp. (in press). 2008.

[Ste2008a] M. Steffen, S. Curtis, R.M. Kirby, J.K. Ryan.
**“Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 3, pp. 680--692. 2008.

[Ste2008b] M. Steffen, R.M. Kirby, M. Berzins.
**“Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM),”** In *International Journal for Numerical Methods in Engineering*, Vol. 76, No. 6, pp. 922--948. 2008.

DOI: 10.1002/nme.2360

[Ste2008c] M. Steffen, P.C. Wallstedt, J.E. Guilkey, R.M. Kirby, M. Berzins.
**“Examination and Analysis of Implementation Choices within the Material Point Method (MPM),”** In *Computer Modeling in Engineering & Sciences*, Vol. 31, No. 2, pp. 107--127. 2008.

[Sti2008a] J.G. Stinstra, M.A. Jolley, J.D. Tate, D.H. Brooks, J.K. Triedman, R.S. MacLeod.
**“The Role of Volume Conductivities in Simulation of Implantable Defibrillators,”** In *Computers in Cardiology*, Bologna, Italy, 2008.

[Sti2008b] J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod.
**“Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,”** In *Proceedings of the 29th Annual International Conference of the IEEE EMBS*, pp. 1422-1425. 2008.

ISBN: 978-1-4244-0787-3

[Sty2008a] M. Styner, I. Oguz, T. Heimann, G. Gerig.
**“Minimum Description Length with Local Geometry,”** In *Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2008)*, pp. 1283--1286. 2008.

DOI: 10.1109/ISBI.2008.4541238

[Sut2008a] D.R. Sutherland, Q. Ni, R.S. MacLeod, R.L. Lux, B.B. Punske.
**“Experimental Measures of Ventricular Activation and Synchrony,”** In *Pacing and Clinical Electrophysiology*, Vol. 31, No. 12, pp. 1560--1570. December, 2008.

[Tac2008a] B. Taccardi, B.B. Punske, E. Macchi, R.S. MacLeod, P.R. Ershler.
**“Epicardial and Intramural Excitation During Ventricular Pacing: Effect of Myocardial Structure,”** In *The American Journal of Physiology - Heart and Circulatory Physiology*, Vol. 294, No. 4, pp. H1753--1766. April, 2008.

DOI: 10.1152/ajpheart.01400.2007

[Tas2008a] T. Tasdizen.
**“Principal Components for Non-Local Means of Image Denoising,”** In *Proceedings of the International Conference on Image Processing (ICIP 2008)*, pp. 1728--1731. 2008.

PubMed ID: 19180227

[Tas2008b] T. Tasdizen , E. Jurrus, R. T. Whitaker.
**“Non-uniform Illumination Correction in Transmission Electron Microscopy,”** In *MICCAI Workshop on Microscopic Image Analysis with Applications in Biology*, 2008.

[Tra2008a] L.T. Tran, J. Kim, M. Berzins.
**“An Introduction to the Material Point Method using a Case Study from Gas Dynamics,”** In *Numerical Analysis and Applied Mathematics: International Conference on Numerical Analysis and Applied Mathematics 2008. AIP Conference Proceedings*, Vol. 1048, Edited by T.E. Simos and G. Psihoyios and Ch. Tsitouras, pp. 26--29. 2008.

ISBN: 978-0-7354-0576-9

[Tri2008a] X. Tricoche, R.S. MacLeod, C.R. Johnson.
**“Visual Analysis of Bioelectric Fields,”** In *Visualization in Medicine and Life Sciences*, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.

[Tri2008b] J.K. Triedman, M. Jolley, J. Stinstra, D.H. Brooks, R.S. MacLeod.
**“Predictive Modeling of Defibrillation Using Hexahedral and Tetrahedral Finite Element Models: Recent Advances,”** In *Journal of Electrocardiology*, Vol. 41, pp. 483--486. 2008.

[Vak2008a] S. Vakkalanka, M. DeLisi, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp.
**“Implementing Efficient Dynamic Formal Verification Methods for MPI Programs,”** In *Recent Advances in Parallel Virtual Machine and Message Passing Interface
Lecture Notes in Computer Science*, Dublin, Ireland, Vol. 5205, pp. 248--256. September, 2008.

[Vak2008b] S. Vakkalanka, M. DeLisi, G. Gopalakrishnan, R.M. Kirby.
**“Scheduling Considerations for Building Dynamic Verification Tools for MPI,”** In *Proceedings of the 6th Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging*, Seattle, WA, PADTAD '08, Vol. 3, ACM, pp. 1--6. 2008.

ISBN: 978-1-60558-052-4

DOI: 10.1145/1390841.1390844

[Vak2008c] S. Vakkalanka, G. Gopalakrishnan, R.M. Kirby.
**“Dynamic Verification of MPI Programs with Reductions in Presence of Split Operations and Relaxed Orderings,”** In *Computer Aided Verification Lecture Notes in Computer Science *, Vol. 5123, pp. 66--79. July, 2008.

DOI: 10.1007/978-3-540-70545-1_9

[Vas2008a] S.X. Vasquez, M.S. Hansen, A.N. Bahadur, M.F. Hockin, G.L. Kindlmann, L. Nevell, I.Q. Wu, D.J. Grunwald, D.M. Weinstein, G.M. Jones, C.R. Johnson, J.L. Vandeberg, M.R. Capecchi, C. Keller.
**“Optimization of Volumetric Computed Tomography for Skeletal Analysis of Model Genetic Organisms,”** In *The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology*, Vol. 291, pp. 475--487. 2008.

PubMed ID: 18286615

[Ver2008a] A.I. Veress, J.A. Weiss, R.H. Huesman, B.W. Reutter, S.E . Taylor, A. Sitek, B. Feng, Y. Yang, G.T. Gullberg.
**“Measuring Regional Changes in the Diastolic Deformation of the Left Ventricle of SHR Rats Using MicroPET Technology and Hyperelastic Warping,”** In *Annals of Biomedical Engingeering*, Vol. 36, No. 7, pp. 1104--1017. 2008.

[Vie2008a] K. Vieira, L. Barbosa, J. Freire, A. Silva.
**“Siphon++: A Hidden-Web Crawler for Keyword-Based Interfaces,”** In *Proceeding of the 17th ACM conference on Information and knowledge management (CIKM)*, pp. 1361--1362. November, 2008.

[Wal2008a] I. Wald, T. Ize, S.G. Parker.
**“Fast, Parallel, and Asynchronous Construction of BVHs for Ray Tracing Animated Scenes,”** In *Computers and Graphics*, Vol. 32, No. 1, pp. 3--13. February, 2008.

[Wan2008a] H. Wang, C.E. Scheidegger, C.T. Silva.
**“Optimal Bandwidth Selection for MLS Surfaces,”** In *IEEE International Conference on Shape Modeling and Applications (SMI) 2008*, pp. 111--120. 2008.

ISBN: 978-1-4244-2260-9

DOI: 10.1109/SMI.2008.4547957

[Whi2008a] R.T. Whitaker, R.M. Kirby, J.G. Sinstra, M.D. Meyer.
**“Multimaterial Meshing of MRI Head Data for Bioelectric Field Simulations,”** In *Proceedings of the 17th International Meshing Roundtable*, 2008.

[Xiu2008a] D. Xiu.
**“Numerical Integration Formulas of Degree Two,”** In *Applied Numerical Mathematics*, Vol. 58, No. 10, pp. 1515--1520. 2008.

DOI: 10.1016/j.apnum.2007.09.004

[Xu2008a] S. Xu, M. Styner, J.H. Gilmore, G. Gerig.
**“Multivariate Longitudinal Statistics for Neonatal-Pediatric Brain Tissue Development,”** In *Proceedings of SPIE Medical Imaging 2008*, Vol. 6914, February, 2008.

DOI: 10.1117/12.773966

[Xu2008b] S. Xu, M. Styner, J. Gilmore, J. Piven, G. Gerig.
**“Multivariate Nonlinear Mixed Model to Analyze Longitudinal Image Data: MRI Study of Early Brain Development,”** In *Proceedings of IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA) 2008*, IEEE Computer Society, pp. 1--8. June, 2008.

ISBN: 978-1-4244-2339-2

DOI: 10.1109/CVPRW.2008.4563011

[Yan2008a] Y. Yang, X. Chen, G. Gopalakrishnan, R.M. Kirby.
**“Efficient Stateful Dynamic Partial Order Reduction,”** In *Proceedings of Model Checking Software: 15th International SPIN Workshop*, Los Angeles, CA, Vol. 5156, pp. 288--305. August, 2008.

DOI: 10.1007/978-3-540-85114-1_20

[Yau2008a] S. Yau, K. Damevski, D. Zorin, V. Karamcheti, S.G. Parker.
**“Result Reuse in Design Space Exploration: A Study in System Support for Interactive Parallel Computing,”** In *Proceedings of the 22nd International Parallel and Distributed Processing Symposium (IPDPS 2008)*, Miami, Florida, pp. 1--12. 2008.

[Zha2008a] F. Zhang, E.R. Hancock, C. Goodlett, G. Gerig.
**“Probabilistic White Matter Fiber Tracking using, Particle Filtering and von Mises-Fisher Sampling,”** In *Medical Image Analysis (MedIA)*, pp. (in print). 2008.

2007

[Adl2007a] G. Adluru, S.P. Awate, T. Tasdizen, R.T. Whitaker, E.V.R. DiBella.
**“Temporally Constrained Reconstruction of Dynamic Cardiac Perfusion MRI,”** In *Magnetic Resonance in Medicine*, Vol. 57, pp. 1027--1036. 2007.

[Adl2007b] G. Adluru, R.T. Whitaker, E.V.R. DiBella.
**“Spatio-Temporal Constrained Reconstruction of Sparse Dynamic Contrast Enhanced Radial MRI Data,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging*, pp. 109--112. 2007.

[Adl2007c] G. Adluru, E. Hsu, E.V.R. DiBella.
**“Constrained Reconstruction of Sparse Cardiac MR DTI Data,”** In *Proceedings of FIMH 2007*, LNCS, No. 4466, pp. 91--99. 2007.

[Alt2007a] O. Alter.
**“Genomic Signal Processing: From Matrix Algebra to Genetic Networks,”** In *Microarray Data Analysis: Methods in Molecular Biology*, Vol. 377, Edited by M.J. Korenberg, Humana Press, Totowa, pp. 17--59. 2007.

DOI: 10.1007/978-1-59745-390-5_2

[And2007b] E.W. Anderson, S.P. Callahan, C.E. Scheidegger, J.M. Schriener, C.T. Silva.
**“Hardware-Assisted Point-Based Volume Rendering of Tetrahedral Meshes,”** In *Proceedings of SIBGRAPI 2007*, pp. 163--170. 2007.

[And2007c] E.W. Anderson, G.A. Preston, C.T. Silva.
**“Towards Development of a Circuit Based Treatment for Impaired Memory: A Multidisciplinary Approach,”** In *Proceedings of IEEE EMBS Neural Engineering 2007*, pp. 163--172. 2007.

[And2007d] A.E. Anderson, B.J. Ellis, J.A. Weiss.
**“Verification, Validation and Sensitivity Studies in Computational Biomechanics,”** In *Computer Methods in Biomechanics and Biomedical Engineering*, Vol. 10, No. 3, pp. 171--184. 2007.

[And2007e] E.W. Anderson, S.P. Callahan, D.A. Koop, E. Santos, C.E. Scheidegger, H.T. Vo, J. Freire, C.T. Silva.
**“VisTrails: Using Provenance to Streamline Data Exploration,”** In *Poster Proceedings of the International Workshop on Data Integration in the Life Sciences (DILS) 2007*, Note: *Poster presentation*, 2007.

[Ate2007a] G.A. Ateshian, B.J. Ellis, J.A. Weiss.
**“Equivalence Between Short-Time Biphasic and Incompressible Elastic Material Response,”** In *Journal of Biomechanical Engineering*, Vol. 129, No. 3, pp. 405--412. 2007.

[Awa2007a] S. Awate, R.T. Whitaker.
**“Feature-Preserving MRI Denoising: A Nonparametric Empirical-Bayes Approach,”** In *IEEE Transactions on Medical Imaging*, Vol. 26, No. 9, pp. 1242--1255. 2007.

[Bah2007a] A.N. Bahadur, I.Q. Wu, D.M. Weinstein, M.D. Davis, D.A. Lewis, P. Kochunov, C. Keller.
**“Multimodality Chamber for Coregistered Anatomical and Molecular Imaging of Small Animals,”** In *Lab Animal*, Vol. 36, No. 8, pp. 29--35. 2007.

[Bar2007a] L. Barbosa, J. Freire.
**“An Adaptive Crawler for Locating Hidden-Web Entry Points,”** In *Proceedings of the 16th international conference on World Wide Web (WWW)*, Banff, Alberta, Canada, pp. 441--450. May, 2007.

[Bar2007b] L. Barbosa, J. Freire.
**“Combining Classifiers to Identify Online Databases,”** In *Proceedings of the 16th International Conference on World Wide Web (WWW)*, Banff, Alberta, Canada, pp. 431--440. May, 2007.

[Bar2007c] L. Barbosa, J. Freire, A. Silva.
**“Organizing Hidden-Web Databases by Clustering Visible Web Documents,”** In *Proceedings of the IEEE 23rd International Conference on Data Engineering, 2007. (ICDE 2007)*, Istanbul, pp. 326--335. 2007.

[Bar2007d] L. Barbosa, S. Tandon, J. Freire.
**“Automatically Constructing a Directory of Molecular Biology Databases,”** In *Data Integration in the Life Sciences*, Lecture Notes in Computer Science (LNCS), Vol. 4544/2007, pp. 6--16. 2007.

ISBN: 978-3-540-73254-9

[Bav2007a] L. Bavoil, S.P. Callahan, A. Lefohn, J.L.D. Comba, C.T. Silva.
**“Multi-Fragment Effects on the GPU using the k-Buffer,”** In *ACM Symposium on Interactive 3D Graphics and Games (i3D)*, pp. 97--104. 2007.

[Bel2007a] M.K. Belmonte, J.C. Mazziotta, N.J. Minshew, A.C. Evans, E. Courchesne, S.R. Dager, S.Y. Bookheimer, E.H. Aylward, D.G. Amaral, R.M. Cantor, D.C. Chugani, A.M. Dale, C. Davatzikos, G. Gerig, M.R. Herbert, J.E. Lainhart, D.G. Murphy, J. Piven, A.L. Reiss, R.T. Schultz, T.A. Zeffiro, S. Levi-Pearl, C. Lajonchere, S.A. Colamarino.
**“Offering to Share: How to Put Heads Together in Autism Neuroimaging,”** In *Journal of Autism and Developmental Disorders JADD*, Vol. 38, pp. 2--13. 2007.

[Ben2007a] C. Benthin, S. Boulos, D. Lacewell, I. Wald.
**“Packet-based Ray Tracing of Catmull-Clark Subdivision Surfaces,”** SCI Institute Technical Report, No. UUSCI-2007-011, *University of Utah*, 2007.

[Ben2007b] J. Bennett, V. Pascucci, K.I. Joy.
**“Genus Oblivious Cross Parameterization: Robust Topological Management of Intersurface Maps,”** In *Proceedings of Pacific Graphics 2007*, 2007.

[Ber2007a] F.F. Bernardon, S.P Callahan, J.L.D. Comba, C.T. Silva.
**“An Adaptive Framework for Visualizing Unstructured Grids with Time-Varying Scalar Fields,”** In *Journal on Parallel Computing*, Vol. 33, No. 6, pp. 391--405. 2007.

[Ber2007b] F.F. Bernardon, L.K. Ha, S.P. Callahan, J.L.D. Comba, C.T. Silva.
**“Interactive Transfer Function Specification for Direct Volume Rendering of Disparate Volumes,”** SCI Institute Technical Report, No. UUSCI-2007-007, *University of Utah*, 2007.

[Ber2007c] M. Berzins.
**“Is there Still More to Science than Computation?,”** In *Computing in Science and Engineering*, Vol. 9, No. 1, pp. 98--101. 2007.

[Ber2007d] M. Berzins.
**“Adaptive Polynomial Interpolation on Evenly Spaced Meshes.,”** In *SIAM Review*, Vol. 49, No. 4, pp. 604-627. 2007.

[Bet2007a] E.W. Bethel, C.R. Johnson, K. Joy, S. Ahern, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, B. Hamann, C.D. Hansen, D. Laney, P. Lindstrom, J. Meredith, G. Ostrouchov, S.G. Parker, C.T. Silva, A.R. Sanderson, X. Tricoche.
**“SciDAC Visualization and Analytics Center for Enabling Technology,”** In *Journal of Physics*, Conference Series, Vol. 78, No. 012032, pp. (published online). 2007.

[Bet2007b] E.W. Bethel, C.R. Johnson, C. Aragon, Prabhat, O. Rübel, G. Weber, V. Pascucci, H. Childs, P.-T. Bremer, B. Whitlock, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann, C. Garth, M. Cole, C.D. Hansen, S.G. Parker, A.R. Sanderson, C.T. Silva, X. Tricoche.
**“DOE's SciDAC Visualization and Analytics Center for Enabling Technologies - Strategy for Petascale Visual Data Analysis Success,”** In *CTWatch Quarterly*, Vol. 3, No. 4, 2007.

[Bou2007a] S. Boulos, D. Edwards, J.D. Lacewell, J. Kniss, J. Kautz, I. Wald, P. Shirley.
**“Packet-based Whitted and Distribution Ray Tracing,”** In *Proceedings of Graphics Interface 2007*, Vol. 234, pp. 177--184. 2007.

[Bre2007a] P.-T. Bremer, E.M. Bringa, M.A. Duchaineau, A. Gyulassy, D. Laney, A. Mascarenhas, V. Pascucci.
**“Topological Feature Extraction and Tracking,”** In *Proceedings of SciDAC 2007 -- Scientific Discovery Through Advanced Computing*, Boston, MA, USA, Vol. 78, Journal of Physics Conference Series, pp. 012032 (5pp). June, 2007.

[Bre2007b] P.-T. Bremer, V. Pascucci.
**“A Practical Approach to Two-Dimensional Scalar Topology,”** In *Mathematics and Visualization*, Springer Verlag, pp. 151--169. 2007.

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

[Bro2007a] D.H. Brooks, A. Keely, A. Ghodrati, G. Tadmor, R.S. MacLeod.
**“Some Spatio-Temporal Approaches to Inverse Electrocardiography,”** In *Proc. Asilomar Conf. on Signals, Systems, and Computers*, Pacific Grove, CA, November, 2007.

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[But2007a] L. Butler, A.J. Stephens.
**“Bullet Ray Vision,”** In *Proceedings of the IEEE Symposium on Interactive Ray Tracing*, pp. 167--170. 2007.

[But2007b] C.R. Butson, C.C. McIntyre.
**“Differences among implanted pulse generator waveforms cause variations in the neural response to deep brain stimulation,”** In *Clinical Neurophysiology*, Vol. 118, pp. 1889--1894. August, 2007.

ISSN: 1388-2457

DOI: 10.1016/j.clinph.2007.05.061

[But2007c] C.R. Butson, S.E. Cooper, J.M. Henderson, C.C. McIntyre.
**“Patient-specific analysis of the volume of tissue activated during deep brain stimulation,”** In *NeuroImage*, Vol. 34, No. 2, pp. 661--670. January, 2007.

ISSN: 1053-8119

DOI: 10.1016/j.neuroimage.2006.09.034

PubMed ID: 17113789

[Cal2007a] M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.
**“BioMesh3D: A Meshing Pipeline for Biomedical Models,”** SCI Institute Technical Report, No. UUSCI-2007-009, *University of Utah*, 2007.

[Cal2007b] M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.
**“A Meshing Pipeline for Biomedical Computing,”** In *Engineering with Computers*, Special Issue on Computational Bioengineering, pp. (in press). 2007.

[Cal2007c] S.P. Callahan, L. Bavoil, V. Pascucci, C.T. Silva.
**“Progressive Volume Rendering of Large Unstructured Grids,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 1, pp. 1307-1314. 2007.

[Cas2007b] C.J. Cascio, G. Gerig, J. Piven.
**“Diffusion Tensor Imaging: Application to the Study of the Developing Brain,”** In *J Am Acad Child Adolesc Psychiatry*, Vol. 46, No. 2, pp. 213--223. February, 2007.

[Cat2007a] J. Cates, P.T. Fletcher, M. Styner, M. Shenton, R.T. Whitaker.
**“Shape Modeling and Analysis with Entropy-Based Particle Systems,”** In *Proceedings of Information Processing in Medical Imaging (IPMI) 2007*, LNCS 4584, pp. 333--345. 2007.

[Chi2007a] D. Chisnall, M. Chen, C.D. Hansen.
**“Ray-Driven Dynamic Working Set Rendering for Complex Volume Scene Graphs Involving Large Point Clouds,”** In *The Visual Computer*, Vol. 23, No. 3, pp. 167--179. 2007.

[Cur2007a] S. Curtis, R.M. Kirby, J.K. Ryan, C.-W. Shu.
**“Post-Processing for the Discontinuous Galerkin Method Over Non-Uniform Meshes,”** In *SIAM Journal of Scientific Computing*, Vol. 30, No. 1, pp. 272--289. 2007.

[Dam2007a] K. Damevski, K. Zhang, S.G. Parker.
**“Practical Parallel Remote Method Invocation for the Babel Compiler,”** In *Proceedings of the 2007 Symposium on Component and Framework Technology in High-Performance and Scientific Computing*, pp. 131--140. 2007.

[Dam2007b] K. Damevski, A. Swaminathan, S.G. Parker.
**“Highly Scalable Distributed Component Framework for Scientific Computing,”** In *Proceedings of the 3rd International Conference on High Performance Computing and Communication (HPCC 2007)*, 2007.

[Dam2007c] K. Damevski, A. Swaminathan, S.G. Parker.
**“CCALoop: Scalable Design of a Distributed Component Framework,”** In *Proceedings of the 16th International High Performance Distributed Computing Symposium (HPDC 2007)*, pp. 213--214. 2007.

[Dan2007a] J.D. Daniels, L. Ha, T. Ochotta, C.T. Silva.
**“Robust Smooth Feature Extraction from Point Clouds,”** In *Proceedings of the 2007 International Conference on Shape Modeling and Applications*, Lyon, France, 2007.

[Dav2007a] B. Davis, P.T. Fletcher, E. Bullitt, S. Joshi.
**“Population Shape Regression From Random Design Data,”** In *Proceedings of the Eleventh IEEE International Conference on Computer Vision (ICCV '07)*, pp. 1-7. 2007.

[Dav2007b] S. Davidson, S. Cohen-Boulakia, A. Eyal, B. Ludascher, T. McPhillips, S. Bowers, J. Freire.
**“Provenance in Scientific Workflow Systems,”** In *IEEE Data Engineering Bulletin*, Vol. 32, No. 4, pp. 44--50. 2007.

[Dou2007a] C.C. Douglas, M.J. Cole, P. Dostert, Y. Efendiev, R.E. Ewing, G. Haase, J. Hatcher, M. Iskandarani, C.R. Johnson, R.A. Lodder.
**“Dynamically identifying and tracking contaminants in water bodies,”** In *Proceedings of the 7th International Conference on Computational Science (ICCS) 2007, Part I*, Beijing, China, Lecture Notes in Computer Science (LNCS), Vol. 4887, Edited by Y. Shi and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra, Springer-Verlag, Berlin Heidelberg, pp. 1002--1009. May, 2007.

[Dou2007b] C.C. Douglas, D. Bansal, J.D. Beezley, L.S. Bennethum, S. Chakraborty, J.L. Coen, Y. Efendiev, R.E. Ewing, J. Hatcher, M. Iskandarani, C.R. Johnson, M. Kim, D. Li, R.A. Lodder, J. Mandel, G. Qin, A. Vodacek.
**“Dynamic data-driven application systems for empty houses, contaminat tracking, and wildland fireline prediction,”** In *Grid-Based Problem Solving Environments*, IFIP series, Edited by P.W. Gaffney and J.C.T. Pool, Springer-Verlag, Berlin, pp. 255-272. 2007.

DOI: 10.1007/978-0-387-73659-4_14

[Fle2007a] P.T. Fletcher, S. Joshi.
**“Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data,”** In *Signal Processing*, Vol. 87, No. 2, pp. 250--262. February, 2007.

[Fle2007b] P.T. Fletcher, R. Tao, W.-K. Jeong, R.T. Whitaker.
**“A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI,”** In *Information Processing in Medical Imaging*, Vol. 4584/2007, pp. 346--358. 2007.

[Fle2007c] P.T. Fletcher, S. Powell, N.L. Foster, S. Joshi.
**“Quantifying Metabolic Asymmetry Modulo Structure in Alzheimer's Disease,”** In *Lecture Notes in Computer Science*, Springer, pp. 446--457. 2007.

DOI: 10.1007/978-3-540-73273-0_37

PubMed ID: 17633720

[Fri2007a] H. Friedrich, I. Wald, P. Slusallek.
**“Interactive Iso-Surface Ray Tracing of Massive Volumetric Data Sets,”** In *Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization*, pp. 109--116. 2007.

[Gar2007a] C. Garth, G. Li, X. Tricoche, C.D. Hansen, H. Hagen.
**“Visualization of Coherent Structures in Transient 2D Flows,”** In *Proceedings of the 2007 Workshop on Topology-Based Method in Visualization (TopoInVis)*, Grimma, Germany, March, 2007.

[Gar2007b] C. Garth, F. Gerhardt, X. Tricoche, H. Hagen.
**“Efficient Computation and Visualization of Coherent Structures in Fluid Flow Applications,”** In *Proceeding of IEEE Visualization 2007*, pp. 1464--1471. 2007.

[Gar2007c] C. Garth, B. Laramee, X. Tricoche, H. Hauser, J. Schneider.
**“Extraction and Visualization of Swirl and Tumble Motion from Engine Simulation Data,”** In * Topology-based Methods in Visualization*, Mathematics and Visualization, Springer Berlin Heidelberg, pp. 121--135. 2007.

ISBN: 978-3-540-70822-3

DOI: 10.1007/978-3-540-70823-0_9

[Gen2007a] S.E. Geneser, R.M. Kirby, D. Xiu, F.B. Sachse.
**“Stochastic Markovian Modeling of Electrophysiology of Ion Channels: Reconstruction of Standard Deviations in Macroscopic Currents,”** In *Journal of Theoretical Biology*, Vol. 245, No. 4, pp. 627--637. 2007.

DOI: 10.1016/j.jtbi.2006.10.016

[Ger2007a] S. Gerber, T. Tasdizen, R.T. Whitaker.
**“Robust Non-linear Dimensionality Reduction using Successive 1-Dimensional Laplacian Eigenmaps,”** In *Proceedings of the 2007 International Conference on Machine Learning (ICML)*, pp. 281--288. 2007.

[Gho2007a] A. Ghodrati, D.H. Brooks, R.S. MacLeod.
**“Methods of Solving Reduced Lead Systems for Inverse Electrocardiography,”** In *IEEE Trans Biomed Eng*, Vol. 54, No. 2, pp. 339--343. February, 2007.

PubMed ID: 17278592

[Gil2007a] J.H. Gilmore, W. Lin, I. Corouge, Y.S. Vetsa, J.K. Smith, C. Kang, H. Gu, R.M. Hamer, J.A. Lieberman, G. Gerig.
**“Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography,”** In *American Journal of Neuroradiology*, Vol. 28, No. 9, pp. 1789--1795. October, 2007.

[Gil2007b] J.H. Gilmore, W. Lin, M.W. Prastawa, C.B. Looney, Y.S.K. Vetsa, R.C. Knickmeyer, D.D. Evans, J.K. Smith, R.M. Hamer, J.A. Lieberman, G. Gerig.
**“Regional Gray Matter Growth, Sexual Dimorphism, and Cerebral Asymmetry in the Neonatal Brain,”** In *Journal of Neuroscience*, Vol. 27, No. 6, pp. 1255--1260. 2007.

[Gil2007c] J.H. Gilmore, L. Smith, C. Kang, R. Hamer, H. Wolfe, B. Hertzberg, J.K. Smith, N. Chescheir, W. Lin, G. Gerig.
**“Neonatal Brain Structure in Children with Prenatal Isolated Mild Ventriculomegaly,”** In *Proceedings American Conference of Neuropharmacology (ACNP) 2007*, Boca Raton, FL, Note: *abstract.*, 2007.

[Gil2007d] J.H. Gilmore, W. Lin, M.W. Prastawa, C.B. Looney, Y.S.K. Vetsa, R.C. Knickmeyer, D.D. Evans, J.K. Smith, R.M. Hamer, J.A. Lieberman, G. Gerig.
**“Regional Gray Matter Growth, Sexual Dimorphism, and Cerebral Asymmetry in the Neonatal Brain,”** In *Journal of Neuroscience*, Vol. 27, No. 6, pp. 1255--1260. 2007.

[Goo2007a] C. Goodlett, P.T. Fletcher, W. Lin, G. Gerig.
**“Quantification of Measurement Error in DTI: Theoretical Predictions and Validation,”** In *Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007)*, Lecture Notes in Computer Science, Vol. 4792, pp. 10--17. November, 2007.

PubMed ID: 18051038

[Goo2007b] C.E. Goodyer, M. Berzins.
**“Parallelisation and Scalability Issues of a Multilevel EHL Solver,”** In *Concurrency and Computation: Practice and Experience*, Vol. 19, No. 4, pp. 369--396. 2007.

[Goo2007c] C.B. Goodlett, P.T. Fletcher, W. Lin, G. Gerig.
**“Noise-Induced Bias in Low-Direction Diffusion Tensor MRI: Replication of Monte-Carlo Simulation with In-Vivo Scans,”** In *Proceedings of ISMRM 2007*, 2007.

[Gor2007a] K. Gorczowski, M. Styner, J.Y. Jeong, J.S. Marron, J. Piven, H.C. Hazlett, S.M. Pizer, G. Gerig.
**“Statistical Shape Analysis of Multi-Object Complexes,”** In *Proceedings of the 2007 IEEE Conference on Computer Vision and Pattern Recognition*, pp. 1--8. 2007.

[Gor2007b] K. Gorczowski, M. Stynera, J.Y. Jeonga, J.S. Marron, J. Piven, H.C. Hazlett, S.M. Pizer, G. Gerig.
**“Discrimination Analysis using Multi-Object Statistics of Shape and Pose,”** In *Proceedings of the 2007 SPIE Conference*, Vol. 6512, January, 2007.

[Gou2007a] S. Gouttard, M. Styner, S. Joshi, R.G. Smith, H.C. Hazlett, G. Gerig.
**“Subcortical Structure Segmentation Using Probabilistic Atlas Priors,”** In *Medical Imaging 2007: Image Processing*, Vol. 6512, No. 65122J, Note: *Presented at Worshop - 3D Segmentation in the Clinic: a Grand Challenge*, Edited by J.P. W. Pluim and J.M. Reinhardt, SPIE Intl Soc Optical Eng, March, 2007.

[Gri2007a] C.P. Gribble, S.G. Parker.
**“Interactive Visualization with Advanced Shading Models using Lazy Evaluation,”** In *Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization*, pp. 37--44. 2007.

[Gri2007b] C.P. Gribble, C. Brownlee, S.G. Parker.
**“Practical Global Illumination for Interactive Particle Visualization,”** In *Computers and Graphics*, Vol. 32, No. 1, pp. 14--24. February, 2007.

[Gyu2007a] A. Gyulassy, V. Natarajan, B. Hamann, V. Pascucci.
**“Efficient Computation of Morse-Smale Complexes for Three-dimensional Scalar Functions,”** In *IEEE Transactions on Visualization and Computer Graphics*, Note: *(presented at IEEE VIS 2007)*, 2007.

[Gyu2007b] A. Gyulassy, V. Natarajan, B. Hamann, M. Duchaineau, V. Pascucci, E. Bringa, A. Higginbotham.
**“Topologically Clean Distance Fields,”** In *IEEE Transactions on Visualization and Computer Graphics*, Note: *(presented at IEEE VIS 2007)*, 2007.

[Ham2007a] C.W. Hamman, R.M. Kirby, M. Berzins.
**“Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations,”** In *Concurrency and Computation: Practice and Experience*, Vol. 14, No. 10, pp. 1403--1422. 2007.

[Ham2007b] C.R. Hamman, R.M. Kirby, M. Berzins.
**“Parallel Direct Simulation of Incompressible Navier Stokes Equations,”** In *Concurrency and Computation*, Vol. 19, No. 10, pp. 1403-1427. 2007.

[Hen2007a] H.B. Henninger, C.J. Underwood, S.A. Maas, R.T. Whitaker, J.A. Weiss.
**“Spatial Distribution and Orientation of Dermatan Sulfate in Human Medial Collateral Ligament,”** In *Journal of Structural Biology*, Vol. 158, No. 1, pp. 33--45. April, 2007.

DOI: 10.1016/j.jsb.2006.10.008

[Hua2007a] X. Huang, Y.Z. Lee, M. McKeown, G. Gerig, H. Gu, W. Lin, M.M. Lewis, S. Ford, A.I. Troster, D.R. Weinberger, Styner.
**“Asymmetrical ventricular enlargement in Parkinson's Disease,”** In *Movement Disorders*, Vol. 22, No. 11, pp. 1657--1660. August 15, 2007.

[Iki2007a] M. Ikits.
**“Interactive Exploration of Volumetric Data Sets With a Combined Visual and Haptic Interface,”** Note: *Ph.D. Thesis*, *University of Utah School of Computing*, 2007.

[Ize2007a] T. Ize, I. Wald, S.G. Parker.
**“Asynchronous BVH Construction for Ray Tracing Dynamic Scenes on Parallel Multi-Core Architectures,”** In *Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization*, pp. 101--108. 2007.

[Ize2007b] T. Ize, P. Shirley, S.G. Parker.
**“Grid Creation Strategies for Efficient Ray Tracing,”** In *Proceedings of the 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing*, pp. 27--32. 2007.

[Jeo2007a] W.-K. Jeong, P.T. Fletcher, R. Tao, R.T. Whitaker.
**“Interactive Visualization of Volumetric White Matter Connectivity in DT-MRI Using a Parallel-Hardware Hamilton-Jacobi Solver,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 6, pp. 1480--1487. 2007.

PubMed ID: 17968100

[Joh2007a] C.R. Johnson, R. Ross, S. Ahern, J. Ahrens, W. Bethel, K.L. Ma, M. Papka, J. van Rosendale, H.W. Shen, J. Thomas.
**“DOE Visualization and Knowledge Discovery,”** Note: *Report from the DOE/ASCR Workshop on Visual Analysis and Data Exploration at Extreme Scale*, October, 2007.

[Jol2007a] M. Jolley, J.G. Stinstra, D.M. Weinstein, S. Pieper, R.S.J. Estepar, G. Kindlmann, R.S. MacLeod, D.H. Brooks, J.K. Triedman.
**“Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement,”** In *Functional Imaging and Modeling of the Heart*, Lecture Notes in Computer Science (LCNS), Vol. 4466/2007, pp. 373--382. 2007.

ISBN: 978-3-540-72906-8

[Jon2007a] B.W. Jones, R.E. Marc, C.B. Watt, K. Kinardi, D. DeMill, J.H. Yang, T. Tasdizen, P. Koshevoy, E. Jurrus, R.T. Whitaker.
**“Structure and Function of Microneuromas in Retinal Remodeling,”** In *The Association for Research in Vision and Ophthalmology (ARVO) Conference*, Note: *(abstract)*, 2007.

[Jon2007b] C. Jones, K.-L. Ma, A.R. Sanderson, L. Myers.
**“Visual Interrogation of Gyrokinetic Particle Simulations,”** In *Journal of Physics*, Conference Series, Vol. 78, pp. 012033 (6pp). 2007.

[Kin2007a] G. Kindlmann, D.B. Ennis, R.T. Whitaker, C.-F. Westin.
**“Diffusion Tensor Analysis With Invariant Gradients and Rotation Tangents,”** In *IEEE Transactions on Medical Imaging*, Vol. 26, No. 11, pp. 1483--1499. 2007.

[Kir2007a] R.M. Kirby, Z. Yosibash, G.E. Karniadakis.
**“Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,”** In *Journal of Computational Physics*, Vol. 223, No. 2, pp. 489--518. 2007.

[Kni2007a] J.M. Kniss, W. Hunt, K. Potter, P. Sen.
**“IStar: A Raster Representation for Scalable Image and Volume Data,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 13, No. 6, pp. 1424--1431. Nov, 2007.

DOI: 10.1109/TVCG.2007.70572

[Kno2007a] A. Knoll, C.D. Hansen, I. Wald.
**“Coherent Multiresolution Isosurface Ray Tracing,”** SCI Institute Technical Report, No. UUSCI-2007-001, *University of Utah*, 2007.

[Kno2007b] A. Knoll, Y. Hijazi, C.D. Hansen, I. Wald, H. Hagen.
**“Interactive Ray Tracing of Arbitrary Implicit Functions,”** SCI Institute Technical Report, No. UUSCI-2007-002, *University of Utah*, 2007.

[Kno2007c] A. Knoll, Y. Hijazi, C.D. Hansen, I. Wald, H. Hagen.
**“Interactive Ray Tracing of Arbitrary Implicits with SIMD Interval Arithmetic,”** In *Proceedings of 2nd IEEE/EG Symposium on Interactive Ray Tracing 2007*, Ulm, Germany, pp. 11--18. 2007.

[Kno2007d] A. Knoll, Y. Hijazi, A. Kensler, M. Schott, C.D. Hansen, H. Hagen.
**“Fast and Robust Ray Tracing of General Implicits on the GPU,”** SCI Institute Technical Report, No. UUSCI-2007-014, *University of Utah*, 2007.

[Kos2007a] P.A. Koshevoy, T. Tasdizen, R.T. Whitaker.
**“Automatic Assembly of TEM Mosaics and Mosaic Stacks Using Phase Correlation,”** SCI Institute Technical Report, No. UUSCI-2007-004, *University of Utah*, 2007.

[Kri2008b] L. Krishnan, J.B. Hoying, H. Ngyuen, H. Song, J.A. Weiss.
**“Interaction of Angiogenic Microvessels with the Extracellular Matrix,”** In *American Journal of Physiology: Heart and Circulation Physiology*, Vol. 293, No. 6, pp. H3650--H36588. 2007.

[Lan2007a] D. Laney, P.-T. Bremer, A. Mascarenhas, P. Miller, V. Pascucci.
**“Understanding the Structure of the Turbulent Mixing Layer in Hydrodynamic Instabilities,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 1, pp. 1053--1060. January, 2007.

[Lew2007a] S. Lew, C. Wolters, A. Anwander, S. Makeig, R.S. MacLeod.
**“Low Resolution Conductivity Estimation to Improve Source Localization,”** In *New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006.*, International Congress Series, Vol. 1300, pp. 149--152. June, 2007.

[Li2007a] G.-S. Li, X. Tricoche, C.D. Hansen.
**“Visualizing Unsteady Flows on Surfaces Using Spherical Parameterization,”** SCI Institute Technical Report, No. UUSCI-2007-013, *University of Utah*, 2007.

[Liv2007a] Y. Livnat, S.G. Parker, C.R. Johnson.
**“Fast Isosurface Extraction Methods for Large Image Data Sets,”** In *Handbook of Medical Imaging: Processing and Analysis*, 2nd Edition, Ch. 44, Edited by Isaac Bankman, Academic Press, 2007.

[Lui2007a] J. Luitjens, M. Berzins, T.C. Henderson.
**“Parallel Space Filling Curve Generation Through Sorting,”** In *Journal of Concurrency and Computation*, Vol. 19, No. 10, pp. 1387--1402. 2007.

[Lui2007b] J. Luitjens, B. Worthen, M. Berzins, T.C. Henderson.
**“Scalable Parallel AMR for the Uintah Multiphysics Code,”** In *Petascale Computing Algorithms and Applications*, Edited by D. Bader, Chapman and Hall/CRC, 2007.

[Lui2007c] J. Luitjens, M. Berzins, T. Henderson.
**“Parallel space-filling curve generation through sorting,”** In *Concurrency and Computation: Practice and Experience*, Vol. 19, No. 10, pp. 1387--1402. July, 2007.

DOI: 10.1002/cpe.1179

[Luj2007a] T.J. Lujan, M.S. Dalton, B.M. Thompson, B.J. Ellis, J.A. Weiss.
**“Effect of ACL Deficiency on MCL Strains and Joint Kinematics,”** In *Journal of Biomechanical Engineering*, Vol. 129, No. 3, pp. 386--392. 2007.

[Luj2007b] T.J. Lujan, C.J. Underwood, H.B. Henninger, B.M. Thompson, J.A. Weiss.
**“Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament,”** In *Journal of Orthopaedic Research*, Vol. 25, No. 7, pp. 894--903. 2007.

[Mal2007a] M. Malik, Y. Birnbaum, R.S. MacLeod, V. Shusterman.
**“Markers of impaired repolarization,”** In *Journal of Electrocardiology*, Vol. 40, No. 1, pp. S54--S57. January, 2007.

[Mey2007a] M.D. Meyer, B. Nelson, R.M. Kirby, R.T. Whitaker.
**“Particle Systems for Efficient and Accurate Finite Element Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 5, pp. 1015--1026. 2007.

[Mey2007b] M.D. Meyer, R.M. Kirby, R.T. Whitaker.
**“Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.

[Nai2007a] D. Nain, M. Styner, M. Niethammer, J.J. Levitt, M.E. Shenton, G. Gerig, A. Bobick, A. Tannenbaum.
**“Statistical Shape Analysis of Brain Structures Using Spherical Wavelets,”** In *Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2007)*, IEEE Press, pp. 209--212. 2007.

[Nem2007a] O. Nemitz, T. Tasdizen, M. Rumpf, R.T. Whitaker.
**“Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data,”** In *Journal of Mathematical Imaging and Vision*, Vol. 7, No. 3, pp. 217--229. 2007.

DOI: 10.1007/s10851-006-0645-2

[New2007a] E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby.
**“Unconditionally Stable Discretizations of the Immersed Boundary Equations,”** In *Journal of Computational Physics*, Vol. 222, No. 2, pp. 702--719. 2007.

[New2007b] E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby.
**“Unconditionally Stable Discretizations of the Immersed Boundary Equations,”** In *Journal of Computational Physics*, Vol. 222, No. 2, pp. 702--719. March, 2007.

[Och2007a] T. Ochotta, C.E. Scheidegger, J. Schreiner, Y. Lima, R.M. Kirby, C.T. Silva.
**“A Unified Projection Operator for Moving Least Squares Surfaces,”** SCI Institute Technical Report, No. UUSCI-2007-006, *University of Utah*, 2007.

[Omb2007a] L. Omberg, G.H. Golub, O. Alter.
**“A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies,”** In *Proceedings of the National Academy of Sciences*, Vol. 104, No. 47, Proceedings of the National Academy of Sciences, pp. 18371–-18376. November, 2007.

DOI: 10.1073/pnas.0709146104

[Pal2007a] R. Palmer, G. Gopalakrishnan, R.M. Kirby.
**“Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs,”** In *Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD)*, London, UK, Note: *Awarded Best Paper*, 2007.

[Par2007a] S.G. Parker, S. Boulos, J. Bigler, A. Robison.
**“RTSL: a Ray Tracing Shading Language,”** In *In 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing*, pp. 149--160. 2007.

[Par2007b] S.G. Parker, R. Armstrong, D. Bernholdt, T. Dahlgren, T. Epperly, J. Kenny, M. Krishnan, G. Kumfert, J. Larson, L.C. McInnes, J. Nieplocha, J. Ray, S. Shasharina.
**“Enabling Advanced Scientific Computing Software,”** In *CTWatch Quarterly*, Vol. 3, No. 4, 2007.

[Pas2007a] V. Pascucci, G. Scorzelli, P.-T. Bremer, A. Mascarenhas.
**“Robust On-line Computation of Reeb Graphs: Simplicity and Speed,”** In *ACM Transactions on Graphics: ACM SIGGRAPH 2007 Papers*, ACM Press, New York, NY, USA pp. 1057--1066. 2007.

[Per2007a] S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Palmer, R. Thakur, W. Gropp.
**“Practical Model Checking Method for Verifying Correctness of MPI Programs,”** In *Recent Advances in Parallel Virtual Machine and Message Passing Interface - Proceedings of EuroPVM-MPI 2007*, Paris, France, Vol. 4757/2007, pp. 344--353. 2007.

[Pha2007a] N.S. Phatak, Q. Sun, S.-E. Kim, D.L. Parker, R.K. Sanders, A.I. Veress, B.J. Ellis, J.A. Weiss.
**“Noninvasive Determination of Ligament Strain with Deformable Image Registration,”** In *Annals of Biomedical Engineering*, Vol. 35, No. 7, pp. 1175--1187. February, 2007.

[Por2007a] A.B. Porter, L. Healy, N.L. Foster, K.A. Josephs.
**“Compulsive Urination as a Presenting Symptom of Frontotemporal Dementia,”** In *European Journal of Neurology*, Vol. 14, Note: *Letter to the Editor*, pp. e16--e17. 2007.

[Pre2007a] G.A. Preston, E.W. Anderson, C.T. Silva.
**“Effects of 10 Hz rTMS on Alpha Spectral Dynamics and Working Memory Performance,”** In *Proceedings of Neuroscience 2007 Poster Session*, Note: *Poster presentation.*, 2007.

[Ree2007a] D. Reed, C.R. Johnson.
**“CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations,”** Note: *Computing Research Association (CRA)*, 2007.

[Sad2007a] N. Sadeghi, T. Tasdizen, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman..
**“Automatic Classification of Alzheimers Disease vs. Frontotemporal Dementia: A Decision Tree Approach with FDG-PET,”** SCI Institute Technical Report, No. UUSCI-2007-016, *University of Utah*, 2007.

[Sch2007b] C.E. Scheidegger, H.T. Vo, D. Koop, J. Freire, C.T. Silva.
**“Querying and Creating Visualizations by Analogy,”** In *Proceeding of IEEE Visualization 2007*, pp. 1560--1567. 2007.

[She2007b] J.F. Shepherd.
**“Topologic and Geometric Constraint-Based Hexahedral Mesh Generation,”** *School of Computing, University of Utah*, May, 2007.

[She2007c] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation for Biomedical Models in SCIRun,”** SCI Institute Technical Report, No. UUSCI-2007-008, *University of Utah*, 2007.

[Sho2007a] S. Shome, R.L. Lux, B.B. Punske, R.S. MacLeod.
**“Ischemic Preconditioning Protects Against Arrhythmogenesis Through Maintenance of Both Active as well as Passive Electrical Properties in Ischemic Canine Hearts,”** In *Journal of Electrocardiology*, Vol. 40, No. 6 supp, pp. S150--S159. Nov-Dec, 2007.

[Sho2007b] S. Shome, J.G. Stinstra, C Henriquez, R.S. Macleod.
**“Influence of Extracellular Potassium and Reduced Extracellular Space on Conduction Velocity During Acute Ischemia: A Simulation Study,”** In *Journal of Electrocardiology*, Vol. 40, No. 4, pp. S5--S6. 2007.

[Sil2007a] C.T. Silva, J. Freire, S.P. Callahan.
**“Provenance for Visualizations: Reproducibility and Beyond,”** In *IEEE Computing in Science and Engineering*, Vol. 9, No. 5, pp. 82--89. 2007.

[Sti2007a] J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod.
**“Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,”** In *Proceedings of the 29th Annual International Conference of the IEEE EMBS*, pp. 1422--1425. 2007.

[Sty2007a] M. Styner, S. Xu, M. El-Sayed, G. Gerig.
**“Correspondence Evaluation in Local Shape Analysis and Structural Subdivision,”** In *Proceedings of ISBI 2007*, IEEE Press, pp. 1192--1195. 2007.

[Sty2007b] M. Styner, I. Oguz, S. Xu, D. Pantazis, G. Gerig.
**“Statistical Group Differences in Anatomical Shape Analysis using Hotelling T2 Metric,”** In *Proceedings of the 2007 SPIE Medical Imaging Conference*, Vol. 6512, 2007.

[Tay2007a] W.D. Taylor, J.R. MacFall, G. Gerig, K.R. Krishnan.
**“Structural Integrity of the Uncinate Fasciculus in Geriatric Depression: Relationship with Age of Onset,”** In *Neuropsychiatric Disease and Treatment*, Vol. 3, No. 5, pp. 669--674. 2007.

[Ter2007a] T.B. Terriberry, J.N. Damon, S.M. Pizer, S. Joshi, G. Gerig.
**“Population-Based Fitting of Medial Shape Models with Correspondence Optimization,”** In *Proceedings of Information Processing in Medical Imaging (IPMI '07)*, Lecture Notes in Computer Science, Vol. 20, pp. 700--712. July, 2007.

[Tra2007a] L.T. Tran, J. Kim, M. Berzins.
**“Solving Time-Dependent PDEs using the Material Point Method, A Case Study from Gas Dynamics,”** SCI Institute Technical Report, No. UUSCI-2007-010, *University of Utah*, 2007.

[Tri2007a] J.K. Triedman, M. Jolley, R.S. MacLeod, J.G. Stinstra, D.H. Brooks, S. Pieper.
**“A System for Image Based Finite Element Modeling of Novel Defibrillation Strategies,”** In *Life Science Systems and Applications Workshop, 2007. LISA 2007*, pp. 63--66. 2007.

[Tri2007c] J.K. Triedman, M. Jolley, R.S. MacLeod, J. Stinstra, D.H. Brooks, S. Pieper.
**“Finite Element Modeling of Novel Defibrillation Approaches in Children and Adults,”** In *Proc. LISSA Conf.*, Bethesda, MD, November, 2007.

[Vas2007a] S.X. Vasquez, A.N. Bahadur, J.T. Johnson III, D.R. Rodriguez, C. Keller.
**“Severe Runting of a Laboratory Mouse (Mus musculus),”** In *Lab Animal*, Vol. 36, No. 1, pp. 19, 22--23. January, 2007.

[Vo2007a] H.T. Vo, S.P. Callahan, P. Lindstrom, V. Pascucci, C.T. Silva.
**“Streaming Simplification of Tetrahedral Meshes,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 1, pp. 145--155. Jan/Feb, 2007.

[Vo2007b] H.T. Vo, S.P. Callahan, N. Smith, C.T. Silva, W. Martin, D. Owen, D.M. Weinstein.
**“iRun: Interactive Rendering of Large Unstructured Grids,”** In *Proceedings of the 7th Eurographics Symposium on Parallel Graphics and Visualization (EGPGV 2007)*, pp. 93--100. 2007.

[Wal2007a] I. Wald, S. Boulos, P. Shirley.
**“Ray Tracing Deformable Scenes using Dynamic Bounding Volume Hierarchies,”** In *ACM Transactions on Graphics*, Vol. 26, No. 1, 2007.

[Wal2007b] I. Wald, H. Friedrich, C.D. Hansen.
**“Interactive Isosurface Ray Tracing of Time-Varying Tetrahedral Volumes,”** SCI Institute Technical Report, No. UUSCI-2007-003, *University of Utah*, 2007.

[Wal2007c] I. Wald, H. Friedrich, A. Knoll, C.D. Hansen.
**“Interactive Isosurface Ray Tracing of Time-Varying Tetrahedral Volumes,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 6, pp. 1727--1734. 2007.

DOI: 10.1109/TVCG.2007.70566

[Wal2007d] I. Wald, C. Gribble, S. Boulos, A. Kensler.
**“SIMD Ray Stream Tracing - SIMD Ray Traversal with Generalized Ray Packets and On-the-fly Re-Ordering -,”** SCI Institute Technical Report, No. UUSCI-2007-012, *University of Utah*, 2007.

[Wal2007e] I. Wald, W.R. Mark, J. Günther, S. Boulos, T. Ize, W. Hunt, S.G. Parker, P. Shirley.
**“State of the Art in Ray Tracing Animated Scenes,”** In *Proceedings of Eurographics 2007*, State of the Art Reports, pp. (accepted). 2007.

[Wal2007f] I. Wald.
**“On fast Construction of SAH based Bounding Volume Hierarchies,”** In *Proceedings of the 2007 Eurographics/IEEE Symposium on Interactive Ray Tracing*, pp. 33--40. 2007.

[Web2007a] G.H. Weber, P.-T. Bremer, V. Pascucci.
**“Topological Landscapes: A Terrain Metaphor for Scientific Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, Note: *(presented at IEEE VIS 2007)*, 2007.

[Web2007b] G.H. Weber, S.E. Dillard, H. Carr, V. Pascucci, B. Hamann.
**“Topology-controlled volume rendering,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 2, pp. 330--341. January, 2007.

[Wie2007a] A. Wiebel, X. Tricoche, D. Schneider, Heike Jänicke, Gerik Scheuermann.
**“Generalized Streak Lines: Analysis and Visualization of Boundary Induced Vortices,”** In *Proceeding of IEEE Visualization 2007*, pp. 1735--1742. 2007.

[Wol2007b] C.H. Wolters, H. Köstler, C. Möller, J. Härtlein, L. Grasedyck, W. Hackbusch.
**“Numerical Mathematics of the Subtraction Method for the Modeling of a Current Dipole in EEG Source Reconstruction Using Finite Element Head Models,”** In *SIAM J. on Scientific Computing*, Vol. 30, No. 1, pp. 24--45. 2007.

[Wol2007c] C.H. Wolters, H. Köstler, C. Möller, J. Härdtlein, A. Anwander.
**“Numerical Approaches for Dipole Modeling in Finite Element Method Based Source Analysis,”** In *New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006.*, International Congress Series, Vol. 1300, pp. 189--192. June, 2007.

[Xiu2007a] D. Xiu, J. Shen.
**“An Efficient Spectral Method for Acoustic Scattering from Rough Surfaces,”** In *Communications in Computational Physics*, Vol. 2, No. 1, pp. 54--72. 2007.

DOI: 10.1.1.111.815

[Xiu2007b] D. Xiu.
**“Efficient Collocational Approach for Parametric Uncertainty Analysis,”** In *Communications in Computational Physics*, Vol. 2, No. 2, pp. 293--309. 2007.

[Xiu2007c] D. Xiu, S.J. Sherwin.
**“Parametric Uncertainty Analysis of Pulse Wave Propagation in a Model of a Human Arterial Networks,”** In *Journal of Computational Physics*, Vol. 226, No. 2, pp. 1385--1407. 2007.

DOI: 10.1016/j.jcp.2007.05.020

[Yan2007a] Y. Yang, X. Chen, G. Gopalakrishnan, R.M. Kirby.
**“Distributed Dynamic Partial Order Reduction Based Verification of Threaded Software,”** In *Proceedings of Model Checking Software: 14th International SPIN Workshop*, Berlin, Germany, Vol. 4595/2007, pp. 58--75. July, 2007.

[Yih2007a] B. Yihnaz, R.S. MacLeod, B.B. Punske, B. Taccardi, and D.H. Brooks.
**“Generalized training subset selection for statistical estimation of epicardial activation maps from intravenous catheter measurements,”** In *Compo in BioI. and Med.*, In *Compo in BioI. and Med.*, Vol. 37, No. 3, pp. 328--336. 2007.

[Yil2007a] B. Yilmaz, R.S. MacLeod.
**“Generalized Training Subset Selection for Statistical Estimation of Epicardial Activation Maps from Intravenous Catheter Measurements,”** In *Computers in Biology and Medicine*, Vol. 37, No. 9, pp. 328--336. March, 2007.

[Zha2007a] F. Zhang, C. Goodlett, E. Hancock, G. Gerig.
**“Probabilistic White Matter Fiber Tracking using Particle Filtering,”** In *Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007)*, Lecture Notes in Computer Science, Vol. 4791, pp. 144--151. November, 2007.

2006

[Adl2006a] G. Adluru, E.V.R. DiBella, R.T. Whitaker.
**“Automatic Segmentation of Cardiac Short Axis Slices in Perfusion MRI,”** In *c-ISBI2006*, pp. 133--136. 2006.

[Adl2006b] G. Adluru, E.V.R. DiBella.
**“Segmentation Based Registration of Myocardium in Cardiac Perfusion Images,”** In *c-ISMRM2006*, Vol. 14, pp. 1223. 2006.

[Adl2006d] G. Adluru, E.V.R. DiBella, M.C. Schabel.
**“Model-Based Registration for Dynamic Cardiac Perfusion MRI,”** In *Journal of Magnetic Resonance Imaging*, Vol. 24, No. 5, Wiley Subscription Services, Inc., A Wiley Company, pp. 1062--1070. 2006.

DOI: 10.1002/jmri.20756

[Alt2006a] I. Altintas, O. Barney, Z. Cheng, T. Critchlow, B. Ludaescher, S.G. Parker, A. Shoshani, M. Vouk.
**“Accelerating the Scientific Exploration Process with Scientific Workflows,”** In *J. Phys. : Conf. Ser.*, Vol. 46, pp. 468--478. 2006.

[Alt2006b] O. Alter.
**“Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data,”** In *Proceedings of the National Academy of Sciences*, Vol. 103, No. 44, Proceedings of the National Academy of Sciences, pp. 16063--16064. October, 2006.

DOI: 10.1073/pnas.0607650103

[Alt2006c] O. Alter, G. H. Golub.
**“Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening,”** In *Proceedings of the National Academy of Sciences*, Vol. 103, No. 32, Proceedings of the National Academy of Sciences, pp. 11828--11833. July, 2006.

DOI: 10.1073/pnas.0604756103

[And2006a] E.W. Anderson, S.P. Callahan, G.T.Y. Chen, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, H.T. Vo.
**“Visualization in Radiation Oncology: Towards Replacing the Laboratory Notebook,”** SCI Institute Technical Report, No. UUSCI-2006-017, *University of Utah*, 2006.

[And2006b] A.E. Anderson, B.J. Ellis, J.A. Weiss.
**“Verification, Validation and Sensitivity Studies in Computational Biomechanics,”** In *Computer Methods in Biomechanics and Biomedical Engineering*, pp. (in press). 2006.

[Arm2006a] R. Armstrong, G. Kumfert, L.C. McInnes, S.G. Parker, B. Allan, M. Sottile, T. Epperly, T. Dahlgren.
**“The CCA Component Model for High-Performance Scientific Computing,”** In *Concurrency and Computation: Practice & Experience*, Vol. 18, No. 2, John Wiley and Sons Ltd., Chichester, UK pp. 215--229. 2006.

ISSN: 1532-0626

[Ate2006a] G.A. Ateshian, B.J. Ellis, J.A. Weiss.
**“Equivalence Between Instantaneous Biphasic and Incompressible Elastic Material Response,”** In *Journal of Biomechanical Engineering*, pp. (in press). November, 2006.

[Att2006a] L. Atty, N. Holzschuch, M. Lapierre, J.-M. Hasenfratz, C.D. Hansen, F.X. Sillion.
**“Soft Shadow Maps: Efficient Sampling of Light Source Visibility,”** In *Computer Graphics Forum*, Vol. 25, No. 4, pp. 725--741. 2006.

[Awa2006a] S.P. Awate, T. Tasdizen, N. Foster, R.T. Whitaker.
**“Adaptive, Nonparametric Markov Modeling for Unsupervised, MRI Brain-Tissue Classification,”** SCI Institute Technical Report, No. UUSCI-2006-008, *University of Utah*, 2006.

[Awa2006b] S.P. Awate, T. Tasdizen, R.T. Whitaker.
**“Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics,”** In *Proceedings of The European Conference on Computer Vision (ECCV) 2006 Springer, Lecture Notes in Computer Science*, pp. 494--507. 2006.

[Awa2006c] S.P. Awate, T. Tasdizen, R.T. Whitaker.
**“Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics,”** SCI Institute Technical Report, No. UUSCI-2006-011, *University of Utah*, 2006.

[Awa2006d] S.P. Awate, R.T. Whitaker.
**“Unsupervised, Information-Theoretic, Adaptive Image Filtering for Image Restoration,”** In *j-PAMI*, Vol. 28, No. 3, pp. 364--376. March, 2006.

PubMed ID: 16526423

[Awa2006e] S.P. Awate, R.T. Whitaker.
**“Adaptive Markov Models for Information-Theoretic Empirical-Bayesian MRI Denoising,”** SCI Institute Technical Report, No. UUSCI-2006-030, *University of Utah*, 2006.

[Awa2006f] S.P. Awate.
**“Adaptive, Nonparametric Markov Models and Information-Theoretic Methods for Image Restoration and Segmentation,”** Note: *PhD Thesis*, *School of Computing, University of Utah*, December, 2006.

[Awa2006g] S.P. Awate, E.V.R. DiBella, T. Tasdizen, R.T. Whitaker.
**“Model-Based Image Reconstruction for Dynamic Cardiac Perfusion MRI from Sparse Data,”** In *Proceedings of the 2006 IEEE Int. Conf. Engineering and Biology Society (EMBC)*, pp. 936--941. 2006.

[Awa2006h] S.P. Awate, T. Tasdizen, N.L. Foster, R.T. Whitaker.
**“Adaptive, Nonparametric Markov Modeling for Unsupervised, MRI Brain-Tissue Classification,”** In *Medical Image Analysis (MEDIA)*, Vol. 10, No. 5, pp. 726--739. 2006.

[Bar2006a] L. Barbosa, J. Freire.
**“Automatically Constructing Collections of Online Databases,”** In *Proceedings of the 15th ACM International Conference on Information and Knowledge Management (CIKM)*, Arlington, pp. 796--797. 2006.

[Bas2006a] S. Basu, P.T. Fletcher, R.T. Whitaker.
**“Rician Noise Removal in Diffusion Tensor MRI,”** In *Medical Image Computing and Computer Assisted Intervention (MICCAI)*, Vol. LNCS 4190, pp. 117--125. October, 2006.

[Bav2006a] L. Bavoil, S.P. Callahan, C.T. Silva.
**“Robust Soft Shadow Mapping with Depth Peeling,”** SCI Institute Technical Report, No. UUSCI-2006-028, *University of Utah*, 2006.

[Bav2006b] L. Bavoil, S.P. Callahan, A. Lefohn, J.L.D. Comba, C.T. Silva.
**“Multi-Fragment Effects on the GPU using the k-Buffer,”** SCI Institute Technical Report, No. UUSCI-2006-032, *University of Utah*, 2006.

[Beb2006a] **“Advances in Visual Computing, Second International Symposium, ISVC 2006, Lake Tahoe, NV, USA, November 6-8, 2006 Proceedings, Part I,”** In *ISVC (1)*, Lecture Notes in Computer Science, Vol. 4291, Edited by 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, Springer, 2006.

ISBN: 3-540-48628-3

[Ben2006a] C. Benthin, I. Wald, P. Slusallek.
**“Techniques for Interactive Ray Tracing of Bezier Surfaces,”** In *Journal of Graphics Tools*, Vol. 11, No. 2, pp. 1--16. 2006.

[Ben2006b] C. Benthin, I. Wald, M. Scherbaum, H. Friedrich.
**“Ray Tracing on the CELL Processor,”** In *Proceedings of the 2006 IEEE Symposium on Interactive Ray Tracing*, pp. 25--32. 2006.

[Ber2006a] F.F. Bernardon, S.P. Callahan, J.L.D. Comba, C.T. Silva.
**“Interactive Volume Rendering of Unstructured Grids with Time-Varying Scalar Fields,”** In *Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization*, pp. 51--58. 2006.

[Ber2006b] M. Berzins.
**“Is there Still More to Science than Simulation?,”** No. UUSCI-2006-031, *SCI Institute, University of Utah*, November, 2006.

[Ber2006c] M. Berzins.
**“Adaptive Polynomial Interpolation on Evenly Spaced Meshes,”** SCI Institute Technical Report, No. UUSCI-2006-033, *University of Utah*, 2006.

[Bet2006a] W. Bethel, C.R. Johnson, C.D. Hansen, S.G. Parker, A.R. Sanderson, C.T. Silva, X. Tricoche, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, D. Laney, P. Lindstrom, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann.
**“VACET: Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies,”** In *J. Phys.: Conf. Ser.*, Vol. 46, pp. 561--569. 2006.

[Big2006a] J. Bigler, A.J. Stephens, S.G. Parker.
**“Design for Parallel Interactive Ray Tracing Systems,”** SCI Institute Technical Report, No. UUSCI-2006-027, *University of Utah*, 2006.

[Big2006b] J. Bigler, J. Guilkey, C. Gribble, C.D. Hansen, S.G. Parker.
**“A Case Study: Visualizing Material Point Method Data,”** In *Proceedings of Euro Vis 2006*, pp. 299--306, 377. May, 2006.

[Big2006c] J. Bigler, A.J. Stephens, S.G. Parker.
**“Design for Parallel Interactive Ray Tracing Systems,”** In *Proceedings of The IEEE Symposium on Interactive Ray Tracing*, pp. 187--196. 2006.

[Bou2006a] S. Boulos, D. Edwards, J.D. Lacewell, J.M. Kniss, J. Kautz, P. Shirley, I. Wald.
**“Interactive Distribution Ray Tracing,”** SCI Institute Technical Report, No. UUSCI-2006-022, *University of Utah*, 2006.

[Bou2006b] S. Boulos, I. Wald, P. Shirley.
**“Geometric and Arithmetic Culling Methods for Entire Ray Packets,”** School of Computing Technical Report, No. UUCS-06-010, *School of Computing, University of Utah*, 2006.

[Bre2006b] P.-T. Bremer, W. Cabot, A. Cook, D. Laney, A. Mascarenhas, P. Miller, V. Pascucci.
**“Understanding the Structure of the Turbulent Mixing Layer in Hydrodynamic Instabilities,”** In *Proceedings of SciDAC 2006 -- Scientific Discovery Through Advanced Computing*, Denver, CO, USA, Vol. 46, Journal of Physics Conference Series, pp. 556--560. June, 2006.

[Bro2006a] S. Browd, L.J. Healy, G. Dobie, J.T. Johnson III, G.M. Jones, L.F. Rodriguez, D.L. Brockmeyer.
**“Morphometric and Qualitative Analysis of Congenital Occipitocervical Instability in Children: Implications for Down Syndrome Patients,”** In *Journal of Neurosurgery: Pediatrics*, Vol. 105, No. 1 , Journal of Neurosurgery Publishing Group, pp. 50--54. July, 2006.

DOI: 10.3171/ped.2006.105.1.50

[But2006a] C.R. Butson, C.B. Maks, C.C. McIntyre.
**“Sources and effects of electrode impedance during deep brain stimulation,”** In *Clinical Neurophysiology*, Vol. 117, No. 2, pp. 447--454. 2006.

DOI: 10.1016/j.clinph.2005.10.007

PubMed ID: 16376143

[But2006b] C.R. Butson, C.C. McIntyre.
**“Role of electrode design on the volume of tissue activated during deep brain stimulation,”** In *Journal of Neural Engineering*, Vol. 3, No. 1, pp. 1--8. March, 2006.

ISSN: 1741-2560

DOI: 10.1088/1741-2560/3/1/001

PubMed ID: 16510937

[Cal2006a] S.P. Callahan, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, H.T. Vo.
**“Managing the Evolution of Dataflows with VisTrails,”** In *Proceedings of The 2006 IEEE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow 2006)*, 2006.

[Cal2006b] S.P. Callahan, J. Freire, E. Santos, C. Scheidegger, C.T. Silva, H.T. Vo.
**“VisTrails: Visualization Meets Data Management,”** In *Proceedings of the 2006 ACM SIGMOD/PODS Conference*, pp. 745--747. 2006.

[Cal2006c] S.P. Callahan, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, H.T. Vo.
**“Using Provenance to Streamline Data Exploration through Visualization,”** SCI Institute Technical Report, No. UUSCI-2006-016, *University of Utah*, 2006.

[Cal2006d] S.P. Callahan, L. Bavoil, V. Pascucci, C.T. Silva.
**“Progressive Volume Rendering of Large Unstructured Grids,”** SCI Institute Technical Report, No. UUSCI-2006-019, *University of Utah*, 2006.

[Cal2006e] S.P. Callahan, L. Bavoil, V. Pascucci, C.T. Silva.
**“Progressive Volume Rendering of Large Unstructured Grids,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 12, No. 5, Note: *Updated version of UUSCI-2006-019.*, pp. 1307--1314. 2006.

DOI: 10.1109/TVCG.2006.171

[Car2006a] C.D. Carbonera, J.F. Shepherd.
**“On the Existence of a Perfect Matching for 4-regular Graphs derived from Quadrilateral Meshes,”** SCI Institute Technical Report, No. UUSCI-2006-021, *University of Utah*, 2006.

[Car2006b] C.D. Carbonera, J.F. Shepherd.
**“A Constructive Approach to Constrained Hexahedral Mesh Generation,”** In *Proceedings of the 15th International Meshing Roundtable*, Birmingham, AL, September, 2006.

[Cas2006a] C.J. Cascio, M. Styner, R.G. Smith, M.D. Poe, G. Gerig, H.C. Hazlett, M. Jomier, R. Bammer, J. Piven.
**“Tractography-Based Segmentation of the Corpus Callosum Reveals a Reduced Relationship to Cortical White Matter Volume in Young Children with Developmental Delay,”** In *Am J Psychiatry*, Vol. 163, pp. 2157--2163. December, 2006.

[Cas2007a] C.J. Cascio, G. Gerig, J. Piven.
**“Diffusion Tensor Imaging: Application to the Study of the Developing Brain,”** In *Journal of the American Academy of Child and Adolescent Psychiatry JAACAP*, August, 2006.

[Cat2006a] J. Cates, M.D. Meyer, P.T. Fletcher, R.T. Witaker.
**“Entropy-Based Particle Systems for Shape Correspondence,”** In *Workshop on Mathematical Foundations of Computational Anatomy, MICCAI 2006*, pp. 90--99. October, 2006.

[Cat2006b] J. Cates, D. Weinsten, M. Davis.
**“The Center for Integrative Biomedical Computing: Advancing Biomedical Science with Open Source,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI) 2006*, 2006.

[Cor2006a] I. Corouge, P.T. Fletcher, S. Joshi, S. Gouttard, G. Gerig.
**“Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis,”** In *Medical Image Analysis*, Vol. 10, No. 5, pp. 786--798. 2006.

[Die2006a] A. Dietrich, I. Wald, H. Schmidt, K. Sons, P. Slusallek.
**“Realtime Ray Tracing for Advanced Visualization in the Aerospace Industry,”** In *Proceedings of the 5th Paderborner Workshop Augmented and Virtual Reality in der Produktentstehung*, 2006.

[Dil2006a] S.E. Dillard, V. Natarajan, G.H. Weber, V. Pascucci, B. Hamann.
**“Tessellation of Quadratic Elements,”** In *ISAAC*, pp. 722--731. 2006.

[Don2006a] S. Dong, P.-T. Bremer, M. Garland, V. Pascucci, J.C. Hart.
**“Spectral Surface Quadrangulation,”** In *ACM Transactions on graphics: ACM SIGGRAPH 2006 Papers*, Boston, Massachusetts, ACM Press, New York, NY, USA pp. 1057--1066. 2006.

ISBN: 1-59593-364-6

[Dou2006a] C.C. Douglas, J.C. Harris, M. Iskandarani, C.R. Johnson, R.J. Lodder, S.G. Parker, M.J. Cole, R. Ewing, Y. Efendiev, R. Lazarov, G. Qin.
**“Dynamic Contaminant Identification in Water,”** In *Proceedings of Computational Science - ICCS 2006: 6th International Conference, Part III*, Reading, UK, May 28-31, 2006, Lecture Notes in Computer Science series, Vol. 3993, Edited by Vassil N. Alexandrov and Geert Dick van Albada and Peter M.A. Sloot and Jack J. Dongarra, Springer-Verlag Heidelberg, pp. 393--400. 2006.

[Ede2006a] H. Edelsbrunner, D. Morozov, V. Pascucci.
**“Persistence-based Simplification of Real-Valued Functions on 2-Manifolds,”** In *Proceedings of the 22nd International Annual Symposium on Computational Geometry*, Note: *To appear*, pp. 212--220. 2006.

[Eid2006a] E. Eide, L. Stoller, T. Stack, J. Freire, J. Lepreau.
**“Integrated Scientific Workflow Management for the Emulab Network Testbed,”** In *Proceedings of the 2006 USENIX Annual Technical Conference*, pp. 33. 2006.

[Ell2006a] B.J. Ellis, R.E. Debski, S.M. Moore, P.J. McMahon, J.A. Weiss.
**“Methodology and Sensitivity Studies for Finite Element Modeling of the Inferior Glenohumeral Ligament Complex,”** In *j-BM*, Vol. 40, No. 3, pp. 603--612. January, 2006.

[Ell2006b] B.J. Ellis, T.J. Lujan, M.S. Dalton, J.A. Weiss.
**“MCL Insertion Site and Contact Forces in the ACL-Deficient Knee,”** In *Journal of Orthopaedic Research*, Vol. 24, No. 4, Elsevier, pp. 800--810. 2006.

[Fle2006a] P.T. Fletcher, S.M. Pizer, S. Joshi.
**“Shape Variation of Medial Axis Representations via Principal Geodesic Analysis on Symmetric Spaces,”** In *Statistics and Analysis of Shapes*, Springer, pp. 29--59. 2006.

DOI: 10.1007/0-8176-4481-4_2

[Fle2006b] P.T. Fletcher, R.T. Whitaker.
**“Riemannian Metrics on the Space of Solid Shapes,”** In *MICCAI Workshop on Mathematical Foundations of Computational Anatomy*, October, 2006.

[Fre2006a] J. Freire, C.T. Silva, S.P. Callahan, E. Santos, C.E. Scheidegger, H.T. Vo.
**“Managing Rapidly-Evolving Scientific Workflows,”** In *Provenance and Annotation of Data*, In *Proceedings of The 2006 International Provenance and Annotation Workshop*, Lecture Notes in Computer Science (LNCS), pp. 10--18. 2006.

[Ger2006a] G. Gerig, B. Davis, P. Lorenzen, S. Xu, M. Jomier, J. Piven, S. Joshi.
**“Computational Anatomy to Assess Longitudinal Trajectory of Brain Growth,”** In *Proceedings of The Third International Symposium on 3D Data Processing, Visualization, and Transmission*, pp. 1041--1047. June, 2006.

[Ger2006b] G. Gerig, S. Joshi, P.T. Fletcher, K. Gorczowski, S. Xu, S.M. Pizer, M. Styner.
**“Statistics of Populations of Images and its Embedded Objects: Driving Applications in Neuroimaging,”** In *Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 1120--1123. April, 2006.

[Gho2006a] A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“Wavefront-based Models for Inverse Electrocardiography,”** In *j-BME*, Vol. 53, No. 9, pp. 1821--1831. 2006.

DOI: 10.1109/TBME.2006.878117

[Gho2006b] A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“Lead Selection for Inverse Electrocardiography,”** In *j-BME*, pp. in press. 2006.

[Gho2006c] A. Ghodrati, A. Keely, G. Tadmor, R.S. MacLeod, D.H. Brooks.
**“A Wavefront-Based Constraint for Potential Surface Solutions in Inverse Electrocardiography,”** In *2006 International Conference of the IEEE Engineering in Medicine and Biology Society*, IEEE, New York, NY, USA August, 2006.

DOI: 10.1109/IEMBS.2006.260373

[Gho2006d] A. Ghodrati, D.H Brooks, G. Tadmor, R.S. MacLeod.
**“A Threshold-Based Method for Inverse Solutions to Reconstruct Complex Obstacles, with Application to the Inverse Problem of Electrocardiography,”** In *SIAM Conference on Imaging Science*, Minneapolis, MN, USA May, 2006.

[Gil2006a] J.H. Gilmore, W. Lin, G. Gerig.
**“IMAGES IN NEUROSCIENCE: Fetal and Neonatal Brain Development,”** In *Am J Psychiatry*, Vol. 163, pp. 2046. December, 2006.

[Goo2006b] C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales.
**“A Grid-enabled Problem Solving Environment for Parallel Computational Engineering Design,”** In *Advances in Engineering Software*, Vol. 37, No. 7, pp. 439--449. 2006.

[Goo2006c] C.E. Goodyer, M. Berzins.
**“Solving Computationally Intensive Engineering Problems on the Grid using Problem Solving Environments,”** In *Grid Computing: Software Environments and Tools*, Edited by J.C. Cunha and O.F. Rana, Springer Verlag, pp. 284--301. 2006.

[Goo2006d] C.E. Goodyer, M. Berzins.
**“Adaptive Timestepping for Elastohydrodynamic Lubrication Solvers,”** In *SIAM Journal on Scientific Computing*, Vol. 28, No. 2, SIAM, pp. 626-650. 2006.

DOI: 10.1137/050622092

[Gri2006a] C. Gribble, T. Ize, A. Kensler, I. Wald, S.G. Parker.
**“A Coherent Grid Traversal Approach to Visualizing Particle-based Simulation Data,”** SCI Institute Technical Report, No. UUSCI-2006-024, *University of Utah*, 2006.

[Gri2006b] C.P. Gribble, A.J. Stephens, J.E. Guilkey, S.G. Parker.
**“Visualizing Particle-Based Simulation Datasets on the Desktop,”** In *Proceedings of the British HCI 2006 Workshop on Combining Visualization and Interaction to Facilitate Scientific Exploration and Discovery*, 2006.

[Gri2006c] C.P. Gribble, S.G. Parker.
**“Enhancing Interactive Particle Visualization with Advanced Shading Models,”** In *Proceedings of the ACM Siggraph Third Symposium on Applied Perception in Graphics and Visualization*, pp. 111--118. 2006.

[Gui2006a] J.E. Guilkey, J.B. Hoying, J.A. Weiss.
**“Computational Modeling of Multicellular Constructs with the Material Point Method,”** In *Journal of Biomechanics*, Vol. 39, No. 11, pp. 2074--2086. 2006.

[Gyu2006a] A. Gyulassy, V. Natarajan, V. Pascucci, P.-T. Bremer, B. Hamann.
**“A Topological Approach to Simplification of Three-Dimensional Scalar Functions,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 12, No. 4, pp. 474--484. August, 2006.

[Ham2006b] C.W. Hamman, R.M. Kirby, J.C. Klewicki.
**“On the Lamb Vector Divergence as a Momentum Field Diagnostic Employed in Turbulent Channel Flow,”** In *Proceedings of the 59th Annual Meeting of the American Physical Society, Division of Fluid Dynamics*, Tampa Bay, Fl, November, 2006.

[Har2006a] D. Hart, C.E. Goodyer, M. Berzins, P.K. Jimack, L. Scales.
**“Adjoint Error Estimation and Spatial Adaptivity for EHL-Like Models,”** In *IUTAM Symposium on Elastohydrodynamics and Micro-elastohydrodynamics*, Springer, pp. 47--58. 2006.

DOI: 10.1007/1-4020-4533-6_3

[Haz2006a] H.C. Hazlett, M.D. Poe, G. Gerig, R.G. Smith, J. Piven.
**“Cortical Gray and White Brain Tissue Volume in Adolescents and Adults with Autism,”** In *Biological Psychiatry*, Vol. 59, No. 1, pp. 1--96. January, 2006.

[Ion2006a] I. Ionescu, J.E. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss.
**“Simulation of Soft Tissue Failure Using the Material Point Method,”** In *Journal of Biomechanical Engineering*, Vol. 128, No. 6, pp. 917--924. 2006.

[Ize2006a] T. Ize, I. Wald, C. Robertson, S.G. Parker.
**“An Evaluation of Parallel Grid Construction for Ray Tracing Dynamic Scenes,”** SCI Institute Technical Report, No. UUSCI-2006-025, *University of Utah*, 2006.

[Ize2006b] T. Ize, I. Wald, C. Robertson, S.G. Parker.
**“An Evaluation of Parallel Grid Construction for Ray Tracing Dynamic Scenes,”** In *Proceedings of the 2006 IEEE Symposium on Interactive Ray Tracing*, Vol. 1, pp. 47--55. 2006.

[Ize2006c] T. Ize, I. Wald, S.G. Parker.
**“Asynchronous BVH Construction for Ray Tracing Dynamic Scenes,”** Note: *UUSCI-2006-034*, *SCI Institute*, 2006.

[Jeo2006a] W-K. Jeong, R.T. Whitaker, M. Dobin.
**“Interactive 3D Seismic Fault Detection on the Graphics Hardware,”** In *Proceedings of the 2006 International Workshop on Volume Graphics*, In *Proceedings of International Workshop on Volume Graphics*, pp. 111--118. 2006.

[Joh2006a] C.R. Johnson, D.M. Weinstein.
**“Biomedical Computing and Visualization,”** In *Proceedings of the Twenty-Ninth Australasian Computer Science Conference (ACSC2006): Conferences in Research and Practice in Information Technology (CRPIT)*, Hobart, Australia, Vol. 48, Edited by Vladimir Estivill-Castro and Gill Dobbie, pp. 3-10. 2006.

[Joh2006c] J.T. Johnson III, M.S. Hansen, I. Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C. Keller.
**“Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,”** In *PLoS Genetics*, Vol. 2, No. 1, pp. 471--477. April, 2006.

[Joh2006d] C.R. Johnson.
**“Computational Methods and Software for Bioelectric Field Problems,”** In *Biomedical Engineering Handbook, 2nd Edition*, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.

[Joh2006e] C.R. Johnson, S.G. Parker.
**“Problem Solving Environments for DDDAS,”** In *Proceedings of the Ninth Copper Mountain Conference on Iterative Methods*, Copper Mountain, CO, Note: *Minisymposium: Actually Doing Dynamic Data-driven Application Simulations*, April, 2006.

[Joh2006f] J.T. Johnson III, M.S. Hansen, I.Q Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C.Keller.
**“Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,”** In *Proceedings of the Teratology 46th Annual Meeting*, Tucson, AZ, 2006.

[Joh2006g] C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T.S. Yoo, (Eds.).
**“NIH/NSF Visualization Research Challenges Report,”** Note: *IEEE Press*, 2006.

ISBN: 0-7695-2733-7

[Jol2006a] M. Jolley, J. Triedman, C.-F. Westin, D.M. Weinstein, R.S. MacLeod, D.H. Brooks.
**“Image Based Modeling of Defibrillation in Children,”** In *Proceedings of the 26th Annual International Conference of the IEEE EMBS*, New York, NY, USA August, 2006.

[Jur2006a] E. Jurrus, T. Tasdizen, P. Koshevoy, P.T. Fletcher, M. Hardy, C-B. Chien, W. Denk, R.T. Whitaker.
**“Axon Tracking in Serial Block-Face Scanning Electron Microscopy,”** In *Workshop on Microscopic Image Analysis with Applications in Biology, MICCAI*, October, 2006.

[Kin2006a] G. Kindlmann, X. Tricoche, C.-F. Westin.
**“Anisotropy Creases Delineate White Matter Structure in Diffusion Tensor MRI,”** In *Proceedings of the Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06)*, Copenhagen, Denmark, Springer Lecture Notes in Computer Science 4190, pp. 126--133. October, 2006.

[Kir2006a] N.D. Kirkpatrick, J.B. Hoying, S.K. Botting, J.A. Weiss, U. Utzinger.
**“In Vitro Model for Endogenous Optical Signatures of Collagen,”** In *Journal of Biomedical Optics*, Vol. 11, No. 5, September/October, 2006.

[Kir2006b] R.M. Kirby, C.R. Johnson, M. Berzins.
**“Involving Undergraduates in Computational Science and Engineering Research: Successes and Challenges,”** In *Proceedings of Computational Science - ICCS 2006: 6th International Conference*, Reading, UK, Lecture Notes in Computer Science, Vol. 3992, May 28-31, 2006.

[Kir2006c] R.M. Kirby, S.J. Sherwin.
**“Stabilisation of Spectral/hp Element Methods Through Spectral Vanishing Viscosity: Application to Fluid Mechanics Modelling,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 195, pp. 3128--3144. 2006.

[Kir2006d] R.M. Kirby, S.J. Sherwin.
**“Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,”** In *Journal of Engineering Mathematics*, Vol. 56, No. 3, pp. 273--288. 2006.

[Kir2006e] R.M. Kirby, Z. Yosibash, G.E. Karniadakis.
**“Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,”** In *Journal of Computational Physics*, Vol. 223, No. 2, pp. 489--518. 2006.

[Kir2006f] R.M. Kirby, S.J. Sherwin.
**“Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,”** In *Journal of Engineering Mathematics*, Vol. 56, pp. 273--288. 2006.

[Kno2006a] A. Knoll, I. Wald, S.G. Parker, C.D. Hansen.
**“Interactive Isosurface Ray Tracing of Large Octree Volumes,”** SCI Institute Technical Report, No. UUSCI-2006-026, *University of Utah*, 2006.

[Kos2006a] P.A. Koshevoy, T. Tasdizen, R.T. Whitaker.
**“Implementation of an Automatic Slice-to-Slice Registration Tool,”** SCI Institute Technical Report, No. UUSCI-2006-018, *University of Utah*, 2006.

[Kos2006b] P.A. Koshevoy, T. Tasdizen, R.T. Whitaker.
**“Implementation of an Automatic Image Registration Tool,”** SCI Institute Technical Report, No. UUSCI-2006-020, *University of Utah*, 2006.

[Kos2006c] P. Koshevoy, T. Tasdizen, R.T. Whitaker, B. Jones, R. Marc.
**“Assembly of Large Three-Dimensional Volumes from Serial-Section Transmission Electron Microscopy,”** In *Proceedings of 2006 MICCAI Workshop on Microscopic Image Analysis with Applications in Biology*, October, 2006.

[Kum2006a] G. Kumfert, D.E. Bernholdt, T.G.W. Epperly, J.A. Kohl, L.C. McInnes, S.G. Parker, J. Ray.
**“How the Common Component Architecture Advances Computational Science,”** In *J. Phys.: Conf. Ser.*, Vol. 46, pp. 479--493. 2006.

[Lef2006a] A. Lefohn, J.M. Kniss, R. Strzodka, S. Sengupta, J. Owens.
**“Glift: Generic, Efficient Random-Access GPU Data Structures,”** In *j-ACM-CG*, Vol. 25, No. 1, pp. 1--37. January, 2006.

[Li2006a] G. Li, X. Tricoche, C.D. Hansen.
**“GPUFLIC: Interactive and Accurate Dense Visualization of Unsteady Flows,”** In *Proceedings of Euro Vis 2006*, pp. 29--34. 2006.

[Li2006b] G. Li, X. Tricoche, C.D. Hansen.
**“Survey of Texture-based Techniques in Flow Visualization,”** In *VIsualization of Large and Unstructured Data Sets - Applications in Geospatial Planning, Modeling, and Engineering*, Dagstuhl, Germany, GI-Edition, Lecture Notes in Informatics - Visualization of Large and Unstructured Data Sets. First workshop of the DFG's International Research Training Group, pp. 11--21. June, 2006.

[Liv2006a] O.E. Livne.
**“Clustering on Single Refinement Level: Berger-Rigoustos Algorithm,”** SCI Institute Technical Report, No. UUSCI-2006-001, *University of Utah*, 2006.

[Liv2006b] O.E. Livne.
**“Minimum and Maximum Patch Size Clustering on a Single Refinement Level,”** SCI Institute Technical Report, No. UUSCI-2006-002, *University of Utah*, 2006.

[Liv2006c] O.E. Livne.
**“Efficient Update of Persistent Patches in the Berger Rigoutsous Algorithm,”** SCI Institute Technical Report, No. UUSCI-2006-003, *University of Utah*, 2006.

[Liv2006d] O.E. Livne.
**“Clustering Patches for Multi-Level Refined Grids: a Hierarchical Approach,”** SCI Institute Technical Report, No. UUSCI-2006-004, *University of Utah*, 2006.

[Liv2006e] O.E. Livne.
**“ShockTube Problem - Status Report 1 Uni-Level Experiments,”** SCI Institute Technical Report, No. UUSCI-2006-005, *University of Utah*, 2006.

[Liv2006f] O.E. Livne.
**“ICE Algorithm and the Davis Advection Scheme,”** SCI Institute Technical Report, No. UUSCI-2006-006, *University of Utah*, 2006.

[Liv2006g] O.E. Livne.
**“ICE Algorithm for the Shocktube Problem,”** SCI Institute Technical Report, No. UUSCI-2006-007, *University of Utah*, 2006.

[Lor2006a] L. Lorenzo, R.S. MacLeod, R.T. Whitaker, G. Adluru, E.V.R. DiBella.
**“Level Sets and Shape Models for Segmentation of Cardiac Perfusion MRI,”** In *c-SPIEMI2006*, Vol. 6144, pp. 1320--1331. 2006.

[Lor2006b] P. Lorenzen, M.W. Prastawa, B. Davis, G. Gerig, E. Bullitt, S. Joshi.
**“Multi-Modal Image Set Registration and Atlas Formation,”** In *Med Image Anal*, Vol. 10, No. 3, pp. 440--451. June, 2006.

[Lu2006a] H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack, M. Walkley.
**“Adaptive High-order Finite Element Solution of Transient Elastohydrodynamic Lubrication Problems,”** In *Proc. IMechE Part J: J. Engrg. Tribology*, Vol. 220, pp. 215--225. 2006.

[Lu2006b] H. Lu, M. Berzins, P.K. Jimack.
**“Application of the Adaptive Discontinuous Galerkin Method to Problems in Elastohydrodynamic Lubrication,”** In *Innovation in Engineering Computational Technology*, Edited by B.H.V. Topping and G. Montero and R. Montenegro, Saxe-Coburg Publications, Stirling, pp. 169--191. 2006.

[Lu2006c] H. Lu.
**“High Order Finite Element Solution of Elastohydrodynamic Lubrication Problems,”** Note: *Advisor: Martin Berzins*, *School of Computing, University of Leeds*, 2006.

[Luj2006a] T.J. Lujan, M.S. Dalton, B.M. Thompson B.J. Ellis, J.A. Weiss.
**“Effect of ACL Deficiency on MCL Strains and Joint Kinematics,”** In *Journal of Biomechanical Engineering*, pp. (in press). November, 2006.

[Luj2006b] T.J. Lujan, C.J. Underwood, H.B. Henninger, B.M. Thompson, J.A. Weiss.
**“Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament,”** In *Journal of Orthopaedic Research*, pp. (in press). October, 2006.

[Mar2006a] H. Marmanis, C.W. Hamman, R.M. Kirby.
**“A One-Dimensional Model of the Navier-Stokes,”** SCI Institute Technical Report, No. UUSCI-2006-012, *University of Utah*, 2006.

[Mci2006a] L.C. McInnes, B.A. Allan, R. Armstrong, S.J. Benson, D.E. Bernholdt, T.L. Dahlgren, L.F. Diachin, M. Krishnan, J.A. Kohl, J.W. Larson, S. Lefantzi, J. Nieplocha, B. Norris, S.G. Parker, J. Ray, S. Zhou.
**“Parallel PDE-Based Simulations Using the Common Component Architecture,”** In *Numerical Solution of Partial Differential Equations on Parallel Computers*, Lecture Notes in Computational Science and Engineering, Edited by A.M. Bruaset and P. Bjorstad and A. Tveito, Springer, pp. 327--284. 2006.

ISBN: 3-540-29076-1

[Mea2006a] S. Means, A.J. Smith, J. Shepherd, J. Shadid, J. Fowler, R. Wojcikiewicz, T. Mazel, G.D. Smith, B.S. Wilson.
**“Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry,”** In *j-BJ*, Vol. 91, pp. 537--557. March, 2006.

[Mel2006a] I. Melatti, R. Palmer, G. Sawaya, Y. Yang, R.M. Kirby, G. Gopalakrishnan.
**“Parallel and Distributed Model Checking in Eddy,”** In *Model Checking Software: Proceedings of the 13th International SPIN Workshop (SPIN 2006)*, Austria, Vol. 3925/2006, pp. 108--125. 2006.

[Mil2006a] P. Miller, P.-T. Bremer, W. Cabot, A. Cook, D. Laney, A. Mascarenhas, V. Pascucci.
**“Application of Morse Theory to Analysis of Rayleigh-Taylor Topology,”** In *10th International Workshop on the Physics of Compressible Turbulent Mixing*, 2006.

[Moo2006a] C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T. Yoo.
**“NIH/NSF Visualization Research Challenges Report Summary,”** Note: *NIH/NSF*, pp. 66-73. 2006.

[Mun2006a] T. Munzner, C.R. Johnson, R. Moorhead, H. Pfister, P. Rheingans, T.S. Yoo.
**“NIH-NSF Visualization Research Challenges Report Summary,”** Note: *NIH-NSF*, pp. 20--24. March/April, 2006.

[Nag2006a] S. Nagarajan, O. Portniaguine, D. Hwang, C.R. Johnson, K. Sekihara.
**“Controlled Support MEG Imaging,”** In *NeuroImage*, Vol. 15;33, No. 3, pp. 878--885. 2006.

[Nat2006a] V. Natarajan, Y. Wang, P.-T. Bremer, V. Pascucci, B. Hamann.
**“Segmenting Molecular Surfaces,”** In *Computer Aided Geometric Design*, Special Issue on Applications of Geometric Modeling in the Life Sciences, Vol. 23, No. 6, Note: *(To appear)*, pp. 495--509. 2006.

[Nel2006a] B. Nelson, R.M. Kirby.
**“Ray-Tracing Polymorphic Multi-Domain Spectral/hp Elements for Isosurface Rendering,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 12, No. 1, pp. 114--125. 2006.

[Nem2006a] O. Nemitz, M. Rumpf, T. Tasdizen, R.T. Whitaker.
**“Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data,”** In *Journal of Mathematical Imaging and Vision*, Vol. 27, No. 3, pp. 217--229. April, 2006.

[Ode2006a] J.T. Oden, J. Fish, C.R. Johnson, A. Laub, D. Srolovitz, T. Belytschko, T.J.R. Hughes, D. Keys, L. Petzold, S. Yip.
**“NSF Blue Ribbon Panel Report on Simulation Based Engineering Science,”** Note: *NSF Report*, 2006.

[Pal2006a] R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby.
**“Gauss: A Framework for Verifying Scientific Computing Software,”** In *Electronic Notes on Theoretical Computer Science (ENTCS)*, Vol. 144, No. 3, pp. 95--106. February, 2006.

[Par2006a] S.G. Parker.
**“A Component-Based Architecture for Parallel Multi-physics PDE Simulation,”** In *Future Generation Computer Systems (FGCS)*, Vol. 22, No. 1-2, Elsevier, pp. 204--216. 2006.

[Par2006b] S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson.
**“Integrating Component-Based Scientific Computing Software,”** In *Parallel Processing for Scientific Computing*, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM Press, pp. 271--288. 2006.

ISBN: 0-89871-619-5

[Par2006c] S.G. Parker, J. Guilkey, T. Harman.
**“A Component-based Parallel Infrastructure for the Simulation of Fluid Structure Interaction,”** In *Engineering with Computers*, Vol. 22, No. 3-4, Springer London, pp. 277--292. 2006.

[Par2006d] S.G. Parker.
**“Composition of Components in Multiphysics Applications,”** In *Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing*, San Francisco, CA, Note: *Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications*, 2006.

[Par2006e] S.G. Parker.
**“Component-Based Multi-Physics Simulations of Fires and Explosions,”** In *Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing*, San Francisco, CA, Note: *Presented at the Minisymposium on Parallel Dynamic Data Management Infrastructures for Scientific & Engineering Applications*, 2006.

[Par2006f] S.G. Parker.
**“Why do Software Engineering Methods Fail for HPC?,”** In *Presented at Architectures and Algorithms for Petascale Computing*, Schloss Dagstuhl, Germany, Vol. Seminar 06071, February, 2006.

[Par2006g] S. Parker, K. Zhang, C. Damevski, C.R. Johnson.
**“Integrating Component-Based Scientific Computing Software,”** In *Parallel Processing for Scientific Computing*, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM, pp. 271--288. January, 2006.

[Pas2006g] V. Pascucci.
**“Topology Diagrams of Scalar Fields in Scientific Visualisation,”** In *Topological Data Structures for Surfaces*, Note: *UCRL-BOOK-200013*, Edited by Sanjay Rana and Jo Wood, Wiley-Blackwell, pp. 121--129. May, 2006.

DOI: 10.1002/0470020288.ch8

[Peg2006a] V. Pegoraro, S.G. Parker.
**“Physically-Based Realistic Fire Rendering,”** In *Proceedings of the 2006 Eurographics Workshop on Natural Phenomena*, pp. 51--59. 2006.

[Per2006a] S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp.
**“Formal Verification of Programs that use MPI One-Sided Communications,”** In *Proceedings of EuroPVM-MPI 2006*, Bonn, Germany, September 17-20, 2006.

[San2006a] A.R. Sanderson, R.M. Kirby, C.R. Johnson, L. Yang.
**“Advanced Reaction-Diffusion Models for Texture Synthesis,”** In *Journal of Graphics Tools*, Vol. 11, No. 3, pp. 47--71. 2006.

[San2006c] A.R. Sanderson, X. Tricoche, C. Garth, S. Kruger, C. Sovinec, E. Held, J. Breslau.
**“Detection of Magnetic Nulls in Toroidal Geometry,”** In *Proceedings of the 48th Annual Meeting of the Division of Plasma Physics*, 2006.

[San2006d] A.R. Sanderson, X. Tricoche, C. Garth, S. Kruger, C. Sovinec, E. Held, J. Breslau.
**“Visualizing Patterns in the Poincare Plot of a Magnetic Field,”** In *IEEE Visualization Conference 2006 Compendium*, 2006.

[Sch2006a] J. Schreiner, C.E. Scheidegger, S. Fleishman, C.T. Silva.
**“Direct (Re)Meshing for Efficient Surface Processing,”** SCI Institute Technical Report, No. UUSCI-2006-013, *University of Utah*, 2006.

[Sch2006b] J. Schreiner, C.E. Scheidegger, S. Fleishman, C.T. Silva.
**“Direct (Re)Meshing for Efficient Surface Processing,”** In *Computer Graphics Forum*, Vol. 25, No. 3, Wiley-Blackwell, pp. 527--536. Sep, 2006.

DOI: 10.1111/j.1467-8659.2006.00972.x

[Sch2006c] J. Schreiner, C.E. Scheidegger, C.T. Silva.
**“High-Quality Extraction of Isosurfaces from Regular and Irregular Grids,”** In *IEEE Trans. Vis. Comp. Graph.*, Vol. 12, No. 5, pp. 1205--1212. 2006.

[Sch2006d] T. Schultz, B. Burgeth, J. Weickert.
**“Flexible Segmentation and Smoothing of DT-MRI Fields Through a Customizable Structure Tensor,”** In *Advances in Visual Computing*, Lecture Notes in Computer Science, Vol. 4291, Edited by 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, Springer, pp. 455--464. 2006.

[Ser2006a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Improved Performance of Bayesian Solutions for Inverse Electrocardiography Using Multiple Information Sources,”** In *j-BME*, Vol. 53, No. 10, pp. 2024--2034. October, 2006.

[She2006a] J.F. Shepherd.
**“Hexahedral Mesh Generation Constraints,”** SCI Institute Technical Report, No. UUSCI-2006-010, *University of Utah*, 2006.

[She2006b] J.F. Shepherd, C.J. Tuttle, C.T. Silva, Y. Zhang.
**“Quality Improvement and Feature Capture in Hexahedral Meshes,”** SCI Institute Technical Report, No. UUSCI-2006-029, *University of Utah*, 2006.

[She2006c] S.J. Sherwin, R.M. Kirby, J. Peiro, R.L. Taylor, O.C. Zienkiewicz.
**“On 2D Elliptic Discontinuous Galerkin Methods,”** In *International Journal of Numerical Methods in Engineering*, Vol. 65, No. 5, pp. 752--784. 2006.

[Ste2006a] A.J. Stephens, S. Boulos, J. Bigler, I. Wald, S.G. Parker.
**“An Application of Scalable Massive Model Interaction using Shared-Memory Systems,”** In *c-EGPGV2006*, pp. 19--26. 2006.

[Sti2006a] J.G. Stinstra, S.F. Roberts, J.B. Pormann, R.S. MacLeod, C.S. Henriquez.
**“A Model of 3D Propagation in Discrete Cardiac Tissue,”** In *Proceedings of Computers in Cardiology 2006*, Vol. 33, pp. 41. 2006.

[Str2006a] J. Strasser, V. Pascucci, K.-L. Ma.
**“Multi-layered Image Caching for Distributed Rendering of Large Multiresolution Datasets,”** In *Eurographics Symposium on Parallel Graphics and Visualization*, Edited by Bruno Raffin and Alan Heirich and Luis Paulo Santos, Eurographics Association, Braga, Portugal pp. 171--177. 2006.

ISBN: 3-905673-40-1

ISSN: 1727-348X

[Sty2006a] M. Styner, M. Jomier, G. Gerig.
**“Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC,”** In *Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI), Special Session: Open Source*, pp. 702--705. 2006.

[Tar2006a] D.M. Tartakovsky, D. Xiu.
**“Stochastic Analysis of Transport in Tubes with Rough Walls,”** In *Journal of Computational Physics*, Vol. 217, No. 1, pp. 248--259. 2006.

DOI: 10.1016/j.jcp.2006.02.029

[Tri2006a] X. Tricoche, X. Zheng, A. Pang.
**“Visualizing the Topology of Symmetric, Second-Order, Time-varying Two-Dimensional Tensor Fields,”** In *Visualization and Processing of Tensor Fields*, Springer, pp. 225--240. 2006.

[Tri2006b] X. Tricoche, C. Garth.
**“Topological Methods for Visualizing Vortical Flows,”** In *Mathematical Foundations of Visualization, Computer Graphics, and Massive Data Exploration*, Springer, 2006.

[Ver2006a] A.I. Veress, W.P. Segars, J.A. Weiss, B.M.W. Tsui, G.T. Gullberg.
**“Normal and Pathological NCAT Image and Phantom Data Based on Physiologically Realistic Left Ventricle Finite Element Models,”** In *IEEE Transactions on Medical Imaging*, Vol. 25, No. 12, pp. 1604--1616. 2006.

[Vie2006a] K. Vieira, A. Silva, N. Pinto, E.S. Moura, J. Cavalcanti, J. Freire.
**“A Fast and Robust Method for Web Page Template Detection and Removal,”** In *Proceedings of the 15th ACM International Conference on Information and Knowledge Management (CIKM)*, Arlington, VA, pp. 258--267. November, 2006.

[Wal2006a] I. Wald, V. Havran.
**“On building fast kd-Trees for Ray Tracing, and on doing that in O(N log N),”** SCI Institute Technical Report, No. UUSCI-2006-009, *University of Utah*, 2006.

[Wal2006b] I. Wald, T. Ize, A. Kensler, A. Knoll, S.G. Parker.
**“Ray Tracing Animated Scenes using Coherent Grid Traversal,”** In *Proceedings of the ACM SIGGRAPH 2006 Conference*, ACM, New York, NY, USA pp. 485--493. 2006.

ISSN: 0730-0301

DOI: 10.1145/1179352.1141913

[Wal2006c] I. Wald, S. Boulosy, P. Shirley.
**“Ray Tracing Deformable Scenes using Dynamic Bounding Volume Hierarchies,”** SCI Institute Technical Report, No. UUSCI-2006-015, *University of Utah*, 2006.

[Wal2006d] I. Wald, T. Ize, A. Kensler, A. Knoll, S.G. Parker.
**“Ray Tracing Animated Scenes using Coherent Grid Traversal,”** SCI Institute Technical Report, No. UUSCI-2006-014, *University of Utah*, 2006.

[Wal2006e] I. Wald, S. Boulos, P. Shirley.
**“Ray Tracing Deformable Scenes using Dynamic Bounding Volume Hierarchies,”** SCI Institute Technical Report, No. UUSCI-2006-023, Note: *Updated version of UUSCI-2006-015*, *University of Utah*, 2006.

[Wal2006f] I. Wald.
**“Realtime Ray Tracing and Interactive Global Illumination,”** In *IT - Information Technology*, Note: *Invited article in german.*, 2006.

[Wal2006g] I. Wald, A. Dietrich, C. Benthin, A. Efremov, T. Dahmen, J. Gunther, V. Havran, P. Slusallek, H.-P. Seidel.
**“Applying Ray Tracing for Virtual Reality and Industrial Design,”** In *Proceedings of the 2006 IEEE Symposium on Interactive Ray Tracing*, pp. 177--185. 2006.

[Wei2006a] J.A. Weiss, B.J. Maakestad.
**“Permeability of Human Medial Collateral Ligament Transverse to the Collagen Fiber Direction,”** In *j-BM*, Vol. 39, No. 2, pp. 276--283. 2006.

[Wei2006b] J.A. Weiss, A.I. Veress, G.T. Gullberg, N.S. Phatak, Q. Sun, D.L. Parker, R.D. Rabbitt.
**“Strain measurement using deformable image registration,”** In *Mechanics of Biological Tissue*, Edited by G.A. Holzapfel, R.W. Ogden, Springer, pp. 489--501. 2006.

DOI: 10.1007/3-540-31184-x_35

[Wol2006a] C.H. Wolters, A. Anwander, X. Tricoche, D.M. Weinstein, M.A. Koch, R.S. MacLeod.
**“Influence of Tissue Conductivity Anisotropy on EEG/MEG Field and Return Current Computation in a Realistic Head Model: A Simulation and Visualization Study Using High-Resolution Finite Element Modeling,”** In *j-NI*, Vol. 30, No. 3, pp. 813--826. April, 2006.

[Wol2006b] C.H. Wolters, A. Anwander, G. Berti, U. Hartmann.
**“Geometry-Adapted Hexahedral Meshes Improve Accuracy of Finite Element Method Based EEG Source Analysis,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 54, No. 8, pp. 1446--1453. August, 2006.

[Wol2006c] D. Güllmar, J. Haueisen, M. Eiselt, F. Giessler, L. Flemming, A. Anwander, T. Knösche, C.H. Wolters, M. Dümpelmann, D.S. Tuch, J.R. Reichenbach.
**“Influence of Anisotropic Conductivity on EEG Source Reconstruction: Investigations in a Rabbit Model,”** In *IEEE Trans. Biomed. Eng.*, Vol. 53, No. 9, pp. 1841--1850. 2006.

[Wym2006a] C. Wyman, S.G. Parker, P. Shirley, C.D. Hansen.
**“Interactive Display of Isosurfaces with Global Illumination,”** In *IEEE Transactions on Visualization and Comptuer Graphics*, Vol. 12, No. 2, March/April, 2006.

[Xiu2006a] D. Xiu, D.M. Tartakovsky.
**“Numerical Methods for Differential Equations in Random Domains,”** In *SIAM Journal on Scientific Computing*, Vol. 28, No. 3, pp. 1167--1185. 2006.

DOI: 10.1137/040613160

[Xu2006a] S. Xu, M. Styner, B. Davis, S. Joshi, G. Gerig.
**“Group Mean Differences of Voxel and Surface Objects via Nonlinear Group Averaging,”** In *Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 758--761. April, 2006.

[Yil2006a] B. Yilmaz, R.S. Macleod.
**“Instance Selection for Estimation of Epicardial Activation Sequence from Venous Catheter Measurements,”** In *Proceedings of the 28th IEEE EMBS Annual International Conference*, pp. 3982--3985. 2006.

[Yus2006a] P.A. Yushkevich, J. Piven, H.C. Hazlett, R.G. Smith, S. Ho, J.C. Gee, G. Gerig.
**“User-Guided 3D Active Contour Segmentation of Anatomical Structures: Significantly Improved Efficiency and Reliability,”** In *NeuroImage*, Vol. 31, Note: *A NeuroImage Top Cited Paper!*, pp. 1116--1128. 2006.

[Zhe2006a] X. Zheng, X. Tricoche, A. Pang.
**“Degenerate 3D Tensors,”** In *Visualization and Processing of Tensor Fields*, Springer, pp. 241--256. 2006.

2005

[Ale2005a] Y. Alexeev, B.A. Allan, R.C. Armstrong, D.E. Bernholdt, T.L. Dahlgren, D. Gannon, C.L. Janssen, J.P. Kenny, M. Krishnan, J.A. Kohl, G. Kumfert, L.C. McInnes, J. Nieplocha, S.G. Parker, C. Rasmussen, T.L. Windus.
**“Component-Based Software for High-Performance Scientific Computing,”** In *Journal of Physics: Conference Series*, Vol. 16, IOP Publishing, pp. 536--540. January, 2005.

DOI: 10.1088/1742-6596/16/1/073

[Alt2005a] O. Alter, G.H. Golub.
**“Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations,”** In *Proceedings of the National Academy of Sciences*, Vol. 102, No. 49, Proceedings of the National Academy of Sciences, pp. 17559--17564. November, 2005.

DOI: 10.1073/pnas.0509033102

[And2005a] A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss.
**“A Subject-Specific Finite Element Model of the Pelvis: Development, Validation and Sensitivity Studies,”** In *j-JBE*, Vol. 127, No. 3, pp. 364--373. 2005.

[Awa2005a] S.P. Awate, T. Tasdizen, R.T. Whitaker.
**“Nonparametric Statistics of Image Neighborhoods for Unsupervised Texture Segmentation,”** SCI Institute Technical Report, No. UUSCI-2005-003, *University of Utah*, 2005.

[Awa2005b] S.P. Awate, R.T. Whitaker.
**“Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,”** SCI Institute Technical Report, No. UUSCI-2005-004, *University of Utah*, 2005.

[Awa2005c] S.P. Awate, R.T. Whitaker.
**“Nonparametric Neighborhood Statistics for MRI Denoising,”** SCI Institute Technical Report, No. UUSCI-2005-005, *University of Utah*, 2005.

[Awa2005e] S.P. Awate, R.T. Whitaker.
**“Nonparametric Neighborhood Statistics for MRI Denoising,”** In *In Proc. Int. Conf. Information Processing in Medical Imaging (IPMI), 2005. Lecture Notes in Computer Science*, Vol. 3565, pp. 677--688. July, 2005.

[Awa2005f] S.P. Awate, R.T. Whitaker.
**“Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,”** In *Proceedings of the IEEE Int. Conf. Computer Vision and Pattern Recognition (CVPR)*, pp. 44--51. 2005.

[Awa2005g] S.P. Awate, R.T. Whitaker.
**“Unsupervised, Information-Theoretic, Adaptive Image Filtering for Image Restoration,”** In *j-PAMI*, Vol. 28, No. 3, pp. 364--376. 2005.

[Bar2005a] L. Barbosa, A.C. Salgado, F. de Carvalho, J. Robin, J. Freire.
**“Looking at both the Present and the Past to Efficiently Update Replicas of Web Content,”** In *Proceedings of the 7th Annual ACM International Workshop on Web Information and Data Management*, pp. 75--80. 2005.

[Bar2005b] D. Barbosa, J. Freire, A. Mendelzon.
**“Designing Information-Preserving Mapping Schemes for XML,”** In *Proceedings of the 31st International Conference on Very Large Data Bases*, Trondheim, Norway, pp. 109--120. 2005.

[Bav2005a] L. Bavoil, S.P. Callahan, P.J. Crossno, J. Freire, C.E. Scheidegger, C.T. Silva, H.T. Vo.
**“Vistrails: Enabling Interactive Multiple-View Visualizations,”** In *c-VIS2005*, pp. 18. 2005.

[Ber2005a] F. Bertrand, R. Bramley, K. Damevski, D. Bernholdt, J. Kohl, J. Larson, A. Sussman.
**“Data Redistribution and Remote Method Invocation in Parallel Component Architectures,”** In *c-IPDPS2005*, Vol. 1, Note: *Awarded Best Paper*, pp. 40--42. 2005.

[Ber2005b] F.F. Bernardon, S.P. Callahan, J.L.D. Comba, C.T. Silva.
**“Volume Rendering of Time-Varying Scalar Fields on Unstructured Meshes,”** SCI Institute Technical Report, No. UUSCI-2005-006, *University of Utah*, 2005.

[Ber2005c] M. Berzins, R.M. Kirby, C.R. Johnson.
**“Integrating Teaching and Research in HPC: Experiences and Opportunities,”** In *c-ICCS2005*, Atlanta, GA, pp. 36--43. 2005.

[Ber2005d] M. Berzins.
**“Preserving Positivity for Hyperbolic PDEs Using Variable-Order Finite Elements with Bounded Polynomials,”** In *Applied Numerical Mathematics*, Vol. 52, No. 2-3, pp. 197--217. February, 2005.

[Bon2005a] C. Bonifasi-Lista, S.P. Lake, M. Small, J.A. Weiss.
**“Viscoelastic Properties of the Human Medial Collateral Ligament Under Longitudinal, Transverse and Shear Loading,”** In *j-OR*, Vol. 23, No. 1, pp. 67--76. January, 2005.

[Bre2005b] P.-T. Bremer, V. Pascucci, B. Hamann.
**“Maximizing Adaptivity in Hierarchical Topological Models,”** In *International Conference on Shape Modeling and Applications 2005*, IEEE, 2005.

DOI: 10.1109/smi.2005.28

[Bul2005a] E. Bullitt, D. Zeng, G. Gerig, S. Aylward, S. Joshi, J.K. Smith, W. Lin, M. Ewend.
**“Vessel Tortuosity and Brain Tumor Malignancy: A Blinded Study,”** In *Acad Radiol*, Vol. 12, No. 10, pp. 1232--1240. October, 2005.

[But2005a] C.R. Butson, C.C. McIntyre.
**“Tissue and electrode capacitance reduce neural activation volumes during deep brain stimulation,”** In *Clinical Neurophysiology*, Vol. 116, No. 10, pp. 2490--500. October, 2005.

DOI: 10.1016/j.clinph.2005.06.023

PubMed ID: 16125463

[Cal2005a] S.P. Callahan, M. Ikits, J.L.D. Comba, C.T. Silva.
**“Hardware-Assisted Visibility Ordering for Unstructured Volume Rendering,”** In *j-TVCG*, Vol. 11, No. 3, IEEE Educational Activities Department, pp. 285--295. 2005.

ISSN: 1077-2626

[Cal2005b] F. Calderero, A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“A Method to Reconstruct Activation Wavefronts Without Isotropy Assumptions Using a Level Sets Approach,”** In *Functional Imaging and Modeling of the Heart: Third International Workshop (FIMH 2005)*, Barcelona, June 2-4, pp. 195. 2005.

[Cal2005c] S.P. Callahan, J.L.D. Comba, P. Shirley, C.T. Silva.
**“Interactive Rendering of Large Unstructured Grids Using Dynamic Level-of-Detail,”** In *c-VIS2005*, pp. 26. 2005.

[Cal2005d] S.P. Callahan.
**“The k-Buffer and its Applications to Volume Rendering,”** Note: *Masters Thesis*, *School of Computing, University of Utah*, 2005.

[Cor2005a] I. Corouge, P.T. Fletcher, S. Joshi, J.H. Gilmore, G. Gerig.
**“Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis,”** In *Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv*, Vol. 8 (Pt. 1), pp. 131--139. 2005.

[Dal2005a] M.S. Dalton, B.J. Ellis, T.J. Lujan, J.A. Weiss.
**“MCL Insertion Site and Contact Forces in the ACL-Deficient Knee,”** In *Proceedings, 51th Annual Orthopaedic Research Society Meeting*, Vol. 30, pp. 814. 2005.

[Deb2005a] R.E. Debski, J.A. Weiss, W.J. Newman, S.M. Moore, P.J. McMahon.
**“Stress and Strain in the Anterior Band of the Inferior Glenohumeral Ligament During a Simulated Clinical Examination,”** In *Journal of Shoulder and Elbow Surgery*, Vol. 14, pp. 24S--31S. 2005.

[Dem2005a] D.E. DeMarle, C.P. Gribble, S. Boulos, S.G. Parker.
**“Memory Sharing for Interactive Ray Tracing on Clusters,”** In *Parallel Computing*, Vol. 31, No. 2, pp. 221--242. 2005.

[Fif2005b] P. Fife, T. Wei, J.C. Klewicki, P.A. McMurtry.
**“Stress Gradient Balance Layers and Scale Hierarchies in Wall-Bounded Flows,”** In *Journal of Fluid Mechanics*, Vol. 532, pp. 165--189. June, 2005.

DOI: 10.1017/S0022112005003988

[Fos2005a] M. Foskey, B. Davis, L. Goyal, S. Chang, E. Chaney, N. Strehl, S. Tomei, J. Rosenman, S. Joshi.
**“Large Deformation Three-Dimensional Image Registration in Image-Guided Radiation Therapy,”** In *Phys Med Biol*, Vol. 50, No. 24, pp. 5869--5892. December 21, 2005.

[Fou2005a] N. Fout, H. Akiba, K-L. Ma, A.E. Lefohn, J.M. Kniss.
**“High-Quality Rendering of Compressed Volume Data Formats,”** In *Proceedings of The Joint EUROGRAPHICS-IEEE VGTC Symposium on Visualization 2005*, 2005.

[Gen2005a] S.E. Geneser, S. Choe, R.M. Kirby, R.S. MacLeod.
**“Influence of Stochastic Organ Conductivity in 2D ECG Forward Modeling: A Stochastic Finite Element Study,”** In *c-BEMNFSI2005*, pp. 5528--5531. 2005.

[Gho2005a] A. Ghodrati, D.H. Brooks, G. Tadmor, B.B. Punske, R.S. MacLeod.
**“Wavefront-based Inverse Electrocardiography using an Evolving Curve State Vector and Phenomenological Propagation and Potential Models,”** In *IJBEM*, Vol. 7, No. 2, pp. 210--213. 2005.

[Goo2005a] C.E. Goodyer, M. Berzins.
**“Parallelisation and Scalability Issues in a Multilevel EHL Solver,”** Report, No. 2005.05, *School of Computing, University of Leeds*, 2005.

[Gra2005a] L. Grady, T. Tasdizen.
**“A Geometric Multigrid Approach to Solving the 2D Inhomogeneous Laplace Equation with Internal Dirichlet Boundary Conditions,”** In *c-ICIP*, Vol. 2, pp. 642--645. September, 2005.

[Gue2004a] C. Guerra, V. Pascucci.
**“Line-Based Object Recognition Using Hausdorff Distance: From Range Images to Molecular Secondary Structure,”** In *Image and Vision Computing*, Vol. 23, No. 4, Note: *UCRL-JRNL-208551*, pp. 405-415. April, 2005.

[Gui2005a] J.E. Guilkey, J.B. Hoying JB, J.A. Weiss.
**“Computational modeling of multicellular constructs with the Material Point Method,”** In *Journal of Biomechanics*, pp. (published online). June, 2005.

[Gul2005a] D. Gullmar, J.R. Reichenbach, A. Anwander, T. Knosche, C.H. Wolters, M. Eiselt, J. Haueisen.
**“Influence of Anisotropic Conductivity of the White Matter Tissue on EEG Source Reconstruction - An FEM Simulation Study,”** In *j-IJBEM*, Vol. 7, No. 1, pp. 108--110. 2005.

[Guo2005a] H. Guo, A. Rangarajan, S. Joshi.
**“3-D Diffeomorphic Shape Registration on Hippocampal Data Sets,”** In *Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv*, Vol. 8 (Pt. 2), pp. 984--991. 2005.

[Gyu2005a] A. Gyulassy, V. Natarajan, V. Pascucci, P.-T. Bremer, B. Hamann.
**“Topology-based Simplification for Feature Extraction from 3D Scalar Fields,”** In *Proceedings of the IEEE Conference on Visualization (VIS-05)*, pp. 275--280. October, 2005.

[Ham2005a] C.W. Hamman, R.M. Kirby, M. Berzins.
**“Parallelization and Scalability of a Spectral Element Solver,”** SCI Institute Technical Report, No. UUSCI-2005-011, *University of Utah*, 2005.

[Han2005a] C.D. Hansen, C.R. Johnson.
**“The Visualization Handbook,”** Elsevier, 2005.

ISBN: 0-12-387582-X

[Han2005b] Q. Han, S.M. Pizer, D. Merck, S. Joshi, J.-Y. Jeong.
**“Multi-figure Anatomical Objects for Shape Statistics,”** In *Lecture Notes in Computer Science*, Edited by G. Christensen and M. Sonka, Springer, pp. 701-712. 2005.

DOI: 10.1007/11505730_58

[Har2005a] D.E. Hart, C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales.
**“Adjoint Error Estimation for EHL-Like Models,”** In *j-IJNMF*, Vol. 47, No. 10-11, pp. 1069--1075. 2005.

[Haw2005a] P. Hawkes, G. Kindlmann, D. Weinstein, G.M. Jones, C. Keller.
**“Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,”** In *Proceedings of 2005 SMI Conference, 4th Annual Meeting of the Society for Molecular Imaging*, Cologne, Germany, 2005.

[Hop2005a] B. Hopenfeld, J.G. Stinstra, R.S. MacLeod.
**“The Effect of Conductivity on ST-Segment Epicardial Potentials Arising from Subendocardial Ischemia,”** In *j-ABE*, Vol. 33, No. 6, pp. 751--763. 2005.

[Iki2005a] M. Ikits, J.D. Brederson.
**“The Visual Haptic Workbench,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 431--447. 2005.

ISBN: 0-12-387582-X

[Ion2005a] I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss.
**“Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method,”** In *Proceedings, Medicine Meets Virtual Reality*, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.

ISBN: 1-58603-498-7

[Kea2005a] P.J. Keall, S. Joshi, S.S. Vedam, J.V. Siebers, V.R. Kini, R. Mohan.
**“Four-Dimensional Radiotherapy Planning for DMLC-Based Respiratory Motion Tracking,”** In *Med Phys*, Vol. 32, No. 4, pp. 942--951. April, 2005.

[Kho2005a] E.G. Khölmovski, E.V.R. DiBella, A.A. Samsonov.
**“Accurate Assessment of the Arterial Input Function using MRI with Radial Sampling,”** In *c-SCMR2005*, Vol. 7, pp. 292--294. 2005.

[Kho2005b] E.G. Khölmovski, D.L. Parker.
**“Application of Phase Consistency to Improve Time Efficiency and Image Quality in Dual Echo Black Blood Carotid Angiography,”** In *Magn Reson Imaging*, Vol. 23, No. 6, pp. 711--722. 2005.

[Kho2005c] E.G. Khölmovski, E.V.R. DiBella, A.A. Samsonov.
**“Perfusion MRI with Radial Sampling: Arterial Input Function and Tissue Enhancement Curve Assessment,”** In *Proc. Intl. Soc. Mag. Reson.*, Note: *Abstract*, pp. 252. 2005.

[Kho2005d] E.G. Khölmovski, A.A. Samsonov.
**“GARSE: Generalized Autocalibrating Reconstruction for Sensitivity Encoded MRI,”** In *Proc. Intl. Soc. Mag. Reson.*, Note: *Abstract*, pp. 2672. 2005.

[Kin2005a] G.L. Kindlmann, D.M. Weinstein, G.M. Jones, C.R. Johnson, M.R. Capecchi, C. Keller.
**“Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,”** In *Journal of Molecular Imaging*, Vol. 4, No. 4, pp. 417--424. 2005.

[Kir2005a] R.M. Kirby, D.F. Keefe, D.H. Laidlaw.
**“Painting and Visualization,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 873--891. 2005.

ISBN: 0-12-387582-X

[Kir2005b] R.M. Kirby, G.E. Karniadakis.
**“Selecting the Numerical Flux in Discontinuous Galerkin Methods for Diffusion Problems,”** In *Journal of Scientific Computing*, Vol. 22/23, pp. 385--411. 2005.

[Kni2005a] J.M. Kniss, G. Kindlmann, C.D. Hansen.
**“Multidimentional Transfer Functions for Volume Rendering,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 189--210. 2005.

ISBN: 0-12-387582-X

[Kni2005b] J.M. Kniss, R. Van Uitert, A.J. Stephens, G. Li, T. Tasdizen.
**“Statistically Quantitative Volume Visualization,”** In *IEEE Visualization 2005*, 2005.

[Kni2005c] J.M. Kniss, A.E. Lefohn, N. Fout.
**“Deferred Filtering: Rendering from Difficult Data Formats,”** In *GPU Gems II: Programming Techniques for High-Performance Graphics and General-Purpose Computation*, Ch. 41, Edited by M. Pharr and R. Fernando, Addison Wesley, pp. 669--677. 2005.

[Kni2005d] J.M. Kniss, A.E. Lefohn, R. Strzodka, S. Sengupta, J.D. Owens.
**“Octree Textures on Graphics Hardware,”** In *Proceedings of the ACM SIGGRAPH 2005 Conference on Abstracts and Applications*, 2005.

[Lai2005a] D.H. Laidlaw, R.M. Kirby, C.D. Jackson, J.S. Davidson, T.S. Miller, M. Silva, W.H. Warren, M. Tarr.
**“Comparing 2D Vector Field Visualization Methods: A User Study,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 11, No. 1, pp. 59--70. 2005.

[Lan2005a] D. Laney, S.P. Callahan, N. Max, C.T. Silva, S. Langer, R. Frank.
**“Hardware-Assisted Simulated Radiography,”** In *c-VIS2005*, pp. 44. 2005.

[Lef2005a] A.E. Lefohn, J.M. Kniss, J. Owens.
**“Implementing Efficient Parallel Data Structures on GPUs,”** In *GPU Gems II: Programming Techniques for High-Performance Graphics and General-Purpose Computation*, Ch. 33, Edited by M. Pharr and R. Fernando, Addison Wesley, pp. 521--545. 2005.

[Lef2005b] A.E. Lefohn, S. Sengupta, J.M. Kniss, R. Strzodka, J.D. Owens.
**“Dynamic Adaptive Shadow Maps on Graphics Hardware,”** In *Proceedings of the ACM SIGGRAPH 2005 Conference on Abstracts and Applications*, 2005.

[Lew2005a] S. Lew, C. Wolters, K. Lee, S. Makeig, G. Worrell, R.S. MacLeod.
**“Epileptogenic Source Localization For Open Skull Head Model of Epilepsy By Independent Component Analysis And Inverse Dipole Fit Method,”** In *1st Annual Mountain West Biomedical Engineering Conference*, 2005.

[Liv2005a] Y. Livnat.
**“Accelerated Isosurface Extraction Approaches,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 39--55. 2005.

ISBN: 0-12-387582-X

[Liv2005b] Y. Livnat, J. Agutter, S. Moon, R.F. Erbacher, S. Foresti.
**“A Visualization Paradigm for Network Intrusion Detection,”** In *IEEE Workshop on Information Assurance and Security 2005*, pp. 30--37. June, 2005.

[Liv2005c] Y. Livnat, J. Agutter, S. Moon, S. Foresti.
**“Visual Correlation for Situational Awareness,”** In *c-IVIS2005*, pp. 13. October, 2005.

[Liv2005d] Y. Livnat, X. Tricoche.
**“Shadows for Incomplete Point-based Isosurfaces,”** SCI Institute Technical Report, No. UUSCI-2005-001, *University of Utah*, 2005.

[Lor2005a] P. Lorenzen, B. Davis, S. Joshi.
**“Unbiased Atlas Formation via Large Deformations Metric Mapping,”** In *Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv (MICCAI)*, Vol. 8 (Pt. 2), Edited by J.S. Duncan and G. Gerig, pp. 411--418. 2005.

[Lu2005a] H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack.
**“High Order Discontinuous Galerkin Method for EHL Line Contact Problems,”** In *Communication in Numerical Methods in Engineering*, Vol. 21, No. 11, pp. 643--650. 2005.

[Luj2005a] T.J. Lujan, S.P. Lake, T.A. Plaizier, B.J. Ellis, J.A. Weiss.
**“Simultaneous Measurement of Three-Dimensional Joint Kinematics and Tissue Strains with Optical Methods,”** In *ASME Journal of Biomechanical Engineering*, Vol. 127, pp. 193--197. 2005.

[Mac2005a] R.S. MacLeod, B. Yilmaz, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Epicardial Activation Mapping from Multielectrode Venous Catheters,”** In *j-JE*, pp. (in press). 2005.

[Mac2005b] R.S. MacLeod, S. Shome, J.G. Stinstra, B.P. Punske, B. Hopenfeld.
**“Mechanisms of Ischemia-Induced ST-Segment Changes,”** In *j-JE*, Vol. 38(4 Suppl), pp. 8--13. November, 2005.

[Mac2005c] R.S. MacLeod.
**“Mechanisms of ischemia-induced ST-segment changes,”** In *Journal of Electrocardiology*, Vol. 38, No. 4 , Elsevier, pp. 8--13. Oct, 2005.

DOI: 10.1016/j.jelectrocard.2005.06.095

[Mac2005e] R.S. MacLeod, F. Kornreich, A. van Oosterom, P. Rautaharju, R. Selvester, G. Wagner, C. Zywietz.
**“Report of the First Virtual Visualization of the Reconstructed Electrocardiographic Display Symposium,”** In *Journal of Electrocardiology*, Vol. 38, pp. 385--399. 2005.

[Mey2005a] M.D. Meyer, H. Pfister, C.D. Hansen, C.R. Johnson.
**“Image-Based Volume Rendering with Opacity Light Fields,”** SCI Institute Technical Report, No. UUSCI-2005-002, *University of Utah*, 2005.

[Mey2005b] M.D. Meyer, P. Georgel, R.T. Whitaker.
**“Robust Particle Systems for Curvature Dependent Sampling of Implicit Surfaces,”** In *In Proceedings of the International Conference on Shape Modeling and Applications (SMI)*, pp. 124--133. June, 2005.

[Moo2005a] S.M. Moore, R.E. Debski, B. Ellis, P.J. McMahon, J.A. Weiss.
**“All Three Regions of the Inferior Glenohumeral Ligament Contribute to Anterior Stability,”** In *Proceedings, 51st Annual Orthopaedic Research Society Meeting*, Vol. 30, pp. 804. 2005.

[Nat2005a] V. Natarajan, V. Pascucci.
**“Volumetric Data Analysis Using Morse-Smale Complexes,”** In *Proceedings of the International Conference Shape Modeling and Applications*, Edited by A.G. Belyaev and A.A. Pasko and M. Spagnuolo, *IEEE Computer Society*, pp. 320--325. June, 2005.

[Pal2005a] R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby.
**“Gauss: A Framework for Verifying Scientific Computing Software,”** In *Proceeding of the Software Model Checking Workshop*, Edinburgh, Scotland, July, 2005.

[Piz2005a] S.M. Pizer, P.T. Fletcher, S. Joshi, A.G. Gash, J. Stough, A. Thall, G. Tracton, E. Chaney.
**“A Method and Software for Segmentation of Anatomic Object Ensembles by Deformable M-Reps,”** In *Med Phys*, Vol. 32, No. 5, pp. 1335--1345. May, 2005.

[Piz2005b] S.M. Pizer, J.Y. Jeong, C. Lu, K. Muller, S. Joshi.
**“Estimating the Statistics of Multi-Object Anatomic Geometry Using Inter-Object Relationships,”** In *Proceedings of International Workshop on Deep Structure, Singularities and Computer Vision (DSSCV)*, Edited by O.F. Olsen and L. Florack and A Kuijper, pp. 60--71. June, 2005.

[Ram2005a] M. Ramanath, L. Zhang, J. Freire, J. Haritsa.
**“IMAX: Incremental Maintenance of Schema-Based XML Statistics,”** In *International Conference on Data Engineering (ICDE)*, IEEE Computer Society, Los Alamitos, CA, USA pp. 273--284. 2005.

ISSN: 1084-4627

[Ree2005a] D. Reed, R. Bajcsy, J.M. Griffiths, J. Dongarra, C.R. Johnson.
**“Computational Science: Ensuring America's Competitiveness,”** Note: *President's Information Technology Advisory Committee (PITAC)*, June, 2005.

[Sac2005a] F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson.
**“Advanced Modeling and Visualization of Cardiothoracic Electrical Fields,”** In *Proceedings of 13th Medicine Meets Virtual Reality (MMVR13)*, 2005.

[Sam2005a] A.A. Samsonov, E.V.R. DiBella, P. Kellman, E.G. Kholmovski, C.R. Johnson.
**“Adaptive k-t BLAST/k-t SENSE for Accelerating Cardiac Perfusion MRI,”** In *c-SCMR2005*, pp. 277--278. 2005.

[Sam2005b] A.A. Samsonov, E.G. Khölmovski, C.R. Johnson.
**“POCS-Enhanced Parallel MRI Correction of MR Image Artifacts,”** In *Proc. Intl. Soc. Mag. Reson.*, Note: *Abstract*, pp. 690. 2005.

[Sch2005a] G. Scheuermann, X. Tricoche.
**“Topological Methods for Flow Visualization,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 341--356. 2005.

ISBN: 0-12-387582-X

[Sch2005b] C. Scheidegger, S. Fleishman, C.T. Silva..
**“Triangulating Point-Set Surfaces With Bounded Error,”** In *Proceedings of the Third Eurographics/ACM Symposium on Geometry Processing*, Eurographics Association, pp. 63--72. 2005.

ISBN: 3-905673-24-X

[Sch2005c] C. Scheidegger, J. Comba, R. Cunha..
**“Practical CFD Simulations on the GPU Using SMAC,”** In *Computer Graphics Forum*, Vol. 24, No. 4, pp. 715--728. 2005.

[Ser2005a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Bayesian Solutions and Performance Analysis in Bioelectric Inverse Problems,”** In *j-BME*, Vol. 52, No. 6, pp. 1009--1020. June, 2005.

[Shi2005a] Y.T. Shiu, J.A. Weiss, J.B. Hoying, M.N. Iwamoto, I.S. Joung, C.T. Quam.
**“The Role of Mechanical Stresses in Angiogenesis,”** In *j-CRBME*, Vol. 33, No. 5, pp. 431--510. 2005.

[Sil2005a] C.T. Silva, J.L.D. Comba, S.P. Callahan, F.F. Bernardon.
**“A Survey of GPU-Based Volume Rendering of Unstructured Grids,”** In *Revista de Informatica Teorica e Aplicada*, Vol. 12, No. 2, pp. 9--29. 2005.

ISSN: 01034308

[Sir2005a] S. Sirisup, G.E. Karniadakis, D. Xiu, I.G. Kevrekidis.
**“Equation-free/Galerkin-free POD-assisted Computation of Incompressible Flows,”** In *Journal of Computational Physics*, Vol. 207, No. 2, pp. 568--587. 2005.

DOI: 10.1016/j.jcp.2005.01.024

[Sti2005a] J.G. Stinstra, D.M. Weinstein, B. Hopenfeld, C.S. Henriquez, R.S. MacLeod.
**“Software Challenges in the New Field of Integrated Cardiac Models,”** In *c-BEMNFSI2005*, Vol. 7, pp. 195--198. 2005.

[Sti2005b] J.G. Stinstra, B. Hopenfeld, R.S. MacLeod.
**“On the Passive Cardiac Conductivity,”** In *j-ABE*, Vol. 33, No. 12, pp. 1743--1751. 2005.

[Sti2005c] J.G. Stinstra, S. Shome, B. Hopenfeld, R.S. MacLeod.
**“Modelling Passive Cardiac Conductivity During Ischaemia,”** In *Med. Biol. Eng. Comput.*, Vol. 43, No. 6, pp. 776--782. 2005.

[Sun2005a] Q. Sun, R.T. Burks, P.E. Greis, N.S. Phatak, J.A. Weiss.
**“Noninvasive Measurement of Meniscus Strain Using Hyperelastic Warping,”** In *51st Annual Orthopaedic Research Society Meeting*, Vol. 30, pp. 478. 2005.

[Suz2005a] T. Suzuki, S. Takahashi, J. Shepherd.
**“An Interior Surface Generation Method for All-Hexahedral Meshing,”** In *Proceedings of The 14th International Meshing Roundtable*, Springer-Verlag, pp. 377--398. September, 2005.

[Tac2005a] B. Taccardi, B.B. Punske, F. Sachse, X. Tricoche, P. Colli-Franzone, L.F. Pavarino, C. Zabawa.
**“Intramural Activation and Repolarization Sequences in Canine Ventricles. Experimental and Simulation Studies,”** In *j-JE*, Vol. 38, No. 4, pp. 131-137. 2005.

[Tas2005a] T. Tasdizen, S.P. Awate, R.T. Whitaker, N. Foster.
**“MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach,”** In *c-MICCAI2005*, pp. 517--525. 2005.

PubMed ID: 16685999

[Tas2005b] T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones.
**“Enhancement of Cell Boundaries in Transmission Micropscopy Images,”** In *c-ICIP*, Vol. 2, pp. 129--132. 2005.

[Tas2005c] T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones.
**“Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images,”** SCI Institute Technical Report, No. UUSCI-2005-008, *University of Utah*, 2005.

[Tas2005d] T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones.
**“Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images,”** SCI Institute Technical Report, No. UUSCI-2005-007, *University of Utah*, 2005.

[Ter2005a] T. Terriberry, S. Joshi, G. Gerig.
**“Hypothesis Testing with Nonlinear Shape Models,”** In *Information Processing in Medical Imaging (IPMI)*, Edited by G Christensen and M Sonka, pp. 15--26. July, 2005.

[Tri2005a] X. Tricoche, C. Garth, G. Scheuermann.
**“Fast and Robust Extraction of Separation Line Features,”** In *Scientific Visualization: The Visual Extraction of Knowledge from Data*, Edited by G.-P. Bonneau and T. Ertl and G.M. Nielson, Springer, pp. 249--264. 2005.

[Ues2005a] D. Uesu, L. Bavoil, S. Fleishman, J. Shepherd, C.T. Silva.
**“Simplication of Unstructured Tetrahedral Meshes by Point Sampling,”** In *Proceedings of the 2005 International Workshop on Volume Graphics*, pp. 157--238. 2005.

[Ver2005a] A.I. Veress, G.T. Gullberg, J.A. Weiss.
**“Measurement of Strain in the Left Ventricle with Cine-MRI and Deformable Image Registration,”** In *j-JBE*, Vol. 127, No. 7, pp. 1195--1207. July 21, 2005.

[Wal2005a] I. Wald, C. Benthin, A. Efremov, T. Dahmen, J. Gunther, A. Dietrich, V. Havran, H. Seidel, P. Slusallek.
**“A Ray Tracing based Virtual Reality Framework for Industrial Design,”** SCI Institute Technical Report, No. UUSCI-2005-009, *University of Utah*, 2005.

[Wal2005b] I. Wald.
**“DIRmaps : Discretized Incident Radiance Maps for High-Quality Global Illumination Walkthroughs in Complex Environments,”** SCI Institute Technical Report, No. UUSCI-2005-010, *University of Utah*, 2005.

[Wei2005a] D.M. Weinstein, S.G. Parker, J. Simpson, K. Zimmerman, G.M. Jones.
**“Visualization in the SCIRun Problem-Solving Environment,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 615--632. 2005.

ISBN: 0-12-387582-X

[Wei2005b] J.A. Weiss, B.J. Maakestad.
**“Permeability of Human Medial Collateral Ligament in Compression Transverse to the Collagen Fiber Direction,”** In *Journal of Biomechanics*, Vol. 39, No. 2, pp. 276--283. 2005.

[Wei2005c] J.A. Weiss, J.C. Gardiner, B.J. Ellis, T.J. Lujan, N.S. Phatak.
**“Three-Dimensional Finite Element Modeling of Ligaments: Technical Aspects,”** In *Medical Engineering and Physics*, Vol. 27, No. 10, Note: *Invited paper for special issue: Advances in the Finite Element Modeling of Soft Tissue Deformation*, pp. 845--861. May 21, 2005.

[Whi2005a] R.T. Whitaker.
**“Isosurfaces and Level-Sets,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 97--123. 2005.

ISBN: 0-12-387582-X

[Wol2005b] C. H. Wolters, A. Anwander, X. Tricoche, S. Lew, C.R. Johnson.
**“Influence of Local and Remote White Matter Conductivity Anisotropy for a Thalamic Source on EEG/MEG Field and Return Current Computation,”** In *Int.Journal of Bioelectromagnetism*, Vol. 7, No. 1, pp. 203--206. 2005.

[Xiu2005a] D. Xiu, S.J. Sherwin, S. Dong, G.E. Karniadakis.
**“Strong and Auxiliary Forms of the Semi-Lagrangian Method for Incompressible Flows,”** In *Journal of Scientific Computing*, Vol. 25, No. 1-2, pp. 323-346. 2005.

DOI: Journal of Scientific Computing

[Xiu2005b] D. Xiu, I.G. Kevrekidis.
**“Equation-free, Multiscale Computation for Unsteady Random Diffusion,”** In *SIAM Journal on Multiscale Modeling and Simulation*, Vol. 4, No. 3, pp. 915--935. 2005.

DOI: 10.1137/040615006

[Xiu2005c] D. Xiu, J.S. Hesthaven.
**“High Order Collocation Methods for Differential Equations with Random Inputs,”** In *SIAM Journal on Scientific Computing*, Vol. 27, No. 3, pp. 1118--1139. 2005.

DOI: 10.1137/040615201

[Xiu2005d] D. Xiu, R. Ghanem, I.G. Kevrekidis.
**“An Equation-free, Multiscale Approach to Uncertainty Quantification,”** In *IEEE Computing in Science and Engineering Journal (CiSE)*, Vol. 7, No. 3, pp. 16--23. 2005.

DOI: 10.1109/MCSE.2005.46

[Yil2005a] B. Yilmaz, R.S. MacLeod, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Training Set Selection for Statistical Estimation of Epicardial Activation Mapping from Intravenous Multielectrode Catheters,”** In *j-BME*, pp. (in press). 2005.

[Yil2005b] B. Yilmaz, R.S. MacLeod, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Venous Catheter Based Mapping of Ectopic Epicardial Activation: Training Data Set Selection for Statistical Estimation,”** In *IEEE Trans Biomed Eng*, Vol. 52, No. 11, pp. 1823--1831. November, 2005.

[Yoo2005a] S.-E. Yoon, P. Lindstrom, V. Pascucci, D. Manocha.
**“Cache-Oblivious Mesh Layouts,”** In *ACM Transactions on Graphics: ACM SIGGRAPH 2005 Papers*, Vol. 24, No. 3, pp. 886--893. August, 2005.

[Yoo2005b] S.-E. Yoon, P. Lindstrom, V. Pascucci, D. Manocha.
**“Cache-Oblivious Layouts of Polygonal Meshes,”** In *Proceedings of Massive 2005 (workshop on Massive Geometric Data Sets)*, pp. 29--33. 2005.

[Yos2005a] Z. Yosibash, R.M. Kirby.
**“Dynamic Response of Various Von-Karman Non-Linear Plate Models and their 3-D Counterparts,”** In *International Journal of Solids and Structures*, Vol. 42, pp. 2517--2531. 2005.

[Zha2005a] S. Zhang, D.H. Laidlaw, G. Kindlmann.
**“Diffusion Tensor MRI Visualization,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 327--340. 2005.

ISBN: 0-12-387582-X

2004

[Alt2004a] O. Alter, G.H. Golub.
**“Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription,”** In *Proceedings of the National Academy of Sciences*, Vol. 101, No. 47, Proceedings of the National Academy of Sciences, pp. 16577--16582. November, 2004.

DOI: 10.1073/pnas.0406767101

[Alt2004b] O. Alter, G.H. Golub, P.O. Brown, D. Botstein.
**“Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models,”** In *Proceedings of the Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer*, Vol. 15, Edited by 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, 2004.

[Ame2004a] S. Amer-Yahia, F. Du, J. Freire.
**“A Comprehensive Solution to the XML-to-Relational Mapping Problem,”** In *Proceedings of the 6th Annual ACM International Workshop on Web Information and Data Management*, Washington DC, USA, pp. 31--38. 2004.

ISBN: 1-58113-978-0

[And2004a] A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss.
**“Development and Validation of a Subject-Specific Finite Element Model of the Pelvis: Assessment of Model Sensitivity,”** In *c-CMBBE2004*, pp. (6 pages). 2004.

[And2004b] A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss.
**“A Subject-Specific Finite Element Model of the Pelvis Accurately Predicts Cortical Strains Under Acetabular Loading,”** In *c-ORS2004*, San Francisco, CA, Vol. 29, pp. 1334. March, 2004.

[Bar2004a] D. Barbosa, J. Freire, A. Mendelzon.
**“Information Preservation in XML-to-Relational Mappings,”** In *Database and XML Technologies*, Lecture Notes in Computer Science (LNCS), Vol. 3186/2004, pp. 66--81. 2004.

ISBN: 978-3-540-22969-8

[Ber2004a] F.F. Bernardon, C.A. Pagot, J.L.D. Comba, C.T. Silva.
**“GPU-based Tiled Ray Casting using Depth Peeling,”** SCI Institute Technical Report, No. UUSCI-2004-006, *University of Utah*, 2004.

[Ber2004b] M. Berzins.
**“Variable Order Finite Elements and Positivity Preservation for Hyperbolic PDEs,”** In *Applied Numerical Mathematics*, Vol. 48, No. 3-4, pp. 253--439. March, 2004.

[Bor2004a] R. Borgo, V. Pascucci, R. Scopigno.
**“Massive Data Pre-Processing with a Cluster Based Approach,”** In *Proceedings of the 2004 Eurographics Symposium on Parallel Graphics and Visualization (EG-PGV-04)*, Note: *UCRL-PROC-208678*, Eurographics Association, Aire-la-Ville, Switzerland pp. 67--74. June, 2004.

[Bre2004a] P.-T. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci.
**“A Topological Hierarchy for Functions on Triangulated Surfaces,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 10, No. 4, Note: *UCRL-JRNL-208700*, pp. 385-396. July/August, 2004.

[Bre2004c] P.-T. Bremer, V. Pascucci, B. Hamann.
**“Maximizing adaptivity in hierarchical topological models,”** In *Trends in Software*, Note: *UCRL-BOOK-200013*, Edited by T. Moeller and B. Hamann and B. Russell, Springer, pp. 121--130. January, 2004.

[Bro2004b] D.H. Brooks, A. Ghodrati, Y. Zhang, G. Tadmor, R.S. MacLeod.
**“Inverse Electrocardiography in the Framework of Dynamic Imaging Problems,”** In *c-EMBS2004*, San Francisco, CA, pp. 3565--3568. September, 2004.

[Bul2004a] E. Bullitt, M.G. Ewend, S. Aylward, W. Lin, G. Gerig, S. Joshi, I. Jung, K. Muller, J. Smith.
**“Abnormal Vessel Tortuosity as a Marker of Treatment Response of Malignant Gliomas: Preliminary Report,”** In *Technol Cancer Res Treat*, Vol. 3, No. 6, pp. 577--584. December, 2004.

[Cal2004a] S.P. Callahan, M. Ikits, J.L.D. Comba, C.T. Silva.
**“Hardware-Assisted Visibility Sorting for Unstructured Volume Rendering,”** SCI Institute Technical Report, No. UUSCI-2004-003, *University of Utah*, June, 2004.

[Cat2004a] J. Cates, A. Lefohn, R.T. Whitaker.
**“GIST: an Interactive, GPU-Based Level Set Segmentation Tool for 3D Medical Images,”** No. UUCS-04-007, *University of Utah School of Computing*, 2004.

[Cat2004b] J. Cates, R.T. Whitaker, G.M. Jones.
**“Case Study: An Evaluation of User-Assisted Hierarchical Watershed Segmentation,”** No. UUCS-04-006, *University of Utah School of Computing*, 2004.

[Cat2004c] J. Cates, A. Lefohn, R.T. Whitaker.
**“GIST: An Interactive, GPU-Based Level Set Segmentation Tool for 3D Medical Images,”** In *Medical Image Analysis*, Vol. 8, No. 3, pp. 217--231. September, 2004.

[Cha2004a] E. Chaney, S. Pizer, S. Joshi, R. Broadhurst, P.T. Fletcher, G. Gash, Q. Han, J.Y. Jeong, C. Lu, D. Merck, J. Stough, G. Tracton, M.D.J. Bechtel, J. Rosenman, Y.Y. Chi, K. Muller.
**“Automatic Male Pelvis Segmentation from CT Images via Statistically Trained Multi-Object Deformable M-rep Models,”** In *Presented at American Society for Therapeutic Radiology and Oncology (ASTRO)*, 2004.

[Che2004a] A.B. Cheryauka, J.N. Lee, A.A. Samsonov, M. Defrise, G.T. Gullberg.
**“MRI Diffusion Tensor Reconstruction with PROPELLER Data Acquisition,”** In *j-JMRI*, Vol. 22, No. 2, pp. 139--148. 2004.

[Col2004a] M. Cole, F.B. Sachse, D.M. Weinstein, S.G. Parker, R.M. Kirby.
**“A Software Framework for Solving Problems of Bioelectricity Applying High-Order Finite Elements,”** In *c-EMBS2004*, Vol. 1, pp. 821--824. 2004.

[Col2004b] K. Cole-McLaughlin, V. Pascucci.
**“Multiresolution Representation of Topology,”** In *Proceedings of the 4th IASTED International Conference on Visualization, Imaging, And Image Processing (VIIP 2004)*, Marbella, Spain, Vol. 2004, Note: *UCRL-PROC-208680*, pp. 282--289. September, 2004.

[Com2004a] J.L.D. Comba, J.S.B. Mitchell, C.T. Silva.
**“On the Convexification of Unstructured Grids From A Scientific Visualization Perspective,”** SCI Institute Technical Report, No. UUSCI-2004-004, *University of Utah*, 2004.

[Cse2004a] J.G. Csernansky, L. Wang, S.C. Joshi, J.T. Ratnanather, M. Miller.
**“Computational Anatomy and Neuropsychiatric Disease: Probabilistic Assessment of Variation and Statistical Inference of Group Difference, Hemispheric Asymmetry, and Time-Dependent Change,”** In *Neuroimage*, Vol. 23 Suppl. 1, pp. S56--S68. 2004.

[Dam2004a] Kostadin Damevski, Steven Parker.
**“Imprecise Exceptions in Distributed Parallel Components,”** In *c-EUP2004*, Lecture Notes in Computer Science, Vol. 3149, pp. 108--116. August/September, 2004.

[Dam2004b] E. Dam, P.T. Fletcher, S.M. Pizer, G. Tracton, J. Rosenman.
**“Prostate Shape Modeling based on Principal Geodesic Analysis Bootstrapping,”** In *Medical Image Computing and Computer-Assisted Intervention (MICCAI)*, pp. 1008--1016. 2004.

[Das2004a] R. Das, L. Krishnan, C. Evensen, J.A. Weiss.
**“MCL Healing at Early Time Points: Biomechanics and Gene Expression,”** In *c-ORS2004*, San Francisco, CA, Vol. 29, pp. 892. March, 2004.

[Dav2004a] B. Davis, D. Prigent, J. Bechtel, J. Rosenman, D.M. Lovelock, S. Joshi.
**“Accommodating Bowel Gas in Large Deformation Image Registration for Adaptive Radiation Therapy of the Prostate,”** In *Proceedings of AAPM Annual Meeting*, July, 2004.

[Dav2004b] B. Davis, P. Lorenzen, S. Joshi.
**“Large Deformation Minimum Mean Squared Error Template Estimation for Computational Anatomy,”** In *Proceedings of the International Symposium on Biomedical Imaging (ISBI)*, Piscataway, NJ, pp. 173--176. April, 2004.

[Dem2004a] D.E. DeMarle, C.P. Gribble, S.G. Parker.
**“Memory-Savvy Distributed Interactive Ray Tracing,”** In *c-EGPGV2004*, Edited by Dirk Bartz and Bruno Raffin and Han-Wei Shen, 2004.

[Det2004a] C. DeTar, A.L. Fogelson, C.R. Johnson, C.A. Sikorski, T. Truong.
**“Computational Engineering and Science Program at the University of Utah,”** In *c-ICCS2004*, Lecture Notes in Computer Science (LNCS) 3039, part 4, Edited by M. Bubak et al, pp. 1202--1209. 2004.

[Du2004a] F. Du, S. Amer-Yahia, J. Freire.
**“ShreX: Managing XML Documents in Relational Databases,”** In *Proceedings of the 13th International Conference on Very Large Data Bases*, Vol. 30, pp. 1297--1300. 2004.

ISBN: 0-12-088469-0

[Ede2004a] H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci.
**“Local and Global Comparison of Continuous Functions,”** In *Proceedings of the IEEE Conference on Visualization (VIS-04)*, Note: *UCRL-PROC-208677*, pp. 275--280. October, 2004.

[Ede2004b] H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci.
**“Time-Varying Reeb Graphs for Continuous Space-Time Data,”** In *SCG '04: Proceedings of the Twentieth Annual Symposium on Computational Geometry*, Brooklyn, New York, USA, Note: *UCRL-PROC-208697*, ACM Press, pp. 366--372. 2004.

ISBN: 1-58113-885-7

[Fle2004a] P.T. Fletcher, C. Lu, S.M. Pizer, S. Joshi.
**“Principal Geodesic Analysis for the Study of Nonlinear Statistics of Shape,”** In *IEEE Trans Med Imaging*, Vol. 23, No. 8, pp. 995--1005. August, 2004.

[Fle2004b] P.T. Fletcher, S. Joshi.
**“Principal Geodesic Analysis on Symmetric Spaces: Statistics of Diffusion Tensors,”** In *Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis*, Springer-Verlag, Lecture Notes In Computer Science, Vol. 3117, pp. 87--98. 2004.

DOI: 10.1109/TMI.2004.831793

[Fle2004c] P.T. Fletcher.
**“Statistical Variability in Nonlinear Spaces: Application to Shape Analysis and DT-MRI,”** Note: *Ph.D. Thesis*, *University of North Carolina Department of Computer Science*, August, 2004.

[Fre2004a] J. Freire, M. Benedikt.
**“Managing XML Data: An Abridged Overview,”** In *Computing in Science and Engineering*, Vol. 6, No. 4, IEEE Computer Society, pp. 12--19. 2004.

ISSN: 1521-9615

[Fre2004b] J. Freire, M. Ramanath, L. Zhang.
**“A Flexible Infrastructure for Gathering XML Statistics and Estimating Query Cardinality,”** In *Proceedings of the 20th International Conference on Data Engineering*, pp. 857. 2004.

ISBN: 0-7695-2065-0

[Gar2004a] C. Garth, X. Tricoche, G. Scheuermann.
**“Tracking of Vector Field Singularities in Unstructured 3D Time-Dependent Datasets,”** In *c-VIS2004*, pp. 329--336. 2004.

[Gar2004b] C. Garth, X. Tricoche, T. Salzbrunn, T. Bobach, G. Scheuermann.
**“Surface Techniques for Vortex Visualization,”** In *Proceedings of Joint Eurographics - IEEE TCVG Symposium on Visualization*, pp. 155--164. May, 2004.

[Gho2004a] A. Ghodrati, D.H. Brooks, R.S. MacLeod.
**“On Selecting and Using Reduced Sets of Leads for Electrocardiographic Imaging Using Reconstruction-Quality Criteria,”** In *Proceedings of The SIAM Conference on Imaging Science 2004*, Salt Lake City, UT, Note: *abstract.*, May, 2004.

[Gho2004b] A. Ghodrati, F. Calderero, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“A Level Sets Algorithm for the Inverse Problem of Electrocardiography,”** In *Proceedings of the Asilomar Conf. on Sig. and Sys.*, Vol. 2, pp. 1590--1594. November, 2004.

[Goo2004a] C.E. Goodyer, R. Fairlie, D.E. Hart, M. Berzins, L.E. Scales.
**“Calculation of Friction in Steady-State and Transient EHL Simulations Transient Processes in Tribology,”** In *Transient Processes in Tribology: Proceeding of the 31st Leeds-Lyon Symposium on Tribology*, Edited by A.A. Lubrecht and G. Dalmaz, Elsevier, pp. 579--590. 2004.

[Gri2004a] C. Gribble, S.G. Parker, C.D. Hansen.
**“Interactive Volume Rendering of Large Datasets Using the Silicon Graphics Onyx4 Visualization System,”** No. UUCS-04-003, *University of Utah School of Computing*, January 27th, 2004.

[Gui2004a] J.E. Guilkey, Y. Zhang, J.B. Hoying, J.A. Weiss.
**“Mechanical Simulation of Multicellular Structures with the Material Point Method,”** In *Proc 6th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering*, Madrid, Spain, Note: *Winner of the Taylor and Francis Prize for Outstanding Innovation in Computer Methods in Biomechanics and Biomedical Engineering*, March, 2004.

[Han2004a] Q. Han, C. Lu, G. Liu, S.M. Pizer, S. Joshi, A. Thall.
**“Representing Multi-Figure Anatomical Objects,”** In *Proceedings of the International Symposium on Biomedical Imaging (ISBI)*, Piscataway, NJ, pp. 1251--1254. 2004.

[Hen2004a] C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson.
**“Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart,”** In *Cardiac Electrophysiology: From Cell to Bedside*, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.

[Hop2004a] B. Hopenfeld, J.G. Stinstra, R.S. MacLeod.
**“Mechanism for ST Depression Associated with Contiguous Subendocardial Ischemia,”** In *j-JCE*, Vol. 15, No. 10, pp. 1200--1206. 2004.

[Iki2004a] M. Ikits, J.M. Kniss, A.E. Lefohn, C.D. Hansen.
**“Volume Rendering Techniques,”** In *GPU Gems: Programming Techniques, Tipsand Tricks for Real-Time Graphics*, Edited by Randima Fernando, Addison Wesley, pp. 667--692. 2004.

[Jeo2004a] Won-Ki Jeong, Tolga Tasdizen, Ross Whitaker.
**“Anisotropic Diffusion of Height Field Data using Multigrid Solver on GPU,”** In *Proceedings ACM Workshop on General Purpose Computing on Graphics Processors, 2004*, 2004.

[Joh2004a] C.R. Johnson.
**“Top Scientific Visualization Research Problems,”** In *IEEE Computer Graphics and Applications: Visualization Viewpoints*, Vol. 24, No. 4, pp. 13--17. July/August, 2004.

[Joh2004b] C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein.
**“Biomedical Computing and Visualization Software Environments,”** In *j-ACM-COM*, Vol. 47, No. 11, pp. 64--71. 2004.

[Jos2004a] S. Joshi, B. Davis, M Jomier, G. Gerig.
**“Unbiased Diffeomorphic Atlas Construction for Computational Anatomy,”** In *Neuroimage*, Vol. 23 Suppl. 1, pp. S151--S160. 2004.

[Kad2004a] A. Kadlag, A.V. Wanjari, J. Freire, J. Haritsa.
**“Supporting Exploratory Queries in Databases,”** In *Database Systems for Advanced Applications*, Lecture Notes in Computer Science (LNCS), Vol. 2973/2004, pp. 25-26. 2004.

[Kin2004a] G Kindlmann.
**“Superquadric Tensor Glyphs,”** In *c-VISSYM2004*, pp. 147--154. May, 2004.

[Kin2004b] G.L. Kindlmann, D.M. Weinstein, A.D. Lee, A.W. Toga, P.M. Thompson.
**“Visualization of Anatomic Covariance Tensor Fields,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference*, 2004.

[Kin2004c] G. Kindlmann, A. L. Alexander, M. Lazar, J. Lee, T. Tasdizen, R.T. Whitaker.
**“An Algorithm for Moment-Based Global Registration of Echo Planar Diffusion-Weighted Images,”** In *Proceedings of 12th Annual ISMRM*, pp. 2200. 2004.

[Kin2004d] G. Kindlmann.
**“Visualization and Analysis of Diffusion Tensor Fields,”** Technical Report, No. UUCS-04-014, Note: *PhD Thesis*, *School of Computing, University of Utah*, 2004.

[Kir2004a] R.M. Kirby, Z. Yosibash.
**“Solution of Von-Karman Dynamic Non-linear Plate Equations Using a Pseudo-spectral Method,”** In *j-CMAME*, Vol. 193, No. 6-8, pp. 575-599. 2004.

[Kir2004b] R.M. Kirby, G.E. Karniadakis.
**“Spectral Element and hp Methods,”** In *Encyclopedia of Computational Mechanics*, Vol. 3, Ch. 3, Edited by E. Stein and R. de Borst and T.J.R. Hughes, John Wiley and Sons, NY, pp. 61--88. 2004.

[Kir2004d] R.M. Kirby, Z. Yosibash.
**“Solution of von-Karman Dynamic Non-Linear Plate Equations Using a Pseudo-Spectral Method,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 193, No. 6-8, pp. 575--599. 2004.

[Kni2004a] J.M. Kniss, J.P. Schulze, U. Wössner, P. Winkler, U. Lang, C.D. Hansen.
**“Medical Applications of Multi-field Volume Rendering and VR Techniques,”** In *c-VISSYM2004*, pp. 249--254. 2004.

[Kri2004a] L. Krishnan, J.A. Weiss, M.D. Wessman MD, J.B. Hoying.
**“Design and Application of a Test System for Viscoelastic Characterization of Collagen Gels,”** In *j-TE*, Vol. 10, No. (1-2), pp. 241--252. 2004.

[Lan2004a] D. Laney, V. Pascucci.
**“Progressive Compression of Volumetric Subdivision Meshes,”** In *Proceedings of the International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT)*, Note: *UCRL-CONF-203679*, pp. 293--300. September, 2004.

[Lef2004a] A.E. Lefohn, J.M. Kniss, C.D. Hansen, R.T. Whitaker.
**“A Streaming Narrow-Band Algorithm: Interactive Deformation and Visualization of Level Sets,”** In *j-TVCG*, pp. 422--433. 2004.

[Lin2004a] L. Linsen, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy.
**“Wavelet-Based Multiresolution with N-th-Root-of-2,”** In *Geometric Modeling, Dagstuhl 2002. Proceedings of the Dagstuhl Seminar on Geometric Modeling*, Note: *UCRL-PROC-208699*, Dagstuhl, Germany May, 2004.

[Lin2004b] L. Linsen, J.T. Gray, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy.
**“Hierarchical Large-scale Volume Representation with 3rd-root-of-2 Subdivision and Trivariate B-spline Wavelets,”** In *Geometric Modeling for Scientific Visualization*, Edited by G. Brunnett and B. Hamann and H. Mueller, Springer-Verlag, pp. 359--377. 2004.

DOI: 10.1007/978-3-662-07443-5_22

[Lin2004c] L. Linsen, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy.
**“Wavelet-Based Multiresolution with n-th-root-of-2,”** In *Proceedings of Geometric Modeling, Dagstuhl 2002*, Dagstuhl, Germany, Note: *UCRL-PROC-208699*, May, 2004.

[Liv2004a] Y. Livnat, X. Tricoche.
**“Interactive Point Based Isosurface Extraction,”** In *c-VIS2004*, pp. 457--464. 2004.

[Lor2004a] P. Lorenzen, B. Davis, S. Joshi.
**“Model Based Symmetric Information Theoretic Large Deformation Multi-Modal Image Registration,”** In *Proceedings of the International Symposium on Biomedical Imaging (ISBI)*, Piscataway, NJ, pp. 720--723. April, 2004.

[Luj2004a] T.J. Lujan, M.S. Dalton, S.P. Lake, B.J. Ellis, T.D. Rosenberg, J.A. Weiss.
**“ACL Injury Alters MCL Strain During Anterior-Posterior but not Varus-Valgus Loading,”** In *c-ORS2004*, San Francisco, CA, Vol. 29, pp. 1272. March, 2004.

[Mac2004a] R.S. Macleod, D.M. Weinstein, J.D. de St. Germain, D.H. Brooks, C.R. Johnson, S.G. Parker.
**“SCIRun/BioPSE: Integrated Problem Solving Environment for Bioelectric Field Problems and Visualization,”** In *Proceedings of the Int. Symp. on Biomed. Imag.*, Arlington, Va, pp. 640--643. April, 2004.

[Mag2004a] M. Magnor, G. Kindlmann, C.D. Hansen, N. Duric.
**“Constrained Inverse Volume Rendering for Planetary Nebulae,”** In *c-VIS2004*, pp. 83--90. 2004.

[Mas2004a] A. Mascarenhas, M. Isenburg, V. Pascucci, J. Snoeyink.
**“Encoding Volumetric Meshes For Streaming Isosurface Extraction,”** In *Proceedings of the International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT)*, Note: *UCRL-PROC-208696*, pp. 293--300. September, 2004.

[Mcc2004a] P. McCormick, J. Inman, J. Ahrens, G. Roth, C.D. Hansen.
**“Hardware-Accelerated System for Quantitatively Driven Visualization and Analysis,”** In *c-VIS2004*, pp. 171--178. 2004.

[Pao2004a] A. Paoluzzi, V. Pascucci, G. Scorzelli.
**“Progressive BSP Representation and Boolean Operations for Dimension-Independent Polyhedra,”** In *ACM Symposium on Solid Modeling*, Note: *UCRL-PROC-208679*, pp. 203-211. June, 2004.

[Pas2004b] V. Pascucci.
**“Isosurface Computation Made Simple: Hardware Acceleration, Adaptive Refinement and Tetrahedral Stripping,”** In *Proceedings of the Joint Eurographics - IEEE TVCG Symposium on Visualization (VisSym)*, Note: *UCRL-CONF-202459*, pp. 293--300. May, 2004.

[Pes2004a] S. Pesco, P. Lindstrom, V. Pascucci, C.T. Silva.
**“Implicit Occluders,”** In *c-VVIS2004*, pp. 47--54. 2004.

[Pha2004a] N.S. Phatak, J.L. McCann, Q. Sun, S.E. Kim, D.L. Parker, E.K. Jeong, R.K. Sanders, A.I. Veress, J.A. Weiss.
**“Noninvasive Measurement of Ligament Strain,”** In *c-ORS2004*, San Francisco, CA, Vol. 29, pp. 893. March, 2004.

[Ram2004a] S.D. Ramsey, J.T. Johnson III, C.D. Hansen.
**“Adaptive Temporal Tone Mapping,”** In *Computer Graphics and Imaging*, pp. 124--128. 2004.

[Sac2004b] F. B. Sachse.
**“Computational Cardiology: Modeling of Anatomy, Electrophysiology, and Mechanics,”** LNCS 2966, Springer, Berlin, Heidelberg, New York 2004.

[Sam2004a] A.A. Samsonov, C.R. Johnson..
**“Removal of Intensity Bias in Magnitude Spin-Echo MRI Images by Nonlinear Diffusion Filtering,”** In *c-MI2004*, San Diego, CA, Vol. 5370, pp. 743--752. 2004.

[Sam2004c] A.A. Samsonov, C.R. Johnson.
**“Non-Cartesian POCSENSE,”** In *c-ISMRM2004*, Kyoto, Japan, pp. 2648. 2004.

[Sam2004d] A.A. Samsonov, C.R. Johnson.
**“Unbiased Nonlinear Filtering of Fast Spin Echo MRI Images,”** In *c-ISMRM2004*, Kyoto, Japan, pp. 760. 2004.

[Sam2004e] A.A. Samsonov, E.G. Kholmovski, C.R. Johnson.
**“Phase-Constrained Reconstruction of Sensitivity-Encoded MRI Data with POCSENSE,”** In *c-ISMRM2004*, Kyoto, Japan, pp. 2647. 2004.

[Sam2004f] A.A. Samsonov, C.R. Johnson.
**“Noise-Adaptive Nonlinear Diffusion Filtering of MR Images with Spatially Varying Noise Levels,”** In *j-MRM*, Vol. 52, pp. 798--806. 2004.

[Sam2004g] A.A. Samsonov, E.G. Kholmovski, D.L. Parker, C.R. Johnson.
**“POCSENSE: POCS-based reconstruction for sensitivity encoded MRI,”** In *j-MRM*, Vol. 52, pp. 1397--1406. 2004.

[Sam2004h] A.A. Samsonov, C.R. Johnson.
**“Multicoil MRI Artifacts Correction Using Parallel Pocs,”** In *c-ISMRM2004*, 2004.

[San2004a] A.R. Sanderson, C.R. Johnson, R.M. Kirby.
**“Display of Vector Fields Using a Reaction Diffusion Model,”** In *c-VIS2004*, pp. 115--122. 2004.

[Sch2004a] U. Schmitt, C.H. Wolters, A. Anwander, T. Knoesche.
**“STR: A New Spatio-Temporal Approach for Accurate and Efficient Current Density Reconstruction,”** In *c-BIOMAG2004*, pp. 591--592. 2004.

[She2004a] H.-W. Shen, G.-S. Li, U. Bordoloi.
**“Interactive Visualization of Three-Dimensional Vector Fields with Flexible Appearance Control,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 10, No. 4, pp. 434--445. 2004.

[Sim2004a] J. Simpson, S.J. Balling.
**“ANNOT3D and Packaging of 3D Visualizations for Educational Purposes,”** In *c-MMVR2004*, Newport Beach, CA, pp. (in press). January, 2004.

[Sta2004a] K.J. Stabile, J. Pfaeffle, J.A. Weiss, K. Fisher, M.M. Tomaino.
**“Bi-directional Mechanical Properties of the Human Forearm Interosseous Ligament,”** In *j-OR*, Vol. 22, No. 3, pp. 607--612. 2004.

[Ste2004a] F. Stenger, T. Cook, R.M. Kirby.
**“Sinc Solution of Biharmonic Problems,”** In *Canadian Applied Mathematics Quarterly*, Vol. 12, No. 3, pp. 391--413. 2004.

[Tas2004a] T. Tasdizen, D.M. Weinstein, J.N. Lee.
**“Automatic Tissue Classification for the Human Head from Multispectral MRI,”** SCI Institute Technical Report, No. UUSCI-2004-001, *University of Utah*, March, 2004.

[Tas2004b] T. Tasdizen, R.T. Whitaker.
**“Higher-order nonlinear priors for surface reconstruction,”** In *j-PAMI*, Vol. 26, No. 7, pp. 878--891. July, 2004.

[Tas2004c] T. Tasdizen, R.T. Whitaker.
**“An Efficient, Geometric Multigrid Solver for the Anisotropic Diffusion Equation in Two and Three Dimensions,”** SCI Institute Technical Report, No. UUSCI-2004-002, *University of Utah*, June, 2004.

[Tri2004a] X. Tricoche, C. Garth, G. Kindlmann, E. Deines, G. Scheuermann, Markus Ruetten, Charles D. Hansen.
**“Visualization of Intricate Flow Structures for Vortex Breakdown Analysis,”** In *c-VIS2004*, pp. 187--194. 2004.

[Tri2004b] X. Tricoche, C. Garth, T. Bobach, G. Scheuermann, M. Ruetten.
**“Accurate and Efficient Visualization of Flow Structures in a Delta Wing Simulation.,”** In *34th AIAA Fluid Dynamics Conference and Exhibit*, Portland, OR., American Institute of Aeronautics and Astronautics AIAA, June, 2004.

[Ues2004a] D. Uesu, L. Bavoil, S. Fleishman, C.T. Silva.
**“Simplification of Unstructured Tetrahedral Meshes by Point-Sampling,”** SCI Institute Technical Report, No. UUSCI-2004-005, *University of Utah*, 2004.

[Van2004a] R. Van Uitert, C.R. Johnson, L. Zhukov.
**“Influence of Head Tissue Conductivity in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models,”** In *j-BME*, Vol. 51, No. 12, pp. 2129--2137. 2004.

[Van2004b] M.J. van Kreveld, R. van Oostrum, C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“Efficient contour tree and minimum seed set construction,”** In *Surface Topological Data Structures: An Introduction for Geographical Information Science*, Note: *UCRL-BOOK-200018*, Edited by Sanjay Rana and Jo Wood, John Wiley & Sons, pp. 71--86. May, 2004.

[Ver2004a] A.I. Veress, N. Phatak, J.A. Weiss.
**“Deformable Image Registration with Hyperelastic Warping,”** In *Topics in Biomedical Engineering International Book Series*, Edited by J.S. Suri and D.L Wilson and S. Laxminarayan, Springer, pp. 487--533. 2004.

DOI: 10.1007/0-306-48608-3_12

[Ver2004b] A.I. Veress, W.P. Segars, B.M.W. Tsui, J.A. Weiss, G.T. Gullberg.
**“Physiologically Realistic LV Models to Produce Normal and Pathological Image and Phantom Data,”** In *Proceedings of the IEEE Medical Imaging Conference*, Rome, October, 2004.

[Wan2004a] X. Wan, D. Xiu, G.E. Karniadakis.
**“Stochastic Solutions for the Two-dimensional Advection-Diffusion Equation,”** In *SIAM Journal on Scientific Computing*, Vol. 26, No. 2, pp. 578--590. 2004.

DOI: 10.1137/S106482750342684X

[Wol2004a] C.H. Wolters, L. Grasedyck, A. Anwander, H. Hackbusch.
**“Efficient Computation of Lead Field Bases and Influence Matrix for the FEM-Based EEG and MEG Inverse Problem,”** In *c-BIOMAG2004*, Boston, MA, pp. 104--107. August, 2004.

[Wol2004b] C.H. Wolters, L. Grasedyck, W. Hackbusch.
**“Efficient Computation of Lead Field Bases and Influence Matrix for the FEM-Based EEG and MEG Inverse Problem,”** In *Inverse Problems*, Vol. 20, No. 4, pp. 1099--1116. 2004.

[Wol2004c] C.H. Wolters, A. Anwander, B. Maess, R.S. MacLeod, A.D. Friederici.
**“The Influence of Volume Conduction Effects on the EEG/MEG Reconstruction of the Sources of the Early Left Anterior Negativity,”** In *c-EMBS2004*, San Francisco, CA, Vol. 5, pp. 3569--3572. September, 2004.

[Wol2004d] C.H. Wolters, A. Anwander, S. Reitzinger, G. Haase.
**“Algebraic Multigrid with Multiple Right-Hand-Side Treatment for an Efficient Computation of EEG and MEG Lead Field Bases,”** In *c-BIOMAG2004*, Boston, MA, pp. 465--466. August, 2004.

[Wol2004e] C.H. Wolters, A. Anwander, S. Reitzinger, G. Haase.
**“Avoiding the Problem of FE Meshing: A Parallel Algebraic Multigrid with Multiple Right-Hand Side Treatment for an Efficient and Memory-Economical Computation of High Resolution EEG and MEG Lead Field Bases,”** In *c-EMBS2004*, San Francisco, CA, Note: *poster*, September, 2004.

[Xiu2004a] D. Xiu, G.E. Karniadakis.
**“Supersensitivity Due to Uncertain Boundary Conditions,”** In *International Journal for Numerical Methods in Engineering*, Vol. 61, No. 12, pp. 2114--2138. 2004.

DOI: 10.1002/nme.1152

[Xiu2004b] D. Xiu, D.M. Tartakovsky.
**“A Two-scale Non-perturbative Approach to Uncertainty Analysis of Diffusion in Random Composites,”** In *SIAM Journal on Multiscale Modeling and Simulation*, Vol. 2, No. 4, pp. 662--674. 2004.

DOI: 10.1137/03060268X

[Yos2004a] Z. Yosibash, R.M. Kirby, D. Gottlieb.
**“Collocation Methods for the Solution of Von-Karman Dynamic Non-Linear Plate Systems,”** In *Journal of Computational Physics*, Vol. 200, No. 2, pp. 432--461. 2004.

[Zha2004a] Y. Zhang, J.E. Guilkey, J.B. Hoying, J.A. Weiss.
**“Mechanical Simulation of Multicellular Structures with the Material Point Method,”** In *c-CMBBE2004*, pp. (6 pages). March, 2004.

[Zha2004b] K. Zhang, K. Damevski, V. Venkatachalapathy, S.G. Parker.
**“SCIRun2: A CCA Framework for High Performance Computing,”** In *c-HIPS2004*, April, 2004.

2003

[Ale2003a] M. Alexa, J. Behr, D. Cohen-Or, S. Fleishman, C.T. Silva, D. Levin.
**“Computing and Rendering Point Set Surfaces,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 9, No. 1, pp. 3--15. 2003.

ISSN: 1077-2626

[Alt2003a] O. Alter, P.O. Brown, D. Botstein.
**“Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms,”** In *Proceedings of the National Academy of Sciences*, Vol. 100, No. 6, Proceedings of the National Academy of Sciences, pp. 3351--3356. March, 2003.

DOI: 10.1073/pnas.0530258100

[Bap2003a] A. Baptista, T. Leen, Y. Zhang, A. Chawla, D. Maier, Wu-chang Feng, Wu-chi Feng, J. Walpole, C.T. Silva, J. Freire.
**“Environmental Observation and Forecasting Systems: Vision, Challenges and Successes of a Prototype,”** In *Proceedings of the International Society for Environmental Information Sciences Annual Conference (ISEIS '2003) on Systems Science and Information Technology for Environmental Applications*, Regina, Sask, Canada, July, 2003.

[Ben2003a] M. Benedikt, C.Y. Chan, W. Fan, J. Freire, R. Rastogi.
**“Capturing Both Types and Constraints in Data Integration,”** In *Proceedings of the 2003 ACM SIGMOD International Conference on Management of Data*, pp. 277--288. 2003.

ISBN: 1-58113-634-X

[Ber2003b] M. Berzins, A.G. Wilson.
**“Spatial Interaction Models and Fisher Information Theory A New Calibration Model,”** In *Environment and Planning*, Vol. 35, pp. 2161--2176. 2003.

[Ber2003c] M. Bertram, X. Tricoche, H. Hagen.
**“Adaptive Smooth Scattered Data Approximation for Largescale Terrain Visualization,”** In *Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2003*, pp. 177--184. 2003.

[Boh2003a] P. Bohannon, J. Freire, J. Haritsa, M. Ramanath, P. Roy, J. Simeon.
**“Bridging the XML-Relational Divide with LegoDB: A Demonstration,”** In *International Conference on Data Engineering*, pp. 759. 2003.

ISSN: 1063-6382

[Bor2003a] R. Borgo, R. Scopigno, P. Cignoni, V. Pascucci.
**“A Progressive Subdivision Paradigm (PSP),”** In *Proceedings of the Conference on Vision, Modeling and Visualization 2003 (VMV-03)*, Note: *UCRL-PROC-208557*, Edited by T. Ertl and B. Girod and G. Greiner and H. Niemann and H.-P. Seidel and E. Steinbach and R. Westermann, Aka GmbH, Berlin, Germany pp. 441--450. Nov, 2003.

[Bre2003a] P.-T. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci.
**“A Multi-resolution Data Structure for Two-dimensional Morse Functions,”** In *Proceedings of IEEE Conference on Visualization (VIS-03)*, Note: *UCRL-JC-154014*, pp. 139--146. October, 2003.

[Cat2003a] J. Cates, R.T. Whitaker.
**“Interactive Medical Image Segmentation Using the Insight Toolkit,”** In *c-RSNA2003*, November, 2003.

[Coh2003a] D. Cohen-Or, Y.L. Chrysanthou, C.T. Silva, F. Durand.
**“A Survey of Visibility for Walkthrough Applications,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 9, No. 3, IEEE Computer Society, Los Alamitos, CA, USA pp. 412--431. 2003.

ISSN: 1077-2626

[Col2003a] M. Cole, S.G. Parker.
**“Dynamic Compilation of C++ Template Code,”** In *Scientific Programming*, Vol. 11, IOS Press, pp. 321--327. 2003.

[Col2003b] K. Cole-McLaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci.
**“Loops in Reeb Graphs of 2-Manifolds,”** In *Proceedings of the 19th ACM Symposium on Computational Geometry*, Note: *UCRL-JC-151933*, pp. 344--350. June, 2003.

[Col2003c] K. Cole-McLaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci.
**“Loops in Reeb Graphs of 2-Manifolds,”** In *Proceedings of the 19th ACM Symposium on Computational Geometry*, Note: *UCRL-JC-151933*, pp. 344--350. June, 2003.

[Cor2003a] A. Corlan, R.S. MacLeod, L.D. Ambroggi.
**“Low Variability of Autocorrelation Maps with Intrathoracic Heart Position,”** In *j-IJBEM*, Vol. 5, No. 1, pp. 139--140. 2003.

[Cor2003b] W. Correa, J. Klosowski, C.T. Silva.
**“Visibility-Based Prefetching for Interactive Out-Of-Core Rendering,”** In *Proceedings of the 2003 IEEE Symposium on Parallel and Large-Data Visualization and Graphics*, pp. 2. 2003.

ISBN: 0-7695-2091-X

[Cor2003c] W. Correa, J. Klosowski, C.T. Silva.
**“Out-Of-Core Sort-First Parallel Rendering for Cluster-Based Tiled Displays,”** In *Parallel Computing*, Vol. 29, No. 3, pp. 325--338. 2003.

[Dam2003b] K. Damevski, S.G. Parker.
**“Parallel Remote Method Invocation and M-by-N Data Redistribution,”** In *Proceedings of the 4th Los Alamos Computer Science Institute Symposium*, pp. (published on CD). 2003.

[Dem2003a] D.E. DeMarle, S.G. Parker, M. Hartner, C. Gribble, C.D. Hansen.
**“Distributed Interactive Ray Tracing for Large Volume Visualization,”** In *IEEE Symposium on Parallel Visualization and Graphics*, Seattle, Wa., pp. 87--94. October, 2003.

[Dou2003a] C.C. Douglas, M. Cole, Y. Efendiev, R. Ewing, V. Ginting, C.R. Johnson, G.M. Jones, R. Lazarov, C. Shannon, J. Simpson.
**“Workshop on Dynamic Data-Driven Application Systems,”** In *ICCS 2003*, Melbourne, Australia, June 2-3, 2003.

[Dou2003b] C.C. Douglas, C.E. Shannon, Y. Efendiev, R.E. Ewing, V. Ginting, R. Lazanov, M.J. Cole, G.M. Jones, C.R. Johnson, J. Simpson.
**“A Note on Dynamic Data Driven Application Simulation (DDDAS) Using Virtual Telemetry,”** In *International Conference on Parallel Algorithms and Computing Environments*, pp. pp.193--198. 2003.

[Ede2003a] H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci.
**“Morse Complexes for Piecewise Linear 3-Manifolds,”** In *Proceedings of the 19th ACM Symposium on Computational Geometry*, Note: *UCRL-PROC-208698*, pp. 361--370. June, 2003.

[Fai2003a] R. Fairlie, C.E. Goodyer, M. Berzins, L.E. Scales.
**“Numerical Modelling of Thermal Effects in Elastohydrodynamic Lubrication Solvers,”** In *Tribological Research and Design for Engineering Systems, Proceedings of the 29th Leeds-Lyon Symposium on Tribology*, Edited by D. Dowson et al., Elsevier, pp. 675--683. 2003.

[Fle2003a] P.T. Fletcher, S. Joshi, C. Lu, S. Pizer.
**“Gaussian Distributions on Lie Groups and Their Application to Statistical Shape Analysis,”** In *Inf Process Med Imaging*, Vol. 18, Note: *Runner-up for the Francois Erbsmann Prize*, pp. 450--462. 2003.

[Fle2003b] P.T. Fletcher, C. Lu, S. Joshi.
**“Statistics of Shape via Principal Component Analysis on Lie Groups,”** In *Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR)*, Los Alamitos, CA, pp. 95--101. June, 2003.

[Fle2003c] S. Fleishman, M. Alexa, D. Cohen-Or, C.T. Silva.
**“Progressive Point Set Surfaces,”** In *ACM Transactions on Graphics (TOG)*, Vol. 22, No. 4, pp. 997--1011. 2003.

ISSN: 0730-0301

[Fre2003a] J. Freire, J. Simeon.
**“Adaptive XML Shredding: Architecture, Implementation, and Challenges,”** In *Efficiency and Effectiveness of XML Tools and Techniques and Data Integration over the Web*, Lecture Notes in Computer Science (LNCS), Vol. 2590/2008, pp. 104--116. 2003.

[Gar2003a] J.C. Gardiner, J.A. Weiss.
**“Subject-Specific Finite Element Analysis of the Human Medial Collateral Ligament During Valgus Knee Loading,”** In *Journal of Orthopaedic Research*, Vol. 21, pp. 1098--1106. 2003.

[Ger2003a] J.D. de St. Germain, S.G. Parker.
**“Software Integration in an Academic Environment,”** In *Software Quality Forum (SQF)*, Arlington, Virginia, pp. (published on CD). March, 2003.

[Ger2003b] J.D. de St. Germain, A. Morris, S.G. Parker, A.D. Malony, S. Shende.
**“Performance Analysis Integration in the Uintah Software Development Cycle,”** In *International Journal of Parallel Programming*, Vol. 31, No. 1, pp. 35--53. 2003.

[Goo2003a] C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales.
**“Grid-Based Numerical Optimisation in a Problem Solving Environment,”** In *Proceedings of Second UK E-Science All-Hands Meeting*, Nottingham, UK, Edited by S.J. Cox, pp. 854--861. 2003.

ISBN: 1-904425-11-9

[Gri2003a] C.P. Gribble, S.G. Parker.
**“A Survey of the Itanium Architecture from a Programmer's Perspective,”** SCI Institute Technical Report, No. UUSCI-2003-003, *University of Utah*, August, 2003.

[Gui2003a] J.E. Guilkey, J.A. Weiss.
**“Implicit Time Integration with the Material Point Method,”** In *International Journal for Numerical Methods in Engineering*, Vol. 57, pp. 1323--1338. 2003.

[Han2003a] C.D. Hansen, C.R. Johnson.
**“Graphics Applications for Grid Computing,”** In *j-CGA*, pp. 20--21. March/April, 2003.

[Her2003a] W. Herrera-Jimenez, W. Correa, C.T. Silva, A. Baptista.
**“Visualizing Spatial and Temporal Variability in Coastal Observatories,”** In *Proceedings of the 14th IEEE Visualization 2003 (VIS'03)*, pp. 75. 2003.

ISBN: 0-7695-2030-8

[Hog2003a] R.E. Hogan, R.D. Bucholz, S. Joshi.
**“Hippocampal Deformation-Based Shape Analysis in Epilepsy and Unilateral Mesial Temporal Sclerosis,”** In *Epilepsia*, Vol. 44, No. 6, pp. 800--806. June, 2003.

[Hub2003a] M.E. Hubbard, M. Berzins.
**“A Positivity Preserving Finite Element Method for Hyperbolic Partial Differential Equations,”** In *Computational Fluid Dynamics 2002*, Edited by S. Armfield and P. Morgan and K. Srinivas, Springer-Verlag, pp. 205--210. 2003.

[Hwa2003a] D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara.
**“Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources,”** In *World Congress on Medical Physics and Biomedical Engineering*, August, 2003.

[Hwa2003b] D. Hwang, S. Nagarajan, O. Portniaguine, K. Sekihara.
**“Multiresolution MEG (Magnetoencephalography) Imaging By Adaptive Beamformer Scanning,”** In *25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society*, Vol. 1, pp. 955--958. September, 2003.

DOI: 10.1109/IEMBS.2003.1279925

[Iba2003a] L. Ibanez, W. Schroeder, L. Ng, J. Cates.
**“The ITK Software Guide,”** Kitware, Inc., 2003.

ISBN: 1-930934-10-6

[Iki2003a] M. Ikits, C.D. Hansen, C.R. Johnson.
**“A Comprehensive Calibration and Registration Procedure for the Visual Haptic Workbench,”** In *Proceedings of the Ninth Eurographics Workshop on Virtual Environments*, Zurich, Switzerland, pp. 247--254. May, 2003.

[Iki2003b] M. Ikits, J.D. Brederson, C.D. Hansen, C.R. Johnson.
**“A Constraint-Based Technique for Haptic Volume Exploration,”** In *Proceedings IEEE Visualization 2003*, Seattle, WA, pp. 263--269. October, 2003.

[Jeo2003a] J. Jeon, A.E. Lefohn, G. A. Voth.
**“An Improved Polarflex Water Model,”** In *The Journal of Chemical Physics*, Vol. 118, No. 16, pp. 7504--7518. 2003.

[Joh2003a] C.R. Johnson, A.R. Sanderson.
**“A Next Step: Visualizing Errors and Uncertainty,”** In *IEEE Computer Graphics and Applications*, Vol. 23, No. 5, pp. 6--10. September/October, 2003.

[Jos2003a] S. Joshi, P. Lorenzen, G. Gerig, E. Bullitt.
**“Structural and Radiometric Asymmetry in Brain Images,”** In *Med Image Anal*, Vol. 7, No. 2, pp. 155--170. June, 2003.

[Kin2003b] G. Kindlmann, R.T. Whitaker, T. Tasdizen, T. Möller.
**“Curvature-Based Transfer Functions for Direct Volume Rendering: Methods and Applications,”** In *Proceedings Visualization 2003*, pp. 67. October, 2003.

[Kir2003a] R.M. Kirby, G.E. Karniadakis.
**“De-Aliasing on Non-Uniform Grids: Algorithms and Applications,”** In *J. Comp. Phys.*, Vol. 191, No. 1, pp. 267--282. October, 2003.

[Kir2003b] G.E. Karniadakis, R.M. Kirby.
**“Parallel Scientific Computing in C++ and MPI: A Seamless Approach to Parallel Algorithms and their Implementation,”** Cambridge University Press, pp. 628 pages. June, 2003.

ISBN: 0521520800

[Kir2003c] R.M. Kirby, G.E. Karniadakis.
**“De-Aliasing on Non-Uniform Grids: Algorithms and Applications,”** In *Journal of Computational Physics*, Vol. 191, pp. 249--264. 2003.

[Kni2003a] J.M. Kniss, S. Premoze, C.D. Hansen, P. Shirley, A. McPherson.
**“A Model for Volume Lighting and Modeling,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 9, No. 2, April - June, 2003.

[Kni2003b] J.M. Kniss, S. Premoze, M. Ikits, A.E. Lefohn, C.D. Hansen, E. Praun.
**“Gaussian Transfer Functions for Multi-Field Volume Visualization,”** In *IEEE Visualization 2003*, Seattle, Wa., pp. 497--504. October, 2003.

[Kni2003c] J.M. Kniss, S. Premoze, M. Ikits, A.E. Lefohn, C.D. Hansen.
**“Closed Form Solution to the Volume Rendering Integral with Gaussian Transfer Functions,”** Technical Report, No. UUCS-03-013, *University of Utah School of Computing*, 2003.

[Lam2003a] E. Lamar, V. Pascucci.
**“A Multi-Layered Image Cache For Scientific Visualization,”** In *Proceedings of IEEE Symposium on Parallel and Large-Data Visualization and Graphics*, Note: *UCRL-JC-152963*, pp. 61--68. October, 2003.

[Lan2003a] M. Langbein, G. Scheuermann, X. Tricoche.
**“An Efficient Point Location Method for Visualization in Large Unstructured Grids,”** In *Proceedings of Vision, Modeling, and Visualization 2003*, IOS Press, pp. 27--36. 2003.

[Laz2003a] M. Lazar, D.M. Weinstein, J.S. Tsuruda, K.M. Hasan, K. Arfanakis, E. Meyer, B. Badie, H.A. Rowley, V. Haughton, A. Field, A.L. Alexander.
**“White Matter Tractography Using Diffusion Tensor Deflection,”** In *Human Brain Mapping*, Vol. 18, pp. 306--321. 2003.

[Lef2003a] A.E. Lefohn, J.M. Kniss, C.D. Hansen, R.T. Whitaker.
**“Interactive Deformation and Visualization of Level Set Surfaces Using Graphics Hardware,”** In *IEEE Visualization 2003*, Seattle, Wa., pp. 75--82. October, 2003.

[Lef2003b] A.E. Lefohn, J. Cates, R.T. Whitaker.
**“Interactive, GPU-Based Level Sets for 3D Brain Tumor Segmentation,”** Technical Report, No. UUCS-03-004, *University of Utah School of Computing*, 2003.

[Lef2003d] A.E. Lefohn, R.T. Caruso, E. Reinhard, B. Budge, P. Shirley.
**“An Ocularist's Approach to Human Iris Synthesis,”** In *IEEE Computer Graphics and Applications*, Vol. 23, No. 6, pp. 70--75. 2003.

[Lef2003e] A.E. Lefohn, J.M. Kniss, C.D. Hansen, R.T. Whitaker.
**“Interactive Deformation and Visualization of Level Set Surfaces Using Graphics Hardware,”** Technical Report, No. UUCS-03-005, *University of Utah School of Computing*, 2003.

[Lef2003f] A.E. Lefohn, J. Cates, R.T. Whitaker.
**“Interactive, GPU-Based Level Sets for 3D Segmentation,”** In *Medical Image Computing and Computer Assisted Intervention (MICCAI)*, pp. 564--572. 2003.

[Leu2003a] C.H. Leung, M. Berzins.
**“A Computational Model for Organism Growth based on Surface Mesh Generation,”** In *Journal of Computational Physics*, Vol. 188, No. 1, pp. 75--99. 2003.

[Li2003a] G. Li, U.D. Bordoloi, H. Shen.
**“Chameleon: An Interactive Texture-based Rendering Framework for Visualizing Three-dimensional Vector Fields,”** In *Proceedings of IEEE Visualization 2003*, pp. 32. Oct, 2003.

[Liv2003a] Y. Livnat, C.D. Hansen.
**“Dynamic View Dependent Isosurface Extraction,”** SCI Institute Technical Report, No. UUSCI-2003-004, *University of Utah*, 2003.

[Lor2003a] P. Lorenzen, S. Joshi.
**“High-Dimensional Multi-modal Image Registration,”** In *Proceedings of the Workshop on Biomedical Image Registration*, pp. 234--243. 2003.

[Lu2003a] A. Lu, C.J. Morris, J. Taylor, D.S. Ebert, C.D. Hansen, P. Rheingans, M. Hartner.
**“Illustrative Interactive Stipple Rendering,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 9, No. 2, pp. 127--138. April, 2003.

[Lu2003b] C. Lu, S. Pizer, S. Joshi.
**“A Markov Random Field Approach to Multi-scale Shape Analysis,”** In *Scale Space Methods in Computer Vision*, Edited by LD Griffin and M Lillholm, pp. 416--431. 2003.

[Luc2003a] D. Lucor, D. Xiu, C.-H. Su, G.E. Karniadakis.
**“Predictability and Uncertainty in CFD,”** In *International Journal for Numerical Methods in Fluids*, Vol. 43, No. 5, pp. 483--505. 2003.

DOI: 10.1002/fld.500

[Max2003a] N. Max, P. Williams, C.T. Silva, R. Cook.
**“Volume Rendering for Curvilinear and Unstructured Grids,”** In *Proceedings of Computer Graphics International, 2003*, pp. 210--215. 2003.

ISBN: 0-7695-1946-6

ISSN: 1530-1052

[Nub2003a] C. Nuber, E.C. LaMar, V. Pascucci, B. Hamann, K.I. Joy.
**“Using Graphs for Fast Error Term Approximation of Time-varying Datasets,”** In *Proceedings of Eurographics VisSym'03 (Data Visualization 2003)*, Note: *UCRL-JC-151965*, Edited by Georges-Pierre Bonneau AND Stefanie Hahmann AND Charles D. Hansen, Association for Computing Machinery, New York, New York 2003.

[Pao2003a] A. Paoluzzi, V. Pascucci, M. Vicentino, C. Baldazzi, S. Protuesi.
**“Geometric Programming for Computer Aided Design,”** John Wiley & Sons, June, 2003.

[Par2003b] S.G. Parker.
**“C-SAFE Uses Linux HPCC in Fire Research,”** In *Syllabus, Technology for Higher Education*, Vol. 16, No. 7, Feburary, 2003.

[Pas2003a] V. Pascucci, K. Cole-McLaughlin.
**“Parallel Computation of the Topology of Level Sets,”** In *Algorithmica*, Vol. 38, No. 1, pp. 249--268. October, 2003.

[Pas2003b] V. Pascucci, D.E. Laney, R. Frank, G. Scorzelli, L. Linsen, B. Hamann, F. Gygi.
**“Real-Time Monitoring of Large Scientific Simulations,”** In *Proceedings of the 18-th annual ACM Symposium on Applied Computing*, Melbourne, Florida, Note: *UCRL-JC-151094*, pp. 194--198. March, 2003.

[Pas2003g] V. Pascucci, R. J. Frank.
**“Hierarchical Indexing for Out-of-Core Access to Multi-Resolution Data,”** In *Mathematics and Visualization*, Note: *UCRL-JC-140581*, Edited by G.Farin and B. Hamann and H. Hagen, Springer-Verlag, pp. 225--241. 2003.

DOI: 10.1007/978-3-642-55787-3_14

[Piz2003a] S.M. Pizer, G. Gerig, S. Joshi, S. Aylward.
**“Multiscale Medial Shape-Based Analysis of Image Objects,”** In *Proceedings of the IEEE*, Vol. 91, No. 10, Edited by C. Roux and J.K. Udupa, IEEE, pp. 1670--1679. October, 2003.

DOI: 10.1109/jproc.2003.817876

[Piz2003b] S.M. Pizer, P.T. Fletcher, Y. Fridman, D.S. Fritsch, A.G. Gash, J.M. Glotzer, S. Joshi, A. Thall, G. Tracton, P. Yushkevich, E.L. Chaney.
**“Deformable M-Reps for 3D Medical Image Segmentation,”** In *International Journal of Computer Vision - Special UNC-MIDAG issue*, Vol. 55, No. 2, Edited by O Faugeras and K Ikeuchi and J Ponce, Kluwer Academic, pp. 85--106. November-December, 2003.

[Piz2003c] S.M. Pizer, P.T. Fletcher, A. Thall, M. Styner, G. Gerig, S. Joshi.
**“Object Models in Multiscale Intrinsic Coordinates via M-reps,”** In *Image and Vision Computing, Special Issue on Generative Model-based Vision*, Vol. 21, No. 1, pp. 5--15. January, 2003.

[Por2003a] O. Portniaguine, C. Bonifasi, E. DiBella, R.T. Whitaker.
**“Inverse Methods for Reduced K-Space Acquisition,”** In *International Society for Magnetic Resonance in Medicine (ISMRM)*, Note: *abstract.*, 2003.

[Pre2003a] S. Premoze, T. Tasdizen, J. Bigler, A.E. Lefohn, R. T. Whitaker.
**“Particle-Based Simulation of Fluids,”** In *Eurographics*, pp. 401--410. 2003.

[Ram2003a] S.D. Ramsey, M. Bertram, C.D. Hansen.
**“Simplification of Arbitrary Polyhedral Meshes,”** In *IASTED Computer Graphics and Imaging (CGIM 2003)*, Honolulu, pp. 117--222. 2003.

[Ram2003b] M. Ramanath, J. Freire, J. Haritsa, P. Roy.
**“Searching for Efficient XML-to-Relational Mappings,”** In *Lecture Notes in Computer Science*, Lecture Notes in Computer Science (LNCS), Vol. 2824, pp. 19--36. 2003.

ISBN: 978-3-540-20055-0

DOI: 10.1007/978-3-540-39429-7_2

[Ril2003a] K. Riley, D. Ebert, C.D. Hansen, J. Levit.
**“Visually Accurate Multi-Field Weather Visualization,”** In *IEEE Visualization 2003*, Seattle, pp. 279--286. 2003.

[Sam2003a] A.A. Samsonov, E.G. Kholmovski, C.R. Johnson.
**“Image Reconstruction from Sensitivity Encoded MRI Data Using Extrapolated Iterations of Parallel Projections Onto Convex Sets,”** In *SPIE Medical Imaging*, Vol. 5032, pp. 1829--1838. 2003.

[Sam2003b] A.A. Samsonov, E.G. Kholmovski, C.R. Johnson.
**“Determination of the Sampling Density Compensation Function Using a Point Spread Function Modeling Approach and Gridding Approximation,”** In *Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM)*, Toronto, pp. 477. 2003.

[Sam2003c] A.A. Samsonov, E.G. Kholmovski, C.R. Johnson.
**“A Modified POCSENSE Technique for Accelerated Iterative Reconstruction from Sensitivity Encoded MRI Data,”** In *Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM)*, Toronto, pp. 477. 2003.

[San2003a] A.R. Sanderson, C.R. Johnson.
**“Display of Vector Fields Using a Reaction-Diffusion Model,”** SCI Institute Technical Report, No. UUSCI-2003-002, *University of Utah*, June, 2003.

[Sch2003a] J. Schpok, J. Simons, D.S. Ebert, C.D. Hansen.
**“A Real-Time Cloud Modeling, Rendering, and Animation System,”** In *ACM Symposium on Computer Animation*, San Diego, pp. 160--166. 2003.

[Ser2003a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Prior Model Selection for Bayesian Inverse Electrocardiography,”** In *Proceedings of the NFSI Conference 2003*, Chieti, Italy, 2003.

[Ser2003b] Y. Serinagaoglu, R.S. MacLeod, D.H. Brooks.
**“A Bayesian Approach to Inclusion and Performance Analysis of Using Extra Information in Bioelectric Inverse Problems,”** In *Proceedings of the IEEE International Conference on Image Processing*, 2003.

[Ser2003c] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Combining Numerical and Physiological Constraints in Inverse Electrocardiography,”** In *j-IJBEM*, Vol. 5, No. 1, pp. 215--217. 2003.

[Sti2003a] J.G. Stinstra, B. Hopenfeld, R.S. MacLeod.
**“A Model for the Passive Cardiac Conductivity,”** In *Int. J. Bioelectromag.*, Vol. 5, No. 1, pp. 185--186. 2003.

[Sty2003a] M. Styner, G. Gerig, S. Pizer, S. Joshi.
**“Automatic and Robust Computation of 3D Medial Models Incorporating Object Variability,”** In *International Journal of Computer Vision - Special UNC-MIDAG issue*, Vol. 55, No. 2, Edited by O Faugeras and K Ikeuchi and J Ponce, Kluwer Academic, pp. 107--122. November-December, 2003.

[Tas2003b] T. Tasdizen, R.T. Whitaker, P. Burchard, S. Osher.
**“Geometric Surface Processing via Normal Maps,”** In *ACM Transactions on Graphics*, 2003.

[Tas2003c] T. Tasdizen, R.T. Whitaker.
**“Cramer-Rao Bounds for Nonparametric Surface Reconstruction from Range Data,”** In *Proceedings of Fourth International Conference on 3-D Imaging and Modeling*, pp. 70--77. October, 2003.

[Tas2003d] T. Tasdizen, R.T. Whitaker.
**“Anisotropic diffusion of surface normals for feature preserving surface reconstruction,”** In *Proceedings of Fourth International Conferenceon 3-D Imaging and Modeling*, pp. 353--360. October, 2003.

[Tas2003e] T. Tasdizen, R.T. Whitaker.
**“Feature preserving variational smoothing of terrain data,”** In *IEEE Workshop on Variational, Geometric and Level Set Methods in Computer Vision*, October, 2003.

[Tri2003a] X. Tricoche, G. Scheuermann.
**“Topology Simplification of Symmetric, Second Order 2D Tensor Fields,”** In *Geometric Modeling Methods in Scientific Visualization*, Springer, Berlin, pp. 171--184. 2003.

[Uit2003a] R. Van Uitert, D. Weinstein, C.R. Johnson.
**“Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models,”** In *Annals of Biomedical Engineering*, Vol. 31, pp. 21--31. 2003.

[Uit2003b] R. Van Uitert, C.R. Johnson.
**“Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models,”** In *The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society*, Vol. 3, pp. 2136--2139. September, 2003.

[Wei2003b] D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson.
**“BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation,”** In *International Journal of Bioelectromagnetism*, Vol. 5, No. 1, pp. 314--315. 2003.

[Wym2003a] C. Wyman, C.D. Hansen.
**“Penumbra Maps: Approximate Soft Shadows in Real-Time,”** In *Eurographics Rendering Symposium*, Belguim, pp. 202--207. 2003.

[Xiu2003a] D. Xiu, G.E. Karniadakis.
**“Modeling Uncertainty in Flow Simulations via Generalized Polynomial Chaos,”** In *Journal of Computational Physics*, Vol. 187, No. 1, pp. 137--167. 2003.

DOI: 10.1016/S0021-9991(03)00092-5

[Xiu2003b] D. Xiu, G.E. Karniadakis.
**“A New Stochastic Approach to Transient Heat Conduction Modeling with Uncertainty,”** In *International Journal of Heat and Mass Transfer*, Vol. 46, No. 24, pp. 4681--4693. 2003.

DOI: 10.1016/S0017-9310(03)00299-0

[Yus2003a] P. Yushkevich, S. Joshi, S.M. Pizer, J.G. Csernansky, L. Wang.
**“Feature Selection for Shape-Based Classification of Biological Objects,”** In *Inf Process Med Imaging*, Vol. 18, pp. 114--125. July, 2003.

[Yus2003b] P. Yushkevich, P.T. Fletcher, S. Joshi, A. Thall, S.M. Pizer.
**“Continuous Medial Representations for Geometric Object Modeling in 2D and 3D,”** In *Image and Vision Computing, Special Issue on Generative Model-based Vision*, Vol. 21, No. 1, pp. 17--27. 2003.

[Zyp2003a] K. Zyp.
**“The Transfer Operator for Multigrid on Inverse Bioelectric Field Problems,”** SCI Institute Technical Report, No. UUSCI-2003-001, Note: *Masters thesis*, *University of Utah*, May, 2003.

2002

[Ben2002a] M. Benedikt, J. Freire, P. Godefroid.
**“VeriWeb: Automatically Testing Dynamic Web Sites,”** In *In Proceedings of 11th International World Wide Web Conference 2002*, 2002.

[Boh2002a] P. Bohannon, J. Freire, J. Haritsa, M. Ramanath, P. Roy, J. Simeon.
**“LegoDB: Customizing Relational Storage for XML Documents,”** In *Proceedings of the 28th international conference on Very Large Data Bases*, Hong Kong, China, pp. 1091--1094. 2002.

[Boh2002b] P. Bohannon, J. Freire, P. Roy, J. Sim\'eon.
**“From XML Schema to Relations: A Cost-Based Approach to XML Storage,”** In *International Conference on Data Engineering*, IEEE Computer Society, Los Alamitos, CA, USA pp. 64. 2002.

ISBN: 0-7695-1531-2

[Che2002a] Z. Chen, S. Pizer, E. Chaney, S. Joshi.
**“Medical Image Synthesis via Monte Carlo Simulation,”** In *Medical Image Computing and Computer-Assisted Intervention (MICCAI)*, Edited by T Dohi and R Kikinis, pp. 347--354. 2002.

[Dur2002a] L.J.K. Durbeck, M. Berzins.
**“Unstructured Tetrahedral Mesh Quality Analysis Using an Interactive Haptic and Visual Interface,”** In *j-CVS*, Vol. 5, No. 3, Springer-Verlag, pp. 179--192. 2002.

[Fle2002a] P.T. Fletcher, S.M. Pizer, G. Gash, S. Joshi.
**“Deformable M-rep segmentation of object complexes,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 26--29. 2002.

[Fre2002a] J. Freire, J. Haritsa, M. Ramanath, P. Roy, J. Simeon.
**“StatiX: Making XML Count,”** In *Proceedings of the 2002 ACM SIGMOD International Conference on Management of Data*, pp. 181--191. 2002.

[Ger2002a] J.D. de St. Germain, A. Morris, S.G. Parker, A.D. Malony, S. Shende.
**“Integrating Performance Analysis in the Uintah Software Development Cycle,”** In *c-ISHPC2002*, pp. 190--206. May 15-17, 2002.

[Goo2002a] C.E. Goodyer, M. Berzins.
**“Eclipse and Ellipse: PSEs for EHL Solutions using IRIS Explorer and SCIRun,”** In *c-ICCS2002*, Amsterdam, The Netherlands, Vol. 2329, Edited by P.M.A. Sloot and C.J.K. Tan and J.J. Dongarra and A.G. Hoekstra, Springer Berlin, pp. 523--532. 2002.

[Goo2002b] C.E. Goodyer, J. Wood, M. Berzins.
**“A Parallel Grid Based PSE for EHL Problems,”** In *c-PARA2002*, Espoo, Finland, Vol. 2367, Edited by J. Fagerholm and J. Haatja and J. Jarvinen and M. Lyly and P. Raback and V. Savolainen, Springer Lecture Notes in Computer Science, pp. 521--530. 2002.

[Gre2002a] J. Gregor, R.T. Whitaker.
**“Indoor Scene Reconstruction for Sets of Noisy Range Images,”** In *Graphical Models*, Vol. 63, No. 5, pp. 304--332. September, 2002.

[Gre2002b] J. Gregor, S.S. Gleason, M.J. Paulus, J. Cates.
**“Fast Feldkamp Reconstruction Based on Focus of Attention and Distributed Computing,”** In *j-IJIST*, Vol. 12, No. 6, pp. 229--234. 2002.

[Gre2002c] B. Gregoski, M. Duchaineau, P. Lindstrom, V. Pascucci, K. Joy.
**“Interactive View-Dependent Rendering of Large Isosurfaces,”** In *Proceedings of IEEE Conference on Visualization (VIS-02)*, Boston, MA, Note: *UCRL-JC-146819*, pp. 475--482. October, 2002.

[Han2002a] K.A. Hansen, J.A. Weiss, J.K. Barton.
**“Recruitment of Tendon Crimp with Applied Tensile Strain,”** In *Journal of Biomechanical Engineering*, Vol. 124, pp. 72--77. 2002.

[Jim2002a] P.K. Jimack, R. Mahmood, M.A. Walkley, M. Berzins.
**“A Multilevel Approach for Obtaining Locally Optimal Finite Element Meshes,”** In *j-AES*, Vol. 33, pp. 403--415. 2002.

[Joh2002a] C.R. Johnson, S.G. Parker, D. Weinstein, S. Heffernan.
**“Component-Based Problem Solving Environments for Large-Scale Scientific Computing,”** In *j-CCPE*, Vol. 14, pp. 1337--1349. 2002.

[Jos2002a] S. Joshi, S. Pizer, P.T. Fletcher, P. Yushkevich, A. Thall, J. Marron.
**“Multiscale Deformable Model Segmentation and Statistical Shape Analysis Using Medial Descriptions,”** In *IEEE Trans Med Imaging*, Vol. 21, No. 5, pp. 538--550. May, 2002.

[Kho2002a] E.G. Kholmovski, A.A. Samsonov, D.L. Parker.
**“POCSENSE: POCS-based method for reconstruction from sensitivity-encoded data,”** In *c-ISMRM2002*, Honolulu, pp. 194. 2002.

[Kho2002b] E.G. Kholmovski, A.A. Samsonov, D.L. Parker.
**“Motion Artifact Reduction Technique for Dual Contrast FSE Imaging,”** In *Magnetic Resonance Imaging*, Vol. 20, No. 6, pp. 455--462. 2002.

[Kir2002a] R.M. Kirby, G.E. Karniadakis.
**“Coarse Resolution Turbulence Simulations With Spectral Vanishing Viscosity - Large-Eddy Simulations (SVV-LES),”** In *j-JFE*, Vol. 124, No. 4, pp. 886-891. 2002.

[Kir2002b] R.M. Kirby, G.E. Karniadakis.
**“Coarse Resolution Turbulence Simulations With Spectral Vanishing Viscosity - Large-Eddy Simulations (SVV-LES),”** In *Journal of Fluids Engineering*, Vol. 124, No. 4, pp. 886--891. 2002.

[Kni2002a] J.M. Kniss, G. Kindlmann, C.D. Hansen.
**“Multidimensional Transfer Functions for Interactive Volume Rendering,”** In *j-TVCG*, Vol. 8, No. 3, pp. 270--285. 2002.

[Kni2002b] J.M. Kniss, C.D. Hansen, M. Grenier, T. Robinson.
**“Volume Rendering Multivariate Data to Visualize Meteorological Simulations: A Case Study,”** In *c-VISSYM2002*, 2002.

[Kni2002c] J.M. Kniss, S. Premoze, C.D. Hansen, D. Ebert.
**“Interactive Translucent Volume Rendering and Procedural Modeling,”** In *c-VIS2002*, 2002.

[Lag2002a] I. Lagzi, A.S. Tomlin, T. Turanyi, L. Haszpra, R. Meszaros, M. Berzins.
**“Modelling Tropospheric Ozone Formation in Hungary Using an Adaptive Gridding Method,”** In *Proceedings from the EUROTRAC-2 Symposium 2002*, Edited by Garmisch-Partenkirchenand P.M. Midgley and M. Reuters, 2002.

[Lag2002b] I. Lagzi, A.S. Tomlin, T. Turanyi, L. Haszpra, R. Meszaros, M. Berzins.
**“Modeling Photochemical Air Pollution in Hungary Using an Adaptive Grid Model,”** In *Air Pollution modeling and Simulation - Proc.2nd International Conference on Air Pollution Modeling and Simulation (APMS'2001)*, pp. 264--273. april, 2002.

ISBN: 3540425152, 9783540425151

[Lef2002a] A.E. Lefohn, R.T. Whitaker.
**“A GPU-Based, Three-Dimensional Level Set Solver with Curvature Flow,”** Technical Report, No. UUCS-02-017, *University of Utah School of Computing*, 2002.

[Lin2002a] P. Lindstrom, V. Pascucci.
**“Terrain Simplification Simplified: A General Framework for View-Dependent Out-of-Core Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 8, No. 3, Note: *UCRL-JC-147847*, pp. 239--254. July-September, 2002.

[Lin2002b] L. Linsen, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy.
**“Hierarchical Representation of Time-varying Volume Data with 4th-root-of-2 Subdivision and Quadrilinear B-spline Wavelets,”** In *Proceedings of Tenth Pacific Conference on Computer Graphics and Applications*, Beijing, China, Note: *UCRL-JC-151063*, pp. 346--355. 2002.

[Liv2002b] Y. Livnat, X. Cavin, C.D. Hansen.
**“PHASE: Progressive Hardware Assisted IsoSurface Extraction Framework,”** SCI Institute Technical Report, No. UUSCI-2002-001, *University of Utah*, 2002.

[Lu2002a] A. Lu, J. Taylor, M. Hartner, D. Ebert, C.D. Hansen.
**“Hardware-Accelerated Interactive Illustrative Stipple Drawing of Polygonal Objects,”** In *c-VMV2002*, Erlangen, Germany, pp. 61--68. November, 2002.

[Lu2002b] A. Lu, C.J. Morris, D. Ebert, P. Rheingans, C.D. Hansen.
**“Non-Photorealistic Volume Rendering Using Stippling Techniques,”** In *c-VIS2002*, Boston, MA, Note: *Awarded Best Paper at the conference*, pp. 211--218. 2002.

[Luk2002a] E. Luke, C.D. Hansen.
**“Semotus Visum: A Flexible Remote Visualization Framework,”** In *c-VIS2002*, Boston, MA, pp. 61--68. 2002.

[Mac2002a] R.S. MacLeod, Q. Ni, B. Taccardi.
**“Modeling Cardiac Bioelectricity in Realistic Volumes: How Real is Real?,”** In *Einthoven 2002*, Leiden, Edited by M.J. Schalij and M.J. Janse and A. van Oosterom and H.J.J. Wellens and E.E. van der Wall, *The Einthoven Foundation*, pp. 45-56. 2002.

[Mac2002b] R.S. MacLeod, E.D. DiBella, B.B. Punske, E.K. Jeong.
**“Multimodal Imaging of Cardiac Activation, Perfusion, and Ischemia,”** In *14th Annual Research Symposium of the Medical Imaging Research Laboratory*, 2002.

[Mar2002a] W. Martin, E. Reinhard, P. Shirly, S.G. Parker, W. Thompson.
**“Temporally Coherent Interactive Ray Tracing,”** In *Journal of Graphics Tools*, Vol. 7, No. 2, pp. 41--48. 2002.

[Nag2002a] S.S. Nagarajan, O. Portniaguine, K. Sekihara, D. Hwang, C.R. Johnson.
**“Performance of a Minimum-Support Imaging Method for Biomagnetic Source Localization,”** In *c-EMBS2002*, Houston, Vol. 3, pp. 2006-2007. October, 2002.

[Nie2002a] T. Nielsen, R.B. West, S.C. Linn, O. Alter, M.A. Knowling, J. O'Connell, S. Zhu, M. Fero, G. Sherlock, J.R. Pollack, P.O. Brown, D. Botstein, M. van de Rijn.
**“Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study,”** In *Lancet*, Vol. 359, No. 9314, pp. 1301–-1307. April, 2002.

DOI: 10.1016/S0140-6736(02)08270-3

[Par2002a] S.G. Parker.
**“Interactive Ray Tracing on a Supercomputer,”** In *In Practical Parallel Rendering*, Edited by A. Chalmers and E. Reinhard, 2002.

[Par2002b] S.G. Parker.
**“A Component-Based Architecture for Parallel Multi-physics PDE Simulation,”** In *c-ICCS2002*, Vol. 2331, pp. 719--734. 2002.

[Pas2002b] V. Pascucci, K. Cole-McLaughlin.
**“Efficient Computation of the Topology of Level Sets,”** In *Proceedings of IEEE Conference on Visualization (VIS-02)*, Boston, MA, Note: *UCRL-JC-149277*, pp. 187--194. October, 2002.

[Pas2002c] V. Pascucci.
**“Slow Growing Subdivision (SGS) in Any Dimension: Towards Removing the Curse Of Dimensionality,”** In *Proceedings of Eurographics 2002*, Saabruken, Germany, Note: *UCRL-ID-144257*, pp. 451--460. September, 2002.

[Pas2002d] V. Pascucci.
**“Slow Growing Volumetric Subdivision for 3D Volumetric Data,”** In *SIGGRAPH 2002 Technical Sketches*, 2002.

[Por2002a] O. Portniaguine, M.S. Zhdanov.
**“3-D Magnetic Inversion with Data Compression and Image Focusing,”** In *j-GEO*, Vol. 67, No. 5, pp. 1532--1541. September - October, 2002.

[Qua2002a] H.W. Quartero, J.G. Stinstra, E.G. Golbach, E.J. Meijboom, M.J. Peters.
**“Clinical Implications of Fetal Magnetocardiography,”** In *Ultrasound Obstet Gynecol*, Vol. 20, No. 2, pp. 142--153. 2002.

[Rei2002a] E. Reinhard, C.D. Hansen, S.G. Parker.
**“Interactive Ray Tracing of Time Varying Data,”** In *c-EGPGV2002*, Germany, pp. 77--82. September, 2002.

[Sam2002a] A.A. Samsonov, R.T. Whitaker, C.R. Johnson.
**“Noise-Adaptive Nonlinear Filtering Technique for SENSE-Reconstructed Images,”** In *c-ISMRM2002*, Honolulu, pp. 74. 2002.

[Sam2002b] A.A. Samsonov, C.R. Johnson.
**“Noise-Adaptive Anisotropic Diffusion Filtering of MRI Images Reconstructed by SENSE (SENSitivity Encoding) Method,”** In *c-ISBI2002*, Washington DC, pp. 701--704. July, 2002.

[Sam2002c] A.A. Samsonov, R.T. Whitaker, E.G. Kholmovski, C.R. Johnson.
**“Parametric Method for Correction of Intensity Inhomogeneity in MRI Data,”** In *c-ISMRM2002*, Honolulu, pp. 154. 2002.

[Sam2002d] A.A. Samsonov, E.G. Kholmovski.
**“Method for Quality Improvement of Images Reconstructed From Sensitivity-Encoded Data,”** In *c-ISMRM2002*, Honolulu, pp. 2408. 2002.

[Ser2002a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Including Sparse Noisy Epicardial Potential Measurements Into Bayesian Inverse Electrocardiography,”** In *Proceedings of EMBC 2002*, 2002.

[Ser2002b] Y. Serinagaoglu, R.S. MacLeod, B. Yilmaz, D.H. Brooks.
**“Multielectrode Venous Catheter Mapping as a High Quality Constraint for Electrocardiographic Inverse Solution,”** In *j-JE*, Vol. 35 (supplement), 2002.

[Sim2002a] J. Simpson, A.R. Sanderson, E. Luke, K. Balling, R. Coffey.
**“Collaborative Remote Visualization,”** In *c-ACMSC2002*, Baltimore, Maryland, November, 2002.

[Sim2002b] J. Simpson, A.R. Sanderson, E. Luke, K. Balling, R. Coffey.
**“Collaborative Remote Visualization,”** In *Presented before the Utah State Legislature*, 2002.

[Sti2002a] J. Stinstra, M. Peters.
**“The Influence of Fetoabdominal Tissues on Fetal ECGs and MCGs,”** In *Arch Physiol Biochem*, Vol. 110, No. 3, pp. 165--176. 2002.

[Tac2002a] B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni.
**“Visualization, Analysis and Physiological Interpretation of Three-dimentional Cardiac Electric Fields,”** In *Proceedings of 24th Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, 2002.

[Tas2002a] T. Tasdizen, R.T. Whitaker, P. Burchard, S. Osher.
**“Geometric Surface Smoothing via Anisotropic Diffusion of Normals,”** In *c-VIS2002*, pp. 125--132. 2002.

[Tri2002a] X. Tricoche, T. Wischgoll, G. Scheuermann, H. Hagen.
**“Topology Tracking for the Visualization of Time-Dependent Two-Dimensional Flows,”** In *Computer & Graphics*, Vol. 26, pp. 249--257. 2002.

[Tri2002b] X. Tricoche, G. Scheuermann, H. Hagen.
**“Scaling the Topology of Symmetric Second Order Tensor Fields,”** In *Hierarchical and Geometrical Methods in Scientific Visualization*, Springer, Berlin, pp. 171-184. 2002.

[Tri2002c] X. Tricoche.
**“Vector and Tensor Topology Simplification, Tracking, and Visualization,”** Note: *Schriftenreihe Fachbereich Informatik (3)*, *Universitat Kaiserslautern*, 2002.

[Uit2002b] R. Van Uitert, C.R. Johnson.
**“Can a Spherical Model Substitute for a Realistic Head Model in Forward and Inverse MEG Simulations?,”** In *c-BIOMAG2002*, Jena, Germany, August, 2002.

[Ver2002a] A.I. Veress, J.A. Weiss, G.T. Gullberg, D.G. Vince, R.D. Rabbitt.
**“Strain Measurement In Coronary Arteries Using Intravascular Ultrasound And Deformable Images,”** In *j-JBE*, Vol. 124, pp. 734--741. 2002.

[Wal2002a] M. Walkley, P.K. Jimack, M. Berzins.
**“Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,”** In *j-IJNMF*, Vol. 40, No. 3-4, pp. 551--559. 2002.

[Wal2002b] M. Walkley, M. Berzins.
**“A finite element model for the two-dimensional extended Boussinesq equations,”** In *International Journal for Numerical Methods in Fluids*, Vol. 39, No. 10, pp. 865--885. 2002.

[Wei2002a] J.A. Weiss, J.C. Gardiner, C. Bonifasi-Lista.
**“Ligament Material Behavior is Nonlinear, Viscoelastic and Rate-Independent Under Shear Loading,”** In *Journal of Biomechanics*, Vol. 35, pp. 943--950. 2002.

[Whi2002a] R.T. Whitaker, V. Elangovan.
**“A Direct Approach to Estimating Surfaces in Tomographic Data,”** In *j-JMIA*, Vol. 6, No. 3, pp. 235--249. 2002.

[Whi2002b] R.T. Whitaker, J. Gregor.
**“A Maximum Likelihood Surface Estimator for Dense Range Data,”** In *j-PAMI*, pp. 1372--1387. 2002.

[Whi2002c] R.T. Whitaker, E. L. Valdes-Juarez.
**“On the Reconstruction of Height Functions and Terrain Maps from Dense Range Data,”** In *j-TIP*, Vol. 11, No. 7, pp. 704--716. 2002.

[Xiu2002a] D. Xiu, G.E. Karniadakis.
**“The Wiener-Askey Polynomial Chaos for Stochastic Differential Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 24, No. 2, pp. 619--644. 2002.

DOI: 10.1137/S1064827501387826

[Xiu2002b] D. Xiu, D. Lucor, C.-H. Su, G.E. Karniadakis.
**“Stochastic Modeling of Flow-Structure Interactions using Generalized Polynomial Chaos,”** In *Journal of Fluids Engineering*, Vol. 124, No. 1, pp. 51--59. 2002.

DOI: 10.1115/1.1436089

[Xiu2002c] D. Xiu, G.E. Karniadakis.
**“Modeling Uncertainty in Steady State Diffusion Problems via Generalized Polynomial Chaos,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 191, No. 43, pp. 4927--4948. 2002.

[Xu2002a] J. Xu, D. Xiu, G.E. Karniadakis.
**“A Semi-Lagrangian Method for Turbulence Simulations Using Mixed Spectral Discretizations,”** In *Journal of Scientific Computing*, Vol. 17, No. 1-4, pp. 585--597. 2002.

DOI: 10.1023/A:1015122714039

2001

[Ahm2001a] I. Ahmad, M. Berzins.
**“MOL Solvers for Hyperbolic PDEs with Source Terms,”** In *Mathematics and Computers in Simulation*, Vol. 56, pp. 1115--1125. 2001.

[Alt2001a] O. Alter, Y. Yamamoto.
**“Quantum Measurement of a Single System,”** Wiley-Blackwell, May, 2001.

ISBN: 9780471283089

DOI: 10.1002/9783527617128

[Alt2001b] O. Alter, P.O. Brown, D. Botstein.
**“Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition,”** In *Microarrays: Optical Technologies and Informatics*, Vol. 4266, Edited by M.L. Bittner and Y. Chen and A.N. Dorsel and E.R. Dougherty (International Society for Optical Engineering Bellingham), pp. 171--186. 2001.

[Ber2001a] M. Bertram, D. Laney, M. Duchaineau, C.D. Hansen, B. Hamann, K. Joy.
**“Wavelet Representation of Contour Sets,”** In *c-VIS2001*, pp. 303--310, 566. 2001.

[Ber2001b] M. Berzins, A.S. Tomlin, S. Ghorai, I. Ahmad J.Ware.
**“Unstructured Mesh Adaptive Mesh MOL Solvers for Atmospheric Reacting Flow Problems,”** In *The Adaptive Method of Lines*, Note: *invited chapter*, Edited by A. Vande Wouwer and Ph. Saucez and W. Schiesser, CRC Press, Boca Raton, Florida, USA., pp. 317--351. 2001.

ISBN: 1-58488-231-X

[Ber2001c] M. Berzins, L. Durbeck.
**“Unstructured Mesh Solvers for Hyperbolic PDEs with Source Terms: Error Estimates and Mesh Quality,”** In *Godunonv Methods: Theory and Applications*, Note: *Proc. of Godunov Conf. October 18-22, Oxford UK*, Edited by E. Toro et al., Kluwer Academic/Plenum, pp. 117--124. 2001.

[Ber2001d] M. Berzins.
**“Modified Mass Matrices and Positivity Preservation for Hyperbolic and Parabolic PDEs,”** In *Communications in Numerical Methods in Engineering*, Vol. 17, pp. 659--666. 2001.

[Bre2001a] J.D. Brederson, M. Ikits, C.R. Johnson, C.D. Hansen.
**“A Prototype System For Synergistic Data Display,”** In *IEEE Virtual Reality 2001*, 2001.

[Bre2001b] D. Breen, R.T. Whitaker.
**“A Level-Set Approach for the Metamorphosis of Solid Models,”** In *j-TVCG*, Vol. 7, No. 2, pp. 173--192. 2001.

[But2001a] C.R. Butson.
**“From Action Potentials to Surface Potentials,”** In *Multilevel Neuronal Modeling Workshop*, Edinburgh, Scotland, May, 2001.

[But2001b] C.R. Butson, G.A. Clark.
**“Random Noise Confers a Paradoxical Improvement in the Ability of a Simulated Hermissenda Photoreceptor Network to Encode Light Intensity,”** In *Society for Neuroscience Conference*, November, 2001.

[Cor2001a] N.M. Cordaro, J.A. Weiss, J.A. Szivek.
**“Strain Transfer Between a CPC Coated Strain Gauge and Cortical Bone During Bending,”** In *Journal of Biomedical Materials Research*, Vol. 58, No. 2, pp. 147--155. 2001.

[DeT2001a] C. DeTar, A.L. Fogelson, C.R. Johnson, C.A. Sikorski.
**“Computational Engineering and Science Program at the University of Utah,”** In *c-ICCS2001*, San Francisco, Edited by V. Alexandrov and J. Dongarra and B. Juliano and R. Renner and K. Tan, pp. 1176--1185. May, 2001.

[Ela2001a] V. Elangovan, R.T. Whitaker.
**“From Sinograms to Surfaces: A Direct Approach to Segmenting Tomographic Data,”** In *c-MICCAI2001*, pp. 213--223. October, 2001.

[Gar2001a] J.C. Gardiner, J.A. Weiss, T.D. Rosenberg.
**“Strain in the Human Medial Collateral Ligament During Valgus Loading,”** In *Clinical Orthopaedics and Related Research*, Vol. 391, pp. 266--274. 2001.

[Gar2001b] J.C. Gardiner, J.A. Weiss.
**“Simple Shear Testing of Parallel-Fibered Planar Soft Tissues,”** In *Journal of Biomechanical Engineering*, Vol. 123, pp. 1--5. 2001.

[Goo2001a] C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales.
**“Adaptive Techniques for Elastohydrodynamic Lubrication Solvers,”** In *Tribology Research: From Model Experiment to Industrial Problem, Proceedings of the 27th Leeds-Lyon Symposium on Tribology*, Edited by G. Dalmaz et al., Elsevier, 2001.

[Goo2001b] C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales.
**“Adaptive Mesh Methods for Elastohydrodynamic Lubrication,”** In *ECCOMAS CFD 2001: Computational Fluid Dynamics Conference Proceedings*, Institute of Mathematics and its Applications, 2001.

ISBN: 0-905-091-12-4

[Goo2001c] C.E. Goodyer.
**“Adaptive Numerical Methods for Elastohydrodynamic Lubrication,”** Note: *Advisor: Martin Berzins*, *School of Computing, University of Leeds*, May, 2001.

[Got2001] A. Gothandaraman, R.T. Whitaker, J. Gregor.
**“Total Variation For The Removal of Blocking Effects in DCT based Encoding,”** In *c-ICIP*, pp. 455--458. October, 2001.

[Gue2001a] C. Guerra, V. Pascucci.
**“Finding Line Segments with Tabu Search,”** In *IEICE Transactions on Information & Systems*, Vol. E84-D, No. 12, pp. 1739-1744. December, 2001.

[Gum2001a] S. Gumhold, X. Wang, R.S. MacLeod.
**“Feature Extraction from Point Clouds,”** In *Proceedings, 10th International Meshing Round Table*, Sandia National Laboratories, pp. 293--305. 2001.

[Hig2001a] G. Higgins, B. Athey, J. Bassingthwaighte, J. Burgess, H. Champion, K. Cleary, P. Dev, J. Duncan, M. Hopmeier, D. Jenkins, C.R. Johnson, H. Kelly, R. Leitch, W. Lorensen, D. Metaxas, V. Spitzer, N. Vaidehi, K. Vosburgh, R. Winslow.
**“Modeling and Simulation in Medicine: Towards an Integrated Framework,”** In *Computer Aided Surgery*, Vol. 6, No. 1, 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.*, 2001.

DOI: 10.1002/igs.1008

[Iki2001] M. Ikits, J.D. Brederson, C.D. Hansen, J.M. Hollerbach.
**“An Improved Calibration Framework for Electromagnetic Tracking Devices,”** In *c-VR2001*, Yokohama, Japan, pp. 63--70. Mar, 2001.

[Iki2001b] M. Ikits, J.D. Brederson, C.D. Hansen, J.M. Hollerbach.
**“Calibration of 6DOF Electromagnetic Tracking Devices,”** In *IEEE VR2001*, Japan, pp. 63--70. 2001.

[Joh2001a] C.R. Johnson, D. Brederson, C.D. Hansen, M. Ikits, G. Kindlmann, Y. Livnat, S.G. Parker, D.M. Weinstein, R.T. Whitaker.
**“Computational Field Visualization,”** In *Computer Graphics*, Vol. 35, No. 4, pp. 5--9. 2001.

[Joh2001b] C.R. Johnson, Y. Livnat, L. Zhukov, D. Hart, G. Kindlmann.
**“Computational Field Visualization,”** In *Mathematics Unlimited -- 2001 and Beyond*, Vol. 2, Edited by B. Engquist and W. Schmid, Springer-Verlag, pp. 605--630. 2001.

[Joh2001c] C.R. Johnson, M. Mohr, U. Ruede, A. Samsonov, K. Zyp.
**“Multilevel Methods for Inverse Bioelelectric Field Problems,”** In *Lecture Notes in Computational Science and Engineering - Multiscale and Multiresolution Methods: Theory and Applications*, Vol. 20, Edited by T.J. Barth and T.F. Chan and R. Haimes, Springer-Verlag Publishing, Heidelberg pp. 331--346. October, 2001.

[Joh2001d] C.R. Johnson.
**“Adaptive Finite Element and Local Regularization Methods for the Inverse ECG Problem,”** In *Inverse Problems in Electrocardiology*, Advances in Computational Biomedicine, Vol. 5, Edited by Peter Johnston, WIT Press, pp. 51--88. 2001.

[Joh2001e] C.R. Johnson.
**“Computational Bioimaging for Medical Diagnosis and Treatment,”** In *Communications of the ACM*, Vol. 44, No. 3, pp. 74--76. March, 2001.

[Jos2001a] S. Joshi, S. Pizer, P.T. Fletcher, A. Thall, G. Tracton.
**“Multi-scale 3-D Deformable Model Segmentation Based on Medial Description,”** In *Information Processing in Medical Imaging (IPMI)*, Edited by MF Insana and RM Leahy, pp. 64--77. June, 2001.

[Kir2001a] R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram.
**“Integrated Simulation for MEMS: Coupling Flow-Structure-Thermal-Electrical Domains,”** In *The MEMS Handbook*, Edited by M. Gad-el-Hak, Informa UK Limited, 2001.

[Kir2001b] R.M. Kirby, G.E. Karniadakis.
**“Under-Resolution and Diagnostics in Spectral Simulations of Complex-Geometry Flows,”** In *Turbulent Flow Computation*, Edited by D. Drikakis and B. Geurts, Springer, pp. 1--42. 2001.

[Kir2001c] R.M. Kirby, G.E. Karniadakis, O. Mikulchenko, K. Mayaram.
**“An Integrated Simulator for Coupled Domain Problems in MEMS,”** In *Journal of Microelectromechanical Systems*, Vol. 10, No. 3, pp. 379--399. 2001.

[Kni2001a] J.M. Kniss, G. Kindlmann, C.D. Hansen.
**“Interactive Volume Rendering Using Multi-Dimensional Transfer Functions and Direct Manipulation Widgets,”** In *c-VIS2001*, pp. 255--262. October, 2001.

[Kni2001b] J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen.
**“Interactive Texture-based Volume Rendering for Large Datasets,”** In *j-CGA*, Vol. 21, No. 4, pp. 52--61. July/August, 2001.

[Kni2001c] J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen.
**“T-Rex, Texture-based Volume Rendering for Extremely Large Datasets,”** In *j-CGA*, Vol. 21, No. 4, pp. 52--61. 2001.

[Lai2001a] D.H. Laidlaw, R.M. Kirby, J.S. Davidson, T.S. Miller, M. da Silva, W.H. Warren, M. Tarr.
**“Quantitative Comparative Evaluation of 2D Vector Field Visualization Methods,”** In *Proceedings of IEEE Visualization 2001*, San Diego, CA, pp. 143--150. October, 2001.

[Leg2001a] I. Lagzi, A.S. Tomlin, T.Turanyi, L.Haszpra, M.Berzins.
**“The Simulation of Photochemical Smog Episodes in Hungary and Central Europe Using Adaptive Gridding Models,”** In *Lecture Notes in Computer Science (LCNS), Computational Science - ICCS 2001*, Vol. 2074/2001, Springer Berlin / Heidelberg, pp. 67--76. 2001.

ISBN: 978-3-540-42233-4

[Lin2001a] P. Lindstrom, V. Pascucci.
**“Visualization of Large Terrains Made Easy,”** In *Proceedings of the 12th Annual IEEE Conference on Visualization (VIS-01)*, San Diego, CA, Note: *UCRL-JC-144753*, *IEEE Computer Society*, pp. 363--370, 574. October 21-26, 2001.

[Liv2001] Y. Livnat, C.D. Hansen, S.G. Parker, C.R. Johnson.
**“Isosurface extraction for large-scale datasets,”** In *Proceedings of Scientific Visualization -Dagstuhl`2000*, Edited by F. Post, 2001.

[Lor2001a] P. Lorenzen, S. Joshi, G. Gerig, E. Bullitt.
**“Tumor-Induced Structural Radiometric Asymmetry in Brain Images,”** In *Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA)*, pp. 163--170. 2001, 2001.

[Ma2001] K. Ma, S.G. Parker.
**“Massively Parallel Software Rendering for Visualizing Large-Scale DataSets,”** In *j-TVCG*, pp. 72--83. July/August, 2001.

[Mac2001a] R.S. MacLeod, B. Yilmaz, B. Taccardi, B.B. Punske, Y. Serina, D.H. Brooks.
**“Direct and Inverse Methods for Cardiac Mapping Using Multielectrode Catheter Measurements,”** In *Journal of Biomedizinische Technik*, Vol. 46(supp), pp. 207--209. 2001.

[Mac2001b] R.S. MacLeod, B.B. Punske, B. Yilmaz, S. Shome, B. Taccardi.
**“The Role of Heart Rate in Myocardial Ischemia From Restricted Coronary Perfusion,”** In *j-JE*, Vol. 34 (supp), Note: *ISCE conference paper*, pp. 43--51. 2001.

[Mcc2001a] J. McCorquodale, J.D. de St. Germain, S.G. Parker, C.R. Johnson.
**“The Uintah Parallelism Infrastructure: A Performance Evaluation on the SGI Origin 2000,”** In *c-HPC2001*, Seattle, Mar, 2001.

[Mil2001] M. Miller, C. Moulding, J. Dongarra, C.R. Johnson.
**“Grid-enabling Problem Solving Environments: A Case Study of SCIRun and Netsolv,”** In *c-HPC2001*, 2001 Advanced Simulation Technologies Conference, *Society for Modeling and Simulation International*, pp. 98--103. April, 2001.

[Pas2001a] V. Pascucci, R.J. Frank.
**“Global Static Indexing for Real-time Exploration of Very Large Regular Grids,”** In *Proceedings of Supercomputing 2001*, Note: *UCRL-JC-144754*, *ACM*, Nov, 2001.

[Pas2001b] V. Pascucci.
**“On the Topology of the Level Sets of a Scalar Field,”** In *Proceedings of the 13th Canadian Conference on Computational Geometry*, Note: *UCRL-JC-142262*, pp. 141--144. August, 2001.

[Pfi2001a] H. Pfister, B. Lorensen, C. Bajaj, G. Kindlmann, W. Schroeder, L.S. Avila, K.M. Raghu, R. Machiraju, J. Lee.
**“The transfer function bake-off,”** In *IEEE Computer Graphics and Applications*, Vol. 21, No. 1, IEEE, pp. 16--22. 2001.

DOI: 10.1109/38.920623

[Piz2001a] S. Pizer, S. Joshi, P.T. Fletcher, M. Styner, G. Tracton, Z. Chen.
**“Segmentation of Single-Figure Objects by Deformable M-reps,”** In *Medical Image Computing and Computer-Assisted Intervention (MICCAI)*, Edited by WJ Niessen and MA Viergever, New York, pp. 862--871. October, 2001.

[Por2001a] O. Portniaguine, D.M. Weinstein, C.R. Johnson.
**“Focusing Inversion of Electroencephalography and Magnetoencephalography Data,”** In *3rd International Symposium On Noninvasive Functional Source Imaging*, Journal of Biomedizinische Technik (special issue), Vol. 46, Innsbruck, Austria pp. 115--117. Sep, 2001.

[Raw2001a] R. Rawat, S.G. Parker, P.J. Smith, C.R. Johnson.
**“Parallelization and Integration of Fire Simulations in the Uintah PSE,”** In *Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing*, Portsmouth, Virginia, March 12-14, 2001.

[Rei2001a] E. Reinhard, P. Shirley, C.D. Hansen.
**“Parallel point reprojection,”** In *Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics*, pp. 29--35. 2001.

DOI: 10.1109/PVGS.2001.964400

[Sch2001a] L.M. Schultz, C.R. Butson, G.A. Clark.
**“Post-light potentiation at type B to A photoreceptor connections in Hermissenda,”** In *Neurobiology of Learning and Memory*, Vol. 76, No. 1, pp. 7--32. July, 2001.

[Sha2001a] A. Shamir, V. Pascucci.
**“Temporal and Spatial Level of Details for Dynamic Meshes,”** In *Proceedings of the ACM Symposium on Virtual Reality Software and Technology 2001*, Banff Center, Canada, *ACM*, November, 2001.

[Tac2001a] B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni.
**“Extracardiac Effects of Myocardial Electrical Anisotropy,”** In *j-BMT*, Vol. 46(suppl 2), pp. 216--218. 2001.

[Tri2001a] X. Tricoche, G. Scheuermann, H. Hagen.
**“Tensor Topology Tracking: A Visualization Method for Time-Dependent 2D Symmetric Tensor Fields,”** In *Computer Graphics Forum*, Vol. 20, No. 3, Wiley-Blackwell, pp. 461-470. Sep, 2001.

DOI: 10.1111/1467-8659.00539

[Tri2001b] X. Tricoche, G. Scheuermann, H. Hagen.
**“Vector and Tensor Topology Simplification on Irregular Grids,”** In *Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2001*, pp. 101--116. 2001.

[Tri2001c] X. Tricoche, G. Scheuermann, H. Hagen.
**“Topology-based Visualization of Time-Dependent 2D Vector Fields,”** In *Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2001*, pp. 117--126. 2001.

[Tri2001d] X. Tricoche, G. Scheuermann, H. Hagen.
**“Continuous Topology Simplification of Planar Vector Fields,”** In *Proceedings of IEEE Visualization 2001*, pp. 159--166. 2001.

[Uit2001] R. Van Uitert, D. Weinstein, C.R. Johnson, L. Zhukov.
**“Finite Element EEG and MEG Simulations for Realistic Head Models: Quadratic vs. Linear Approximations,”** In *j-BMT*, Vol. 46, pp. 32--34. 2001.

[Wal2001a] M. Walkley, P.K. Jimack, M. Berzins.
**“Mesh Quality for Three-dimensional Finite Element Solutions on Anisotropic Meshes,”** In *Proceedings of FEM3D*, GUKUTO International Series, Mathematical Sciences and Applications, Vol. 15, pp. 310--321. 2001.

[Wal2001b] M. Walkley, P.K. Jimack, M. Berzins.
**“Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,”** In *Numerical Methods for Fluid Dynamics VII*, Edited by M.J. Baines, ICFD, Oxford, pp. 525--531. 2001.

ISBN: 0 9524929 2 X

[Wal2001c] M. Walkley, P.K. Jimack, M. Berzins.
**“Mesh Quality and Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,”** In *Proceedings of ECCOMAS Computational Fluid Dynamics Conference 2001*, Swansea, UK, 2001.

ISBN: 0 905 091 12 4

[Wan2001a] L. Wang, S.C. Joshi, M.I. Miller, J. Csernansky.
**“Statistical Analysis of Hippocampal Asymmetry in Schizophrenia,”** In *Neuroimage*, Vol. 14, No. 3, pp. 531--545. September, 2001.

[Wei2001a] D. Weinstein, O. Portniaguine, L. Zhukov.
**“A Comparison of Dipolar and Focused Inversion for EEG Source Localization,”** In *j-BMT*, Vol. 46 (special issue), pp. 121--123. Sep, 2001.

[Wei2001b] J.A. Weiss, J.C. Gardiner.
**“Computational Modeling of Ligament Mechanics,”** In *Critical Reviews in Biomedical Engineering*, Vol. 29, No. 3, pp. 1--70. 2001.

[Wes2001a] R. Westermann, C.R. Johnson, T. Ertl.
**“Topology Preserving Smoothing of Vector Fields,”** In *j-TVCG*, Vol. 7, No. 3, pp. 222--229. 2001.

DOI: 10.1109/2945.942690

[Whi2001a] R.T. Whitaker.
**“Reconstructing Terrain Maps from Dense Range Data,”** In *c-ICIP*, pp. 165--168. October, 2001.

[Whi2001b] R.T. Whitaker, X. Xue.
**“Variable-Conductance, Level-Set Curvature for Image Denoising,”** In *IEEE International Conference on Image Processing*, pp. 142--145. October, 2001.

[Xiu2001a] D. Xiu, G.E. Karniadakis.
**“A Semi-Lagrangian High-Order Method for Navier-Stokes Equations,”** In *Journal of Computational Physics*, Vol. 172, No. 2, pp. 658--684. 2001.

DOI: 10.1006/jcph.2001.6847

[Yus2001a] P. Yushkevich, S.M. Pizer, S. Joshi, J.S. Marron.
**“Intuitive, Localized Analysis of Shape Variability,”** In *Information Processing in Medical Imaging (IPMI)*, pp. 402--408. June, 2001.

[Zhu2001] L. Zhukov, D.M. Weinstein, C.R. Johnson, R.S. Macleod.
**“Spatio-temporal Multi-dipole Source Localization Using ICA and Lead-Fields in FEM Head Models,”** In *c-EMBS2001*, Istanbul, Turkey Oct, 2001.

2000

[Alt2000a] O. Alter, P.O. Brown, D. Botstein.
**“Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling,”** In *Proceedings of the National Academy of Sciences*, Vol. 97, No. 18, Proceedings of the National Academy of Sciences, pp. 10101--10106. August, 2000.

DOI: 10.1073/pnas.97.18.10101

[Ape2000a] Th. Apel, M. Berzins, P.K. Jimack, G. Kunert, A. Plaks, I. Tsukerman, M. Walkley.
**“Mesh Shape and Anistropic Elements: Theory and Practice,”** In *The Mathematics of Finite Elements and Applications X*, Edited by J.R. Whiteman, Elsevier, pp. 367--376. 2000.

[Ber2000a] M. Berzins, L. Durbeck, P.K. Jimack, M. Walkley.
**“Mesh Quality and Moving and Meshes for 2D and 3D Unstructured Mesh Solvers,”** In *Von Karman Institute for Fluid Mechanics 31st Lecture Series on Computational Fluid Mechanics*, Edited by N.P. Weatherill and H. Deconinck, Von Karman Institute, March, 2000.

ISSN: 0377-8312

[Ber2000b] M. Berzins.
**“An Introduction to Mesh Quality,”** In *Lectures notes for 31st Lecture Series on Computational Fluid Mechanics*, Rhode st Genessee, Brussels, Belgium, Edited by N.P. Weatherill and H. Deconink, *Von Karman Institute for Fluid Mechanics*, pp. 21 pages. March, 2000.

ISSN: 0377-8312

[Ber2000d] M. Berzins.
**“Solution-Based Mesh Quality Indicators for Triangular and Tetrahedral Meshes,”** In *International Journal of Computational Geometry and Applications*, Vol. 10, No. 3, pp. 333-346. June, 2000.

[Ber2000e] M. Berzins.
**“A New Metric for Dynamic Load Balancing,”** In *Applied Mathematical Modelling*, Vol. 25, Note: *Special issue on dynamic load balancing*, pp. 141--151. 2000.

[Ber2000g] M. Berzins.
**“A Data-Bounded Quadratic Interpolant on Triangles and Tetrahedra,”** In *SIAM Journal on Scientific Computing*, Vol. 22, No. 1, pp. 177--197. 2000.

[Bra2000a] R. Bramley, C.R. Johnson, D. Gannon, J. Reynders, T. Hewett, J. Rice.
**“Workshop on Scientific Knowledge, Information and Computing, SIDEKIC 98,”** In *Enabling Technologies for Computational Science*, Springer, pp. 19-32. 2000.

DOI: 10.1007/978-1-4615-4541-5_2

[Bre2000a] J.D. Brederson, M. Ikits, C.R. Johnson, C.D. Hansen, J.M. Hollerbach.
**“The Visual Haptic Workbench,”** In *Proceedings of the Fifth PHANToM Users Group Workshop*, pp. 46--49. October, 2000.

[Cse2000a] J.G. Csernansky, L. Wang, S. Joshi, J.P. Miller, M. Gado, D. Kido, D. McKeel, J.C. Morris, M. Miller.
**“Early DAT is Distinguished from Aging by High-Dimensional Mapping of the Hippocampus. Dementia of the Alzheimer Type,”** In *Neurology*, Vol. 55, No. 11, pp. 1636--1643. December 12, 2000.

[Des2000a] A. Deshmukh, C.C. Douglas, M. Ball, R.E. Ewing, C.R. Johnson, C. Kesselman, C. Lee.
**“Dynamic Data Driven Application Systems: Creating a dynamic and symbiotic coupling of application/simulations with measurements/experiments,”** Note: *28 pages*, Edited by W. Powell, R. Sharpley, National Science Foundation, 2000.

[Due2000a] B.S. Duerstock, C.L. Bajaj, V. Pascucci, D.R. Schikore, K. Lin, R.B. Borgens.
**“Advances in Three-Dimensional Reconstruction of the Experimental Spinal Cord Injury,”** In *Computerized Medical Imaging and Graphics*, Vol. 24, No. 6, pp. 389--406. 2000.

[For2000a] A. Forsberg, R.M. Kirby, D.H. Laidlaw, G.E. Karniadakis, A. van Dam, J. Elion.
**“Immersive Virtual Reality for Visualizing Flow Through an Artery,”** In *Proceedings of IEEE Visualization 2000*, Salt Lake City, UT, pp. 457--460. October, 2000.

[Ger2000a] J.D. de St. Germain, J. McCorquodale, S.G. Parker, C.R. Johnson.
**“Uintah: A Massively Parallel Problem Solving Environment,”** In *Ninth IEEE International Symposium on High Performance and Distributed Computing*, IEEE, Piscataway, NJ, pp. 33--41. Nov, 2000.

[Gho2000a] S. Ghorai, A.S. Tomlin, M. Berzins.
**“Resolution of pollutant concentrations in the boundary layer using a fully 3-D adaptive gridding technique,”** In *Atmospheric Environment*, Vol. 34, No. 18, pp. 2851-2863. 2000.

[Goo2000a] C.E. Goodyer, R. Fairlie, M. Berzins, L.E. Scales.
**“An In-depth Investigation of the Multigrid Approach to Steady and Transient EHL Problems,”** In *Thinning Films and Tribological InterfacesProceedings of the 26th Leeds-Lyon Symposium on Tribology*, Tribology Series, Vol. 38, Edited by 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, Elsevier, pp. 95--102. 2000.

ISSN: 0167-8922

[Goo2000b] C.E. Goodyera, R. Fairliea, M. Berzinsa, L.E. Scales.
**“An in-depth investigation of the multigrid approach to steady and transient EHL problems,”** In * 26th Leeds-Lyon Symposium on Tribology*, Vol. 38, Elsevier, pp. 95-102. 2000.

[Hog2000a] R.E. Hogan, K.E. Mark, L. Wang, S. Joshi, M.I. Miller, R. Bucholz.
**“Mesial Temporal Sclerosis and Temporal Lobe Epilepsy: MR Imaging Deformation-Based Segmentation of the Hippocampus in Five Patients,”** In *Radiology*, Vol. 216, No. 1, pp. 291--297. July, 2000.

[Hog2000b] R.E. Hogan, K.E. Mark, I. Choudhuri, L. Wang, S. Joshi, M.I. Miller, R. Bucholz.
**“Magnetic Resonance Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,”** In *J Digit Imaging*, Vol. 13, No. 2 (Suppl. 1), pp. 217--218. May, 2000.

[Hog2000c] R.E. Hogan, R.D. Bucholz, I. Choudhuri, K.E. Mark, C.S. Butler, S. Joshi.
**“Shape-analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis,”** In *Journal of Digital Imaging*, Vol. 13, No. 2, pp. 39--42. 2000.

[Itk2000] M. Ikits.
**“Coregistration of Pose Measurement Devices Using Nonlinear Least Squares Parameter Estimation,”** School of Computing Technical Report, No. UUCS-00-018, *University of Utah*, 2000.

[Joh2000b] C.R. Johnson, S.G. Parker, D. Weinstein.
**“Large-Scale Computational Science Applications Using the SCIRun Problem Solving Environment,”** In *c-ISC2000*, 2000.

[Jos2001b] S. Joshi, M.I. Miller.
**“Landmark Matching Via Large Deformation Diffeomorphisms,”** In *IEEE Transactions on Image Processing*, Vol. 9, No. 8, pp. 1357--1370. August, 2000.

[Kin2000] G.L. Kindlmann, D.M. Weinstein, D. Hart.
**“Strategies for Direct Volume Rendering of Diffusion Tensor Fields,”** In *j-TVCG*, Vol. 6, No. 2, pp. 124--138. April-June, 2000.

[Liv2000] Y. Livnat, S.G. Parker, C.R. Johnson.
**“Fast Isosurface Extraction Methods for Large Image Data Sets,”** In *Handbook of Medical Imaging*, Edited by A.N. Bankman, Academic Press, San Diego, CA pp. 731--745. Nov, 2000.

[Par2000a] S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson.
**“Computational Steering and the SCIRun Integrated Problem Solving Environment,”** In *Proceedings of Dagstuhl 1997 Workshop on Scientific Visualization*, Note: *Invited and peer reviewed*, Edited by Hans Hagen and Greg Nielson and Frits Post, pp. 257--266. 2000.

[Pas2000a] V. Pascucci, C.L. Bajaj.
**“Time Critical Isosurface Refinement and Smoothing,”** In *Proceedings of the ACM/IEEE Volume Visualization and Graphics Symposium 2000*, Salt lake City, Utah, Note: *UCRL-JC-139628*, pp. 33--42. October, 2000.

[Rei2000a] E. Reinhard, B. Smits, C.D. Hansen.
**“Dynamic Acceleration Structures for Interactive Ray Tracing,”** In *Proceedings Eurographics Workshop on Rendering*, Brno, Czech Republic, pp. 299--306. June, 2000.

[Rei2000b] E. Reinhard, C.D. Hansen.
**“A Comparison of Parallel Compositing Techniques on Shared Memory Architectures,”** In *c-EGPGV2000*, Spain, pp. 115--124. September, 2000.

[Sch2000a] G. Scheuermann, W. Kollmann, X. Tricoche, T. Wischgoll.
**“Evolution of Topology in Axi-Symmetric and 3D Viscous Flows,”** In *Numerical Simulations of Incompressible Flows*, World Scientific Publishing, New Jersey, pp. 622--643. 2000.

[Sha2000a] A. Shamir, V. Pascucci, C.L. Bajaj.
**“Multi-Resolution Dynamic Meshes with Arbitrary Deformations,”** In *Proceedings of IEEE Conference on Visualization (VIS-00)*, Salt lake City, Utah, Note: *UCRL-JC-139680*, pp. 423--430. 2000.

[Sut2000a] P. Sutton, C.D. Hansen.
**“Accelerated Isosurface Extraction in Time-varying Fields,”** In *j-TVCG*, Vol. 6, No. 2, pp. 98--107. 2000.

[Sut2000b] P.M. Sutton, C.D. Hansen, H.W. Shen, D. Schikore.
**“A Case Study of Isosurface Extraction Algorithm Performance,”** In *c-VISSYM2000*, Amsterdam, pp. 259--268. May, 2000.

[Tas2000a] T. Tasdizen, J.-P. Tarel, D.B. Cooper.
**“Improving the Stability of Algebraic Curves for Applications,”** In *IEEE Transactions on Image Processing*, Vol. 9, No. 3, pp. 405--416. March, 2000.

[Tas2000b] T. Tasdizen, D.B. Cooper.
**“Boundary Estimation from Intensity/Color Images with Algebraic Curve Models,”** In *Proceedings 15th International Conference on Pattern Recognition. ICPR-2000*, IEEE, 2000.

DOI: 10.1109/icpr.2000.905308

[Tom2000a] A.S. Tomlin, S. Ghorai, G. Hart, M. Berzins.
**“3-D Adaptive Unstructured Meshes in Air Pollution Modelling,”** In *Environmental Modeling and Software*, Vol. 15, No. 4, pp. 681--692. 2000.

[Tou2000a] N. Touheed, P. Selwood, P.K. Jimack, M. Berzins.
**“A Comparison of Some Dynamic Load Balancing Algorithms for a Parallel Adaptive Flow Solver,”** In *Parallel Computing*, Vol. 26, No. 12, pp. 1535--1554. 2000.

[Tri2000a] X. Tricoche, G. Scheuermann, H. Hagen.
**“Higher Order Singularities in Piecewise Linear Vector Fields,”** In *The Mathematics of Surfaces IX*, Springer, London, pp. 99--113. 2000.

[Tri2000b] X. Tricoche, G. Scheuermann, H. Hagen.
**“A Topology Simplification Method for 2D Vector Fields,”** In *Proceedings of IEEE Visualization 2000*, pp. 359--366. 2000.

[Van2000a] D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller.
**“Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,”** In *Adv Neurol*, Vol. 84, pp. 23--34. 2000.

[Wei2000a] D.M. Weinstein, L. Zhukov, G. Potts.
**“Localization of Multiple Deep Epileptic Sources in a Realistic Head Model via Independent Component Analysis,”** School of Computing Technical Report, No. UUCS-2000-004, *University of Utah*, February, 2000.

[Wei2000b] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“Lead-Field Bases for EEG Source Imaging,”** In *j-ABE*, Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.

[Wei2000c] D. Weinstein.
**“Scanline Surfacing: Building Separating Surfaces from Planar Contours,”** In *c-VIS2000*, pp. 283--289. 2000.

[Wei2000d] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“An Inverse EEG Problem Solving Environment and its Applications to EEG Source Localization,”** In *NeuroImage (suppl.)*, pp. 921. 2000.

[Wei2000e] M. Weiler, R. Westermann, C.D. Hansen, K. Zimmerman, T. Ertl.
**“Level-Of-Detail Volume Rendering via 3D Textures,”** In *c-VVIS2000*, SLC, Utah, pp. 7--13. October, 2000.

[Wei2000f] D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen.
**“Interactive Source Imaging with BioPSE,”** In *Chicago 2000 World Congress on Medical Physics and Biomedical Engineering*, Chicago, IL., Note: *Refereed abstract.*, July, 2000.

[Wei2000g] D.M. Weinstein, P. Krysl, C.R. Johnson.
**“The BioPSE Inverse EEG Modeling Pipeline,”** In *ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations*, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.

[Wes2000] R. Westermann, C.R. Johnson, T. Ertl.
**“A Level-Set Method for Flow Visualization,”** In *c-VIS2000*, IEEE Computer Society, Salt Lake City pp. 147--154. 2000.

[Zhu2000a] L. Zhukov, D. Weinstein, C.R. Johnson.
**“Statistical Analysis For FEM EEG Source Localization in Realistic Head Models,”** School of Computing Technical Report, No. UUCS-2000-003, *University of Utah*, February, 2000.

[Zhu2000b] L. Zhukov, D.M. Weinstein, C.R. Johnson.
**“Reciprocity Basis for EEG Source Imaging,”** In *NeuroImage (suppl.)*, pp. 598. 2000.

[Zhu2000c] L. Zhukov, D. Weinstein, C.R. Johnson.
**“Independent Component Analysis for EEG Source Localization in Realistic Head Models,”** In *IEEE Engineering in Medicine and Biology*, Vol. 19, No. 3, pp. 87--96. 2000.

1999

[Alt1999a] O. Alter, Y. Yamamoto.
**“Fundamental Quantum Limit to External Force Detection via Monitoring a Single Harmonic Oscillator or Free Mass,”** In *Physics Letters A*, Vol. 236, No. 4-6, pp. 226--231. 1999.

DOI: 10.1016/S0375-9601(99)00743-4

[Arm99a] R. Armstrong, D. Gannon, A. Geist, K. Keahey, S. Kohn, L. McInnes, S.G. Parker, B. Smolinksi.
**“Toward a Common Component Architecture for High-Performance Scientific Computing,”** In *Proceedings of the 8th IEEE International Symposium on High Performance Distributed Computation (HPDC)*, August, 1999.

[Baj1999a] C.L. Bajaj, C. Baldazzi, S. Cutchin, A. Paoluzzi, V. Pascucci, M. Vicentino.
**“A Programming Approach for Complex Animations,”** In *Computer Aided Design*, Vol. 31, No. 11, pp. 695--710. 1999.

[Baj1999b] C.L. Bajaj, V. Pascucci, G. Zhuang.
**“Single Resolution Compression of Arbitrary Triangular Meshes with Properties,”** In *Computational Geometry: Theory and Applications*, Vol. 14, No. 1--3, pp. 167--186. 1999.

ISSN: 0925-7721

DOI: 10.1016/S0925-7721(99)00026-7

[Baj1999c] C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“Data Visualization Techniques,”** Trends in Software, Vol. 6, Ch. 3: Accelerated IsoContouring of Scalar Fields, John Wiley & Sons, pp. 31--47. 1999.

[Baj1999d] C.L. Bajaj, V. Pascucci, G. Zhuang.
**“Progressive Compression and Transmission of Arbitrary Triangular Meshes,”** In *Proceedings of the 10th Annual IEEE Conference on Visualization (VIS-99)*, San Francisco, CA, pp. 307--316. October 24-29, 1999.

[Baj1999e] C.L. Bajaj, V. Pascucci, D. Thompson, X.Y. Zhang.
**“Parallel Accelerated Isocontouring for Out-Of-Core Visualization,”** In *Proceedings of First Parallel Visualization and Graphics Symposium 1999*, San Francisco, CA, *IEEE Computer Society*, October, 1999.

[Baj1999f] C.L. Bajaj, V. Pascucci, G. Zhuang.
**“Single Resolution Compression of Arbitrary Triangular Meshes with Properties,”** In *Proceedings of DCC: Data Compression Conference 1999*, *IEEE Computer Society*, Snowbird, Utah March, 1999.

[Baj1999g] C.L. Bajaj, S. Cutchin, V. Pascucci, A. Paoluzzi, C. Morgia.
**“Web Based Collaborative CAAD,”** In *Proceedings of the 5th Symposium on Solid Modeling and Applications*, 1999.

[Baj1999h] C. Bajaj, V. Pascucci, E. Petajan, G. Zhuang.
**“Polygonal Model Coding Evaluation for Low bit-rate Communication,”** In *Proceedings of the International Workshop on Synthetic - Natural Hybrid Coding and Three Dimensional Imaging*, September, 1999.

[Ber1999a] M. Berzins, L.J.K. Durbeck.
**“Unstructured Mesh Methods Applied to Hyperbolic PDEs with Source Terms: Error Estimates and Mesh Quality,”** In *Godunov Methods: Theory and Applications Conference and Short Course*, Oxford. numeritek Ltd.URL, October, 1999.

[Ber1999c] M. Berzins, J. Nash, P. Selwood.
**“Parallel Solution of Reacting Flow Problems using Unstructured Tetrahedral Meshes,”** In *Proceedings of 9th SIAM Parallel Processing for Scientific Computing*, Philadelphia, PA, 1999.

ISBN: 0-89871-435-4

[Ber1999e] M. Berzins.
**“A Solution Based H1 Norm Triangular Mesh Quality Indicator,”** In *Grid Generation and Adaptive Algorithms*, Edited by Marshal W. Bern, Joseph E. Flaherty, Mitchell Luskin, Springer, pp. 77-88. 1999.

[Ber99d] M. Berzins.
**“Mesh Quality - Geometry, Error Estimates or Both?,”** In *Engineering and Computers*, Vol. 15, pp. 236--247. 1999.

[Bot1999a] D. Botstein, L. Smarr, D. Agard, M. Levitt, D. Lippman, D. Herrington, C.R. Johnson, G Rose, G. Rubin, A. Levison, M. Spence, H. Smith, C. Peskin, G. Jacobs.
**“NIH Biomedical Information Science and Technology Initiative (BISTI),”** Note: *Prepared by the Working Group on Biomedical Computing Advisory Committee to the Director*, National Institutes of Health, July, 1999.

[Bre99] J.D. Brederson.
**“The I3Stick: An Inexpensive, Immersive, Interaction Device,”** School of Computing Technical Report, No. UUCS-99-014, *University of Utah*, November, 1999.

[Bro1999a] D.H. Brooks, G.F. Ahmad, R.S. MacLeod, G.M. Maratos.
**“Inverse Electrocardiography by Simultaneous Imposition of Multiple Constraints,”** In *j-BME*, Vol. 46, No. 1, pp. 3--18. 1999.

[Chi1999a] T.H.C. Childs, M. Berzins, G.R. Ryder, A. Towtoni.
**“Selective Laser Sintering of an Amorphous Polymer-Simulations and Experiments,”** In *Proceedings of the Institution of Mechanical Engineers Part B: Journal of Engineering Manufacture*, Vol. 213, No. B4, pp. 333--349. 1999.

[Dur99c] L. Durbeck.
**“Evaporation: A Technique for Visualizing Mesh Quality,”** In *8th International Meshing Roundtable*, *Sandia National Laboratories*, pp. 259--265. Oct, 1999.

[Gue1999a] C. Guerra, V. Pascucci.
**“On Matching Sets of 3D Segments,”** In *Proceedings of SPIE Vision Geometry VIII*, Denver, USA pp. 157-167. 1999.

[Gue1999b] C. Guerra, V. Pascucci.
**“3D Segment Matching Using the Hausdorff Distance,”** In *Proceedings of the IEEE Conference on Image Processing and its Applications, IPA99*, pp. 18--22. 1999.

[Gue1999c] C. Guerra, V. Pascucci.
**“Segment Matching for Protein Secondary Structure Comparison,”** In *Proceedings of the Third International Conference on Computational Molecular Biology, RECOMB'99*, *ACM*, Lyon, France pp. 30. 1999.

[Han99a] C.D. Hansen, T. Udeshi, S.G. Parker, P. Shirley.
**“Parallel Methods for Isosurface Visualization,”** In *Ninth SIAM Conference on Parallel Processing for Scientific Computing*, Note: *extended abstract*, 1999.

[Hog1999a] R.E. Hogan, K.E. Mark, L. Wang, S.C. Joshi, M.I. Miller, R.D. Bucholz.
**“MR Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,”** In *Epilepsia*, Vol. 40, No. 7, 1999.

[Joh99b] C.R. Johnson, S.G. Parker.
**“The SCIRun Parallel Scientific Computing Problem Solving Environment,”** In *Ninth SIAM Conference on Parallel Processing for Scientific Computing*, 1999.

[Joh99c] C.R. Johnson, S.G. Parker, C.D. Hansen, G.L. Kindlmann, Y. Livnat.
**“Interactive Simulation and Visualization,”** In *IEEE Computer*, Vol. 32, No. 12, pp. 59--65. Dec, 1999.

[Jos1999a] M. Joshi, J. Cui, K. Doolittle, S. Joshi, D.C. Van Essen, L. Wang, M. Miller.
**“Brain Segmentation and the Generation of Cortical Surfaces,”** In *Neuroimage*, Vol. 9, No. 5, pp. 461--476. May, 1999.

[Kar1999a] G.-S. Karamanos, C. Evangelinos, R.C. Boes, R.M. Kirby, G.E. Karniadakis.
**“Direct Numerical Simulation of Turbulence with a PC/Linux Cluster: Fact or Fiction?,”** In *Proceedings of SuperComputing 1999*, Portland, OR, November, 1999.

[Kin99] G.L. Kindlmann, D.M. Weinstein.
**“Hue-Balls and Lit-Tensors for Direct Volume Rendering of Diffusion Tensor Fields,”** In *Proceedings of the IEEE Visualization 99*, pp. 183--189. 1999.

[Kir1999a] R.M. Kirby, T.C. Warburton, I. Lomtev, G.E. Karniadakis.
**“A Discontinuous Galerkin Spectral/hp Method on Hybrid Grids,”** In *Journal of Applied Numerical Mathematics*, Vol. 33, pp. 393--405. 1999.

[Kir1999b] R.M. Kirby, H. Marmanis, D.H. Laidlaw.
**“Visualizing Multivalued Data from 2D Incompressible Flows Using Concepts from Painting,”** In *Proceedings of IEEE Visualization 1999*, San Francisco, CA, pp. 333--340. October, 1999.

[Liv99a] Y. Livnat.
**“NOISE, WISE and SAGE: Algorithms for Rapid Isosurface Extraction,”** SCI Institute Technical Report, No. UUSCI-1999-001, *University of Utah*, December, 1999.

[Lom1999a] I. Lomtev, R.M. Kirby, G.E. Karniadakis.
**“A Discontinuous Galerkin ALE Method for Compressible Viscous Flows in Moving Domains,”** In *Journal of Computational Physics*, Vol. 155, pp. 128--159. 1999.

[Mcc99a] P. McCormick, C.D. Hansen, E. Angel.
**“The Deferred Accumulation Buffer,”** In *Journal for Graphics Tools*, Vol. 4, No. 3, pp. 35--46. 1999.

[Mil1999a] M. Miller, C.D. Hansen, C.R. Johnson.
**“The SCIRun Problem Solving Environment: Implementation within a Distributed Environment,”** In *Ninth SIAM Conference on Parallel Processing for Scientific Computing*, Note: *extended abstract*, 1999.

[Mil1999b] M.I. Miller, S.C. Joshi, G.E. Christensen.
**“Large Deformation Fluid Diffeomorphisms For Landmark and Image Matching,”** In *Brain Warping*, Edited by A. W. Toga and John Mazziotta, pp. 115--131. 1999.

[Nas1999a] J. Nash, P. Dew, M. Berzins.
**“Using SADTs to Support Irregular Computational Problems,”** In *International Symposium on Parallel Architectures, Algorithms, and Networks*, IEEE Computer Society, Los Alamitos, CA, USA pp. 338--344. 1999.

ISSN: 1087-4089

DOI: 10.1109/ISPAN.1999.778961

[Nas1999b] J. Nash, M. Berzins, P. Selwood.
**“A Structured SADT Approach to the Support of a Parallel Adaptive 3D CFD Code,”** In *Euro-Par'99 Parallel Processing*, Springer Nature, pp. 651--658. 1999.

DOI: 10.1007/3-540-48311-x_91

[Nur1999a] E.M. Nurgat, M. Berzins, L.E. Scales.
**“Solving EHL Problems Using Iterative Multigrid and Homotopy Methods,”** In *ASME Journal of Tribology*, Vol. 121, pp. 28--34. January, 1999.

[Par99a] S.G. Parker, M. Parker, Y. Livnat, P.P. Sloan, C.D. Hansen, P. Shirley.
**“Interactive Ray Tracing for Volume Visualization,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 5, No. 3, pp. 238--250. July-September, 1999.

[Par99b] S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan, M. Parker.
**“Interacting with Gigabyte Volume Datasets on the Origin 2000,”** In *The 41st Annual Cray User's Group Conference*, 1999.

[Par99c] S.G. Parker, W. Martin, P.-P. Sloan, P. Shirley, B. Smits, C.D. Hansen.
**“Interactive Ray Tracing,”** In *Symposium on Interactive 3D Graphics: Interactive 3D*, pp. 119--126. April 26-28, 1999.

[Ric1999a] M. Richards, N.A. Waanders, J.A. Weiss, V. Bhatia, L.E. Senunas, M.B. Schaffler, S.A. Goldstein, J.A. Goulet.
**“Reduced Gap Strains Induce Changes in Bone Regeneration During Distraction,”** In *Journal of Biomechanical Engineering*, Vol. 121, pp. 348--355. 1999.

[Sch1999a] G. Scheuermann, X. Tricoche, H. Hagen.
**“C1-Interpolation for Vector Field Topology Visualization,”** In *Proceeding IEEE Visualization 1999*, pp. 271--278. 1999.

[Sel99a] P. Selwood, M. Berzins.
**“Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,”** In *Concurrency*, Vol. 11, No. 13, pp. 1--22. 1999.

[Slo99] P.P. Sloan, C.D. Hansen.
**“Parallel Lumigraph Reconstruction,”** In *Parallel Visualization and Graphics Symposium 1999*, pp. 7--14. October, 1999.

[Sut99] P. Sutton, C.D. Hansen.
**“Isosurface Extraction in Time-varying Fields Using a Temporal Branch-on-Need Tree (T-BON),”** In *IEEE Visualization 1999*, pp. 147--153. Oct, 1999.

[Tas1999a] T. Tasdizen, J.-P. Tarel, D. B. Cooper.
**“Algebraic curves that work better,”** In *Proceedings. 1999 IEEE Computer Society Conference on Computer Vision and Pattern Recognition*, IEEE, 1999.

DOI: 10.1109/cvpr.1999.784605

[Tom1999a] A. Tomlin, S. Ghorai, G. Hart, M. Berzins.
**“3D adaptive unstructured meshes for air pollution modelling,”** In *Environmental Management and Health*, Vol. 10, No. 4, pp. 267-275. 1999.

DOI: 10.1108/09566169910276238

[Ude99] T. Udeshi, C.D. Hansen.
**“Towards Interactive Photo-Realistic Rendering of Indoor Scenes: A Hybrid Approach,”** In *Proceedings of the Tenth Eurographics Workshop on Rendering*, pp. 63--76. June, 1999.

[Ude99b] T. Udeshi, C.D. Hansen.
**“Parallel Multipipe Rendering for Very Large Isosurface Visualization,”** In *Joint EUROGRAPHICS - IEEE TCCG Symposium on Visualization*, 1999.

[Wal99] B. Walter, G. Drettakis, S.G. Parker.
**“Interactive Rendering Using the Render Cache,”** In *Rendering techniques '99 (Proceedings of the10thEurographics Workshop on Rendering)*, Vol. 10, Springer-Verlag/Wien, New York pp. 235--246. 1999.

[Wal99a] M. Walkley, M. Berzins.
**“A finite element model for the one-dimensional extended Boussinesq equations,”** In *International Journal for Numerical Methods in Fluids*, Vol. 29, pp. 143--157. 1999.

[Wei1999a] J.A. Weiss, L.E. Paulos.
**“Mechanical Testing of Ligament Fixation Devices,”** In *Techniques in Orthopaedics*, Vol. 14, No. 1, pp. 14--21. 1999.

[Wei1999b] D.M. Weinstein, G. Kindlmann, E. Lundberg.
**“Tensorlines: Advection-Diffusion Based Propagation Through Diffusion Tensor Fields,”** In *IEEE Visualization*, pp. 249--253. 1999.

[Wei1999c] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“Lead Field Basis for FEM Source Localization,”** School of Computing Technical Report, No. UUCS-99-014, *University of Utah*, Salt Lake City, UT October, 1999.

[Wei1999d] D.M. Weinstein, G. Kindlmann, E. Lundberg.
**“Stream Bundles - Cohesive Advection through Flow Fields,”** University of Utah Technical Report, No. UUCS-99-005, *School of Computing*, 1999.

[Zhu99a] L. Zhukov, D.M. Weinstein, C.R. Johnson.
**“Independent Component Analysis For EEG Source Localization In Realistic Head Models,”** In *Third International Conference on Inverse Problems in Engineering*, 1999.

1998

[Alt1998a] O. Alter, Y. Yamamoto.
**“Impossibility of Determining the Unknown Wavefunction of a Single Quantum System: Quantum Non-Demolition Measurements, Measurements without Entanglement and Adiabatic Measurements,”** In *Fortschritte der Physik*, Vol. 46, No. 6-8, pp. 817--827. November, 1998.

[Baj1998a] C.L. Bajaj, V. Pascucci, R.J. Holt, A.N. Netravali.
**“Dynamic Maintenance and Visualization of Molecular Surfaces,”** In *Proceedings of the 10th Canadian Conference on Computational Geometry (CCCG)*, Montreal, Quebec, Canada, Edited by Mike Soss, School of Computer Science, McGill University, pp. 68--69. August, 1998.

[Baj1998b] C.L. Bajaj, V. Pascucci, G. Rabbiolo, D.R. Schikore.
**“Hypervolume Visualization: A Challenge in Simplicity,”** In *Proceedings of the 1998 IEEE Symposium on Volume Visualization*, pp. 95--102. 1998.

[Baj1998c] C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“Visualization of Scalar Topology for Structural Enhancement,”** In *Proceedings of the 9th Annual IEEE Conference on Visualization (VIS-98)*, *IEEE Computer Society*, New York pp. 51--58. October, 1998.

ISBN: 1-58113-106-2

[Ber98b] M. Berzins, P.J. Capon, P.K. Jimack.
**“On Spatial Adaptivity and Interpolation When Using the Method of Lines,”** In *Applied Numerical Mathematics*, Vol. 26, pp. 117--134. 1998.

[Ber98c] M. Berzins.
**“A Solution-Based Triangular and Tetrahedral Mesh Quality Indicator,”** In *SIAM Journal on Scientific Computing*, Vol. 19, pp. 2051--2060. 1998.

[Ber98d] M. Berzins, R. Fairlie, S.V. Pennington, J.M. Ware, L.E. Scales.
**“SPRINT2D: Adaptive Software for PDEs,”** In *ACM Transactions on Mathematical Software*, Vol. 24, No. 4, pp. 475--499. December, 1998.

[Bow1998a] A.E. Bowden, R.D. Rabbitt, J.A. Weiss.
**“Anatomical Registration and Segmentation by Warping Template Finite Element Models,”** In *Proc. SPIE (Laser-Tissue Interaction IX)*, Vol. 3254, pp. 469--476. 1998.

[Cse1998a] J.C. Csernansky, S. Joshi, L. Wang, M. Gado, J.P. Miller, U. Grenander, M.I. Miller.
**“Hippocampal Morphometry in Schizophrenia by High Dimensional Brain Mapping,”** In *Proceedings of the National Academy of Science*, Vol. 95, pp. 11406--11411. September, 1998.

[Dur98a] L.J.K Durbeck, N.J. Macias, D.M. Weinstein C.R., J.M. Hollerbach.
**“SCIRun/Haptic Display for Flow Fields,”** In *Proceedings of the Third PHANTOM Users Group Workshop*, AI Lab Technical Report No. 1643 and RLE Technical Report No. 624, Edited by J.K. Salisbury and M.A. Srinivasan, pp. 71--75. Dec, 1998.

[Han98a] C.D. Hansen.
**“EUROGRAPHICS '97 Conference Report,”** In *Computer Graphics Quarterly*, Vol. 32, No. 1, pp. 39. February, 1998.

[Han98b] C.D. Hansen.
**“EUROGRAPHICS '97: Budapest, Hungary, September 4-8, 1997: Meeting Report,”** In *Computer Graphics Forum*, Vol. 16, No. 5, pp. 323--324. February, 1998.

[Har1998a] G. Hart, A. Tomlin, J. Smith, M. Berzins.
**“Multi-scale Atmospheric Dispersion Modelling by the Use of Adaptive Grid Techniques,”** In *Environmental Monitoring and Assessment*, Vol. 52, pp. 225--228. 1998.

[Joh98a] C.R. Johnson, R.S. MacLeod.
**“Adaptive local regularization methods for the inverse ECG problem,”** In *Progress in Biophysics and Biochemistry*, Vol. 69, No. 2/3, pp. 405. Dec, 1998.

[Joh98b] C.R. Johnson.
**“Computer Visualization in Medicine,”** In *National Forum*, Vol. Fall, pp. 17--21. 1998.

[Joh98c] C.R. Johnson, M. Berzins, L. Zhukov, R. Coffey.
**“SCIRun: Applications to Atmospheric Diffusion Using Unstructured Meshes,”** In *Numerical Methods for Fluid Dynamics VI*, Edited by M.J. Baines, Oxford University Press, pp. 111--122. 1998.

[Kin98a] G. Kindlmann, J. Durkin.
**“Semi-Automatic Generation of Transfer Functions for Direct Volume Rendering,”** In *IEEE Symposium on Volume Visualization*, IEEE Press, pp. 79--86. Oct, 1998.

[Liv98] Y. Livnat, C.D. Hansen.
**“View Dependent Isosurface Extraction,”** In *IEEE Visualization '98*, pp. 175--180. Oct, 1998.

[Mil98a] M. Miller, C.D. Hansen, C.R. Johnson.
**“Simulation Steering with SCIRun in a Distributed Memory Environment,”** In *Lecture Notes in Computer Science, Springer-Verlag*, In *Applied Parallel Computing, 4th International Workshop, PARA'98*, Lecture Notes in Computer Science, Vol. 1541, Edited by B. Kagstrom and J. Dongarra and E. Elmroth and J. Wasniewski, Springer-Verlag, Berlin pp. 366--376. 1998.

[Mil98b] M. Miller, C.D. Hansen, S.G. Parker, C.R. Johnson.
**“Simulation Steering with SCIRun in a Distributed Memory Environment,”** In *Seventh IEEE International Symposium on High Performance Distributed Computing (HPDC-7)*, Jul, 1998.

[Pan98a] J. Pan, C.G.W. Sheppard, A. Tindall, M. Berzins, S.V. Pennington, J.M. Ware.
**“End Gas Inhomogeneity, Autoignition and Knock,”** SAE meeting technical report, San Fransisco, CA, No. 982616, *SAE*, 1998.

[Par98a] S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan.
**“Interactive Ray Tracing for Isosurface Extraction,”** In *IEEE Visualization '98*, pp. 233--238. October, 1998.

[Par98b] S.G. Parker, P. Shirley, B. Smits.
**“Single Sample Soft Shadows,”** School of Computing Technical Report, No. UUCS-98-019, *University of Utah*, October, 1998.

[Par98c] S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson, P.-P. Sloan.
**“An Integrated Problem Solving Environment: The SCIRun Computational Steering System,”** In *31st Hawaii International Conference on System Sciences (HICSS-31)*, Vol. VII, Edited by H. El-Rewini, pub-IEEE, pp. 147--156. January, 1998.

[Pot98] G.F. Potts, D.M. Weinstein, B.F. O'Donnell M.E., C.R. Johnson, R.W. McCarley.
**“Bioelectric Modeling of the P300 in Schizophrenia,”** In *Biological Psychiatry (suppl.)*, pp. 396. 1998.

[Pot98a] G.F. Potts, C.G. Wible, M.E. Shenton, D.M. Weinstein, I.A. Fisher, M.E. Levention, L.D. Gugino, R.W. McCarley.
**“Localization of Visual Cortex with Coregistered Functional Magnetic Resonance Imaging, Bioelectrically Modeled Cortical Visual Evoked Potential, and Transcranial Magnetic Stimulation Induced Visual Suppression,”** In *Journal of Cognitive Neuroscience (suppl.)*, pp. 42. 1998.

[Pus1998a] M.A. Puso, J.A. Weiss.
**“Finite Element Implementation of Anisotropic Quasilinear Viscoelasticity Using a Discrete Spectrum Approximation,”** In *Journal of Biomechanical Engineering*, Vol. 120, pp. 62--70. 1998.

[Qua1998a] K.M. Quapp, J.A. Weiss.
**“Material Characterization of Human Medial Collateral Ligament,”** In *Journal of Biomechanical Engineering*, Vol. 120, pp. 757--763. 1998.

[Ric1998a] M. Richards, J.A. Goulet, J.A. Weiss, N.A. Waanders, M.B. Schaffler, S.A. Goldstein.
**“Bone Regeneration and Fracture Healing: Experience with Distraction Osteogenesis Model,”** In *Clinical Orthopaedics and Related Research*, Vol. 355S, pp. 191--204. 1998.

[Sel1998a] P.Selwood, M.Berzins, J. Nash, P.M. Dew.
**“Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,”** In *Proceedings of Irregular 98 Conference*, Lecture Notes in Computer Science (LNCS), Vol. 1457, Edited by A. Ferreira et al., Springer, pp. 56--67. 1998.

[Sle98a] P.A. Sleigh, M. Berzins, P.H. Gaskell, N.G. Wright.
**“An Unstructured Finite Volume Algorithm for Predicting Flow in Rivers and Estuaries,”** In *Computers and Fluids*, Vol. 27, No. 4, pp. 479--508. 1998.

[Slo98] P.P.J. Sloan, D.M. Weinstein, J.D. Brederson.
**“Importance Driven Texture Coordinate Optimization,”** In *Eurographics 98*, Sep, 1998.

[Ste1998a] R. Stevens, H. Fuchs, A. van Dam, P. Hanrahan, C.R. Johnson, C. McMillan, P. Heermann, S. Louis, T. Defanti, D. Reed, E. Cohen.
**“Data and Visualization Corridors: Report on the 1998 DVC Workshop Series,”** Note: *DOE Report*, September, 1998.

[Tas1998a] T. Tasdizen, L. Akarun, C. Ersoy.
**“Color Quantization with Genetic Algorithms,”** In *Signal Processing: Image Communication*, Vol. 12, pp. 49--57. 1998.

[Tou98a] N. Touheed, P. Selwood, P.K. Jimack, M. Berzins.
**“Parallel Dynamic Load-Balancing for the Solution of Transient CFD Problems Using Adaptive Tetrahedral Meshes,”** In *Parallel Computational Fluid Dynamics - Recent Developments and Advances Using Parallel Computers*, Edited by D.R. Emerson and A. Ecer and J. Periaux and N. Satufoka and P. Fox, Elsevier Science, pp. 81--88. 1998.

[Van1998a] D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller.
**“Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,”** In *Proceedings of the National Academy of Sciences*, Vol. 95, No. 3, Proceedings of the National Academy of Sciences, pp. 788--795. February, 1998.

DOI: 10.1073/pnas.95.3.788

[Wei1998a] J.A. Weiss, R.D. Rabbitt, A.E. Bowden.
**“Incorporation of Medical Image Data in Finite Element Models to Track Strain in Soft Tissues,”** In *Proc SPIE (Laser-Tissue Interaction IX)*, Vol. 3254, pp. 477--484. 1998.

[Wei98a] D.M. Weinstein.
**“The Analytic 3-D Transform for the Least-Squared Fit of Three Pairs of Corresponding Points,”** School of Computing Technical Report, No. UUCS-98-005, *University of Utah*, Salt Lake City, UT 1998.

[Whi98a] R.T. Whitaker.
**“A Level-Set Approach to 3D Reconstruction From Range Data,”** In *International Journal of Computer Vision*, Vol. 29, No. 3, pp. 203--231. 1998.

1997

[Ahm97a] I. Ahmad, M. Berzins.
**“An Algorithm for ODEs from Atmospheric Dispersion Problems,”** In *Applied Numerical Mathematics*, Vol. 25, pp. 137--149. 1997.

[Alt1997a] O. Alter, Y. Yamamoto.
**“Reply to the Comment on 'Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State',”** In *Physical Review A*, Vol. 56, No. 1, pp. 1057--1059. July, 1997.

DOI: 10.1103/PhysRevA.56.1057

[Alt1997b] O. Alter, Y. Yamamoto.
**“Quantum Zeno Effect and the Impossibility of Determining the Quantum State of a Single System,”** In *Physical Review A*, Vol. 55, No. 4, pp. R2499--R2502. April, 1997.

DOI: 10.1103/PhysRevA.55.R2499

[Baj1997a] C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“The Contour Spectrum,”** In *Proceedings of the 8th Annual IEEE Conference on Visualization (VIS-97)*, Edited by Roni Yagel and Hans Hagen, *IEEE Computer Society*, pp. 167--175. November, 1997.

[Baj1997b] C. Bajaj, H.Y. Lee, R. Merkert, V. Pascucci.
**“NURBS based B-rep Models for Macromolecules and their Properties,”** In *Proceedings of the 4th Symposium on Solid Modeling and Applications*, Edited by Christoph Hoffmann and Wim Bronsvort, ACM Press, New York pp. 217--228. May, 1997.

ISBN: 0-89791-946-7

[Baj1997d] C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“Fast Isocontouring for Structured and Unstructured Meshes in Any Dimension,”** In *Late Breaking Hot Topics Proceedings of the 8th Annual IEEE Conference on Visualization (VIS-97)*, Edited by Amitabj Varshney and David S. Ebert, *IEEE Computer Society*, pp. 25--28. November, 1997.

[Bea97] D.M. Beazley.
**“Using SWIG to control, prototype, and debug C program with Python,”** In *4th International Python Conference*, 1997.

[Ber1997b] M. Berzins, S.V. Pennington, P.R. Pratt, J.M. Ware.
**“SPRINT2D Software for Convection Dominated PDEs,”** In *Modern Software Tools in Scientific Computing*, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, 1997.

[Ber1997c] M. Berzins, P.J. Capon, P.K. Jimack.
**“On Spatial Adaptivity and Interpolation when Using the Method of Lines,”** In *Applied Numerical Mathematics: Transactions of IMACS*, Vol. 26, No. 1--2, pp. 117--133. 1997.

[Chr1997a] G.E. Christensen, S.C. Joshi, M. Miller.
**“Volumetric Transformation of Brain Anatomy,”** In *IEEE Trans Med Imaging*, Vol. 16, No. 6, pp. 864--877. December, 1997.

[Chr1997b] G.E. Christensen, S.C. Joshi, M.I. Miller.
**“Volumetric Transformation of Brain Anatomy,”** In *IEEE Transactions on Medical Imaging*, Vol. 16, No. 6, pp. 864--877. December, 1997.

[Cre1997a] D.J. Creasey, D.E. Heard, M. Pilling, B.J. Whitaker, M. Berzins, R. Fairlie.
**“Visualisation of a Supersonic Free-Jet Expansion Using Laser-Induced Fluorescence Spectroscopy: Application to the Measurement of Rate Constants at Ultralow Temperatures,”** In *Applied Physics B: Lasers and Optics*, Vol. 65, pp. 375--391. 1997.

[Hal1997a] J.W. Haller, A. Banerjee, G.E. Christensen, M. Gado, S. Joshi, M.I. Miller, Y. Sheline, M.W. Vannier, J. Csernansky.
**“Three-Dimensional Hippocampal MR Morphometry with High-Dimensional Transformation of a Neuroanatomic Atlas,”** In *Radiology*, Vol. 202, No. 2, pp. 504--510. February, 1997.

[Han97a] C.D. Hansen, M. Krogh, J. Painter.
**“Parallel Rendering Techniques for Massively Parallel Visualization,”** In *International Symposium on Parallel Algorithms/Architecture Synthesis*, Aizu-Wakamatsu, Japan, pp. 276--281. March, 1997.

[Joh97a] C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein.
**“Applications of Large-Scale Computing and Scientific Visualization in Medicine,”** SCI Institute Technical Report, No. UUSCI-1997-001, *University of Utah*, 1997.

[Joh97d] C.R. Johnson.
**“Computational and Numerical Methods for Bioelectric Field Problems,”** In *Critical Reviews in BioMedical Engineering*, Vol. 25, No. 1, pp. 1--81. 1997.

[Jos1997a] S.C. Joshi, M.I. Miller, U. Grenander.
**“On the Geometry and Shape of Brain Sub-Manifolds,”** In *International Journal of Pattern Recognition and Artificial Intelligence, special issue on Magnetic Resonance Imaging*, Vol. 11, No. 8, pp. 1317--1343. 1997.

[Jos1997b] S. Joshi, A. Banerjee, G.E. Christensan, J.G. Csernansky, J.W. Haller, M.I. Miller, L. Wang.
**“Gaussian Random Fields on Sub-Manifolds for Characterizing Brain Surfaces,”** In *Proceedings of the International Conference on Image Processing in Medical Imaging (IPMI)*, 1997.

[Kle97a] R.N. Klepfer, C.R. Johnson, R.S. MacLeod.
**“The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 44, No. 8, pp. 706--719. August, 1997.

[Kre1997a] M. van Kreveld, R. van Oostrum, C. Bajaj, V. Pascucci, D.R. Schikore.
**“Contour Trees and Small Seed Sets for Isosurface Traversal,”** In *Proceedings of the 13th International Annual Symposium on Computational Geometry (SCG-97)*, ACM Press, New York pp. 212--220. June, 1997.

ISBN: 0-89791-878-9

[Kro97a] M. Krogh, J. Painter, C.D. Hansen.
**“Parallel Sphere Rendering,”** In *Parallel Computing*, Vol. 23, No. 7, pp. 961--974. 1997.

[Lei1997a] Z. Lei, T. Tasdizen, D.B. Cooper.
**“PIMS and Invariant Parts for Shape Recognition,”** In *Sixth International Conference on Computer Vision*, Narosa Publishing House, 1997.

DOI: 10.1109/iccv.1998.710813

[Lev1997a] A.L. Levy, T.J. Schaewe, M.I. Miller, K.R. Smith, A.M. Hammoud, J.M. Henderson, S. Joshi, K.E. Mark, C.D. Sturm, L.L. McDurmont Jr, R. Bucholz.
**“An Internet-Connected, Patient-Specific, Deformable Brain Atlas Integrated into a Surgical Navigation System,”** In *J Digit Imaging*, Vol. 10, No. 3 (Suppl. 1), pp. 231--237. August, 1997.

[Mil1997a] M. Miller, A. Banerjee, G. Christensen, S. Joshi, N. Khaneja, U. Grenander, L. Matejic.
**“Statistical Methods in Computational Anatomy,”** In *Stat Methods Med Res*, Vol. 6, No. 3, pp. 267--299. September, 1997.

[Mil1997b] M.I. Miller, S. Joshi.
**“Discussion of Mathematics for Object Recognition Shape, Invariance and Deformations,”** In *Proceedings of the Workshop on Mathematics for Object Recognition Shape, Invariance and Deformations*, Edited by L. Younes, November, 1997.

[Par1997a] S.G. Parker, D.M. Weinstein, C.R. Johnson.
**“The SCIRun Computational Steering Software System,”** In *Modern Software Tools in Scientific Computing*, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, Boston pp. 1--40. 1997.

[Par97b] S.G. Parker, D.M. Beazley, C.R. Johnson.
**“Computational Steering Software Systems and Strategies,”** In *IEEE Computational Science and Engineering*, Vol. 4, No. 4, pp. 50--59. 1997.

[Sel96a] P. Selwood, N.A. Verhoeven, J.M. Nash, M. Berzins, N.P. Weatherill, P.M. Dew, K. Morgan.
**“Parallel Mesh Generation and Adaptivity : Partitioning and Analysis,”** In *Parallel C.F.D.- Proc. of Parallel CFD 96 Conference*, Capri, Italy, Edited by A.Ecer and J.Periaux and N.Satufoka and P.Schiano, Elesvier Science BV, May, 1997.

ISBN: 0-444 823271

[Sel97a] P. Selwood, M. Berzins, P.M. Dew.
**“3D Parallel Mesh Adaptivity: Data Structures and Algorithms,”** In *Proc. of SIAM Conf. on Parallel Processing for Scientific Computing*, Minneapolis, MN, USA, pp. (CD-Rom). March, 1997.

ISBN: 0-89871-395-1

[Slo97] P.P.J. Sloan, M.F. Cohen, S.J. Gortler.
**“Time Critical Lumigraph Rendering,”** In *1997 Symposium on Interactive 3D Graphics*, Apr, 1997.

[Spe97a] W. Speares, M. Berzins.
**“A 3D Unstructured Mesh Adaptation Algorithm for Time Dependent Shock Dominated Problems,”** In *Int. Jour Numerical Methods in Fluids*, Vol. 25, pp. 81--104. 1997.

[Tom97a] A. Tomlin, M. Berzins, J.M. Ware, J. Smith, M. Pilling.
**“On the use of adaptive gridding methods for modelling chemical transport from multi-scale sources,”** In *Atmospheric Env.*, Vol. 31, No. 18, pp. 2945--2959. 1997.

[Wei97a] D.M. Weinstein, C.R. Johnson.
**“Effects of Geometric Uncertainty on the Inverse EEG Problem,”** In *Computational, Experimental, and Numerical Methods for Solving Ill-Posed Inverse Imaging Problems:Medical and Nonmedical Applications*, SPIE '97, Vol. 3171, Edited by R.L. Barbour and M.J. Carvlin and M.A. Fiddy, SPIE, pp. 138--145. 1997.

[Wei97b] D.M. Weinstein, C.R. Johnson.
**“Cache-rings for Memory Efficient Isosurface Construction,”** School of Computing Technical Report, No. UUCS-97-016, *University of Utah*, Salt Lake City, UT 1997.

[Yu97a] F. Yu, Y. Livnat, C.R. Johnson.
**“An Automatic Adaptive Refinement and Derefinement Method for 3D Elliptic Problems,”** In *Applied Numerical Mathematics*, 1997.

1996

[Alt1996a] O. Alter, Y. Yamamoto.
**“Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State,”** In *Physical Review A*, Vol. 53, No. 5, pp. R2911--R2914. May, 1996.

DOI: 10.1103/PhysRevA.53.R2911

[Alt1996b] O. Alter, Y. Yamamoto.
**“Inhibition of the Measurement of the Wavefunction of a Single Quantum System and the Projection Postulate,”** In *Quantum Physics, Chaos Theory and Cosmology*, Edited by M. Namiki and I. Ohba and K. Maeda and Y. Aizawa, American Institute of Physics, pp. 151--172. 1996.

DOI: 10.1103/PhysRevLett.74.4106

[Alt1996c] O. Alter, Y. Yamamoto.
**“The Quantum Zeno Effect of a Single System is Equivalent to the Indetermination of the Quantum State of a Single System,”** In *Quantum Interferometry*, Edited by F. De Martini and G. Denardo and Y. Shih, VCH, pp. 539--544. 1996.

DOI: 10.1103/PhysRevA.55.R2499

[Alt1996d] O. Alter, Y. Yamamoto.
**“The Unknown Wavefunction of a Single System Cannot Be Inferred Using Repeated Quantum Measurements,”** In *Quantum Coherence and Decoherence*, Edited by K. Fujikawa and Y. A. Ono, Elsevier Science, Amsterdam, Netherlands, pp. 31--34. 1996.

[Baj1996a] C.L. Bajaj, V. Pascucci, D.R. Schikore.
**“Fast Isocontouring for Improved Interactivity,”** In *1996 Volume Visualization Symposium*, *IEEE Computer Society*, pp. 39--46. October, 1996.

ISBN: 0-89791-741-3

[Baj1996b] C.L. Bajaj, V. Pascucci.
**“Splitting a Complex of Convex Polytopes in any Dimension,”** In *Proceedings of the Twelfth Annual Symposium On Computational Geometry (ISG '96)*, ACM Press, New York pp. 88--97. May, 1996.

ISBN: 0-89791-832-0

[Baj1996c] C.L. Bajaj, F. Bernardini, V. Pascucci, D.R. Schikore.
**“Interrogative Visualization of the Visible Human Datasets,”** In *Proceedings of the The Visible Human Project Conference*, 1996.

[Bea96a] D.M. Beazley.
**“Using SWIG to control, prototype, and debug C programs with Python,”** In *4th International Python Conference*, 1996.

[Ber1996c] M. Berzins, T.H.C. Childs, G.R. Ryder.
**“The Selective Laser Sintering of Polycarbonate,”** In *CIRP Annals*, Vol. 45, No. 1, pp. 187--190. 1996.

ISSN: 0007-8506

DOI: 10.1016/S0007-8506(07)63044-3

[Ber96a] M. Berzins, J.M. Ware.
**“Solving Convection and Convection Reaction Problems Using the M.O.L.,”** In *Applied Numerical Mathematics*, Vol. 20, pp. 83--99. 1996.

[Coo1996a] M.L. Cooper, A.D. Lanterman, S.C. Joshi, M.I. Miller.
**“Representing The Variation of Thermodynamic State Via Principal Components Analysis,”** In *Proceedings of the Third Workshop On Conventional Weapon ATR*, pp. 481--490. November, 1996.

[Git96] C.S. Gitlin, C.R. Johnson.
**“MeshView: A tool for exploring 3D unstructured tetrahedral meshes,”** In *5th International Meshing Roundtable*, pp. 333--345. 1996.

[Hal1996a] J.W. Haller, G.E. Christensen, S.C. Joshi, J.W. Newcomer, M.I. Miller, J.G. Csernansky, M. Vannier.
**“Hippocampal MR Imaging Morphometry by Means of General Pattern Matching,”** In *Radiology*, Vol. 199, No. 3, pp. 787--791. June, 1996.

[Joh96b] C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein.
**“Applications of Large-Scale Computing and Scientific Visualization in Medicine,”** In *International Journal on Supercomputer Applications and High Performance Computing*, 1996.

[Joh96e] C.R. Johnson, R.S. MacLeod.
**“Local regularization and adaptive methods for the inverse Laplace problem,”** In *Biomedical and Life Physics*, Edited by D.N. Ghista, Vieweg-Verlag, Braunschweig pp. 224--234. 1996.

[Kle96] R.N. Klepfer, C.R. Johnson, R.S. MacLeod.
**“The effects of inhomogeneities and anisotropies on electrocardiographic fields: A three-dimensional finite element study,”** In *IEEE Trans. on Biomedical Engineering*, 1996.

[Liv96] Y. Livnat, H.W. Shen, C.R. Johnson.
**“A Near Optimal Isosurface Extraction Algorithm Using the Span Space,”** In *IEEE Transactions on Visual Computer Graphics*, Vol. 2, No. 1, pp. 73--84. 1996.

[Nur1996a] E. Nurgat, M. Berzins.
**“A new relaxation scheme for solving EHL Problems,”** In *23rd Leeds-Lyon Symposium on Tribology, Tribology Series*, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125a-134. 1996.

ISBN: 0444828095

[Nur96a] E. Nurgat, M. Berzins.
**“A new relaxation scheme for solving EHL Problems,”** In *Proceedings of 23rd Leeds-Lyon Symposium on Tribology*, Tribology Series, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125A--134. 1996.

ISBN: 0444828095

[Pai96a] J. Painter, H.P. Bunge, Y. Livnat.
**“Case Study: Mantle Convection Visualization on the Cray T3D,”** In *IEEE Visualization `96*, pp. 409--412. 1996.

[Pai96b] J. Painter, M. Krogh, C.D. Hansen.
**“Parallel Sphere Rendering,”** In *EUROGRAPHICS Workshop on Parallel Graphics and Visualization*, Bristol, England, September, 1996.

[Par96a] S.G. Parker, C.R. Johnson.
**“SCIRun: Applying Interactive Computer Graphics to Scientific Problems,”** In *SIGGRAPH (applications/demo)*, 1996.

[Pas1996a] V. Pascucci, V. Ferrucci, A. Paoluzzi.
**“Dimension-Independent Convex-Cell Based HPC: Skeletons and Product,”** In *International Journal of Shape Modeling*, Vol. 2, pp. 37--67. 1996.

[Pra1996a] P. Pratt, M. Berzins.
**“Shock preserving quadratic interpolation for visualization on triangular meshes,”** In *Computers & Graphics*, Vol. 20, No. 5, pp. 723--730. 1996.

DOI: 10.1016/S0097-8493(96)00046-5

[Ryd96a] G.J. Ryder, M. Berzins, T.H.C. Childs.
**“Modelling Simple Feature Creation in Selective Laser Sintering,”** In *Proc 7th Symposium on Solid Free Form Fabrication*, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 567--574. 1996.

[She96a] H.W. Shen, C.R. Johnson, K.L. Ma.
**“Global and Local Vector Field Visualization Using Enhanced Line Integral Convolution,”** In *Symposium on Volume Visualization*, IEEE Press, pp. 63--70. 1996.

[She96b] H.W. Shen, C.D. Hansen, Y. Livnat, C.R. Johnson.
**“Isosurfacing in Span Space with Utmost Efficiency,”** In *IEEE Visualization `96*, IEEE Press, pp. 287--294. 1996.

[Sle1996a] P.A. Sleigh, M. Berzins, P.H. Gaskell.
**“A Reliable and Accurate Technique for the Modelling of Complex Hydraulic Flows,”** In *Proceedings of the First International Symposium on Finite Volumes for Complex Applications*, Hermes, Paris, pp. 635--642. 1996.

ISBN: 2-86601-556-8

[Smi1996a] J.D.B. Smith, A.S. Tomlin, M. Berzins, V. Pennington, M.J. Pilling.
**“Modelling the effects of Concentrated Emissions Sources on Tropospheric Ozone,”** In *Proceedings of the 3rd Workshop on Modelling of Chemical Reaction Systems*, Heidelberg, Germany, Published on CD-ROM, July, 1996.

ISBN: 3-932217-00-4

[Wei1996a] J.A. Weiss, B.N. Maker, S. Govindjee.
**“Finite Element Implementation of Incompressible, Transversely Isotropic Hyperelasticity,”** In *Computer Methods in Applied Mechanics and Engineering*, Vol. 135, pp. 107--128. 1996.

1995

[Ahr95a] J. Ahrens, C.D. Hansen.
**“Cost-Effective Data-Parallel Load Balancing,”** In *International Conference on Parallel Processing*, Oconomowoc, Wi., pp. 14--18. August, 1995.

[Alt1995a] O. Alter, Y. Yamamoto.
**“Inhibition of the Measurement of the Wave Function of a Single Quantum System in Repeated Weak Quantum Nondemolition Measurements,”** In *Physical Review Letters*, Vol. 74, No. 21, American Physical Society, pp. 4106--4109. May, 1995.

DOI: 10.1103/PhysRevLett.74.4106

[Alt1995b] O. Alter, Y. Yamamoto.
**“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,”** In *Fundamental Problems in Quantum Theory*, Vol. 755, Edited by D.M. Greenberger and A. Zeilinger, New York Academy of Sciences, New York, NY, pp. 103--109. 1995.

DOI: 10.1111/j.1749-6632.1995.tb38960.x

[Ban1995a] A. Banerjee, G.E. Christensen, J. Haller, S. Joshi, M.E. Raichle, M.I. Miller.
**“Accommodating anatomical variability in functional imaging via deformable templates,”** In *Proc. 33rd Annual Allerton Conference on Communication, Control and Computing*, pp. 275--284. 1995.

[Ber1995a] M. Berzins, J.M. Ware.
**“Positive Cell Centered Finite Volume Discretisation Methods for Hyperbolic Equations on Irregular Meshes,”** In *Applied Numerical Mathematics*, Vol. 16, pp. 417--438. 1995.

[Ber1995d] M. Berzins, P. Gaskell, A. Sleigh, A.S. Tomlin, J. Ware.
**“An adaptive CFD solver for time-dependent environmental flow problems,”** In *Proceedings of the Institute of Computational Fluid Dynamics Conference*, Edited by K.W. Morton, M.J. Baines, Oxford University Press, pp. 311-317. 1995.

[Ber95a] M. Berzins, T.H.C. Childs, K.W. Dalgarno, G.R. Ryder, G. Stein.
**“Densification and Distortion in Selective Laser Sintering of Polycarbonate,”** In *Proc 6th Symposium on Solid Free Form Fabrication*, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 196--203. 1995.

[Ber95c] M. Berzins.
**“Temporal Error Control in the Method of Lines for Convection Dominated Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 16, pp. 558--580. 1995.

[Chr1995a] G.E. Christensen, R.D. Rabbitt, M.I. Miller, S.C. Joshi, U. Grenander, T.A. Coogan.
**“Topological Properties of Smooth Anatomic Maps,”** In *Information Processing in Medical Imaging*, pp. 101--112. 1995.

[Gha95] P. Gharpure, C.R. Johnson.
**“A Cellular Automaton Model of Electrical Activation in Canine Ventricles: A Validation Study,”** SCI Institute Technical Report, No. UUSCI-1995-002, *University of Utah*, 1995.

[Hal1995a] J.W. Haller, M.I. Miller, G.E. Christensen, S. Joshi, M. Gado, J. Csernansky, M.W. Vannier.
**“A Comparison of Automated and Manual Segmentation of Hippocampus MR Images,”** In *Proceedings of SPIE Medical Imaging*, pp. 206--215. March, 1995.

[Hal1995b] J.W. Haller, G.E. Christensen, S. Joshi, M.I. Miller, M.W. Vannier.
**“Digital Atlas-Based Segmentation of the Hippocampus,”** In *Computer Assisted Radiology: Proceedings of the International Symposium on Computer and Communications Systems for Image Guided Diagnosis and Therapy*, Edited by C.C. Jaffe and H.U. Lemke and K. Inamura and M.W. Vannier, pp. 152--157. June, 1995.

[Han95a] C.D. Hansen, G.C. de Verdiere, M. Krogh, J. Painter, R. Troutman.
**“Binary-Swap Volumetric Rendering on the T3D,”** In *Cray Users Group Conference*, Denver, Co., pp. 61--69. March, 1995.

[Han95b] C.D. Hansen, M. Krogh, W. White.
**“Massively Parallel Visualization: Parallel Rendering,”** In *SIAM Parallel Computation Conference*, San Francisco, Ca., pp. 790--795. February, 1995.

[Hen95a] C.S. Henriquez, C.R. Johnson, K.A. Henneberg L.J., A.E. Pollard.
**“Large Scale Biomedical Modeling and Simulation: From Concepts to Results,”** SCI Institute Technical Report, No. UUSCI-1995-001, *University of Utah*, 1995.

[Hod1995a] D.C. Hodgson, P.K. Jimack, P. Selwood, M. Berzins.
**“Scalable, Parallel Generation of Partitioned Unstructured Meshes,”** In *Parallel C.F.D. -- Implementations and Results using Parallel Computers*, Parallel CFD Conference 1995, pasadena, California, Edited by A. Ecer and J. Periaux and N. Satufoka and S. Taylor, pp. 665-672. June, 1995.

ISBN: 0-444 823220

[Joh95a] C.R. Johnson, R.S. MacLeod, J.A. Schmidt.
**“Software Tools for Modeling, Computation, and Visualization in Medicine,”** In *CompMed 94 Proceedings*, World Scientific, 1995.

[Joh95b] C.R. Johnson, S.G. Parker.
**“Applications in Computational Medicine using SCIRun: A Computational Steering Programming Environment,”** In *Supercomputer `95*, Edited by H.W. Meuer, Springer-Verlag, pp. 2--19. 1995.

[Joh95c] C.R. Johnson.
**“Direct and Inverse Bioelectric Field Problems,”** In *Computational Science Education Project*, Edited by E. Oliver and M. Strayer and V. Meiser and D. Zachmann and R. Giles, DOE, Washington, D.C. 1995.

[Joh95d] C.R. Johnson.
**“Numerical Methods for Bioelectric Field Problems,”** In *The Biomedical Engineering Handbook*, Edited by J.D. Bronzino, CRC Press, Boca Ratan pp. 161--188. 1995.

[Jos1995a] S.C. Joshi, M.I. Miller, G.E. Christensen, A. Banerjee, T.A. Coogan, U. Grenander.
**“Hierarchical brain mapping via a generalized Dirichlet solution for mapping brain manifolds,”** In *Proc. of the SPIE International Symposium on Optical Science, Engineering, and Instrumentation*, pp. 278--289. August, 1995.

[Jos1995b] S.C. Joshi, J. Wang, M.I. Miller, D.V. Essen, U. Grenander.
**“On the Differential Geometry of the Cortical Surface,”** In *Proceedings of SPIE 1995 International Symposium: Vision Geometry IV*, San Diego, CA, pp. 304--311. August, 1995.

[Kle95a] R.N. Klepfer, C.R. Johnson, R.S. MacLeod.
**“The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study,”** In *IEEE Engineering in Medicine and Biology Society 17th Annual International Conference*, IEEE Press, pp. 233--234. 1995.

[Pai95a] J. Painter, P. McCormick, M. Krogh, C.D. Hansen, G.C. de Verdiere.
**“ACLMPL: Portable and Efficient Message Passing for MPPs,”** In *First European T3D User's Group Workshop*, Lausanne Switzerland, pp. 4--10. November, 1995.

[Pao1995a] A. Paoluzzi, V. Pascucci, M. Vicentino.
**“Geometric Programming: A Programming Approach to Geometric Design,”** In *ACM Transactions on Graphics*, Vol. 14, No. 3, pp. 266--306. July, 1995.

[Pao1995b] A. Paoluzzi, V. Pascucci.
**“Building Design Programming with a Functional Language,”** In *Proceedings of 6th Conference on Computing in Civil and Building Engineering*, Berlin, Germany, AA Balkema, Rotterdam, July, 1995.

[Pao1995c] A. Paoluzzi, V. Pascucci, C. Sansoni.
**“Prototype Shape Modeling with a Design Language,”** In *Proceedings of the Sixth Int. Conf. on Computer-Aided Architectural Design Futures*, The Global Design Studio, Edited by Milton Tan and Robert Teh, Centre for Advanced Studies in Architecture, National University of Singapore pp. 59--78. 1995.

[Par1995a] S.G. Parker, C.R. Johnson.
**“SCIRun: A Scientific Programming Environment for Computational Steering,”** In *Proceedings of the 1995 ACM/IEEE Conference on Supercomputing*, San Diego, California, USA, Supercomputing '95, No. 52, ACM, New York, NY, USA 1995.

ISBN: 0-89791-816-9

DOI: 10.1145/224170.224354

[Pas1995a] V. Pascucci, V. Ferrucci, A. Paoluzzi.
**“Dimension-independent convex-cell based HPC: representation scheme and implementation issues,”** In *SMA '95: Proceedings of the Third Symposium on Solid Modeling and Applications*, Note: *held May 17-19, 1995 in Salt Lake City, Utah*, *ACM*, pp. 163--174. May, 1995.

[Rab1995a] R.D. Rabbitt, J.A. Weiss, G.E. Christensen, M.I. Miller.
**“Mapping of Hyperelastic Deformable Templates Using the Finite Element Method,”** In *Proc SPIE (Vision Geometry IV)*, Vol. 2573, pp. 252--265. 1995.

[Sch95a] J.A. Schmidt, C.R. Johnson, J.C. Eason, R.S. MacLeod.
**“Applications of Automatic Mesh Generation and Adaptive Methods in Computational Medicine,”** In *Modeling, Mesh Generation, and AdaptiveMethodsforPartial Differential Equations*, Edited by I. Babuska and J.E. Flaherty and W.D. Henshaw and J.E. Hopcroft and J.E. Oliger and T. Tezduyar, Springer-Verlag, pp. 367--390. 1995.

[Sch95b] J.A. Schmidt, C.R. Johnson.
**“Defibsim: An Interactive Defibrillation Device Design Tool,”** In *IEEE Engineering in Medicine and Biology Society 17th Annual International Conference*, IEEE Press, pp. 305--306. 1995.

[Sch95c] J.A. Schmidt, C.R. Johnson, R.S. MacLeod.
**“An Interactive Computer Model for Defibrillation Device Design,”** In *International Congress on Electrocardiology*, ICE, pp. 160--161. 1995.

[She95a] H.W. Shen, C.R. Johnson.
**“Sweeping Simplices: A Fast Iso-surface Extraction Algorithm for Unstructured Grids,”** In *IEEE Visualization `95*, IEEE Press, pp. 143--150. 1995.

[Sle95a] P.A. Sleigh, P.H. Gaskell, M. Berzins, J.M. Ware, N.G. Wright.
**“A Reliable and Accurate Technique for the Modelling of Practically Occurring Open Channel Flow,”** In *Proceedings of the Ninth International Conference on Numerical Methods in Laminar and Turbulent Flow*, Pineridge Press, pp. 881--892. 1995.

[Spe1995a] W. Speares, M. Berzins.
**“A Fast 3-D Unstructured Mesh Adaptation Algorithm with Time-Dependent Upwind Euler Shock Diffraction Calculations,”** In *Proc. of 6th International Symposium on Computational Fluid Dynamics*, Vol. 3, Edited by M. Hafez and K. Oshima, pp. 1181--1188. 1995.

[Spe1995b] W. Speares, M. Berzins.
**“A 3D Unstructured Mesh Adaption Algorithm for Time Dependent Shock Dominated Problems,”** School of Computer Studies Research Report, No. 95.33, *University of Leeds*, 1995.

[Tom1995a] A. Tomlin, J.M. Ware, J. Smith, M. Berzins, M.J. Pilling.
**“Efficient High Resolution Methods for Air Pollution Models,”** In *International Conference on Air Pollution - Proceedings*, Vol. 1, Computational Mechanics Inc, pp. 201--208. 1995.

[Tro95a] R. Troutman, C.D. Hansen.
**“Binary-Swap Shear-Warp Volume Renderer on the T3D,”** In *Cray Users Group Conference*, Fairbanks, Ak., pp. 93--102. September, 1995.

[Tun95a] W.B. Tung, C.D. Hansen, D.R. Jones, W.H. Chen, H.A. Al-Sunaidi.
**“Development of an Interactive Reservoir Simulation and Visualization System for a Massively Parallel Processor,”** In *5th ARCHIE Conference: Visualization Technology to Find and Develop more Oil and Gas*, The Woodlands, Texas, Note: *Refereed abstract.*, pp. 105--107. May, 1995.

[Wal1995b] C. Walshaw, M. Berzins.
**“Dynamic Load-Balancing For PDE Solvers On Adaptive Unstructured Meshes,”** In *Concurrency*, Vol. 7, No. 1, pp. 17--28. 1995.

[Wal95a] C. Walshaw, M. Berzins.
**“Adaptive Time-dependent CFD on Distributed Unstructured Meshes,”** In *Parallel Computational Fluid Dynamics: New Trends and Advances*, Elsevier Science, pp. 191--198. 1995.

[War1995a] J.M. Ware, M. Berzins.
**“Adaptive Finite Volume Methods for Time-dependent P.D.E.s.,”** In *Modeling, Mesh Generation and Adaptive Numerical Methods for PDEs.*, IMA Volumes in Mathematics and Its Applications Series, Vol. 75, Springer Verlag, pp. 417--430. 1995.

[Wei95a] D.M. Weinstein, C.R. Johnson, J.A. Schmidt.
**“Effects of Adaptive Refinement on the Inverse EEG Solution,”** In *SPIE*, In *Experimental and Numerical Methods for Solving Ill-Posed Inverse Problems*, Vol. 2570, SPIE, pp. 2--11. 1995.

[Wei95b] D.M. Weinstein, C.R. Johnson.
**“Hierarchical Data Structures for Interactive Volume Visualization,”** School of Computing Technical Report, No. UUCS-95-012, *University of Utah*, Salt Lake City, UT 1995.

[Whi95a] R.T. Whitaker.
**“Algorithms for Implicit Deformable Models,”** In *Fifth International Conference on Computer Vision'95*, pp. 822--827. 1995.

1994

[Ade94a] S. Adelson, C.D. Hansen.
**“Fast Stereoscopic Images with Ray-Traced Volume Rendering,”** In *Symposium on Volume Visualization*, Washington, DC., pp. 3--9. October, 1994.

[Ber1994a] M. Berzins, J.M. Ware.
**“Reliable Finite Volume Methods for the Navier Stokes Equations.,”** In *Numerical methods for the Navier-Stokes equations*, Notes on Numerical Fluid Mechanics, No. 47, Edited by F.K. Hebeker and R. Rannacher and G. Wittum, Springer, pp. 1-8. 1994.

DOI: 10.1007/978-3-663-14007-8_1

[Git94a] C.S. Gitlin, C.R. Johnson.
**“Techniques for Visualizing 3D Unstructured Meshes,”** School of Computing Technical Report, No. UUCS-94-018, *University of Utah*, 1994.

[Han94a] C.D. Hansen T.Crockett, S. Whitman.
**“Parallel Rendering,”** In *IEEE Parallel and Distributed Technology*, Vol. 2, No. 2, Note: *Guest editors' introduction*, pp. 7. Summer, 1994.

[Hen94a] C.S. Henriquez, C.R. Johnson, K.A. Henneberg, L.J. Leon, A.E. Pollard..
**“Large Scale Biomedical Modeling and Simulation: From Concepts to Results,”** In *Frontiers in Biomedical Computing*, Edited by N. Thakor, IEEE Press, Philadelphia 1994.

[Joh94a] C.R. Johnson, S.G. Parker.
**“A Computational Steering Model Applied to Problems in Medicine,”** In *Supercomputing 94*, IEEE Press, pp. 540--549. 1994.

[Joh94e] C.R. Johnson, P. Alfeld.
**“Computational Engineering and Science at the University of Utah,”** In *IEEE Computational Science and Engineering*, pp. 7--9. 1994.

[Ma94a] K.L. Ma, J. Painter, C.D. Hansen, M. Krogh.
**“Parallel Volume Rendering Using Binary-Swap Compositing,”** In *IEEE Computer Graphics and Applications*, Vol. 14, No. 4, pp. 59--68. 1994.

[Mac94d] R.S. MacLeod, P.R. Ershler, C.R. Johnson M.A..
**“Map3d: Scientific Visualization Program for Multichannel Time Series Data on Unstructured, Three-Dimensional Meshes. Program User's Guide,”** School of Computing Technical Report, No. UUCS-94-016, *University of Utah*, 1994.

[Mac94e] R.S. MacLeod, C.R. Johnson, P.R. Ershler.
**“Construction of a Human Torso Model from Magnetic Resonance Images for Problems in Computational Electrocardiography,”** School of Computing Technical Report, No. UUCS-94-017, *University of Utah*, 1994.

[Mil1994a] M.I. Miller, S. Joshi, D.R. Maffitt, J.G. McNally, U. Grenander.
**“Membranes, Mitochondria and Amoebae: Shape Models,”** In *Journal of Applied Statistics*, Vol. 21, No. 1, 2, Edited by Kanti Mardia, pp. 141--163. 1994.

[Par94] S.G. Parker, D.M. Weinstein, C.R. Johnson.
**“A Morphing Algorithm for Generating Near Optimal Grids: Applications in Computational Medicine,”** School of Computing Technical Report, No. UUCS-94-014, *University of Utah*, 1994.

[Par94b] S.G. Parker, C.R. Johnson.
**“Interactive Manipulation of Contour Data Using the Layers Program - User Guide,”** School of Computing Technical Report, No. UUCS-94-014, *University of Utah*, 1994.

[Pen94b] S.V. Pennington, M. Berzins.
**“New NAG Library Software for First-Order Partial Differential Equations,”** In *ACM Transactions on Mathematical Software*, Vol. 20, No. 1, pp. 63--99. March, 1994.

[She94a] H.W. Shen, P.B. Gharpure, C.R. Johnson.
**“Visualization of 3-D wave prorogation in the heart - a new technique,”** In *IEEE Engineering in Medicine and Biology Society 16th Annual International Conference*, IEEE Press, pp. 684--685. 1994.

[She94b] H.W. Shen, C.R. Johnson.
**“Semi-automatic image segmentation: A bimodel thresholding approach,”** School of Computing Technical Report, No. UUCS-94-019, *University of Utah*, 1994.

[She94c] H.W. Shen, C.R. Johnson.
**“Differential volume rendering: A fast alogrithm for scalar field animation,”** In *Visualization 94*, IEEE Press, pp. 180--187. 1994.

[Str1994a] C.B. Straight, E.P. France, T.D. Rosenberg, L.E. Paulos, J.A. Weiss.
**“Soft Tissue Fixation to Bone: A More Biomechanical Analysis of Spiked Soft Tissue Washers,”** In *American Journal of Sports Medicine*, Vol. 22, pp. 339--343. 1994.

[Wei94a] D.M. Weinstein, S.G. Parker, C.R. Johnson.
**“A Physically Based Mesh Generation Algorithm: Applications in Computational Medicine,”** In *IEEE Engineering in Medicine and Biology Society 16th Annual International Conference*, IEEE Press, pp. 718--719. 1994.

[Whi94a] S. Whitman, C.D. Hansen, T.W. Crockett.
**“Recent Developments in Parallel Rendering,”** In *IEEE Computer Graphics and Applications*, Vol. 14, No. 4, Note: *Guest editors' introduction*, pp. 21--22. July, 1994.

[Yu94a] F. Yu, C.R. Johnson.
**“An Automatic Adaptive Refinement and Derefinement Method,”** In *Proceedings of the 14th IMACS World Congress*, pp. 1555--1557. 1994.

1993

[Bag1993a] C.M. Bagi, M. Mecham, J.A. Weiss, S.C. Miller.
**“Comparative Morphometric Changes in Rat Cortical Bone Following Ovariectomy and/or Immobilization,”** In *Bone*, Vol. 14, pp. 877--883. 1993.

[Ber1993a] F. Bernardini, V. Ferrucci, A. Paoluzzi, V. Pascucci.
**“Product Operator on Cell Complexes,”** In *SMA '93: Proceedings of the Second Symposium on Solid Modeling and Applications*, Note: *held May 19-21, 1993 in Montreal, Quebec, Canada*, *ACM*, pp. 43--52. May, 1993.

[Ber1993b] M. Berzins, J.M. Ware.
**“Reliable Finite Volume Methods for Time-Dependent Partial Differential Equations,”** In *MAFELAP 1993 Highlights*, Edited by J.R. Whiteman and John Wiley, pp. 299--306. 1993.

[Fra1993a] E.P. France, J.A. Weiss, L.E. Paulos.
**“Allograft Ligament Reconstruction: Biomechanical Issues and Testing,”** In *Sports Medicine and Arthroscopy Review*, Vol. 1, pp. 47--60. 1993.

[Gha93a] P.B. Gharpure, C.R. Johnson.
**“A 3D Cellular Automata Model of the Heart,”** In *IEEE Engineering in Medicine and Biology Society 15th Annual International Conference*, IEEE Press, pp. 752--753. 1993.

[Han93a] C.D. Hansen, S. Tenbrink.
**“The Impact of Gigabit Network Research on Scientific Visualization,”** In *The Visual Computer*, Vol. 9, No. 6, pp. 318--323. 1993.

[Han93b] C.D. Hansen, M. Krogh.
**“Visualization on Massively Parallel Computers using CM/AVS,”** In *AVS Users Conference*, Orlando, Fl., pp. 129--137. May, 1993.

[Hin93a] P. Hinker, C.D. Hansen.
**“Geometric Optimization,”** In *Visualization 1993*, San Jose, Ca., pp. 189--195. October, 1993.

[Joh93a] C.R. Johnson, R.S. MacLeod.
**“Inverse Solutions for Electric and Potential Field Imaging,”** In *Physiological Imaging, Spectroscopy, andEarlyDetection Diagnostic Methods*, Vol. 1887, Edited by R.L. Barbour and M.J. Carvlin, SPIE, pp. 130--139. 1993.

[Joh93b] C.R. Johnson, R.S. MacLeod, M.A. Matheson.
**“Computational Medicine: Bioelectric Field Problems,”** In *IEEE Computer*, Vol. 26, No. 26, pp. 59--67. Oct, 1993.

[Joh93c] C.R. Johnson, R.S. MacLeod.
**“High Performance Computing in Medicine: Direct and Inverse Problems in Cardiology,”** In *IEEE Engineering in Medicine and Biology Society 15th Annual International Conference*, pp. 582--583. 1993.

[Joh93d] C.R. Johnson, R.S. MacLeod, M.A. Matheson, C. Zimmerman.
**“The Body Electric,”** In *Discover Magazine*, pp. 72--77. February, 1993.

[Jos1993a] S. Joshi, M. Miller.
**“Maximum a Posteriori Estimation with Good's Roughness for Three-Dimensional Optical-Sectioning Microscopy,”** In *J Opt Soc Am A*, Vol. 10, No. 5, pp. 1078--1085. May, 1993.

[Ma93a] K.L. Ma, J. Painter, C.D. Hansen, M. Krogh.
**“A Data Distributed, Parallel Algorithm for Ray-Traced Volume Rendering,”** In *Proceedings of the Parallel Rendering Symposium 1993*, San Jose, Ca., pp. 15--22. October, 1993.

[Ma93b] K.L. Ma, J.S. Painter, C.D. Hansen, M.F. Krogh.
**“A Data Distributed Parallel Algorithm for Ray-Traced Volume Rendering,”** ICASE Report, Hampton, VA, *Institute for Computer Applications in Science and Engineering, NASA Langley Research Center*, pp. 15--22. August, 1993.

[Mac93] R.S. MacLeod, C.R. Johnson, M.A. Matheson.
**“Visualization of Bioelectric Fields,”** In *IEEE Computer Graphics and Applications*, Vol. 14, pp. 10--12. Jul, 1993.

[Mac93b] R.S. MacLeod, C.R. Johnson.
**“Map3d: Interactive Scientific Visualization for Bioengineering Data,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 15th Annual International Conference*, IEEE Press, pp. 30--31. 1993.

[Ort93a] F. Ortega, C.D. Hansen, J. Ahrens.
**“Fast Data Parallel Polygon Rendering,”** In *Supercomputing 1993*, Portland, Or., pp. 709--718. November, 1993.

[Pao1993a] A. Paoluzzi, V. Pascucci, M. Vicentino.
**“PLASM Functional Approach to Design: Representation of Geometry,”** In *Proceedings of the Fifth International Conference on Computer-Aided Design Futures (CAAD Futures '93)*, Edited by U. Flemming and S. Van Wyk, North-Holland, pp. 127--141. 1993.

[Pao1993b] A. Paoluzzi, V. Pascucci, M. Vicentino.
**“Un linguaggio di progettazione orientato al Solid Modeling (A Design Language oriented to Solid Modeling),”** In *Atti del convegno IcoGraphics '93*, Note: *In Italian*, Mondadori Informatica, Milano, Italy pp. 60--66. March, 1993.

[Par93a] J. Parker, M. Berzins, J.M. Cameron, K.A. Collins, C.M. Sawyer.
**“Final Report on SERC/DTI Parallel Applications Programme Collaboration Between EPCC, Rolls Royce ands Leeds University,”** *Edinburgh Parallel Computing Centre*, September, 1993.

[Wal93a] C. Walshaw, M. Berzins.
**“Enhanced Dynamic Load Balancing of Adaptive Unstructured Meshes,”** In *Proc. of 1993 SIAM Conference on Parallel Processing for Scientific Computing*, Vol. 2, pp. 971--978. 1993.

1992

[And1992a] D.R. Anderson, J.A. Weiss, S. Takai, K.J. Ohland, S.L-Y. Woo.
**“Healing of the Medial Collateral Ligament Following a Triad Injury: A Biomechanical and Histological Study of the Knee in Rabbits,”** In *Journal of Orthopaedic Research*, Vol. 10, pp. 485--495. 1992.

[Ber1992b] M. Berzins, A.J. Preston, P.M. Dew, L.E. Scales.
**“Towards Efficient D.A.E. Solvers for the Solution of Dynamic Simulation Problems,”** In *Proc of I.M.A. 1989 O.D.E. Conference*, Edited by I. Gladwell and J. Cash and A. Iserles, Oxford University Press, pp. 299--308. 1992.

ISBN: 0-19-853659-3

[Ber1992c] M. Berzins, R.M. Furzeland.
**“An Adaptive Theta Method for the Solution of Stiff and Non-stiff Differential Equations,”** In *Applied Numerical Mathematics*, Vol. 9, pp. 1--19. 1992.

[Ber92d] M. Berzins, P.M. Dew, S. Hillen.
**“Exploiting Parallelism for Adaptive CFD Software,”** In *Parallelogram*, pp. 14--16. February, 1992.

[Bro1992a] K.W. Brodlie, M. Berzins, P.M. Dew, A. Poon, H. Wright.
**“Visualization and its Use in Scientific Computation,”** In *Programming Environments for High-Level Scientific Problem Solving*, Elsevier, pp. 293--303. 1992.

[For92a] D. Forslunk, P. Hinker, C.D. Hansen, W.St. John, S. Tenbrink, J. Brewton.
**“High-speed Networks, Visualization and Massive Parallelism in the Advanced Computing Laboratory,”** In *Computing Systems in Engineering*, Vol. 3, No. 1-4, 1992.

[Han92a] C.D. Hansen, P. Hinker.
**“Massively Parallel Isosurface Extraction,”** In *Visualization 1992*, Boston, Ma., pp. 77--83. October, 1992.

[Han92b] C.D. Hansen, D. Butler.
**“Visualization '91 Workshop Report: Scientific Visualization Environments,”** In *Computer Graphics Quarterly*, Vol. 26, No. 3, pp. 213--216. August, 1992.

[Joh1992e] C.R. Johnson, R.S. MacLeod, P.R. Ershler.
**“A Computer Model for the Study of Electrical Current Flow in the Human Thorax,”** In *Computers in Biology and Medicine*, Vol. 22, No. 5, Elsevier BV, pp. 305--323. 1992.

[Joh92b] C.R. Johnson, R.S. MacLeod, M.A. Matheson.
**“Computer Simulations Reveal Complexity of Electrical Activity in the Human Thorax,”** In *Computers in Physics*, Vol. 6, pp. 230--237. May/June, 1992.

[Joh92d] C.R. Johnson, R.S. MacLeod, A. Dutson.
**“Effects of Anistropy and Inhomogeneity on Electrocardiographic Fields: A Finite Element Study,”** In *Engineering in Medicine and Biology Society 14th Annual International Conference*, IEEE Press, pp. 2009--2010. 1992.

[Joh92e] C.R. Johnson, R.S. MacLeod.
**“Computational Studies of Forward and Inverse Problems in Electrocardiology,”** In *Biomedical Modeling and Simulation*, Edited by J. Eisenfeld and D.S. Levine and M. Witten, Elsevier Science Publishers, Elsevier, Amsterdam pp. 283--290. 1992.

[Joh92f] C.R. Johnson, R.S. MacLeod.
**“Nonuniform Spatial Mesh Adaption Using a Posteriori Error Estimate: Applications to Forward and Inverse Problems,”** In *Adaptive Methods for Partial Differential Equations*, Vol. 14, Edited by J.E. Flaherty and M.S. Shephard, Elsevier, pp. 311--326. 1992.

[Law1992a] J. Lawson, M. Berzins.
**“Towards an Automatic Algorithm for the Numerical Solution of Parabolic P.D.E.s Using the Method of Lines,”** In *proc of I.M.A. 1989 O.D.E. Conference*, Edited by I. Gladwell and J. Cash and A. Iserles, Oxford University Press, pp. 309--322. 1992.

ISBN: 0-19-853659-3

[Mac92c] R.S. MacLeod, C.R. Johnson, M.A. Matheson.
**“Visualization Tools for Computational Electrocardiology,”** In *Visualization in Biomedical Computing*, pp. 433--444. 1992.

[Mac92d] R.S. MacLeod, C.R. Johnson, M.A. Matheson.
**“Visualization of cardiac bioelectricity --- a case study,”** In *IEEE Visualization `92*, pp. 411--418. 1992.

[Mac92e] R.S. MacLeod, C.R. Johnson, M.J. Gardner B.M..
**“Localization of Ischemia during Coronary Angioplasty using Body Surface Potential Mapping and an Electrocardiographic Inverse Solution,”** In *Computers in Cardiology*, IEEE Press, pp. 251--254. 1992.

[Pas1992a] A. Pascucci, V. Pascucci.
**“Uso del calcolatore nella produzione, elaborazione ed archiviazione di proiezioni parallele (Using the computer for generating, processing and archiving parallel projections),”** In *Atti del convegno L'immagine nel rilievo*, Edited by C. Cundari, Gangemi, pp. 540--561. 1992.

[Wal1992a] C. Walshaw, M. Berzins.
**“Dynamic Load Balancing for PDE Solvers on Adaptive Unstructured Meshes,”** School of Computer Studies Research Report, No. 92.32, *University of Leeds*, December, 1992.

[War1992a] J.M. Ware, M. Berzins.
**“Finite Volume Techniques for Time-dependent Fluid-Flow Problems,”** In *Advances in Comp. Meths. for P.D.E.s VII*, New Jersey, *Rutgers Univ.*, pp. 794--798. 1992.

[Wil92a] C. Williams, J. Rasure, C.D. Hansen.
**“The State of the Art of Visual Languages for Visualization,”** In *Visualization 1992*, Boston, Ma., pp. 202--209. October, 1992.

1991

[Ber1991a] M. Berzins, P. Baehmann, J.E. Flaherty, J. Lawson.
**“Towards An Automated Finite Element Solver for Time-Dependent Fluid-Flow Problems,”** In *MAFELAP 90*, Edited by J.R. Whiteman, Academic Press, pp. 181--188. 1991.

[Ber1991b] M. Berzins, P.M. Dew.
**“Chebyshev Polynomial Software for Elliptic-Parabolic Systems of P.D.E.s,”** In *A.C.M. Transactions on Mathematical Software*, Vol. 17, No. 2, pp. 178--206. June, 1991.

[Ber1991c] M. Berzins.
**“Balancing Space and Time Errors for Spectral Methods used with the Method of Lines for Parabolic equations,”** 1991.

[Han91a] C.D. Hansen, S. Tenbrink.
**“The Impact of Gigabit Networking on Imaging,”** In *Digital Imaging*, Anaheim, Ca., pp. 191--194. April, 1991.

[Joh91a] C.R. Johnson, R.S. MacLeod.
**“Computer Models for Calculating Transthoracic Current Flow,”** In *IEEE Engineering in Medicine and Biology Society 13th Annual International Conference*, IEEE Press, pp. 768--769. 1991.

[Law1991a] J. Lawson, M. Berzins, P.M. Dew.
**“Balancing Space and Time Errors in the Method of Lines for Parabolic Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 12, No. 3, pp. 573--594. 1991.

[Mac91a] R.S. MacLeod, C.R. Johnson, P.R. Ershler.
**“Construction of an Inhomogeneous Model of the Human Torso for Use in Computational Electrocardiography,”** In *IEEE Engineering in Medicine and Biology Society 13th Annual International Conference*, IEEE Press, pp. 688--689. 1991.

[Pre1991a] A.J. Preston, M. Berzins.
**“On Algorithms for the Location of Discontinuities for Dynamic Simulation Problems,”** In *Computers in Chemical Engineering*, Vol. 15, No. 10, pp. 701--713. 1991.

[Sus91a] S. Susswein, T.C. Henderson, J. Zachary, C.D. Hansen, P. Hinker, G. Marsden.
**“Parallel Path Consistency,”** In *International Journal of Parallel Programming*, Vol. 20, No. 6, pp. 453--473. 1991.

[Wei1991a] J.A. Weiss, S.L-Y. Woo, K.J. Ohland, S. Horibe, P.O. Newton.
**“Evaluation of a New Injury Model to Study Medial Collateral Ligament Healing: Primary Repair vs Nonoperative Treatment,”** In *Journal of Orthopaedic Research*, Vol. 9, pp. 516--528. 1991.

[Zac1991a] O. Zachar, O. Alter.
**“Interpretation of the Curious Results of the New Quantum Formalism of Pre- and Post-Selected Systems,”** In *Foundations of Physics*, Vol. 21, No. 7, pp. 803-–820. July, 1991.

DOI: 10.1007/BF00733346

1990

[Alt1990a] O. Alter, O. Zachar.
**“Achilles and the Turtle in the Maze of the Weak Measurement,”** Tel Aviv University Report, No. TAUP 90-1832, *Tel Aviv University*, 1990.

[Ber1990a] M. Berzins, A.J. Preston, P.M. Dew.
**“Integration Algorithms for the Dynamic Simulation of Production Processes,”** In *Proc of Third European Conference for Mathematics in Industry*, Edited by J. Manley et al., Kluwer Academic Publishers, Stuttgart., pp. 265--271. 1990.

[Han90a] C.D. Hansen.
**“High-level Tools for Scientific Visualization,”** In *Computer Use By Engineers (CUBE) Symposium*, Sante Fe, NM., Note: *Refereed abstract.*, November, 1990.

[Joh90a] C.R. Johnson, A.E. Pollard.
**“Electrical Activation of the Heart: Computational Studies of the Forward and Inverse Problems in Electrocardiography,”** In *Computer Assisted Analysis and Modeling*, MIT Press, pp. 583--628. 1990.

[Ske1990a] R.D. Skeel, M. Berzins.
**“A Method for the Spatial Discretisation of Parabolic Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 11, No. 1, pp. 1--32. January, 1990.

[Woo1990a] S.L-Y. Woo, K.J. Ohland, J.A. Weiss.
**“The Effects of Aging and Sex on the Biomechanical Properties of the Medial Collateral Ligament,”** In *Mechanisms of Ageing and Development*, Vol. 56, pp. 129--142. 1990.

[Woo1990b] S.L-Y. Woo, J.A. Weiss, M.A. Gomez, D.A. Hawkins.
**“Measurement of Changes in Ligament Tension with Knee Motion and Skeletal Maturation,”** In *Journal of Biomechanical Engineering*, Vol. 112, pp. 46--51. 1990.

1989

[Ber1989a] M. Berzins.
**“Developments in NAG Library Software for Parabolic Equations,”** In *Scientific Software Systems*, Edited by J.C. Mason and M.G. Cox, Chapman and Hall, pp. 59--72. July, 1989.

ISBN: 0412345706

[Ber1989b] M. Berzins, P.M. Dew, R.M. Furzeland.
**“Developing Software for Time-Dependent Problems Using the Method of Lines and Differential Algebraic Integrators,”** In *Applied Numerical Mathematics*, Vol. 5, pp. 375--397. 1989.

[Han89a] C.D. Hansen, T. Henderson.
**“CAGD-Based Computer Vision,”** In *IEEE Pattern Recognition and Machine Intelligence*, Vol. 11, No. 10, pp. 1181--1193. November, 1989.

[Hen89a] T. Henderson, C.D. Hansen, R. Grupen.
**“CAD-Based 3-D Object Recognition,”** In *IEEE Systems, Man and Cybernetics Conference*, Boston, Ma., pp. 168--172. November, 1989.

1988

[Aya1988a] N. Ayache, C.D. Hansen.
**“Rectification of Images for Binocular and Trinocular Stereovision,”** In *Proceedings of the 9th International Conference on Pattern Recognition*, Rome, Italy, Vol. 1, pp. 11--16. November, 1988.

DOI: 10.1109/ICPR.1988.28160

[Ber1988b] M. Berzins.
**“Global Error Estimation in the Method of Lines for Parabolic Equations,”** In *SIAM Journal on Scientific Computing*, Vol. 9, pp. 687--703. 1988.

[Ber1988c] M. Berzins, R. Brankin, I. Gladwell.
**“Design of Stiff Integrators in the N.A.G. Library,”** In *Signum Bulletin*, Vol. 23, No. 2, pp. 16--24. April, 1988.

[Gru88a] R. Grupen, C.D. Hansen, T. Henderson.
**“Apparent Symmetries in Range Data,”** In *Pattern Recognition Letters*, Vol. 7, pp. 107--111. February, 1988.

[Han88a] C.D. Hansen, T. Henderson.
**“Automatic Generation of Recognition Strategies,”** In *International Conference on Computer Vision*, Tampa, Florida, pp. 275--279. December, 1988.

[Han88b] C.D. Hansen, N. Ayache, F. Lustman.
**“Towards Real-time Trinocular Stereo,”** In *International Conference on Computer Vision*, Tampa, Florida, pp. 129--133. December, 1988.

[Han88c] C.D. Hansen, N. Ayache, Francis Lustman.
**“Efficient Depth Estimation using Trinocular Stereo,”** In *SPIE Conference on Intelligent Robots*, Cambridge, Massachusetts, Note: *Refereed abstract.*, November, 1988.

[Hen88a] T.C. Henderson, A. Mitiche, E. Weitz, C.D. Hansen.
**“Multisensor Knowledge Systems: Interpreting 3-D structure,”** In *International Journal of Robotics Research, Special Issue on Multisensor Integration*, Vol. 7, No. 6, pp. 114--137. December, 1988.

[Hen88b] T. Henderson, C.D. Hansen.
**“CAD-Based Computer Vision,”** In *SPIE Conference*, Orlando, Florida, April, 1988.

1987

[Ber1987a] M. Berzins, P.M. Dew.
**“A Note on C0 Chebyshev Methods for Parabolic Equations,”** In *I.M.A. Journal of Numerical Analysis*, Vol. 7, pp. 15--37. 1987.

[Han87a] C.D. Hansen, T. Henderson.
**“CAGD-Based Computer Vision,”** In *IEEE Computer Vision Workshop*, Miami Beach, Florida, pp. 100--106. December, 1987.

[Hen87a] T. Henderson, C.D. Hansen, Bir Bhanu.
**“Intrinsic Characteristics as the Interface between CAD and Machine Vision Systems,”** In *Pattern Recognition Theory and Applications*, NATO-ASI Series, Edited by P. Devijver and J. Kittler, Springer-Verlag, pp. 461--470. 1987.

[Hen87b] T.C. Henderson, C.D. Hansen, A. Samal, C.C. Ho, B. Bhanu.
**“CAD-Based Robotics,”** In *IEEE Conference on Robotics and Automation*, Raleigh, NC., pp. 631--635. May, 1987.

1986

[Ber1986a] M. Berzins.
**“A C1 Interpolant for Codes Based on Backward Differentiation Formulae,”** In *Applied Numerical Mathematics*, Vol. 2, pp. 109--118. 1986.

[Hen86a] T. Henderson, C.D. Hansen, B. Bhanu.
**“The Specification of Distributed Sensing and Control,”** In *Journal of Robotic Systems*, Vol. 2, No. 4, pp. 387--396. 1986.

[Hen86b] T.C. Henderson, C.D. Hansen, A. Samal, C.C. Ho, B. Bhanu.
**“CAGD Based 3-D Visual Recognition,”** In *International Conference on Pattern Recognition*, Paris, France, pp. 230--232. October, 1986.

1985

[Hen85a] T.C. Henderson, C.D. Hansen, W.S. Fai.
**“Organizing Spatial Data for Robotics Systems,”** In *Computers in Industry*, Vol. 6, No. 5, pp. 331--344. October, 1985.

[Hen85b] T.C. Henderson, C.D. Hansen, B. Bhanu.
**“A Framework for Distributed Sensing and Control,”** In *International Joint Conference on Artificial Intelligence*, Los Angeles, Ca., pp. 1106--1109. August, 1985.

[Hen85c] T.C. Henderson, C.D. Hansen.
**“A Kernel for Multi-sensor Robotics Systems,”** In *Proceedings of the CAD/CAM, Robotics, and Automation Institute and Conference*, Tucson, Arizona, pp. 217--222. February, 1985.

[Hen85d] T.C. Henderson, C.D. Hansen, B. Bhanu.
**“The Synthesis of Logical Sensor Specifications,”** In *SPIE Conference on Intelligent Robots*, Cambridge, Massachusetts, Note: *refereed abstract.*, September, 1985.

1984

[Ber84a] M. Berzins, T.F. Buckley, P.M. Dew.
**“Path Pascal Simulation of Multi-Processor Lattice Architectures for Numerical Computations,”** In *Progress in the Use of Vector and Array processors*, Edited by D.J. Paddon and J.D. Pryce, Academic Press, 1984.

[Hen84a] T.C. Henderson, W.S. Fai, C.D. Hansen.
**“MKS: A Multi-sensor Kernel System,”** In *IEEE Transactions on Systems, Man and Cybernetics*, Vol. SMC-14, No. 5, pp. 784--791. September/October, 1984.

[Hen84b] T.C. Henderson, C.D. Hansen, B. Bhanu.
**“ASP: An Algorithm and Sensor Performance Evaluation System,”** In *PECORA IX Conference on Spatial Information Technologies for Remote Sensing Today and Tomorrow*, Sioux Falls, S.D., pp. 201-207. October, 1984.

[Hen84c] T.C. Henderson, E. Shilcrat, C.D. Hansen.
**“A Fault Tolerant Sensor Scheme,”** In *International Conference on Pattern Recognition*, Montreal, Canada, pp. 663--665. August, 1984.

[Hen84d] T.C. Henderson, B. Bhanu, C.D. Hansen.
**“Distributed Control in the Multi-sensor Kernel System,”** In *SPIE Conference on Intelligent Robots*, Cambridge, Massachusetts, Note: *refereed abstract.*, pp. 253--255. November, 1984.

1983

[Ber1983a] M. Berzins, P.M. Dew, R.M. Furzeland.
**“Software for time-dependent problems,”** In *P.D.E. Software: Modules, Interfaces and Systems; Proc. of 1983 IFIPS Conference*, North Holland, Edited by B. Engquist and J. Rice, 1983.

[Dew1983a] P.M. Dew, T.F. Buckley, M. Berzins.
**“Systolic Architectures for the Iterative Solution of Sparse Matrix Problems,”** In *Parallel Computing*, North Holland, Edited by U. Schendal, 1983.

[Dew83b] P.M. Dew, T.F. Buckley, M. Berzins.
**“Application of VLSI Devices to Computational Problems in the Gas Industry,”** Dept. of Computer Studies Technical Report, No. 163, *The University of Leeds*, 1983.

[Hen83a] T.C. Henderson, C.D. Hansen, E. Shilcrat, W.S. Fai.
**“Logical Sensor Specification,”** In *SPIE Conference on Intelligent Robots*, Cambridge, Massachusetts, Note: *refereed abstract.*, pp. 578--583. November, 1983.

1981

[Ber1981a] M. Berzins, P.M. Dew.
**“A Generalized Chebyshev Method for Non-linear Parabolic Equations in One Space Variable,”** In *I.M.A. Journal on Numerical Analysis*, Vol. 1, pp. 469--487. 1981.

1980

[Ber1980a] M. Berzins, P.M. Dew.
**“A note on the extension of the Chebyshev method to quasi-linear parabolic P.D.E.s.,”** In *International Journal on Computer Mathematics*, Vol. 8, pp. 249--263. 1980.