The NIH/NIGMS
Center for Integrative Biomedical Computing

SCI Publications

2008


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


2007


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.



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.



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.



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.
DOI: 10.1109/ACSSC.2007.4487316



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.



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.



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.



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

ABSTRACT

Markovian models of ion channels have proven useful in the reconstruction of experimental data and prediction of cellular electrophysiology. We present the stochastic Galerkin method as an alternative to Monte Carlo and other stochastic methods for assessing the impact of uncertain rate coefficients on the predictions of Markovian ion channel models. We extend and study two different ion channel models: a simple model with only a single open and a closed state and a detailed model of the cardiac rapidly activating delayed rectifier potassium current. We demonstrate the efficacy of stochastic Galerkin methods for computing solutions to systems with random model parameters. Our studies illustrate the characteristic changes in distributions of state transitions and electrical currents through ion channels due to random rate coefficients. Furthermore, the studies indicate the applicability of the stochastic Galerkin technique for uncertainty and sensitivity analysis of bio-mathematical models.

Keywords: Stochastic Galerkin, Polynomial chaos, Stochastic processes, Markov modeling, Ion channels



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



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



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



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.



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.



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.



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.



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.



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.



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.



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.