Computational Biology Lab

URL: http://people.cs.vt.edu/~ycao

Contact: Yang Cao

Our group focuses on the development of multiscale, multiphysics modeling and simulation methods and tools that help biologists build, simulate and analyze complex biological systems, simulate their dynamics and analyze their functions. Typical biological models include gene expression models, protein interaction networks, and cell cycle models. We are paricularly interested in applications where multiple scales and multiple physics are presented, and has to be modeled in a hybrid way that include both discrete and continuous variables, deterministic and stochastic equations.

We work at the interface of mathematics, computer science, biology and other related subjects. Due to the interdisciplinary feature, we collaborate with other groups with different background.
2012
Liu, Z., Y. Pu, F. Li, C. A. Shaffer, S. Hoops, J. J. Tyson, and Y. Cao, "Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle", {JOURNAL OF CHEMICAL PHYSICS}, vol. {136}, no. {3}, {CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, {AMER INST PHYSICS}, {JAN 21}, 2012. Abstract
Arendt, D., and Y. Cao, "EFFECTIVE GPU ACCELERATION OF LARGE SCALE, ASYNCHRONOUS SIMULATIONS ON GRAPHS", {ADVANCES IN COMPLEX SYSTEMS}, vol. {15}, no. {8}, {5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE}, {WORLD SCIENTIFIC PUBL CO PTE LTD}, {DEC}, 2012. Abstract
Arendt, D., and Y. Cao, "EVOLUTIONARY MOTIFS FOR THE AUTOMATED DISCOVERY OF SELF-ORGANIZING DIMER AUTOMATA", {ADVANCES IN COMPLEX SYSTEMS}, vol. {15}, no. {8}, {5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE}, {WORLD SCIENTIFIC PUBL CO PTE LTD}, {DEC}, 2012. Abstract
Wang, S., and Y. Cao, "Efficient Implementation of the Hybrid Method for Stochastic Simulation of Biochemical Systems", 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Orlando, Florida, 2012.
2011
Belal, N. A., and L. S. Heath, "A Theoretical Model for Whole Genome Alignment", Journal of Computational Biology, vol. 18, no. 5, pp. 705-728, 2011.
Ball, D. A., T. - H. Ahn, P. Wang, K. C. Chen, Y. Cao, J. J. Tyson, J. Peccoud, and W. T. Baumann, "Stochastic exit from mitosis in budding yeast Model predictions and experimental observations", CELL CYCLE, vol. 10, no. 6, 1806 RIO GRANDE ST, AUSTIN, TX 78702 USA, LANDES BIOSCIENCE, pp. 999-1009, MAR 15, 2011. Abstract
Song, Z., Y. Cao, and D. C. Samuels, "Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study", PLoS Comput Biol, vol. 7, no. 11: Public Library of Science, pp. e1002287, 11, 2011.
2010
Vasquez-Robinet, C., J. I. Watkinson, A. A. Sioson, N. Ramakrishnan, L. S. Heath, and R. Grene, "Differential Expression of Heat Shock Protein Genes in Preconditioning for Photosynthetic Acclimation in Water-Stressed Loblolly Pine", Plant Biochemistry and Physiology, vol. 48, pp. 256-264, 2010.
Zhang, J., L. T. Watson, C. A. Beattie, and Y. Cao, "RADIAL BASIS FUNCTION COLLOCATION FOR THE CHEMICAL MASTER EQUATION", INTERNATIONAL JOURNAL OF COMPUTATIONAL METHODS, vol. 7, no. 3, 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE, WORLD SCIENTIFIC PUBL CO PTE LTD, pp. 477-498, SEP, 2010. Abstract
Zhang, L., and L. T. Watson, "The expected fitness cost of a mutation fixation under the one-dimensional Fisher model", Internat. J. Pure Appl. Math., vol. 62, pp. 129--150, 2010.
2009
Gillespie, D., Y. Cao, K. Sanft, and L. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", J. Chem. Phys. , 2009.
Heath, L. S., and A. A. Sioson, "Multimodal Networks: Structure and Operations", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 321-332, 2009. Abstract
Heath, L. S., and A. A. Sioson, "Semantics of Multimodal Network Models", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 271-280, 2009.
2008
Barik, D., M. Paul, W. Baumann, Y. Cao, and J. Tyson, "Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Time Scales", Biophysics Journal, vol. 95, 2008.
Mane, S. P., C. Vasquez-Robinet, A. Ulanov, R. Schafleitner, L. Tincopa, A. Gaudin, G. Nomberto, C. Alvarado, C. Solis, L. A. Bolivar, et al., "Molecular and Physiological Adaptation to Prolonged Drought Stress in the Leaves of two Andean Potato Genotypes", Functional Plant Biology, vol. 35, pp. 669-688, 2008.
Barik, D., M. R. Paul, W. T. Baumann, Y. Cao, and J. J. Tyson, "Stochastic simulation of enzyme-catalyzed reactions with disparate timescales", BIOPHYSICAL JOURNAL, vol. 95, no. 8, 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA, CELL PRESS, pp. 3563-3574, OCT 15, 2008. Abstract