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.

2017
2016
Dutta, T., L. S. Heath, A. V. S. Kumar, and M. V. Marathe, "Labeled Cuts in Graphs", Theoretical Computer Science, vol. 648, pp. 34-39, 2016.
2015
2014
Cao, Y., and R. Erban, "Stochastic Turing Patterns: Analysis of Compartment-Based Approaches", Bulletin of Mathematical Biology: Springer US, pp. 1-19, 2014.
Badr, E., and L. S. Heath, "Identifying Splicing Regulatory Elements with de Bruijn Graphs", Journal of Computational Biology, vol. 21, pp. 880-897, 2014.
Eid, F. E., H. Elmarakeby, L. Heath, and M. Elhefnawi, "Human MicroRNAs Targeting Hepatitis C Virus", Middle East Conference on Biomedical Engineering (MECBME), pp. 184-187, 2014.
Jin, F., W. Wang, L. Zhao, E. Dougherty, Y. Cao, C. - T. Lu, and N. Ramakrishnan, "Misinformation Propagation in the Age of Twitter", COMPUTER, vol. 47, no. 12, {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA}, {IEEE COMPUTER SOC}, pp. 90-94, 12/2014. Abstract
2013
Pu, Y., S. Lee, D. C. Samuels, L. T. Watson, and Y. Cao, "The effect of unhealthy beta-cells on insulin secretion in pancreatic islets", BMC MEDICAL GENOMICS}, vol. 6, no. 3, {236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND}, {BIOMED CENTRAL LTD}, NOV 11, 2013.
Li, F., and Y. Cao, "Multigrid Discretization Method for PopZ Polarization in Caulobacter Cell Cycle", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), Shanghai, China, 12/2013.
Jin, F., E. Dougherty, P. Saraf, Y. Cao, and N. Ramakrishnan, "Modeling of News and Rumors on Twitter", The 7thWorkshop on Social Network Mining and Analysis (SNA KDD), Chicago, IL, 08/2013.
Fernandez, P. L., L. S. Heath, N. Ramakrishnan, M. Tan, and J. P. C. Vergara, "Mining Posets from Linear Orders", Discrete Mathematics, Algorithms and Applications, vol. 5, pp. 15 pages, 2013.
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
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
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.
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
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