Biblio

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2007
Randhawa, R., C. A. Shaffer, and J. J. Tyson, "Fusing and Composing Macromolecular Regulatory Network Models", Proceedings of the 2007 High Performance Computing Symposium (HPC 2007), pp. 337–344, March, 2007.
2006
Allen, N. A., K. C. Chen, C. A. Shaffer, J. J. Tyson, and L. T. Watson, "Computer Evaluation of Network Dynamics Models with Application to Cell Cycle Control in Budding Yeast", IEE Proceedings – Systems Biology, vol. 153, no. 1, pp. 13–21, January, 2006.
Vass, M., C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson, "The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. Vol. 3, no. 2, pp. 155–164, April-June, 2006.
Panning, T. D., L. T. Watson, N. A. Allen, C. A. Shaffer, and J. J. Tyson, "Deterministic Global Parameter Estimation for a Budding Yeast Model", Proceedings of the 2006 High Performance Computing Symposium (HPC'06), pp. 195–201, 2006.
2005
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "Globally optimized parameters for a model of mitotic control in frog egg extracts", IEE Systems Biol., vol. 152, pp. 81-92, 2005.
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "“Parameter estimation for a mathematical model of the cell cycle in frog eggs", J. Comput. Biology, vol. 12, pp. 48–63, 2005.
2004
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "Finding all steady state solutions of chemical kinetic models", Nonlinear Anal.: Real World Appl., vol. 5, pp. 801-814, 2004.
He, J., M. Sosonkina, C. A. Shaffer, J. J. Tyson, L. T. Watson, J. W. Zwolak, and J. Meyer, "A Hierarchical Parallel Scheme for a Global Search Algorithm", Proceedings of the 2004 High Performance Computing Symposium (HPC'04): Society for Modeling and Simulation International, pp. 43–50, 2004.
2003
Allen, N., L. Calzone, K. C. Chen, A. Ciliberto, N. Ramakrishnan, C. A. Shaffer, J. C. Sible, J. J. Tyson, M. Vass, L. T. Watson, et al., "Modeling Regulatory Networks at Virginia Tech", Omics Journal of Integrative Biology, vol. Vol. 7, no. 3, pp. pages 285–300, Fall, 2003.
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "Finding all steady state solutions of chemical kinetic models", Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 47-53, 2003.
2002
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "Parameter estimation in a cell cycle model for frog egg extracts", Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 67-74, 2002.
2001
Zwolak, J. W., J. J. Tyson, and L. T. Watson, "Estimating rate constants in cell cycle models", Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 53–57, 2001.