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JigCell Publications and Presentations

Recent Publications

• Tae-Hyuk Ahn, Layne T. Watson, Yang Cao, Clifford A. Shaffer, and William T. Baumann, Cell Cycle Modeling for Budding Yeast with Stochastic Simulation Algorithms, Submitted.
• Tae-Hyuk Ahn, Pengyuan Wang, Layne T. Watson, Yang Cao, Clifford A. Shaffer, and William T. Baumann, Stochastic Cell Cycle Modeling for Budding Yeast, High Performance Computing and Simulation Symposium (HPCS 2009), 2009, in San Diego, USA. [pdf]
• N. Ramakrishnan, U.S. Bhalla, and J.J. Tyson, Computing with Proteins, IEEE Computer, Vol. 42, No. 1, p47-56, Jan 2009 [pdf].
• D. Barik, M. Paul, W. Baumann, Y. Cao and J. Tyson, Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Time Scales, Biophysical Journal, Vol. 95, Issue 8, p3563-3574, 2008.
• Pengyuan Wang, Ranjit Randhawa, Clifford A. Shaffer, Yang Cao and William Baumann, Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation, High Performance Computing and Simulation Symposium (HPCS 2008), 2008, in Ottawa, Canada. (HPCS 2008 Best Paper Award)
• Tae-Hyuk Ahn, Yang Cao, and Layne T. Watson, Stochastic Simulation Algorithms for Chemical Reactions, Proceedings of the 2008 International Conference on BioInformatics & Computational Biology, July 2008, p431-436. [paper, presentation]

Older Publications

• Allen, N.A., L. Calzone, K.C. Chen, A. Ciliberto, N. Ramakrishnan, C.A. Shaffer, J.C. Sible, J.J. Tyson, M.T. Vass, L.T. Watson, and J.W. Zwolak, Modeling Regulatory Networks at Virginia Tech, OMICS, A Journal of Integrative Biology 7, 3(2003), 285-299. [pdf, Journal]
• Allen, N.A., C.A. Shaffer, M.T. Vass, N. Ramakrishnan, and L.T. Watson, Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment, Simulation 79, 12(Dec 2003), 674-688. [pdf, Journal]
• Allen, N.A., C.A. Shaffer, M.T. Vass, N. Ramakrishnan, and L.T. Watson, Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment. In Proceedings of the 2003 Winter Simulation Conference, S. Chick, P.J. Sanchez, D. Ferrin, and D.J. Morrice, eds., 2003, 782-790. [pdf]
• Borisuk, M. and J.J. Tyson, Bifurcation analysis of a model of mitotic control in frog eggs, Journal of Theoretical Biology 195, (1998), 69-85. [pdf]
• Chen, K.C., A. Csikasz-Nagy, B. Gyorffy, J. Val, B. Novak, and J.J. Tyson, Kinetic Analysis of a molecular model of the budding yeast cell cycle, Molecular Biology of the Cell 11, (January 2000), 369-391. [pdf]
• Chen, K.C., L. Calzone, A. Csikasz-Nagy, F.R. Cross, B. Novak, and J.J. Tyson, Integrative analysis of cell cycle control in budding yeast, Molecular Biology of the Cell 15, (August 2004), 3841-3862. [pdf]
• He, J., L.T. Watson, N. Ramakrishnan, C.A. Shaffer, A. Verstak, J. Jiang, K. Bae, and W.H. Tranter, Dynamic Data Structures for a Direct Search Algorithm, Computational Optimization and Applications 23, 1(October 2002), 5-25. [pdf]
• He, J., M. Sosonkina, C.A. Shaffer, J.J. Tyson, L.T. Watson, and J.W. Zwolak, ``A hierarchical parallel scheme for a global search algorithm'', in Proceedings of the High Performance Computing Symposium 2004, J. Meyer (ed.), Society for Modeling and Simulation International, San Diego, CA, 2004, 43-50. [pdf]
• He., J., M. Sosonkina, C.A. Shaffer, J.J. Tyson, L.T. Watson, J.W. Zwolak, "A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology", in Proceedings of IPDPS (International Parallel and Distributed Processing Symposium) CD-ROM, Santa Fe, New Mexico, April, 2004. [pdf]
• Marlovits, G, C.J. Tyson, B. Novak, and J.J. Tyson, Modeling M-phase Control in Xenopus Oocyte Extracts: the Surveillance Mechanism for Unreplicated DNA, Biophysical Chemistry 72, (1998), 169-184. [.pdf]
• Novák, B. and J.J. Tyson, Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. Journal of Cell Science 106 (1993), 1153-1168. [pdf]
• Novák, B. and J.J. Tyson, Quantitative analysis of a molecular model of mitotic control in fission yeast, Journal of Theoretical Biology 173, (1995), 283-305.
• Novák, B. and J.J. Tyson, Modeling the control of DNA replication in fission yeast. Proceedings of the National Academy of Science 94, (1997), 9147-9152. [pdf]
• Novak, B., A. Csikasz-Nagy, B. Gyorffy, K. Nasmyth, and J.J. Tyson, Model scenarios for evolution of the eukaryotic cell cycle. Phil. Transactions Royal Society London B 353, (1998), 2063-2076. [pdf]
• Novak, B., Z. Pataki, A. Ciliberto and J.J. Tyson, Mathematical model of the cell division cycle of fission yeast Chaos 11, 1(March, 2001), 277-286. [pdf]
• Randhawa, R., C.A. Shaffer, and J.J Tyson, "The Role of Composition and Aggregation in Modeling Macromolecular Regulatory Networks"; poster presented at the International Conference on Systems Biology in Yokohama, Japan, October 2006. [pdf]
• Randhawa, R., C.A. Shaffer, and J.J Tyson, "The Role of Composition and Aggregation in Modeling Macromolecular Regulatory Networks", in Proceedings of the 2006 Winter Simulation Conference, Monterrey, CA, December 2006. [pdf]
• Sha W., J. Moore, K. Chen, A.D. Lassaletta, C.-S. Yi, J.J. Tyson, and J.C. Sible, Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts, Proceedings of the National Academy of Science 100, (2003), 975-980. [pdf]
• Shaffer, C.A., R. Randhawa, and J.J. Tyson, The Role of Composition and Aggregation in Modeling Macromolecular Regulatory Networks. To appear in Proceedings of the 2006 Winter Simulation Conference, L. F. Perrone, F. P. Wieland, J. Liu, B. G. Lawson, D. M. Nicol, and R. M. Fujimoto, eds, Monterey, CA, December 2006. [pdf-preprint]
• Sveiczer, A., J.J. Tyson, and B. Novak, Modeling the fission yeast cell cycle, Briefings in Fuctional Genomics and Proteomics 2, (2004), 298-307.
• Tyson, J.J., K. Chen, and B. Novak, Network dynamics and cell physiology, Nature Reviews Molecular Cell Biology 2, (2001), 908-916. [pdf]
• Tyson J.J., A. Csikasz-Nagy, and B. Novak, The dynamics of cell cycle regulation, Bioessays 24: (2002), 1095-1109. [pdf]
• Tyson, J.J. and B. Novak, Regulation of the Eukaryotic Cell Cycle: Molecular Antagonism, Hysteresis, and Irreversible Transitions, Journal of Theoretical Biology (2001), 249-263. [pdf]
• Tyson, J.J., K.C. Chen, and B. Novak, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell, Current Opinion in Cell Biology 15, 2(2003), 221-31. [pdf]
• Vass, M.T., and P. Schoenhoff, "Error detection support in a cellular modeling end-user programming environment," in IEEE 2002 Symposia on Human Centric Languages and Environments, 2002, 104-106.
• Vass, M., J.M. Carroll, and C.A. Shaffer, "Supporting Creativity in Problem Solving Environments," in Proceedings of the Fourth Creativity & Cognition Conference, Loughborough, Leicestershire, UK, October 2002, 31-37. [pdf]
• Vass, M., N Allen, C.A. Shaffer, N. Ramakrishnan, L.T. Watson, and J.J. Tyson, The JigCell Model Builder and Run Manager, Bioinformatics 20, 18(2004), 3680-3681. [Journal]
• Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Estimating rate constants in cell cycle models," in Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego,CA 2001, 53-57. [ pdf]
• Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Estimating Rate Constants in Cell Cycle Models" (poster). Virginia Tech Workshop on Bioinformatics and Computational Biology, March 19, 2001. Also, Annual Student Research Symposium, Virginia Tech, March 26, 2001. [ PowerPoint]
• Zwolak, J.W., "Parameter Estimation in Biological Cell Cycle Models Using Deterministic Optimization". Masters Thesis. Virginia Tech, October 31, 2001. [pdf]
• Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Parameter Estimation in a Cell Cycle Model for Frog Egg Extracts," in Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. For Modeling and Simulation Internat., San Diego, CA, 2002, 67-74. [pdf]
• Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Finding All Steady States in Biological Models"; poster presented at the International Conference on Systems Biology in Stockholm, Sweden, December 2002. [pdf]
• Zwolak, J.W., J.J. Tyson, and L.T. Watson, "Finding all steady state solutions of chemical kinetic models" in Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2003, 47-53. [pdf]

Presentations

• John Tyson's presentation at the DARPA BioSPICE PI meeting, 2001.
• John Tyson's presentation on cell cycle modeling.
• Cliff Shaffer's presentation to the American Cancer Society meeting on JigCell, Blacksburg, VA, 2003.
• John Tyson and Cliff Shaffer's presentation at the DARPA BioSPICE PI meeting, May 2003.
• Cliff Shaffer's presentation to VBI on JigCell and BioSPICE, Blacksburg, VA, 2003.
• John Tyson's web seminar presentation for BioSPICE, November 2004.
• The JigCell poster. used in various venues.
• Cliff Shaffer's presentation at Winter Simulation Conference on model composition.