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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
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
2010
Randhawa, R., C. A. Shaffer, and J. J. Tyson, "Model Composition for Macromolecular Regulatory Networks", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 278-287, 2010.
2009
Ramakrishnan, N., U. S. Bhalla, and J. J. Tyson, "Computing with Proteins", IEEE Computer, vol. 42, no. 1, 01/2009.
Randhawa, R., C. A. Shaffer, and J. J. Tyson, "Model aggregation: a building-block approach to creating large macromolecular regulatory networks", Bioinformatics, vol. 25, no. 24, pp. 3289-3295, 2009.
Shaffer, C. A., J. W. Zwolak, R. Randhawa, and J. J. Tyson, "Modeling Molecular Regulatory Networks with JigCell and PET", Systems Biology, no. 500: Humana Press, pp. 81-111, 2009.
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
Panning, T. D., L. T. Watson, N. A. Allen, K. C. Chen, C. A. Shaffer, and J. J. Tyson, "Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle", Journal of Global Optimization, vol. 40, no. 4, Hingham, MA, USA, Kluwer Academic Publishers, pp. 719–738, 2008.
2007
Panning, T. D., L. T. Watson, C. A. Shaffer, and J. J. Tyson, "A Mathematical Programming Formulation for the Budding Yeast Cell Cycle", Simulation, vol. 83, no. 7, San Diego, CA, USA, Society for Computer Simulation International, pp. 497–514, 2007.
2006
Sauro, H. M., D. Harel, M. Kwiatkowska, C. A. Shaffer, A. M. Uhrmacher, M. Hucka, P. Mendes, L. Strömback, and J. J. Tyson, "Challenges for modeling and simulation methods in systems biology", WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1720–1730, 2006.
Shaffer, C. A., R. Randhawa, and J. J. Tyson, "The role of composition and aggregation in modeling macromolecular regulatory networks", WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1628–1636, 2006.
2004
Vass, M., N. Allen, C. A. Shaffer, N. Ramakrishnan, L. T. Watson, and J. J. Tyson, "The JigCell Model Builder and Run Manager", Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.