Biblio

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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
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.
Kang, P., N. Selvarasu, N. Ramakrishnan, C. J. Ribbens, D. Tafti, Y. Cao, and S. Varadarajan, "Implementing modular adaptation of scientific software", Jnl. of Computational Science, vol. 3, pp. 28-45, 2012.
2011
Song, Z., Y. Cao, and D. C. Samuels, "Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study", PLOS COMPUTATIONAL BIOLOGY, vol. 7, no. 11, 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA, PUBLIC LIBRARY SCIENCE, NOV, 2011. Abstract
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
Pu, Y., L. T. Watson, and Y. Cao, "Stiffness detection and reduction in discrete stochastic simulation of biochemical systems", JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 5, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, FEB 7, 2011. Abstract
Wu, S., J. Fu, Y. Cao, and L. Petzold, "Michaelis-Menten speeds up tau-leaping under a wide range of conditions", JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 13, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, APR 7, 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
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, J., L. T. Watson, and Y. Cao, "A modified uniformization method for the solution of the chemical master equation", COMPUTERS & MATHEMATICS WITH APPLICATIONS, vol. 59, no. 1, THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, PERGAMON-ELSEVIER SCIENCE LTD, pp. 573-584, JAN, 2010. Abstract
2009
Wendelsdorf, K. V., Z. Song, Y. Cao, and D. C. Samuels, "An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors", PLOS COMPUTATIONAL BIOLOGY, vol. 5, no. 1, 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA, PUBLIC LIBRARY SCIENCE, JAN, 2009. Abstract
Gillespie, D. T., Y. Cao, K. R. Sanft, and L. R. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", JOURNAL OF CHEMICAL PHYSICS, vol. 130, no. 6, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, FEB 14, 2009. Abstract
Gillespie, D., Y. Cao, K. Sanft, and L. Petzold, "The subtle business of model reduction for stochastic chemical kinetics", J. Chem. Phys. , 2009.
Cao, Y., and D. C. Samuels, "DISCRETE STOCHASTIC SIMULATION METHODS FOR CHEMICALLY REACTING SYSTEMS", METHODS IN ENZYMOLOGY: COMPUTER METHODS, VOL 454, PT A, vol. 454, no. Part A, 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA, ELSEVIER ACADEMIC PRESS INC, pp. 115-140, 2009. Abstract
Cao, Y., and D. C. Samuels, Methods in EnzymologyComputer Methods, Part AChapter 5 Discrete Stochastic Simulation Methods for Chemically Reacting Systems, , vol. 454: Elsevier, pp. 115 - 140, 2009.
Kang, P., Y. Cao, N. Ramakrishnan, C. J. Ribbens, and S. Varadarajan, "Modular Implementation of Adaptive Decisions in Stochastic Simulations", Proceedings of the 24th Annual ACM Symposium on Applied Computing (SAC'09): ACM, New York, pp. 995-1001, 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
Li, H., Y. Cao, L. R. Petzold, and D. T. Gillespie, "Algorithms and software for stochastic simulation of biochemical reacting systems", BIOTECHNOLOGY PROGRESS, vol. 24, no. 1, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, AMER CHEMICAL SOC, pp. 56-61, JAN-FEB, 2008. Abstract
Wang, P., R. Randhawa, C. A. Shaffer, Y. Cao, and W. T. Baumann, "Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation", Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 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.
Cao, Y., and L. Petzold, "Slow-scale tau-leaping method", COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, vol. 197, no. 43-44, PO BOX 564, 1001 LAUSANNE, SWITZERLAND, ELSEVIER SCIENCE SA, pp. 3472-3479, 2008. Abstract
2007
Cao, Y., D. T. Gillespie, and L. R. Petzold, "Adaptive explicit-implicit tau-leaping method with automatic tau selection", JOURNAL OF CHEMICAL PHYSICS, vol. 126, no. 22, CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA, AMER INST PHYSICS, JUN 14, 2007. Abstract
Cao, Y., D. T. Gillespie, and L. R. Petzold, "Adaptive explicit-implicit tau-leaping method with automatic tau selection", The Journal of Chemical Physics, vol. 126, issue 22, pp. 224101, 2007.