INVITED TALKS

Stiffness in discrete stochastic simulation for chemically reacting systems, 5th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heldelberg, Germany, Sep. 22-23, 2008.
Multiscale Discrete Stochastic Simulation for Biochemical Systems, NDSSL seminar, VBI, Virginia Tech, 2007.
Y. Cao, Multiscale discrete stochastic simulation for biochemical systems, Michigan State University, March, 2007.
Y. Cao, Slow-scale stochastic simulation algorithm, Workshop on Stochastic Simulation Methods, Princeton University, Oct. 2006.
Y. Cao, Application and software tools in discrete stochastic modeling and simulation for biochemical systems, ICMSB06, LMU Biozentrum, Munich, Germany. 31 July - 4 August 2006.
Y. Cao, Multiscale stochastic simulation for biochemical systems, Huazhong University of Science and Technology, July 2006.
Y. Cao, Stochastic Simulation Algorithms for Multiscale Problems, Workshop on Stochastic Dynamics in Complex Networks, Peking University, June 2006 .
Y. Cao, Multiscale stochastic simulation for biochemical systems, Tsinghua University, June, 2006.

Journal PUBLICATION LIST

Note: Due to copyright consideration, the published version is not posted here. For some publications, links to the journal website are provided. If you can not access the journal link, just download the author version (in double space).

Jingwei Zhang, Layne T. Watson, Yang Cao, Adaptive aggregation method for the Chemical Master Equation International Journal of Computational Biology and Drug Design 2009 - Vol. 2, No.2 pp. 134 - 148, journal link
DT Gillespie, Y Cao, K Sanft, and LR Petzold, The subtle business of model reduction for stochastic chemical kinetics J. Chem. Phys. 130, 064103 (2009). journal link
Y Cao and D Samuels, Discrete Stochastic Simulation Methods for Chemically Reacting Systems, Methods in Enzymology, vol 454, pp. 115-140, 2009. journal link
K Wendelsdorf, Z Song, Y Cao and D Samuels, An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Polymerase-gamma Inhibition by Nucleoside Reverse Transcriptase Inhibitor, PLos Computational Biology, vol 5, Jan 2009. journal link
(pdf file) D Barik, M Paul, W Baumann, Y Cao and J Tyson Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Time Scales, Biophys. J. 95, 3563-3574, 2008. journal link
(pdf file) Liu Z and Cao Y, Detailed Comparison between StochSim and SSA, IET Systems Biology, 2, 334-341, 2008. journal link
(pdf file) Y. Cao and L. Petzold, Slow Scale Tau-leaping Method, Computer Methods in Applied Mechanics and Engineering, Volume 197, Issues 43-44, 1 August 2008. journal link
(pdf file) H. Li, Y. Cao, L. Petzold and D. Gillespie, Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems, Biotechnology Progress, 24(1), 56-61, 2008.
(pdf file) Cao Y, Gillespie D. and Petzold L., The adaptive explicit-implicit tau-leaping method with automatic tau selection, J. Chem. Phys. 126, 224101, 2007. journal link
(pdf file) D. T. Gillespie, L. R. Petzold, and Y. Cao, Comment on “Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates”, J. Chem. Phys. 126, 137101, 2007. journal link
(pdf file) Petzold L, Li ST, Cao Y, Serban R, Sensitivity analysis of differential-algebraic equations and partial differential equations, COMPUTERS & CHEMICAL ENGINEERING 30 (10-12): 1553-1559, 2006.
Y. Cao, D. Gillespie and L. Petzold, Efficient Stepsize Selection for the Tau-Leaping Method, 124, 044109, J. Chem. Phys. 2006. (author version) (journal link)

Y. Cao and L. Petzold, Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems, Journal of Computational Physics, 212(1), Pages 6-24, 10 February 2006. (author version) (journal link)

Y. Cao , D. Gillespie and L. Petzold, Avoiding Negative Populations in Explicit Tau Leaping, J. Chem. Phys. 123, 054104 (2005). (author version) (journal link)

Y. Cao, D. Gillespie and L. Petzold, Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction, J. Chem. Phys., 123(14), 144917, 08 Oct 2005. (author version) (journal link)

Y. Cao and L. Petzold, Trapezoidal tau-lepaing formula for the stochastic simulation of biochemical systems, Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), Pages 149-152. (author version)

Y. Cao, D. Gillespie and L. Petzold, Multiscale Stochastic Simulation Algorithm with Stochastic Partial Equilibrium Assumption for Chemically Reacting Systems, J. Comput. Phys., Volume 206, Issue 2, 1 July 2005, Pages 395-411. (author version) (Journal Link)

R. Gunawan, Y. Cao, L. Petzold and F. Doyle III, Sensitivity analysis of discrete stochastic systems, Biophys. J. 88: 2530-2540, 2005. (author version) (journal version)

M. Rathinam, L. Petzold, Y. Cao, D. Gillespie, Consistency and stability of tau leaping schemes for chemical reaction systems, SIAM Multiscale Modeling and Simulation, vol 4, 867-895, 2005. (pdf file)

Y. Cao, D. Gillespie and L. Petzold, The slow-scale stochastic simulation algorithm, J. Chem. Phys., 122(1), 014116, 2005. (author version) (journal link)

Y. Cao, L. Petzold, M. Rathinam, D. Gillespie, The numerical stability of leaping methods for stochastic simulation of chemically reacting systems, J. Chem. Phys. 121(24), 12169-12178, 2004. (author version) (journal link)

Y. Cao, H. Li and L. Petzold, Efficient formulation of the stochastic simulation algorithm for chemically reacting system, J. Chem. Phys. 121(9), pp. 4059-4067, 2004. (author version) (journal link)

Yang Cao and Linda Petzold, A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method, SIAM J. Scientific Computing, 26(2), 359-374, 2004. (pdf file)

Yang Cao and Linda Petzold, An error estimate for matrix equations, Applied Numerical Mathematics, 50(3-4), 395-407, 2004. (author version) (journal link)

M. Rathinam, Y. Cao, L. Petzold, D. Gillespie, Stiffness in Stochastic Chemically Reacting Systems: The Implicit Tau-Leaping Method, J. Chemical Physics, 119(24), p12784-94, 2003. (author version) (journal link)

(pdf file) Adaptive Numerical Methods for Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations L. Petzold, Y. Cao, S. Li and R. Serban, Proceedings, Workshop on Modelling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003.

Yang Cao and Linda Petzold, A subspace error estimate for linear systems(PS file), SIAM J. Mat. Anal. Appl., 24(3), 787-801, 2003.

(pdf file)Yang Cao, Shengtai Li, Linda Petzold and Radu Serban, Adjoint sensitivity analysis for differential-algebraic equations: the adjoint DAE system and its numerical solution, SIAM J. Sci. Comput. 24(3), 1076--1089, 2002,

(pdf file)Yang Cao, Shengtai Li and Linda Petzold, Adjoint Sensitivity Analysis for Differential-Algebraic Equations: Algorithms and Software, J. Comp. Appl. Math. 149 (1), 171--191, 2002.

Sensitivity Analysis and Design Optimization of Differential-Algebraic Equation Systems(PS file). L. Petzold, R. Serban, S. Li, S. Raha and Y. Cao, Proc. NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion, 2001.

Yang Cao, Qing-Yang Li, Multistep discretization of Index 3 DAEs. Journal of Computational Mathematics, vol.18, (no.3), ICMSEC Chinese Acd. Sci, May 2000. p.325-36.

Yang Cao, Qingyang Li, Predictor-corrector formula for solving index-2 differential-algebraic equations. Mathematica Numerica Sinica, vol.21, (no.1), Math. , , 1999. p.65-74.

Yang Cao and Qingyang Li, Highest order multistep formula for solving index-2 differential algebraic equations, BIT, vol 38, no.4, 1998

Yang Cao and Qingyang Li, A-stable explicit nonlinear Runge-Kutta methods, Tsinghua Science & Technoloty, 1998

Yang Cao and Qingyang Li, Nonlinear Runge-Kutta methods for solving differential-algebraic equations. Chinese J. Numer. Math. Appl. 20, 1998, p.75--85.

Conference PUBLICATION LIST

J. Zhang, M. Sosonkina, L. T. Watson, and Y. Cao, Parallel solution of the chemical master equation, {\sl Proc. 2009 Spring Simulation Multiconference: HPC}, G. Wainer, M. Chinni, P. Roman, H. Rajaei, B. Zeigler, and C. Ribbens (eds.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2009, 563--567.
T.-H. Ahn, P. Wang, L. T. Watson, Y. Cao, C. A. Shaffer, and W. T. Baumann, Stochastic cell cycle modeling for budding yeast, {\sl Proc. 2009 Spring Simulation Multiconference: HPC}, G. Wainer, M. Chinni, P. Roman, H. Rajaei, B. Zeigler, and C. Ribbens (eds.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2009, 569--574.
P Kang, Y Cao, N Ramakrishnan, CJ Ribbens and SV Jan, Modular Implementation of Adaptive Decisions in Stochastic Simulations, ACM SAC 2009, Honolulu, Hawaii, 2009.
Y Cao, The stiffness in discrete stochastic simulation of chemically reacting systems, proceedings of the 5th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Sep, 2008.
J Zhang, L Watson and Y Cao, Adaptive Aggregation Method for the Chemical Master Equation, 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE), August 2008.
Y Cho, N Ramakrishnan, and Y Cao, Reconstructing Chemical Reaction Networks: Data Mining meets System Identification, ACM SIGKDD 2008, Las Vegas, Aug, 2008.
J Zhang, L Watson, M Sosonkina, and Y Cao, Analysis of Goldbeter-Koshland Switch Using the Chemical Master Equation, WORLDCOMP'08 Congress, Las Vegas, July, 2008.
T Ahn, Y Cao, and L Watson, Stochastic Simulation Algorithms for Chemical Reactions, WORLDCOMP'08 Congress, Las Vegas, July, 2008.
P Wang, R Randhawa, C Shaffer, Y Cao, and W Baumann, Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation ({\bf Best paper award}), High Performance Computing and Simulation Symposium (HPCS 2008).
Y. Cao and L. Petzold, Trapezoidal tau-lepaing formula for the stochastic simulation of biochemical systems, Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), Pages 149-152, Aug, 2005.