A Subspace Error Estimate for Linear Systems. - Yang Cao 001; Linda R. Petzold (SIAM J. Matrix Anal. Appl., 2003)

Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution. - Yang Cao 001; Shengtai Li; Linda R. Petzold; Radu Serban (SIAM J. Sci. Comput., 2003)

A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method. - Yang Cao 001; Linda R. Petzold (SIAM J. Sci. Comput., 2004)

Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems. - Muruhan Rathinam; Linda R. Petzold; Yang Cao 001; Daniel T. Gillespie (Multiscale Model. Simul., 2005)

Sensitivity analysis of differential-algebraic equations and partial differential equations. - Linda R. Petzold; Shengtai Li; Yang Cao 001; Radu Serban (Comput. Chem. Eng., 2006)

Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems. - Yang Cao 001; Linda R. Petzold (J. Comput. Phys., 2006)

Adaptive aggregation method for the chemical master equation. - Jingwei Zhang 002; Layne T. Watson; Yang Cao 001 (BIBE, 2008)

Stochastic Simulation Algorithms for Chemical Reactions. - Tae-Hyuk Ahn; Yang Cao 001; Layne T. Watson (BIOCOMP, 2008)

Analysis of Goldbeter-Koshland Switch Using the Chemical Master Equation. - Jingwei Zhang 002; Layne T. Watson; Masha Sosonkina; Yang Cao 001 (BIOCOMP, 2008)

Reconstructing chemical reaction networks: data mining meets system identification. - Yong Ju Cho; Naren Ramakrishnan; Yang Cao 001 (KDD, 2008)

Converting macromolecular regulatory models from deterministic to stochastic formulation. - Pengyuan Wang 005; Ranjit Randhawa; Clifford A. Shaffer; Yang Cao 001; William T. Baumann (SpringSim, 2008)

Modeling of Metabolic Oscillations in Mitochondria and Their Coupling in a Cell. - Yang Pu; Saangho Lee; Zhen Liu; David C. Samuels; Layne T. Watson; Yang Cao 001 (BIOCOMP, 2009)

Radial Basis Function Collocation for the Chemical Master Equation. - Jingwei Zhang 002; Layne T. Watson; Yang Cao 001 (BIOCOMP, 2009)

Modular implementation of adaptive decisions in stochastic simulations. - Pilsung Kang 002; Yang Cao 001; Naren Ramakrishnan; Calvin J. Ribbens; Srinidhi Varadarajan (SAC, 2009)

Stochastic cell cycle modeling for budding yeast. - Tae-Hyuk Ahn; Pengyuan Wang 005; Layne T. Watson; Yang Cao 001; Clifford A. Shaffer; William T. Baumann (SpringSim, 2009)

Parallel solution of the chemical master equation. - Jingwei Zhang 002; Masha Sosonkina; Layne T. Watson; Yang Cao 001 (SpringSim, 2009)

Hybrid Modeling and Simulation of Insulin Secretion Pathway in Pancreatic Islets. - Yang Pu; Saangho Lee; David C. Samuels; Layne T. Watson; Yang Cao 001 (BIBE, 2010)

Stiffness detection and reduction in discrete stochastic simulation of biochemical systems. - Yang Pu; Layne T. Watson; Yang Cao 001 (SpringSim, 2010)

Multistate modeling and simulation for regulatory networks. - Zhen Liu; Umme Juka Mobassera; Clifford A. Shaffer; Layne T. Watson; Yang Cao 001 (WSC, 2010)

A modified uniformization method for the solution of the chemical master equation. - Jingwei Zhang 002; Layne T. Watson; Yang Cao 001 (Comput. Math. Appl., 2010)

Efficient implementation of the hybrid method for stochastic simulation of biochemical systems. - Shuo Wang; Yang Cao 001 (BCB, 2012)

Approximation of a multi-scale model based on multiple site phosphorylation. - Zhen Liu; Yang Cao 001 (BIBM Workshops, 2012)

The effect of unhealthy β-cells in synchronized insulin secretion. - Yang Pu; Saangho Lee; David C. Samuels; Layne T. Watson; Yang Cao 001 (BIBM, 2012)

Effective GPU Acceleration of Large Scale, Asynchronous Simulations on Graphs. - Dustin Arendt; Yang Cao 001 (Adv. Complex Syst., 2012)

Evolutionary motifs for the Automated Discovery of Self-Organizing dimer Automata. - Dustin Arendt; Yang Cao 001 (Adv. Complex Syst., 2012)

Implementing modular adaptation of scientific software. - Pilsung Kang 002; Naresh K. C. Selvarasu; Naren Ramakrishnan; Calvin J. Ribbens; Danesh K. Tafti; Yang Cao 001; Srinidhi Varadarajan (J. Comput. Sci., 2012)

Multigrid discretization method for PopZ polarization in Caulobacter cell cycle. - Fei Li 013; Yang Cao 001 (BIBM, 2013)

Epidemiological modeling of news and rumors on Twitter. - Fang Jin; Edward R. Dougherty; Parang Saraf; Yang Cao 001; Naren Ramakrishnan (SNAKDD, 2013)

Misinformation Propagation in the Age of Twitter. - Fang Jin; Wei Wang 064; Liang Zhao 002; Edward R. Dougherty; Yang Cao 001; Chang-Tien Lu; Naren Ramakrishnan (Computer, 2014)

Two-dimensional model of bipolar PopZ polymerization in caulobacter crescentus. - Minghan Chen; Fei Li 013; Kartik Subramanian; John J. Tyson; Yang Cao 001 (BCB, 2015)

A Framework to Analyze the Performance of Load Balancing Schemes for Ensembles of Stochastic Simulations. - Tae-Hyuk Ahn; Adrian Sandu; Layne T. Watson; Clifford A. Shaffer; Yang Cao 001; William T. Baumann (Int. J. Parallel Program., 2015)

Stochastic Modeling and Simulation of Reaction-Diffusion System with Hill Function Dynamics. - Minghan Chen; Fei Li 013; Shuo Wang; Yang Cao 001 (BCB, 2016)

A Hybrid Stochastic Model of the Budding Yeast Cell Cycle Control Mechanism. - Shuo Wang; Mansooreh Ahmadian; Minghan Chen; John J. Tyson; Young Cao (BCB, 2016)

Efficient implementation of the hybrid method for stochastic simulation of biochemical systems. - Shuo Wang; Yang Pu; Layne T. Watson; Yang Cao 001 (CoRR, 2016)

Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study. - Mansooreh Ahmadian; Shuo Wang; John J. Tyson; Young Cao (BCB, 2017)

Modelling Propagation of Public Opinions on Microblogging Big Data Using Sentiment Analysis and Compartmental Models. - Youjia Fang; Xin Chen; Zheng Song 001; Tianzi Wang; Yang Cao 001 (Int. J. Semantic Web Inf. Syst., 2017)

A Stochastic Model of Size Control in the Budding Yeast Cell Cycle. - Mansooreh Ahmadian; John J. Tyson; Yang Cao 001 (BCB, 2018)

Analysis and Remedy of Negativity Problem in Hybrid Stochastic Simulation Algorithm and its Application: Extended Abstract. - Minghan Chen; Yang Cao 001 (BCB, 2018)

Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application. - Minghan Chen; Yang Cao 001 (BMC Bioinform., 2019)

Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle. - Minghan Chen; Brandon D. Amos; Layne T. Watson; John J. Tyson; Young Cao; Clifford A. Shaffer; Michael W. Trosset; Cihan Oguz; Gisella Kakoti (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Cell cycle control and environmental response by second messengers in Caulobacter crescentus. - Chunrui Xu; Bronson R. Weston; John J. Tyson; Yang Cao 001 (BMC Bioinform., 2020)

A spatiotemporal model of polarity and spatial gradient establishment in caulobacter crescentus. - Chunrui Xu; Yang Cao 001 (BCB, 2021)

Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle. - Chunrui Xu; Henry Hollis; Michelle Dai; Xiangyu Yao; Layne T. Watson; Yang Cao 001; Minghan Chen (PLoS Comput. Biol., 2022)