Third Generation Cellular Automation for Modeling Excitable Media. - Jörg R. Weimar; John J. Tyson; Layne T. Watson (PP, 1991)

The Dynamics of Scroll Waves in Excitable Media. - James P. Keener; John J. Tyson (SIAM Rev., 1992)

On Traveling Wave Solutions of Fisher's Equation in Two Spatial Dimensions. - John J. Tyson; Pavel K. Brazhnik (SIAM J. Appl. Math., 2000)

A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology. - Jian He; Masha Sosonkina; Clifford A. Shaffer; John J. Tyson; Layne T. Watson; Jason W. Zwolak (IPDPS, 2004)

The JigCell Model Builder and Run Manager. - Marc Vass; Nicholas A. Allen; Clifford A. Shaffer; Naren Ramakrishnan; Layne T. Watson; John J. Tyson (Bioinform., 2004)

Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs. - Jason W. Zwolak; John J. Tyson; Layne T. Watson (J. Comput. Biol., 2005)

Challenges for modeling and simulation methods in systems biology. - Herbert M. Sauro; David Harel; Marta Z. Kwiatkowska; Clifford A. Shaffer; Adelinde M. Uhrmacher; Michael Hucka; Pedro Mendes 001; Lena Strömbäck; John J. Tyson (WSC, 2006)

The role of composition and aggregation in modeling macromolecular regulatory networks. - Clifford A. Shaffer; Ranjit Randhawa; John J. Tyson (WSC, 2006)

The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models. - Marc Vass; Clifford A. Shaffer; Naren Ramakrishnan; Layne T. Watson; John J. Tyson (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Fusing and composing macromolecular regulatory network models. - Ranjit Randhawa; Clifford A. Shaffer; John J. Tyson (SpringSim (2), 2007)

Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation. - Andrea Ciliberto; Fabrizio Capuani; John J. Tyson (PLoS Comput. Biol., 2007)

A Mathematical Programming Formulation for the Budding Yeast Cell Cycle. - Thomas D. Panning; Layne T. Watson; Clifford A. Shaffer; John J. Tyson (Simul., 2007)

Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. - Thomas D. Panning; Layne T. Watson; Nicholas A. Allen; Katherine C. Chen; Clifford A. Shaffer; John J. Tyson (J. Glob. Optim., 2008)

A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells. - Shenghua Li; Paul Brazhnik; Bruno W. S. Sobral; John J. Tyson (PLoS Comput. Biol., 2008)

Model aggregation: a building-block approach to creating large macromolecular regulatory networks. - Ranjit Randhawa; Clifford A. Shaffer; John J. Tyson (Bioinform., 2009)

Computing with Proteins. - Naren Ramakrishnan; Upinder S. Bhalla; John J. Tyson (Computer, 2009)

Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus. - Shenghua Li; Paul Brazhnik; Bruno W. S. Sobral; John J. Tyson (PLoS Comput. Biol., 2009)

Model Composition for Macromolecular Regulatory Networks. - Ranjit Randhawa; Clifford A. Shaffer; John J. Tyson (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells. - Tian Hong; Jianhua Xing; Liwu Li 002; John J. Tyson (PLoS Comput. Biol., 2011)

A Hybrid Model of Mammalian Cell Cycle Regulation. - Rajat Singhania; R. Michael Sramkoski; James W. Jacobberger; John J. Tyson (PLoS Comput. Biol., 2011)

A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. - Tian Hong; Jianhua Xing; Liwu Li 002; John J. Tyson (BMC Syst. Biol., 2012)

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells. - Yan Fu; Trevor Glaros; Meng Zhu; Ping Wang; Zhanghan Wu; John J. Tyson; Liwu Li 002; Jianhua Xing (PLoS Comput. Biol., 2012)

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. - Cihan Oguz; Teeraphan Laomettachit; Katherine C. Chen; Layne T. Watson; William T. Baumann; John J. Tyson (BMC Syst. Biol., 2013)

Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. - Christopher L. Poirel; Richard R. Rodrigues; Katherine C. Chen; John J. Tyson; T. M. Murali 001 (J. Comput. Biol., 2013)

Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus. - Kartik Subramanian; Mark R. Paul; John J. Tyson (PLoS Comput. Biol., 2013)

Global parameter estimation for a eukaryotic cell cycle model in systems biology. - T. M. Andrew; Brandon D. Amos; David R. Easterling; Cihan Oguz; William T. Baumann; John J. Tyson; Layne T. Watson (SummerSim, 2014)

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 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)

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 2015)

Cell Cycle Control by a Minimal Cdk Network. - Claude Gérard; John J. Tyson; Damien Coudreuse; Béla Novák (PLoS Comput. Biol., 2015)

Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models. - Kartik Subramanian; Mark R. Paul; John J. Tyson (PLoS Comput. Biol., 2015)

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)

A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. - Debashis Barik; David A. Ball; Jean Peccoud; John J. Tyson (PLoS Comput. Biol., 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)

GraphSpace: stimulating interdisciplinary collaborations in network biology. - Aditya Bharadwaj; Divit P. Singh; Anna M. Ritz; Allison N. Tegge; Christopher L. Poirel; Pavel K. Brazhnik; Neil Adames; Kurt Luther; Shiv D. Kale; Jean Peccoud; John J. Tyson; T. M. Murali 001 (Bioinform., 2017)

Predicting network modules of cell cycle regulators using relative protein abundance statistics. - Cihan Oguz; Layne T. Watson; William T. Baumann; John J. Tyson (BMC Syst. Biol., 2017)

CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. - Aditya Pratapa; Neil Adames; Pavel K. Kraikivski; Nicholas Franzese; John J. Tyson; Jean Peccoud; T. M. Murali 001 (BCB, 2018)

CrossPlan: systematic planning of genetic crosses to validate mathematical models. - Aditya Pratapa; Neil Adames; Pavel K. Brazhnik; Nicholas Franzese; John J. Tyson; Jean Peccoud; T. M. Murali 001 (Bioinform., 2018)

Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. - Dorjsuren Battogtokh; Shihoko Kojima; John J. Tyson (PLoS Comput. Biol., 2018)

Dilution and titration of cell-cycle regulators may control cell size in budding yeast. - Frank S. Heldt; Reece Lunstone; John J. Tyson; Béla Novák (PLoS Comput. Biol., 2018)

JigCell Model Connector: building large molecular network models from components. - Thomas C. Jones Jr; Stefan Hoops; Layne T. Watson; Alida Palmisano; John J. Tyson; Clifford A. Shaffer (Simul., 2018)

A stochastic model of size control in the budding yeast cell cycle. - Mansooreh Ahmadian; John J. Tyson; 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)

Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy. - Jae Kyoung Kim; John J. Tyson (PLoS Comput. Biol., 2020)

Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock. - Xiangyu Yao; Benjamin L. Heidebrecht; Jing Chen 029; John J. Tyson (PLoS Comput. Biol., 2022)