John J. Tyson

Publication Activity (10 Years)

Years Active: 1991-2022
Publications (10 Years): 16

Top Topics

Systems Biology

Saccharomyces Cerevisiae

Protein Interaction

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

Publications

Xiangyu Yao, Benjamin L. Heidebrecht, Jing Chen, John J. Tyson
Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock. PLoS Comput. Biol. 18 (3) (2022)
Chunrui Xu, Bronson R. Weston, John J. Tyson, Yang Cao
Cell cycle control and environmental response by second messengers in Caulobacter crescentus. BMC Bioinform. (14) (2020)
Jae Kyoung Kim, John J. Tyson
Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy. PLoS Comput. Biol. 16 (10) (2020)
Minghan Chen, Brandon D. Amos, Layne T. Watson, John J. Tyson, Young Cao, Clifford A. Shaffer, Michael W. Trosset, Cihan Oguz, Gisella Kakoti
Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Mansooreh Ahmadian, John J. Tyson, Yang Cao
A stochastic model of size control in the budding yeast cell cycle. BMC Bioinform. (12) (2019)
Mansooreh Ahmadian, John J. Tyson, Yang Cao
A Stochastic Model of Size Control in the Budding Yeast Cell Cycle. BCB (2018)
Aditya Pratapa, Neil Adames, Pavel K. Brazhnik, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
CrossPlan: systematic planning of genetic crosses to validate mathematical models. Bioinform. 34 (13) (2018)
Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák
Dilution and titration of cell-cycle regulators may control cell size in budding yeast. PLoS Comput. Biol. 14 (10) (2018)
Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson
Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. PLoS Comput. Biol. 14 (2) (2018)
Thomas C. Jones Jr, Stefan Hoops, Layne T. Watson, Alida Palmisano, John J. Tyson, Clifford A. Shaffer
JigCell Model Connector: building large molecular network models from components. Simul. 94 (11) (2018)
Aditya Pratapa, Neil Adames, Pavel K. Kraikivski, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. BCB (2018)
Cihan Oguz, Layne T. Watson, William T. Baumann, John J. Tyson
Predicting network modules of cell cycle regulators using relative protein abundance statistics. BMC Syst. Biol. 11 (1) (2017)
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
GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinform. 33 (19) (2017)
Mansooreh Ahmadian, Shuo Wang, John J. Tyson, Young Cao
Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study. BCB (2017)
Shuo Wang, Mansooreh Ahmadian, Minghan Chen, John J. Tyson, Young Cao
A Hybrid Stochastic Model of the Budding Yeast Cell Cycle Control Mechanism. BCB (2016)
Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson
A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. PLoS Comput. Biol. 12 (12) (2016)
Minghan Chen, Fei Li, Kartik Subramanian, John J. Tyson, Yang Cao
. BCB (2015)
Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák
Cell Cycle Control by a Minimal Cdk Network. PLoS Comput. Biol. 11 (2) (2015)
Kartik Subramanian, Mark R. Paul, John J. Tyson
: A Theoretical Investigation of Alternative Models. PLoS Comput. Biol. 11 (7) (2015)
Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Syst. Biol. 9 (2015)
Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Syst. Biol. 8 (2014)
T. M. Andrew, Brandon D. Amos, David R. Easterling, Cihan Oguz, William T. Baumann, John J. Tyson, Layne T. Watson
Global parameter estimation for a eukaryotic cell cycle model in systems biology. SummerSim (2014)
Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, T. M. Murali
Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. J. Comput. Biol. 20 (5) (2013)
Kartik Subramanian, Mark R. Paul, John J. Tyson
. PLoS Comput. Biol. 9 (9) (2013)
Cihan Oguz, Teeraphan Laomettachit, Katherine C. Chen, Layne T. Watson, William T. Baumann, John J. Tyson
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC Syst. Biol. 7 (2013)
Yan Fu, Trevor Glaros, Meng Zhu, Ping Wang, Zhanghan Wu, John J. Tyson, Liwu Li, Jianhua Xing
Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells. PLoS Comput. Biol. 8 (5) (2012)
Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson
T cells. BMC Syst. Biol. 6 (2012)
Rajat Singhania, R. Michael Sramkoski, James W. Jacobberger, John J. Tyson
A Hybrid Model of Mammalian Cell Cycle Regulation. PLoS Comput. Biol. 7 (2) (2011)
Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson
A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells. PLoS Comput. Biol. 7 (7) (2011)
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
Model Composition for Macromolecular Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (2) (2010)
Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson
. PLoS Comput. Biol. 5 (8) (2009)
Naren Ramakrishnan, Upinder S. Bhalla, John J. Tyson
Computing with Proteins. Computer 42 (1) (2009)
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinform. 25 (24) (2009)
Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson
Stalked Cells. PLoS Comput. Biol. 4 (1) (2008)
Thomas D. Panning, Layne T. Watson, Nicholas A. Allen, Katherine C. Chen, Clifford A. Shaffer, John J. Tyson
Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. J. Glob. Optim. 40 (4) (2008)
Thomas D. Panning, Layne T. Watson, Clifford A. Shaffer, John J. Tyson
A Mathematical Programming Formulation for the Budding Yeast Cell Cycle. Simul. 83 (7) (2007)
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
Fusing and composing macromolecular regulatory network models. SpringSim (2) (2007)
Andrea Ciliberto, Fabrizio Capuani, John J. Tyson
Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation. PLoS Comput. Biol. 3 (3) (2007)
Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson
Challenges for modeling and simulation methods in systems biology. WSC (2006)
Marc Vass, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson
The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (2) (2006)
Clifford A. Shaffer, Ranjit Randhawa, John J. Tyson
The role of composition and aggregation in modeling macromolecular regulatory networks. WSC (2006)
Jason W. Zwolak, John J. Tyson, Layne T. Watson
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs. J. Comput. Biol. 12 (1) (2005)
Jian He, Masha Sosonkina, Clifford A. Shaffer, John J. Tyson, Layne T. Watson, Jason W. Zwolak
A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology. IPDPS (2004)
Marc Vass, Nicholas A. Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson
The JigCell Model Builder and Run Manager. Bioinform. 20 (18) (2004)
John J. Tyson, Pavel K. Brazhnik
On Traveling Wave Solutions of Fisher's Equation in Two Spatial Dimensions. SIAM J. Appl. Math. 60 (2) (2000)
James P. Keener, John J. Tyson
The Dynamics of Scroll Waves in Excitable Media. SIAM Rev. 34 (1) (1992)
Jörg R. Weimar, John J. Tyson, Layne T. Watson
Third Generation Cellular Automation for Modeling Excitable Media. PPSC (1991)