John J. Tyson

47 papers A 1Misc 2Journal 36Unranked 8
YearRankTypeTitle / Venue / Authors
2022 J jnl
Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock.
PLoS Comput. Biol.
Xiangyu Yao, Benjamin L. Heidebrecht, Jing Chen, John J. Tyson
2020 J jnl
Cell cycle control and environmental response by second messengers in Caulobacter crescentus.
BMC Bioinform.
Chunrui Xu, Bronson R. Weston, John J. Tyson, Yang Cao
2020 J jnl
Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy.
PLoS Comput. Biol.
Jae Kyoung Kim, John J. Tyson
2019 J jnl
A stochastic model of size control in the budding yeast cell cycle.
BMC Bioinform.
Mansooreh Ahmadian, John J. Tyson, Yang Cao
2019 J jnl
Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle.
IEEE ACM Trans. Comput. Biol. Bioinform.
Minghan Chen, Brandon D. Amos, Layne T. Watson, John J. Tyson, Young Cao, Clifford A. Shaffer, Michael W. Trosset, Cihan Oguz, Gisella Kakoti
2018 — conf
A Stochastic Model of Size Control in the Budding Yeast Cell Cycle.
BCB
Mansooreh Ahmadian, John J. Tyson, Yang Cao
2018 — conf
CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models.
BCB
Aditya Pratapa, Neil Adames, Pavel K. Kraikivski, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
2018 J jnl
CrossPlan: systematic planning of genetic crosses to validate mathematical models.
Bioinform.
Aditya Pratapa, Neil Adames, Pavel K. Brazhnik, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
2018 J jnl
Dilution and titration of cell-cycle regulators may control cell size in budding yeast.
PLoS Comput. Biol.
Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák
2018 J jnl
JigCell Model Connector: building large molecular network models from components.
Simul.
Thomas C. Jones Jr, Stefan Hoops, Layne T. Watson, Alida Palmisano, John J. Tyson, Clifford A. Shaffer
2018 J jnl
Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network.
PLoS Comput. Biol.
Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson
2017 J jnl
GraphSpace: stimulating interdisciplinary collaborations in network biology.
Bioinform.
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
2017 — conf
Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study.
BCB
Mansooreh Ahmadian, Shuo Wang, John J. Tyson, Young Cao
2017 J jnl
Predicting network modules of cell cycle regulators using relative protein abundance statistics.
BMC Syst. Biol.
Cihan Oguz, Layne T. Watson, William T. Baumann, John J. Tyson
2016 — conf
A Hybrid Stochastic Model of the Budding Yeast Cell Cycle Control Mechanism.
BCB
Shuo Wang, Mansooreh Ahmadian, Minghan Chen, John J. Tyson, Young Cao
2016 J jnl
A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability.
PLoS Comput. Biol.
Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson
2015 J jnl
Cell Cycle Control by a Minimal Cdk Network.
PLoS Comput. Biol.
Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák
2015 J jnl
Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of
PLoS Comput. Biol.
Kartik Subramanian, Mark R. Paul, John J. Tyson
2015 J jnl
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations.
BMC Syst. Biol.
Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
2015 — conf
Two-dimensional model of bipolar PopZ polymerization in
BCB
Minghan Chen, Fei Li, Kartik Subramanian, John J. Tyson, Yang Cao
2014 — conf
Global parameter estimation for a eukaryotic cell cycle model in systems biology.
SummerSim
T. M. Andrew, Brandon D. Amos, David R. Easterling, Cihan Oguz, William T. Baumann, John J. Tyson, Layne T. Watson
2014 J jnl
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.
BMC Syst. Biol.
Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
2013 J jnl
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model.
BMC Syst. Biol.
Cihan Oguz, Teeraphan Laomettachit, Katherine C. Chen, Layne T. Watson, William T. Baumann, John J. Tyson
2013 J jnl
Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of
PLoS Comput. Biol.
Kartik Subramanian, Mark R. Paul, John J. Tyson
2013 J jnl
Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes.
J. Comput. Biol.
Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, T. M. Murali
2012 J jnl
A simple theoretical framework for understanding heterogeneous differentiation of CD4
BMC Syst. Biol.
Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson
2012 J jnl
Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells.
PLoS Comput. Biol.
Yan Fu, Trevor Glaros, Meng Zhu, Ping Wang, Zhanghan Wu, John J. Tyson, Liwu Li, Jianhua Xing
2011 J jnl
A Hybrid Model of Mammalian Cell Cycle Regulation.
PLoS Comput. Biol.
Rajat Singhania, R. Michael Sramkoski, James W. Jacobberger, John J. Tyson
2011 J jnl
A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells.
PLoS Comput. Biol.
Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson
2010 J jnl
Model Composition for Macromolecular Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
2009 J jnl
Computing with Proteins.
Computer
Naren Ramakrishnan, Upinder S. Bhalla, John J. Tyson
2009 J jnl
Model aggregation: a building-block approach to creating large macromolecular regulatory networks.
Bioinform.
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
2009 J jnl
Temporal Controls of the Asymmetric Cell Division Cycle in
PLoS Comput. Biol.
Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson
2008 J jnl
A Quantitative Study of the Division Cycle of
PLoS Comput. Biol.
Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson
2008 J jnl
Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle.
J. Glob. Optim.
Thomas D. Panning, Layne T. Watson, Nicholas A. Allen, Katherine C. Chen, Clifford A. Shaffer, John J. Tyson
2007 J jnl
A Mathematical Programming Formulation for the Budding Yeast Cell Cycle.
Simul.
Thomas D. Panning, Layne T. Watson, Clifford A. Shaffer, John J. Tyson
2007 — conf
Fusing and composing macromolecular regulatory network models.
SpringSim (2)
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson
2007 J jnl
Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation.
PLoS Comput. Biol.
Andrea Ciliberto, Fabrizio Capuani, John J. Tyson
2006 Misc conf
Challenges for modeling and simulation methods in systems biology.
WSC
Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson
2006 J jnl
The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models.
IEEE ACM Trans. Comput. Biol. Bioinform.
Marc Vass, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson
2006 Misc conf
The role of composition and aggregation in modeling macromolecular regulatory networks.
WSC
Clifford A. Shaffer, Ranjit Randhawa, John J. Tyson
2005 J jnl
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs.
J. Comput. Biol.
Jason W. Zwolak, John J. Tyson, Layne T. Watson
2004 A conf
A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology.
IPDPS
Jian He, Masha Sosonkina, Clifford A. Shaffer, John J. Tyson, Layne T. Watson, Jason W. Zwolak
2004 J jnl
The JigCell Model Builder and Run Manager.
Bioinform.
Marc Vass, Nicholas A. Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson
2000 J jnl
On Traveling Wave Solutions of Fisher's Equation in Two Spatial Dimensions.
SIAM J. Appl. Math.
John J. Tyson, Pavel K. Brazhnik
1992 J jnl
The Dynamics of Scroll Waves in Excitable Media.
SIAM Rev.
James P. Keener, John J. Tyson
1991 — conf
Third Generation Cellular Automation for Modeling Excitable Media.
PP
Jörg R. Weimar, John J. Tyson, Layne T. Watson