John J. Tyson

According to our database1, John J. Tyson authored at least 46 papers between 1991 and 2022.

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Bibliography

2022
Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock.
PLoS Comput. Biol., 2022

2020
Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy.
PLoS Comput. Biol., 2020

Cell cycle control and environmental response by second messengers in Caulobacter crescentus.
BMC Bioinform., 2020

2019
Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

A stochastic model of size control in the budding yeast cell cycle.
BMC Bioinform., 2019

2018
JigCell Model Connector: building large molecular network models from components.
Simul., 2018

Dilution and titration of cell-cycle regulators may control cell size in budding yeast.
PLoS Comput. Biol., 2018

Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network.
PLoS Comput. Biol., 2018

CrossPlan: systematic planning of genetic crosses to validate mathematical models.
Bioinform., 2018

CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
Predicting network modules of cell cycle regulators using relative protein abundance statistics.
BMC Syst. Biol., 2017

GraphSpace: stimulating interdisciplinary collaborations in network biology.
Bioinform., 2017

Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016
A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability.
PLoS Comput. Biol., 2016

A Hybrid Stochastic Model of the Budding Yeast Cell Cycle Control Mechanism.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015
Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of <i>Caulobacter crescentus</i>: A Theoretical Investigation of Alternative Models.
PLoS Comput. Biol., 2015

Cell Cycle Control by a Minimal Cdk Network.
PLoS Comput. Biol., 2015

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations.
BMC Syst. Biol., 2015

Two-dimensional model of bipolar PopZ polymerization in <i>caulobacter crescentus</i>.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.
BMC Syst. Biol., 2014

Global parameter estimation for a eukaryotic cell cycle model in systems biology.
Proceedings of the 2014 Summer Simulation Multiconference, 2014

2013
Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of <i>Caulobacter crescentus</i>.
PLoS Comput. Biol., 2013

Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes.
J. Comput. Biol., 2013

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model.
BMC Syst. Biol., 2013

2012
Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells.
PLoS Comput. Biol., 2012

A simple theoretical framework for understanding heterogeneous differentiation of CD4<sup>+</sup> T cells.
BMC Syst. Biol., 2012

2011
A Hybrid Model of Mammalian Cell Cycle Regulation.
PLoS Comput. Biol., 2011

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells.
PLoS Comput. Biol., 2011

2010
Model Composition for Macromolecular Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

2009
Temporal Controls of the Asymmetric Cell Division Cycle in <i>Caulobacter crescentus</i>.
PLoS Comput. Biol., 2009

Computing with Proteins.
Computer, 2009

Model aggregation: a building-block approach to creating large macromolecular regulatory networks.
Bioinform., 2009

2008
A Quantitative Study of the Division Cycle of <i>Caulobacter crescentus</i> Stalked Cells.
PLoS Comput. Biol., 2008

Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle.
J. Glob. Optim., 2008

2007
A Mathematical Programming Formulation for the Budding Yeast Cell Cycle.
Simul., 2007

Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation.
PLoS Comput. Biol., 2007

Fusing and composing macromolecular regulatory network models.
Proceedings of the 2007 Spring Simulation Multiconference, 2007

2006
The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

The role of composition and aggregation in modeling macromolecular regulatory networks.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Challenges for modeling and simulation methods in systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

2005
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs.
J. Comput. Biol., 2005

2004
The JigCell Model Builder and Run Manager.
Bioinform., 2004

A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

2000
On Traveling Wave Solutions of Fisher's Equation in Two Spatial Dimensions.
SIAM J. Appl. Math., 2000

1992
The Dynamics of Scroll Waves in Excitable Media.
SIAM Rev., 1992

1991
Third Generation Cellular Automation for Modeling Excitable Media.
Proceedings of the Fifth SIAM Conference on Parallel Processing for Scientific Computing, 1991


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