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2020 – today
- 2022
[j36]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)- 2020
- [j35]Chunrui Xu, Bronson R. Weston, John J. Tyson, Yang Cao:
Cell cycle control and environmental response by second messengers in Caulobacter crescentus. BMC Bioinform. 21-S(14): 408 (2020) - [j34]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)
2010 – 2019
- 2019
- [j33]Mansooreh Ahmadian, John J. Tyson, Yang Cao:
A stochastic model of size control in the budding yeast cell cycle. BMC Bioinform. 20-S(12): 322:1-322:13 (2019) - [j32]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): 301-311 (2019) - 2018
- [j31]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): 2237-2244 (2018) - [j30]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) - [j29]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) - [j28]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) - [c11]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: 567 - [c10]Mansooreh Ahmadian, John J. Tyson, Yang Cao:
A Stochastic Model of Size Control in the Budding Yeast Cell Cycle. BCB 2018: 589-590 - 2017
- [j27]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): 3134-3136 (2017) - [j26]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): 30:1-30:24 (2017) - [c9]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: 464-473 - 2016
- [j25]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) - [c8]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: 261-270 - 2015
- [j24]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: 95 (2015) - [j23]Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák:
Cell Cycle Control by a Minimal Cdk Network. PLoS Comput. Biol. 11(2) (2015) - [j22]Kartik Subramanian, Mark R. Paul, John J. Tyson:
Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models. PLoS Comput. Biol. 11(7) (2015) - [c7]Minghan Chen, Fei Li, Kartik Subramanian, John J. Tyson, Yang Cao:
Two-dimensional model of bipolar PopZ polymerization in caulobacter crescentus. BCB 2015: 37-46 - 2014
- [j21]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: 42 (2014) - [c6]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: 45 - 2013
- [j20]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: 53 (2013) - [j19]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): 409-418 (2013) - [j18]Kartik Subramanian, Mark R. Paul, John J. Tyson:
Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus. PLoS Comput. Biol. 9(9) (2013) - 2012
- [j17]Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson:
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. BMC Syst. Biol. 6: 66 (2012) - [j16]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) - 2011
- [j15]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) - [j14]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) - 2010
- [j13]Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson:
Model Composition for Macromolecular Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 278-287 (2010)
2000 – 2009
- 2009
- [j12]Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson:
Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinform. 25(24): 3289-3295 (2009) - [j11]Naren Ramakrishnan, Upinder S. Bhalla, John J. Tyson:
Computing with Proteins. Computer 42(1): 47-56 (2009) - [j10]Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson:
Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j9]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): 719-738 (2008) - [j8]Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson:
A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells. PLoS Comput. Biol. 4(1) (2008) - 2007
- [j7]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) - [j6]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): 497-514 (2007) - [c5]Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson:
Fusing and composing macromolecular regulatory network models. SpringSim (2) 2007: 337-344 - 2006
- [j5]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): 155-164 (2006) - [c4]Clifford A. Shaffer, Ranjit Randhawa, John J. Tyson:
The role of composition and aggregation in modeling macromolecular regulatory networks. WSC 2006: 1628-1636 - [c3]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: 1720-1730 - 2005
- [j4]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): 48-63 (2005) - 2004
- [j3]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): 3680-3681 (2004) - [c2]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 - 2000
- [j2]John J. Tyson, Pavel K. Brazhnik:
On Traveling Wave Solutions of Fisher's Equation in Two Spatial Dimensions. SIAM J. Appl. Math. 60(2): 371-391 (2000)
1990 – 1999
- 1992
- [j1]James P. Keener, John J. Tyson:
The Dynamics of Scroll Waves in Excitable Media. SIAM Rev. 34(1): 1-39 (1992) - 1991
- [c1]Jörg R. Weimar, John J. Tyson, Layne T. Watson:
Third Generation Cellular Automation for Modeling Excitable Media. PP 1991: 376-381
Coauthor Index
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