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John Tyson

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Eukaryotic Cells

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Publications

TOP 3
Christopher L Poirel; Richard R Rodrigues; John J Tyson; Katherine C Chen; TM Murali
Top-down network analysis to drive bottom-up modeling of physiological processes.
Claude Gérard; John J Tyson; Béla Novák
Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates.
Anael Verdugo; P K Vinod; John J Tyson; Bela Novak
Molecular mechanisms creating bistable switches at cell cycle transitions.

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All Publications

2013: Christopher L Poirel; Richard R Rodrigues; John J Tyson; Katherine C Chen; TM Murali
Top-down network analysis to drive bottom-up modeling of physiological processes.
Journal of computational biology : a journal of computational molecular cell biology 2013;20(5):409-18.
2013: Claude Gérard; John J Tyson; Béla Novák
Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates.
Biophysical journal 2013;104(6):1367-79.
2013: Anael Verdugo; P K Vinod; John J Tyson; Bela Novak
Molecular mechanisms creating bistable switches at cell cycle transitions.
Open biology 2013;3(3):120179.
2012: Zhen Liu; Yang Pu; Clifford A Shaffer; John J Tyson; Stefan Hoops; Fei Li; Yang Cao
Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.
The Journal of chemical physics 2012;136(3):034105.
2012: Tian Hong; Liwu Li; Jianhua Xing; John J Tyson
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells.
BMC systems biology 2012;6():66.
2012: Yan Fu; Trevor Glaros; Liwu Li; John J Tyson; Ping Wang; Zhanghan Wu; Meng Zhu; Jianhua Xing
Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells.
PLoS computational biology 2012;8(5):e1002526.
2012: Baris Hancioglu; John J Tyson
A mathematical model of mitotic exit in budding yeast: the role of Polo kinase.
PloS one 2012;7(2):e30810.
2011: Tian Hong; Liwu Li; Jianhua Xing; John J Tyson
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells.
PLoS computational biology 2011;7(7):e1002122.
2011: John J Tyson; Anael Verdugo; Yue Wang; Louis M Weiner; William T Baumann; Chun Chen; Iman Tavassoly; Robert Clarke
Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells.
Nature reviews. Cancer 2011;11(7):523-32.
2011: Enuo He; Orsolya Kapuy; Raquel A Oliveira; John J Tyson; Frank Uhlmann; Béla Novák
System-level feedbacks make the anaphase switch irreversible.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(24):10016-21.
2011: David A Ball; Tae-Hyuk Ahn; Pengyuan Wang; Katherine C Chen; Yang Cao; John J Tyson; Jean Peccoud; William T Baumann
Stochastic exit from mitosis in budding yeast: model predictions and experimental observations.
Cell cycle (Georgetown, Tex.) 2011;10(6):999-1009.
2011: John J Tyson; Bela Novak
Cell cycle: who turns the crank?
Current biology : CB 2011;21(5):R185-7.
2011: David A Ball; William T Baumann; Katherine C Chen; Julie Marchand; Magaly Poulet; John J Tyson; Jean Peccoud
Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry.
PloS one 2011;6(10):e26272.
2011: Rajat Singhania; R Michael Sramkoski; James W Jacobberger; John J Tyson
A hybrid model of mammalian cell cycle regulation.
PLoS computational biology 2011;7(2):e1001077.
2010: Bela Novak; Orsolya Kapuy; Maria Rosa Domingo-Sananes; John J Tyson
Regulated protein kinases and phosphatases in cell cycle decisions.
Current opinion in cell biology 2010;22(6):801-8.
2010: Debashis Barik; William T Baumann; MR Paul; Bela Novak; John J Tyson
A model of yeast cell-cycle regulation based on multisite phosphorylation.
Molecular systems biology 2010;6():405.
2010: Ranjit Randhawa; Clifford A Shaffer; John J Tyson
Model composition for macromolecular regulatory networks.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2010;7(2):278-87.
2010: John J Tyson; Béla Novák
Functional motifs in biochemical reaction networks.
Annual review of physical chemistry 2010;61():219-40.
2009: Orsolya Kapuy; Enuo He; Sandra López-Avilés; Frank Uhlmann; John J Tyson; Béla Novák
System-level feedbacks control cell cycle progression.
FEBS letters 2009;583(24):3992-8.
2009: Ranjit Randhawa; Clifford A Shaffer; John J Tyson
Model aggregation: a building-block approach to creating large macromolecular regulatory networks.
Bioinformatics (Oxford, England) 2009;25(24):3289-95.
2009: Jason Zwolak; Nassiba Adjerid; Elife Z Bagci; John J Tyson; Jill C Sible
A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts.
Journal of theoretical biology 2009;260(1):110-20.
2009: Orsolya Kapuy; Debashis Barik; Maria Rosa Domingo Sananes; John J Tyson; Béla Novák
Bistability by multiple phosphorylation of regulatory proteins.
Progress in biophysics and molecular biology 2009;100(1-3):47-56.
2009: Shenghua Li; Paul Brazhnik; Bruno Sobral; John J Tyson
Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus.
PLoS computational biology 2009;5(8):e1000463.
2009: Tongli Zhang; Paul Brazhnik; John J Tyson
Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death.
Biophysical journal 2009;97(2):415-34.
2009: Sandip Kar; William T Baumann; MR Paul; John J Tyson
Exploring the roles of noise in the eukaryotic cell cycle.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(16):6471-6.
2009: Clifford A Shaffer; Jason W Zwolak; Ranjit Randhawa; John J Tyson
Modeling molecular regulatory networks with JigCell and PET.
Methods in molecular biology (Clifton, N.J.) 2009;500():81-111.
2009: Attila Csikàsz-Nagy; Orsolya Kapuy; Attila Tóth; Csaba Pál; Lars Juhl Jensen; Frank Uhlmann; John J Tyson; Béla Novák
Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation.
Molecular systems biology 2009;5():236.
2008: Béla Novák; John J Tyson
Design principles of biochemical oscillators.
Nature reviews. Molecular cell biology 2008;9(12):981-91.
2008: Debashis Barik; MR Paul; William T Baumann; Yang Cao; John J Tyson
Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.
Biophysical journal 2008;95(8):3563-74.
2008: John J Tyson; Bela Novak
Temporal organization of the cell cycle.
Current biology : CB 2008;18(17):R759-R768.
2008: John J Tyson; Reka Albert; Albert Goldbeter; Peter Ruoff; Jill Sible
Biological switches and clocks.
Journal of the Royal Society, Interface / the Royal Society 2008;5 Suppl 1():S1-8.
2008: Mohsen Sabouri-Ghomi; Andrea Ciliberto; Sandip Kar; Bela Novak; John J Tyson
Antagonism and bistability in protein interaction networks.
Journal of theoretical biology 2008;250(1):209-18.
2008: Attila Csikàsz-Nagy; Béla Novák; John J Tyson
Reverse engineering models of cell cycle regulation.
Advances in experimental medicine and biology 2008;641():88-97.
2008: Shenghua Li; Paul Brazhnik; Bruno Sobral; John J Tyson
A quantitative study of the division cycle of Caulobacter crescentus stalked cells.
PLoS computational biology 2008;4(1):e9.
2008: Attila Csikàsz-Nagy; Béla Gyorffy; Wolfgang Alt; John J Tyson; Béla Novák
Spatial controls for growth zone formation during the fission yeast cell cycle.
Yeast (Chichester, England) 2008;25(1):59-69.
2007: Bela Novak; John J Tyson; Bela Gyorffy; Attila Csikàsz-Nagy
Irreversible cell-cycle transitions are due to systems-level feedback.
Nature cell biology 2007;9(7):724-8.
2007: Attila Csikàsz-Nagy; Orsolya Kapuy; Béla Gyorffy; John J Tyson; Béla Novák
Modeling the septation initiation network (SIN) in fission yeast cells.
Current genetics 2007;51(4):245-55.
2007: Andrea Ciliberto; Fabrizio Capuani; John J Tyson
Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.
PLoS computational biology 2007;3(3):e45.
2007: John J Tyson
Bringing cartoons to life.
Nature 2007;445(7130):823.
2007: Jill C Sible; John J Tyson
Mathematical modeling as a tool for investigating cell cycle control networks.
Methods (San Diego, Calif.) 2007;41(2):238-47.
2007: Christian I Hong; Emery D Conrad; John J Tyson
A proposal for robust temperature compensation of circadian rhythms.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(4):1195-200.
2007: Laurence Calzone; Denis Thieffry; John J Tyson; Bela Novak
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos.
Molecular systems biology 2007;3():131.
2007: Tongli Zhang; Paul Brazhnik; John J Tyson
Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis.
Cell cycle (Georgetown, Tex.) 2007;6(1):85-94.
2006: Attila Csikàsz-Nagy; Dorjsuren Battogtokh; Katherine C Chen; Béla Novák; John J Tyson
Analysis of a generic model of eukaryotic cell-cycle regulation.
Biophysical journal 2006;90(12):4361-79.
2006: Dorjsuren Battogtokh; Kazuyuki Aihara; John J Tyson
Synchronization of eukaryotic cells by periodic forcing.
Physical review letters 2006;96(14):148102.
2006: Marc T 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 transactions on computational biology and bioinformatics / IEEE, ACM 2006;3(2):155-64.
2006: Paul Brazhnik; John J Tyson
Cell cycle control in bacteria and yeast: a case of convergent evolution?
Cell cycle (Georgetown, Tex.) 2006;5(5):522-9.
2006: N A Allen; Katherine C Chen; Clifford A Shaffer; John J Tyson; Layne T Watson
Computer evaluation of network dynamics models with application to cell cycle control in budding yeast.
Systems biology 2006;153(1):13-21.
2006: Dorjsuren Battogtokh; John J Tyson
Periodic forcing of a mathematical model of the eukaryotic cell cycle.
Physical review. E, Statistical, nonlinear, and soft matter physics 2006;73(1 Pt 1):011910.
2005: Andrea Ciliberto; Anna Lukács; Attila Tóth; John J Tyson; Béla Novák
Rewiring the exit from mitosis.
Cell cycle (Georgetown, Tex.) 2005;4(8):1107-12.
2005: Jason W Zwolak; John J Tyson; Layne T Watson
Globally optimised parameters for a model of mitotic control in frog egg extracts.
Systems biology 2005;152(2):81-92.
2005: Andrea Ciliberto; Bela Novak; John J Tyson
Steady states and oscillations in the p53/Mdm2 network.
Cell cycle (Georgetown, Tex.) 2005;4(3):488-93.
2005: Jason W Zwolak; John J Tyson; Layne T Watson
Parameter estimation for a mathematical model of the cell cycle in frog eggs.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(1):48-63.
2004: Marc T Vass; Nicholas Allen; Clifford A Shaffer; Naren Ramakrishnan; Layne T Watson; John J Tyson
the JigCell model builder and run manager.
Bioinformatics (Oxford, England) 2004;20(18):3680-1.
2004: Béla Novák; John J Tyson
A model for restriction point control of the mammalian cell cycle.
Journal of theoretical biology 2004;230(4):563-79.
2004: Dorjsuren Battogtokh; John J Tyson
Bifurcation analysis of a model of the budding yeast cell cycle.
Chaos (Woodbury, N.Y.) 2004;14(3):653-61.
2004: Dorjsuren Battogtokh; John J Tyson
Turbulence near cyclic fold bifurcations in birhythmic media.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(2 Pt 2):026212.
2004: Katherine C Chen; Laurence Calzone; Attila Csikàsz-Nagy; Frederick R Cross; Bela Novak; John J Tyson
Integrative analysis of cell cycle control in budding yeast.
Molecular biology of the cell 2004;15(8):3841-62.
2004: Brian R Thornton; Katherine C Chen; Frederick R Cross; John J Tyson; David P Toczyski
Cycling without the cyclosome: modeling a yeast strain lacking the APC.
Cell cycle (Georgetown, Tex.) 2004;3(5):629-33.
2004: John J Tyson
A precarious balance.
Current biology : CB 2004;14(7):R262-3.
2004: Akos Sveiczer; John J Tyson; Bela Novak
Modelling the fission yeast cell cycle.
Briefings in functional genomics & proteomics 2004;2(4):298-307.
2003: Andrea Ciliberto; Bela Novak; John J Tyson
Mathematical model of the morphogenesis checkpoint in budding yeast.
The Journal of cell biology 2003;163(6):1243-54.
2003: Béla Novák; John J Tyson
Modelling the controls of the eukaryotic cell cycle.
Biochemical Society transactions 2003;31(Pt 6):1526-9.
2003: Andrea Ciliberto; Matthew J Petrus; John J Tyson; Jill C Sible
A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos.
Biophysical chemistry 2003;104(3):573-89.
2003: John J Tyson; Katherine C Chen; Bela Novak
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
Current opinion in cell biology 2003;15(2):221-31.
2003: Wei Sha; Jonathan Moore; Katherine Chen; Antonio D Lassaletta; Chung-Seon Yi; John J Tyson; Jill C Sible
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(3):975-80.
2003: Nicholas A Allen; Laurence Calzone; Katherine C Chen; Andrea Ciliberto; Naren Ramakrishnan; Clifford A Shaffer; Jill C Sible; John J Tyson; Marc T Vass; Layne T Watson; Jason W Zwolak
Modeling regulatory networks at Virginia Tech.
Omics : a journal of integrative biology 2003;7(3):285-99.
2002: John J Tyson; Attila Csikàsz-Nagy; Bela Novak
The dynamics of cell cycle regulation.
BioEssays : news and reviews in molecular, cellular and developmental biology 2002;24(12):1095-109.
2001: John J Tyson; K Chen; Bela Novak
Network dynamics and cell physiology.
Nature reviews. Molecular cell biology 2001;2(12):908-16.
2001: Akos Sveiczer; John J Tyson; Bela Novak
A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation.
Biophysical chemistry 2001;92(1-2):1-15.
2001: John J Tyson; Bela Novak
Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions.
Journal of theoretical biology 2001;210(2):249-63.
2000: Akos Sveiczer; Attila Csikàsz-Nagy; Béla Gyorffy; John J Tyson; Bela Novak
Modeling the fission yeast cell cycle: quantized cycle times in wee1- cdc25Delta mutant cells.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(14):7865-70.
2000: Andrea Ciliberto; John J Tyson
Mathematical model for early development of the sea urchin embryo.
Bulletin of mathematical biology 2000;62(1):37-59.
2000: Katherine C Chen; Attila Csikàsz-Nagy; Béla Gyorffy; J Val; Bela Novak; John J Tyson
Kinetic analysis of a molecular model of the budding yeast cell cycle.
Molecular biology of the cell 2000;11(1):369-91.
1999: John J Tyson; C I Hong; C D Thron; B Novak
A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM.
Biophysical journal 1999;77(5):2411-7.
1999: Béla Novák; A Tóth; Attila Csikàsz-Nagy; B Györffy; John J Tyson; K Nasmyth
Finishing the cell cycle.
Journal of theoretical biology 1999;199(2):223-33.
1998: Bela Novak; Attila Csikàsz-Nagy; Béla Gyorffy; K Nasmyth; John J Tyson
Model scenarios for evolution of the eukaryotic cell cycle.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1998;353(1378):2063-76.
1998: Bela Novak; Attila Csikàsz-Nagy; Béla Gyorffy; K Chen; John J Tyson
Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions.
Biophysical chemistry 1998;72(1-2):185-200.
1998: G Marlovits; C J Tyson; Bela Novak; John J Tyson
Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA.
Biophysical chemistry 1998;72(1-2):169-84.
1997: C I Hong; John J Tyson
A proposal for temperature compensation of the circadian rhythm in Drosophila based on dimerization of the per protein.
Chronobiology international 1997;14(5):521-9.
1997: Bela Novak; John J Tyson
Modeling the control of DNA replication in fission yeast.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(17):9147-52.
1996: John J Tyson; Bela Novak; G M Odell; K Chen; C D Thron
Chemical kinetic theory: understanding cell-cycle regulation.
Trends in biochemical sciences 1996;21(3):89-96.
1995: John J Tyson; Bela Novak; K Chen; J Val
Checkpoints in the cell cycle from a modeler's perspective.
Progress in cell cycle research 1995;1():1-8.
1993: Bela Novak; John J Tyson
Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos.
Journal of cell science 1993;106 ( Pt 4)():1153-68.
1991: John J Tyson
Modeling the cell division cycle: cdc2 and cyclin interactions.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(16):7328-32.
1990: John J Tyson; K C Chen; M Lederman; R C Bates
Analysis of the kinetic hairpin transfer model for parvoviral DNA replication.
Journal of theoretical biology 1990;144(2):155-69.
1990: M Gerhardt; H Schuster; John J Tyson
A cellular automation model of excitable media including curvature and dispersion.
Science (New York, N.Y.) 1990;247(4950):1563-6.
1989: K C Chen; John J Tyson; M Lederman; E R Stout; R C Bates
A kinetic hairpin transfer model for parvoviral DNA replication.
Journal of molecular biology 1989;208(2):283-96.
1989: John J Tyson; J D Murray
Cyclic AMP waves during aggregation of Dictyostelium amoebae.
Development (Cambridge, England) 1989;106(3):421-6.
1987: John J Tyson
Size control of cell division.
Journal of theoretical biology 1987;126(4):381-91.