Research Topics
| John TysonSummaryAffiliation: Virginia Polytechnic Institute and State University Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Rewiring the exit from mitosisAndrea Ciliberto
Molecular Network Dynamics Research Group of Hungarian Academy of Sciences and Budapest University of Technology and Economics, Budapest, Hungary
Cell Cycle 4:1107-12. 2005..We show that the new wiring permits oscillations with a simpler and smaller network than previously envisaged and that the antagonism between MPF and Cdc20 suggests a new interpretation of the spindle checkpoint...
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cellsTian Hong
Genetics, Bioinformatics, and Computational Biology Program, Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
BMC Syst Biol 6:66. 2012..Therefore, conceptual understanding of induced heterogeneous differentiation will shed light on the mechanisms controlling the response of populations of CD4+ T cells under physiological conditions...- Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitionsJ J Tyson
Department of Biology, Virginian Polytechnic Institute and State University, Blacksburg, VA 24061, USA
J Theor Biol 210:249-63. 2001..Then we add new pieces to the "puzzle" until we obtain reasonable models of the control systems in yeast cells, frog eggs, and cultured mammalian cells... - Temporal organization of the cell cycleJohn J Tyson
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Curr Biol 18:R759-R768. 2008..The model accounts for the fundamental physiological properties of mitotic cell divisions, evokes a new view of the meiotic program, and suggests how the control system may have evolved in the first place... 
Functional motifs in biochemical reaction networksJohn J Tyson
Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Annu Rev Phys Chem 61:219-40. 2010..We show that such functional motifs exist and review the experimental evidence that they control cellular responses as expected...- A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIMJ J Tyson
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Biophys J 77:2411-7. 1999..In addition, the model suggests how an endogenous circadian oscillator could have evolved from a more primitive, light-activated switch... - Cell cycle: who turns the crank?John J Tyson
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
Curr Biol 21:R185-7. 2011..The oscillating activity of a single CDK-cyclin fusion protein can drive the orderly progression of yeast cells through DNA replication, mitosis and cell division... - A precarious balanceJohn J Tyson
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Curr Biol 14:R262-3. 2004 - Dynamic modelling of oestrogen signalling and cell fate in breast cancer cellsJohn J Tyson
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Nat Rev Cancer 11:523-32. 2011.... - Biological switches and clocksJohn J Tyson
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
J R Soc Interface 5:S1-8. 2008..We review recent advances in modelling the gene-protein interaction networks that control circadian rhythms, cell cycle progression, signal processing and the design of synthetic gene networks... - Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cellJohn J Tyson
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Curr Opin Cell Biol 15:221-31. 2003..These models shed light on the design principles of biological control systems and make predictions that have been verified experimentally... - The dynamics of cell cycle regulationJohn J Tyson
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg 24061, USA
Bioessays 24:1095-109. 2002..These claims are demonstrated by an analysis of cell cycle regulation in fission yeast... - Network dynamics and cell physiologyJ J Tyson
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Nat Rev Mol Cell Biol 2:908-16. 2001..To understand this dance, a new breed of theoretical molecular biologists reproduces these networks in computers and in the mathematical language of dynamical systems... - Hysteresis drives cell-cycle transitions in Xenopus laevis egg extractsWei Sha
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA
Proc Natl Acad Sci U S A 100:975-80. 2003..All three predictions were validated. These observations confirm hysteresis as the driving force for cell-cycle transitions into and out of mitosis... - Mathematical model of the morphogenesis checkpoint in budding yeastAndrea Ciliberto
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
J Cell Biol 163:1243-54. 2003..The model supports the idea that the morphogenesis checkpoint, like other checkpoints, raises the cell size threshold for progression from one phase of the cell cycle to the next... - Modeling regulatory networks at Virginia TechNicholas A Allen
The Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
OMICS 7:285-99. 2003..The software tools developed at Virginia Tech are designed to meet general requirements of modeling regulatory networks and are collected in a problem-solving environment called JigCell... - Exploring the roles of noise in the eukaryotic cell cycleSandip Kar
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Proc Natl Acad Sci U S A 106:6471-6. 2009..If these mRNA molecules are longer-lived (perhaps 2 min), then the intrinsic noise in our simulations is too large, and there must be some additional noise suppression mechanisms at work in cells... - Antagonism and bistability in protein interaction networksMohsen Sabouri-Ghomi
Department of Biological Sciences, Virginia Polytechnic Institute and State University, M C 0406, Blacksburg, VA 24061, USA
J Theor Biol 250:209-18. 2008..Once an equivalent model is formulated in terms of elementary chemical reactions, it can be simulated accurately either by deterministic differential equations or by Gillespie's stochastic simulation algorithm... - Turbulence near cyclic fold bifurcations in birhythmic mediaDorjsuren Battogtokh
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0106, USA
Phys Rev E Stat Nonlin Soft Matter Phys 70:026212. 2004..We also find similar turbulence in a cell cycle model. These findings suggest that weak turbulence may be universal in biochemical birhythmic media exhibiting cyclic fold bifurcations... - A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryosAndrea Ciliberto
Biology Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0406, USA
Biophys Chem 104:573-89. 2003..The model's predictions about embryos injected with Xic1, a stoichiometric inhibitor of cyclin E/Cdk2, were experimentally validated... - Integrative analysis of cell cycle control in budding yeastKatherine C Chen
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0406, USA
Mol Biol Cell 15:3841-62. 2004.... - The JigCell model builder: a spreadsheet interface for creating biochemical reaction network modelsMarc T Vass
Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0106, USA
IEEE/ACM Trans Comput Biol Bioinform 3:155-64. 2006..All four paradigms had similar data entry times. The spreadsheet and scripting language approaches require significantly fewer screens to view the models than do the wizard or graphical layout approaches... - Bifurcation analysis of a model of the budding yeast cell cycleDorjsuren Battogtokh
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Chaos 14:653-61. 2004..In a three-variable model exhibiting birhythmicity (two stable oscillatory states), we explore possible effects of extrinsic fluctuations on cell cycle progression... - Synchronization of eukaryotic cells by periodic forcingDorjsuren Battogtokh
Department of Biology, Virginia Polytechnic Institute and State University Blacksburg, VA 24061 0106, USA
Phys Rev Lett 96:148102. 2006..We also discuss the effects of intrinsic mitotic fluctuations, asymmetric division, and weak mutual coupling on the pace of synchronization... - Analysis of a generic model of eukaryotic cell-cycle regulationAttila Csikasz-Nagy
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0406, USA
Biophys J 90:4361-79. 2006.... - Cell cycle control in bacteria and yeast: a case of convergent evolution?Paul Brazhnik
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0406, USA
Cell Cycle 5:522-9. 2006.... - Mathematical modeling as a tool for investigating cell cycle control networksJill C Sible
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0406, USA
Methods 41:238-47. 2007.... - Parameter estimation for a mathematical model of the cell cycle in frog eggsJason W Zwolak
Department of Computer Science, 660 McBryde Hall, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0106, USA
J Comput Biol 12:48-63. 2005..These tools are sufficiently general to attack more complicated problems, where guesstimation is impractical or unreliable... - Modeling molecular regulatory networks with JigCell and PETClifford A Shaffer
Department of Computer Science, Virginia Tech, Blacksburg, 24061, USA
Methods Mol Biol 500:81-111. 2009..We show how parameter estimation tools automatically generate rate constants that fit a model to experimental data... - A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extractsJason Zwolak
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, 24061, USA
J Theor Biol 260:110-20. 2009..The model provides a validated framework upon which to build additional aspects of the cell cycle checkpoint signaling network, including those control signals in the mammalian cell cycle that are commonly mutated in cancer... - Temporal controls of the asymmetric cell division cycle in Caulobacter crescentusShenghua Li
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
PLoS Comput Biol 5:e1000463. 2009..g., Rhizobium, Brucella)... - Bringing cartoons to lifeJohn J Tyson
Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Nature 445:823. 2007 - Model aggregation: a building-block approach to creating large macromolecular regulatory networksRanjit Randhawa
Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
Bioinformatics 25:3289-95. 2009..To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined... - the JigCell model builder and run managerMarc Vass
Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106, USA
Bioinformatics 20:3680-1. 2004..AVAILABILITY: JCMB and JCRM are part of the JigCell suite available at http://jigcell.biol.vt.edu... - Stochastic simulation of enzyme-catalyzed reactions with disparate timescalesDebashis Barik
Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Biophys J 95:3563-74. 2008..In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation... - A quantitative study of the division cycle of Caulobacter crescentus stalked cellsShenghua Li
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
PLoS Comput Biol 4:e9. 2008..crescentus are conserved among many genera of alpha-proteobacteria, the proposed mechanism may be applicable to other species of importance in agriculture and medicine... - Computational analysis of dynamical responses to the intrinsic pathway of programmed cell deathTongli Zhang
Department of Biological Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
Biophys J 97:415-34. 2009..Cells first undergo cell cycle arrest and DNA repair, and then apoptosis if the damage is beyond repair. The model ascribes this cell-fate transition to a transformation of p53 from "helper" to "killer" forms... - Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosisTongli Zhang
Department of Biological Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
Cell Cycle 6:85-94. 2007..The proposal accounts for basic features of p53-mediated responses to DNA damage and suggests new experiments to probe the dynamics of p53 signaling... - Arthur T. Winfree (1942-2002)John J Tyson
J Theor Biol 230:433-9. 2004 - Modelling the fission yeast cell cycleAkos Sveiczer
Department of Agricultural Chemical Technology at Budapest University of Technology and Economics, Hungary
Brief Funct Genomic Proteomic 2:298-307. 2004..It is proposed that the key physiological variable driving progression through the cell cycle during balanced growth and division is the mass/DNA ratio, rather than the mass/nucleus ratio... - Cycling without the cyclosome: modeling a yeast strain lacking the APCBrian R Thornton
Cancer Research Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, USA
Cell Cycle 3:629-33. 2004..We discuss a few minor inconsistencies between the model and experiment, and how these may inform future revisions to the model... - Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximationAndrea Ciliberto
The FIRC Institute for Molecular Oncology, Milan, Italy
PLoS Comput Biol 3:e45. 2007.... - A model for restriction point control of the mammalian cell cycleBela Novak
Molecular Network Dynamics Research Group of Hungarian Academy of Sciences and Budapest University of Technology and Economics, Gellert ter 4, 1521 Budapest, Hungary
J Theor Biol 230:563-79. 2004.... - Steady states and oscillations in the p53/Mdm2 networkAndrea Ciliberto
Molecular Network Dynamics Research Group of Hungarian Academy of Sciences, Budapest University of Technology and Economics, Budapest, Hungary
Cell Cycle 4:488-93. 2005..The model reproduces experimental data in quantitative detail. We suggest new experiments for dissecting the contributions of negative and positive feedbacks to the generation of oscillations... - Reverse engineering models of cell cycle regulationAttila Csikasz-Nagy
Materials Structure and Modeling Research Group of the Hungarian Academy of Sciences, Budapest, Hungary
Adv Exp Med Biol 641:88-97. 2008.... - Dynamical modeling of syncytial mitotic cycles in Drosophila embryosLaurence Calzone
Molecular Network Dynamics Research Group of Hungarian Academy of Sciences and Budapest University of Technology and Economics, Budapest, Gellért tér, Hungary
Mol Syst Biol 3:131. 2007..The model can be used to predict the phenotypes of novel mutations and effective ranges of the unmeasured rate constants and transport coefficients in the proposed mechanism... - Irreversible cell-cycle transitions are due to systems-level feedbackBela Novak
Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
Nat Cell Biol 9:724-8. 2007..This systems-level view of irreversibility is supported by many experimental observations... - Spatial controls for growth zone formation during the fission yeast cell cycleAttila Csikasz-Nagy
Materials Structure and Modelling Research Group of the Hungarian Academy of Sciences, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
Yeast 25:59-69. 2008..Based on these results, we propose that fission yeast cells have specific size ranges in which they can exhibit two or more different stable patterns of growth... - Modeling the septation initiation network (SIN) in fission yeast cellsAttila Csikasz-Nagy
Materials Structure and Modeling Research Group of the Hungarian Academy of Sciences and Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111, Budapest, Szt Gellert ter 4, Hungary
Curr Genet 51:245-55. 2007..The model predicts phenotypes of some uncharacterized mutant cells and shows how a cytokinesis checkpoint can stop the cell cycle if septation fails... - Another turn for p53John J Tyson
Mol Syst Biol 2:2006.0032. 2006
Research Grants
- Problem Solving Environment for Modeling the Cell CycleJohn Tyson; Fiscal Year: 2002..and some outstanding collaborators (Sible and Cross, experimental cell cycle research; Kitano and Bolouri, software development for molecular cell biology; and Kohn, bioinformatics of mammalian cell cycle controls). ..
- Experimental and Computational Studies of Exit from Mitosis in Budding YeastJohn J Tyson; Fiscal Year: 2010..g., embryonic development, tissue regeneration, wound healing, and carcinogenesis. ..
- Stochastic Models of Cell Cycle Regulation in EukaryotesJohn Tyson; Fiscal Year: 2009..g., embyronic development, tissue regeneration, wound healing, and carcinogenesis. ..
- Stochastic Models of Cell Cycle Regulation in EukaryotesJohn Tyson; Fiscal Year: 2007..g., embyronic development, tissue regeneration, wound healing, and carcinogenesis. ..
- Experimental and Computational Studies of Exit from Mitosis in Budding YeastJohn Tyson; Fiscal Year: 2007..g., embryonic development, tissue regeneration, wound healing, and carcinogenesis. ..
- Stochastic Models of Cell Cycle Regulation in EukaryotesJohn J Tyson; Fiscal Year: 2010..Hence, a validated stochastic model of the eukaryotic cell cycle is essential to progress in the field of molecular systems biology. ..