John Tyson

Summary

Affiliation: Virginia Polytechnic Institute and State University
Country: USA

Publications

  1. ncbi request reprint Rewiring the exit from mitosis
    Andrea 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
  2. pmc Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
    Cihan Oguz
    Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
    BMC Syst Biol 7:53. 2013
  3. pmc A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells
    Tian 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
  4. ncbi request reprint Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions
    J J Tyson
    Department of Biology, Virginian Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    J Theor Biol 210:249-63. 2001
  5. pmc Biological switches and clocks
    John J Tyson
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    J R Soc Interface 5:S1-8. 2008
  6. pmc Functional motifs in biochemical reaction networks
    John 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
  7. pmc A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM
    J J Tyson
    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Biophys J 77:2411-7. 1999
  8. ncbi request reprint A precarious balance
    John J Tyson
    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Curr Biol 14:R262-3. 2004
  9. doi request reprint 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
  10. pmc Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells
    John J Tyson
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Nat Rev Cancer 11:523-32. 2011

Collaborators

Detail Information

Publications51

  1. ncbi request reprint Rewiring the exit from mitosis
    Andrea 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...
  2. pmc Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
    Cihan Oguz
    Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA
    BMC Syst Biol 7:53. 2013
    ....
  3. pmc A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells
    Tian 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...
  4. ncbi request reprint Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions
    J 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...
  5. pmc Biological switches and clocks
    John 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...
  6. pmc Functional motifs in biochemical reaction networks
    John 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...
  7. pmc A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM
    J 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...
  8. ncbi request reprint A precarious balance
    John J Tyson
    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Curr Biol 14:R262-3. 2004
  9. doi request reprint 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...
  10. pmc Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells
    John J Tyson
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Nat Rev Cancer 11:523-32. 2011
    ....
  11. pmc Temporal organization of the cell cycle
    John 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...
  12. ncbi request reprint Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
    John 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...
  13. ncbi request reprint The dynamics of cell cycle regulation
    John 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...
  14. ncbi request reprint Network dynamics and cell physiology
    J 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...
  15. pmc Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts
    Wei 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...
  16. ncbi request reprint Modeling regulatory networks at Virginia Tech
    Nicholas 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...
  17. pmc Mathematical model of the morphogenesis checkpoint in budding yeast
    Andrea 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...
  18. ncbi request reprint Antagonism and bistability in protein interaction networks
    Mohsen 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...
  19. pmc Exploring the roles of noise in the eukaryotic cell cycle
    Sandip 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...
  20. ncbi request reprint Bifurcation analysis of a model of the budding yeast cell cycle
    Dorjsuren 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...
  21. pmc Modeling molecular regulatory networks with JigCell and PET
    Clifford 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...
  22. pmc A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts
    Jason 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...
  23. pmc Integrative analysis of cell cycle control in budding yeast
    Katherine C Chen
    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0406, USA
    Mol Biol Cell 15:3841-62. 2004
    ....
  24. ncbi request reprint The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models
    Marc 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...
  25. ncbi request reprint Synchronization of eukaryotic cells by periodic forcing
    Dorjsuren 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...
  26. ncbi request reprint Turbulence near cyclic fold bifurcations in birhythmic media
    Dorjsuren 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...
  27. ncbi request reprint A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos
    Andrea 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...
  28. ncbi request reprint Parameter estimation for a mathematical model of the cell cycle in frog eggs
    Jason 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...
  29. pmc Mathematical modeling as a tool for investigating cell cycle control networks
    Jill C Sible
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0406, USA
    Methods 41:238-47. 2007
    ....
  30. ncbi request reprint 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
    ....
  31. pmc Analysis of a generic model of eukaryotic cell-cycle regulation
    Attila Csikasz-Nagy
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0406, USA
    Biophys J 90:4361-79. 2006
    ....
  32. pmc Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus
    Shenghua Li
    Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
    PLoS Comput Biol 5:e1000463. 2009
    ..g., Rhizobium, Brucella)...
  33. ncbi request reprint the JigCell model builder and run manager
    Marc 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...
  34. pmc Stochastic simulation of enzyme-catalyzed reactions with disparate timescales
    Debashis 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...
  35. pmc A quantitative study of the division cycle of Caulobacter crescentus stalked cells
    Shenghua 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...
  36. pmc Model aggregation: a building-block approach to creating large macromolecular regulatory networks
    Ranjit 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...
  37. ncbi request reprint Bringing cartoons to life
    John J Tyson
    Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    Nature 445:823. 2007
  38. pmc Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death
    Tongli 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...
  39. ncbi request reprint Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis
    Tongli 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...
  40. ncbi request reprint Reverse engineering models of cell cycle regulation
    Attila Csikasz-Nagy
    Materials Structure and Modeling Research Group of the Hungarian Academy of Sciences, Budapest, Hungary
    Adv Exp Med Biol 641:88-97. 2008
    ....
  41. ncbi request reprint Steady states and oscillations in the p53/Mdm2 network
    Andrea 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...
  42. ncbi request reprint Cycling without the cyclosome: modeling a yeast strain lacking the APC
    Brian 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...
  43. ncbi request reprint Modelling the fission yeast cell cycle
    Akos 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...
  44. ncbi request reprint A model for restriction point control of the mammalian cell cycle
    Bela 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
    ....
  45. ncbi request reprint Arthur T. Winfree (1942-2002)
    John J Tyson
    J Theor Biol 230:433-9. 2004
  46. pmc Dynamical modeling of syncytial mitotic cycles in Drosophila embryos
    Laurence 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...
  47. pmc Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation
    Andrea Ciliberto
    The FIRC Institute for Molecular Oncology, Milan, Italy
    PLoS Comput Biol 3:e45. 2007
    ....
  48. ncbi request reprint Irreversible cell-cycle transitions are due to systems-level feedback
    Bela 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...
  49. ncbi request reprint Modeling the septation initiation network (SIN) in fission yeast cells
    Attila 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...
  50. pmc Another turn for p53
    John J Tyson
    Mol Syst Biol 2:2006.0032. 2006
  51. ncbi request reprint Spatial controls for growth zone formation during the fission yeast cell cycle
    Attila 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...

Research Grants12

  1. Problem Solving Environment for Modeling the Cell Cycle
    John 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). ..
  2. Experimental and Computational Studies of Exit from Mitosis in Budding Yeast
    John J Tyson; Fiscal Year: 2010
    ..g., embryonic development, tissue regeneration, wound healing, and carcinogenesis. ..
  3. Stochastic Models of Cell Cycle Regulation in Eukaryotes
    John Tyson; Fiscal Year: 2009
    ..g., embyronic development, tissue regeneration, wound healing, and carcinogenesis. ..
  4. Stochastic Models of Cell Cycle Regulation in Eukaryotes
    John Tyson; Fiscal Year: 2007
    ..g., embyronic development, tissue regeneration, wound healing, and carcinogenesis. ..
  5. Experimental and Computational Studies of Exit from Mitosis in Budding Yeast
    John Tyson; Fiscal Year: 2007
    ..g., embryonic development, tissue regeneration, wound healing, and carcinogenesis. ..
  6. Stochastic Models of Cell Cycle Regulation in Eukaryotes
    John 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. ..