All Stories

  1. A dynamical model of growth and maturation in Drosophila

    Article • Proceedings of the National Academy of Sciences, November 2023, Proceedings of the National Academy of Sciences

    Alexander Shingleton, Professor John J Tyson

  2. Evolutionary Stability of Small Molecular Regulatory Networks That Exhibit Near-Perfect Adaptation

    Article • Biology, June 2023, MDPI AG

    Professor John J Tyson

  3. The oscillation of mitotic kinase governs cell cycle latches in mammalian cells

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  4. Turing-pattern model of scaffolding proteins that establish spatial asymmetry during the cell cycle of Caulobacter crescentus

    Article • iScience, April 2023, Elsevier

    Professor John J Tyson

  5. Feedback in the β-catenin destruction complex imparts bistability and cellular memory

    Article • Proceedings of the National Academy of Sciences, January 2023, Proceedings of the National Academy of Sciences

    Curtis Thorne, Professor John J Tyson

  6. A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle

    Article • Scientific Reports, November 2022, Springer Science + Business Media

    Professor John J Tyson

  7. Nucleation of stem cell domains in a bistable activator–inhibitor model of the shoot apical meristem

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, September 2022, American Institute of Physics

    Professor John J Tyson

  8. BubR1 recruitment to the kinetochore via Bub1 enhances spindle assembly checkpoint signaling

    Article • Molecular Biology of the Cell, September 2022, American Society for Cell Biology (ASCB)

    Professor John J Tyson

  9. Time-keeping and decision-making in living cells: Part II

    Article • Interface Focus, June 2022, Royal Society Publishing

    Professor John J Tyson

  10. Time-keeping and decision-making in the cell cycle

    Article • Interface Focus, June 2022, Royal Society Publishing

    Professor John J Tyson

  11. Time-keeping and decision-making in living cells: Part I

    Article • Interface Focus, April 2022, Royal Society Publishing

    Professor John J Tyson

  12. Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock

    Article • PLoS Computational Biology, March 2022, PLOS

    Professor John J Tyson

  13. From the Belousov–Zhabotinsky reaction to biochemical clocks, traveling waves and cell cycle regulation

    Article • Biochemical Journal, January 2022, Portland Press Ltd.

    Professor John J Tyson

  14. Understanding virtual patients efficiently and rigorously by combining machine learning with dynamical modelling

    Article • Journal of Pharmacokinetics and Pharmacodynamics, January 2022, Springer Science + Business Media

    Professor John J Tyson

  15. The oscillation of mitotic kinase governs cell cycle latches

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  16. Computational modeling of unphosphorylated CtrA:Cori binding in the Caulobacter cell cycle

    Article • iScience, December 2021, Elsevier

    Professor John J Tyson

  17. Mechanisms of signalling-memory governing progression through the eukaryotic cell cycle

    Article • Current Opinion in Cell Biology, April 2021, Elsevier

    Professor John J Tyson

  18. Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy

    Article • PLoS Computational Biology, October 2020, PLOS

    Professor Jae Kyoung Kim, Professor John J Tyson

  19. Mathematical Analysis of Robustness of Oscillations in Models of the Mammalian Circadian Clock

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  20. Cell cycle control and environmental response by second messengers in Caulobacter crescentus

    Article • BMC Bioinformatics, September 2020, Springer Science + Business Media

    Professor John J Tyson

  21. Mechanisms of signalling-memory governing progression through the eukaryotic cell cycle

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  22. A stochastic model for error correction of kinetochore-microtubule attachments in budding yeast

    Article • PLoS ONE, August 2020, PLOS

    Professor John J Tyson

  23. A Dynamical Paradigm for Molecular Cell Biology

    Article • Trends in Cell Biology, July 2020, Elsevier

    Professor John J Tyson

  24. Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants

    Article • npj Systems Biology and Applications, May 2020, Springer Science + Business Media

    Professor John J Tyson

  25. A hybrid stochastic model of the budding yeast cell cycle

    Article • npj Systems Biology and Applications, March 2020, Springer Science + Business Media

    Professor John J Tyson

  26. Modeling and Analysis of the Macronutrient Signaling Network in Budding Yeast

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  27. Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  28. A single light-responsive sizer can control multiple-fission cycles in Chlamydomonas

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  29. A stochastic model for error correction of kinetochore-microtubule attachments and its coupling to the spindle assembly checkpoint

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  30. Modeling the dynamic behavior of biochemical regulatory networks

    Article • Journal of Theoretical Biology, February 2019, Elsevier

    Professor John J Tyson

  31. Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, January 2019, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  32. Ectopic Activation of the Spindle Assembly Checkpoint Signaling Cascade Reveals Its Biochemical Design

    Article • Current Biology, January 2019, Elsevier

    Professor John J Tyson

  33. Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB)

    Article • January 2019, Springer Science + Business Media

    Professor John J Tyson

  34. Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock

    Article • Biophysical Journal, November 2018, Elsevier

    Professor John J Tyson

  35. Dilution and titration of cell-cycle regulators may control cell size in budding yeast

    Article • PLoS Computational Biology, October 2018, PLOS

    Professor John J Tyson

  36. Mathematical Analysis of Cytokine-Induced Differentiation of Granulocyte-Monocyte Progenitor Cells

    Article • Frontiers in Immunology, September 2018, Frontiers

    Professor John J Tyson

  37. Genome stability during cell proliferation: A systems analysis of the molecular mechanisms controlling progression through the eukaryotic cell cycle

    Article • Current Opinion in Systems Biology, June 2018, Elsevier

    Professor John J Tyson

  38. Dilution and titration of cell-cycle regulators may control cell size in budding yeast

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Professor John J Tyson

  39. Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network

    Article • PLoS Computational Biology, February 2018, PLOS

    Professor John J Tyson

  40. JigCell Model Connector: building large molecular network models from components

    Article • SIMULATION, February 2018, SAGE Publications

    Professor John J Tyson

  41. CrossPlan: systematic planning of genetic crosses to validate mathematical models

    Article • Bioinformatics, February 2018, Oxford University Press (OUP)

    Professor John J Tyson

  42. Cell-cycle transitions: a common role for stoichiometric inhibitors

    Article • Molecular Biology of the Cell, November 2017, American Society for Cell Biology (ASCB)

    Professor John J Tyson

  43. GraphSpace: stimulating interdisciplinary collaborations in network biology

    Article • Bioinformatics, June 2017, Oxford University Press (OUP)

    Professor John J Tyson

  44. Predicting network modules of cell cycle regulators using relative protein abundance statistics

    Article • BMC Systems Biology, February 2017, Springer Science + Business Media

    Professor John J Tyson

  45. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus

    Article • January 2017, Springer Science + Business Media

    Professor John J Tyson

  46. A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability

    Article • PLoS Computational Biology, December 2016, PLOS

    Professor John J Tyson

  47. Cell Division: Flipping the Mitotic Switches

    Article • Current Biology, December 2016, Elsevier

    Professor John J Tyson

  48. Model-driven experimental approach reveals the complex regulatory distribution of p53 by the circadian factor Period 2

    Article • Proceedings of the National Academy of Sciences, November 2016, Proceedings of the National Academy of Sciences

    Professor Jae Kyoung Kim, Professor John J Tyson

  49. A Hybrid Stochastic Model of the Budding Yeast Cell Cycle Control Mechanism

    Article • October 2016, ACM (Association for Computing Machinery)

    Professor John J Tyson

  50. A stochastic spatiotemporal model of a response-regulator network in theCaulobacter crescentuscell cycle

    Article • Physical Biology, June 2016, Institute of Physics Publishing

    Professor John J Tyson

  51. A Bistable Switch Mechanism for Stem Cell Domain Nucleation in the Shoot Apical Meristem

    Article • Frontiers in Plant Science, May 2016, Frontiers

    Professor John J Tyson

  52. A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks

    Article • PLoS ONE, May 2016, PLOS

    Professor John J Tyson

  53. From START to FINISH: computational analysis of cell cycle control in budding yeast

    Article • npj Systems Biology and Applications, December 2015, Springer Science + Business Media

    Professor John J Tyson

  54. Two-dimensional model of bipolar PopZ polymerization in caulobacter crescentus

    Article • September 2015, ACM (Association for Computing Machinery)

    Professor John J Tyson

  55. Dynamic Modeling of the Interaction Between Autophagy and Apoptosis in Mammalian Cells

    Article • CPT Pharmacometrics & Systems Pharmacology, April 2015, Wiley

    Executive Director, The Hormel Institute Robert Clarke, Professor John J Tyson

  56. A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2

    Article • PLoS ONE, May 2014, PLOS

    Professor John J Tyson

  57. Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer

    Article • Journal of The Royal Society Interface, May 2014, Royal Society Publishing

    Executive Director, The Hormel Institute Robert Clarke, Professor John J Tyson

  58. Control of cell growth, division and death: information processing in living cells

    Article • Interface Focus, April 2014, Royal Society Publishing

    Professor John J Tyson

  59. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

    Article • BMC Systems Biology, January 2014, Springer Science + Business Media

    Professor John J Tyson

  60. Role for regulated phosphatase activity in generating mitotic oscillations in Xenopus cell-free extracts

    Article • Proceedings of the National Academy of Sciences, December 2013, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  61. Measurement and modeling of transcriptional noise in the cell cycle regulatory network

    Article • Cell Cycle, October 2013, Taylor & Francis

    Professor John J Tyson

  62. Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus

    Article • PLoS Computational Biology, September 2013, PLOS

    Professor John J Tyson

  63. Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells

    Article • FEBS Letters, August 2013, Wiley

    Executive Director, The Hormel Institute Robert Clarke, Professor John J Tyson

  64. Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model

    Article • BMC Systems Biology, June 2013, Springer Science + Business Media

    Professor John J Tyson

  65. Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer

    Article • Interface Focus, June 2013, Royal Society Publishing

    Executive Director, The Hormel Institute Robert Clarke, Professor John J Tyson

  66. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes

    Article • Journal of Computational Biology, May 2013, Mary Ann Liebert Inc

    Professor John J Tyson

  67. Molecular mechanisms creating bistable switches at cell cycle transitions

    Article • Open Biology, March 2013, Royal Society Publishing

    Professor John J Tyson

  68. Minimal Models for Cell-Cycle Control Based on Competitive Inhibition and Multisite Phosphorylations of Cdk Substrates

    Article • Biophysical Journal, March 2013, Elsevier

    Professor John J Tyson

  69. Cell Cycle Dynamics, Irreversibility

    Article • January 2013, Springer Science + Business Media

    Professor John J Tyson

  70. Cell Cycle Model Analysis, Bifurcation Theory

    Article • January 2013, Springer Science + Business Media

    Professor John J Tyson

  71. Cell Cycle Modeling, Differential Equation

    Article • January 2013, Springer Science + Business Media

    Professor John J Tyson

  72. Cell Cycle Dynamics, Bistability and Oscillations

    Article • January 2013, Springer Science + Business Media

    Professor John J Tyson

  73. Cell Cycle, Budding Yeast

    Article • January 2013, Springer Science + Business Media

    Professor John J Tyson

  74. Irreversible Transitions, Bistability and Checkpoint Controls in the Eukaryotic Cell Cycle

    Article • January 2013, Elsevier

    Professor John J Tyson

  75. A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells

    Article • BMC Systems Biology, June 2012, Springer Science + Business Media

    Professor John J Tyson

  76. Endoplasmic Reticulum Stress, the Unfolded Protein Response, Autophagy, and the Integrated Regulation of Breast Cancer Cell Fate

    Article • Cancer Research, March 2012, American Association for Cancer Research (AACR)

    Executive Director, The Hormel Institute Robert Clarke, Professor John J Tyson

  77. A Mathematical Model of Mitotic Exit in Budding Yeast: The Role of Polo Kinase

    Article • PLoS ONE, February 2012, PLOS

    Professor John J Tyson

  78. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle

    Article • The Journal of Chemical Physics, January 2012, American Institute of Physics

    Professor John J Tyson

  79. Oscillatory Dynamics of Cell Cycle Proteins in Single Yeast Cells Analyzed by Imaging Cytometry

    Article • PLoS ONE, October 2011, PLOS

    Professor John J Tyson

  80. A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells

    Article • PLoS Computational Biology, July 2011, PLOS

    Professor John J Tyson

  81. System-level feedbacks make the anaphase switch irreversible

    Article • Proceedings of the National Academy of Sciences, May 2011, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  82. Stochastic exit from mitosis in budding yeast

    Article • Cell Cycle, March 2011, Taylor & Francis

    Professor John J Tyson

  83. Cell Cycle: Who Turns the Crank?

    Article • Current Biology, March 2011, Elsevier

    Professor John J Tyson

  84. A Hybrid Model of Mammalian Cell Cycle Regulation

    Article • PLoS Computational Biology, February 2011, PLOS

    Professor John J Tyson

  85. Regulated protein kinases and phosphatases in cell cycle decisions

    Article • Current Opinion in Cell Biology, December 2010, Elsevier

    Professor John J Tyson

  86. A model of yeast cell-cycle regulation based on multisite phosphorylation

    Article • Molecular Systems Biology, August 2010, EMBO

    Professor John J Tyson

  87. Model Composition for Macromolecular Regulatory Networks

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, April 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  88. Functional Motifs in Biochemical Reaction Networks

    Article • Annual Review of Physical Chemistry, March 2010, Annual Reviews

    Professor John J Tyson

  89. Systems Biologists Seek Fuller Integration of Systems Biology Approaches in New Cancer Research Programs

    Article • Cancer Research, January 2010, American Association for Cancer Research (AACR)

    Professor John J Tyson

  90. Model aggregation: a building-block approach to creating large macromolecular regulatory networks

    Article • Bioinformatics, October 2009, Oxford University Press (OUP)

    Professor John J Tyson

  91. An interview with Dr. John J. Tyson on his highly cited paper published inCell Cycle

    Article • Cell Cycle, October 2009, Taylor & Francis

    Professor John J Tyson

  92. A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts

    Article • Journal of Theoretical Biology, September 2009, Elsevier

    Professor John J Tyson

  93. Bistability by multiple phosphorylation of regulatory proteins

    Article • Progress in Biophysics and Molecular Biology, September 2009, Elsevier

    Professor John J Tyson

  94. System-level feedbacks control cell cycle progression

    Article • FEBS Letters, August 2009, Wiley

    Professor John J Tyson

  95. Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus

    Article • PLoS Computational Biology, August 2009, PLOS

    Professor John J Tyson

  96. Computational Analysis of Dynamical Responses to the Intrinsic Pathway of Programmed Cell Death

    Article • Biophysical Journal, July 2009, Elsevier

    Professor John J Tyson

  97. Exploring the roles of noise in the eukaryotic cell cycle

    Article • Proceedings of the National Academy of Sciences, April 2009, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  98. Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

    Article • Molecular Systems Biology, January 2009, EMBO

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  99. Computing with Proteins

    Article • Computer, January 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  100. Modeling Molecular Regulatory Networks with JigCell and PET

    Article • January 2009, Springer Science + Business Media

    Professor John J Tyson

  101. Design principles of biochemical oscillators

    Article • Nature Reviews Molecular Cell Biology, October 2008, Springer Science + Business Media

    Professor John J Tyson

  102. Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Timescales

    Article • Biophysical Journal, October 2008, Elsevier

    Professor John J Tyson

  103. The Interleukin-1 Receptor-Associated Kinase M Selectively Inhibits the Alternative, Instead of the Classical NFκB Pathway

    Article • Journal of Innate Immunity, September 2008, Karger Publishers

    Professor John J Tyson

  104. Temporal Organization of the Cell Cycle

    Article • Current Biology, September 2008, Elsevier

    Professor John J Tyson

  105. Biological switches and clocks

    Article • Journal of The Royal Society Interface, June 2008, Royal Society Publishing

    Professor John J Tyson

  106. Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle

    Article • Journal of Global Optimization, February 2008, Springer Science + Business Media

    Professor John J Tyson

  107. Spatial controls for growth zone formation during the fission yeast cell cycle

    Article • Yeast, January 2008, Wiley

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  108. Antagonism and bistability in protein interaction networks

    Article • Journal of Theoretical Biology, January 2008, Elsevier

    Professor John J Tyson

  109. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

    Article • Molecular Systems Biology, July 2007, EMBO

    Professor John J Tyson, Professor Denis Thieffry

  110. Irreversible cell-cycle transitions are due to systems-level feedback

    Article • Nature Cell Biology, July 2007, Springer Science + Business Media

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  111. A Mathematical Programming Formulation for the Budding Yeast Cell Cycle

    Article • SIMULATION, July 2007, SAGE Publications

    Professor John J Tyson

  112. Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation

    Article • PLoS Computational Biology, March 2007, PLOS

    Professor John J Tyson

  113. Modeling the septation initiation network (SIN) in fission yeast cells

    Article • Current Genetics, March 2007, Springer Science + Business Media

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  114. Bringing cartoons to life

    Article • Nature, February 2007, Springer Science + Business Media

    Professor John J Tyson

  115. Mathematical modeling as a tool for investigating cell cycle control networks

    Article • Methods, February 2007, Elsevier

    Professor John J Tyson

  116. A proposal for robust temperature compensation of circadian rhythms

    Article • Proceedings of the National Academy of Sciences, January 2007, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  117. Exploring Mechanisms of the DNA-Damage Response: p53 Pulses and their Possible Relevance to Apoptosis

    Article • Cell Cycle, January 2007, Taylor & Francis

    Professor John J Tyson

  118. The Role of Composition and Aggregation in Modeling Macromolecular Regulatory Networks

    Article • December 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  119. Challenges for Modeling and Simulation Methods in Systems Biology

    Article • December 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  120. Another turn for p53

    Article • Molecular Systems Biology, June 2006, EMBO

    Professor John J Tyson

  121. Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation

    Article • Biophysical Journal, June 2006, Elsevier

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  122. Synchronization of Eukaryotic Cells by Periodic Forcing

    Article • Physical Review Letters, April 2006, American Physical Society (APS)

    Professor John J Tyson

  123. The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, April 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Professor John J Tyson

  124. Cell Cycle Control in Bacteria and Yeast: A Case of Convergent Evolution?

    Article • Cell Cycle, February 2006, Taylor & Francis

    Professor John J Tyson

  125. Periodic forcing of a mathematical model of the eukaryotic cell cycle

    Article • Physical Review E, January 2006, American Physical Society (APS)

    Professor John J Tyson

  126. Computer evaluation of network dynamics models with application to cell cycle control in budding yeast

    Article • Systems Biology, January 2006, the Institution of Engineering and Technology (the IET)

    Professor John J Tyson

  127. Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs

    Article • Journal of Computational Biology, February 2005, Mary Ann Liebert Inc

    Professor John J Tyson

  128. Steady States and Oscillations in the p53/Mdm2 Network

    Article • Cell Cycle, February 2005, Taylor & Francis

    Professor John J Tyson

  129. A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor John J Tyson

  130. Globally optimised parameters for a model of mitotic control in frog egg extracts

    Article • Systems Biology, January 2005, the Institution of Engineering and Technology (the IET)

    Professor John J Tyson

  131. Finding all steady state solutions of chemical kinetic models

    Article • Nonlinear Analysis Real World Applications, December 2004, Elsevier

    Professor John J Tyson

  132. Arthur T. Winfree (1942–2002)

    Article • Journal of Theoretical Biology, October 2004, Elsevier

    Professor John J Tyson

  133. A model for restriction point control of the mammalian cell cycle

    Article • Journal of Theoretical Biology, October 2004, Elsevier

    Professor John J Tyson

  134. Bifurcation analysis of a model of the budding yeast cell cycle

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, September 2004, American Institute of Physics

    Professor John J Tyson

  135. Turbulence near cyclic fold bifurcations in birhythmic media

    Article • Physical Review E, August 2004, American Physical Society (APS)

    Professor John J Tyson

  136. The JigCell Model Builder and Run Manager

    Article • Bioinformatics, July 2004, Oxford University Press (OUP)

    Professor John J Tyson

  137. Integrative Analysis of Cell Cycle Control in Budding Yeast

    Article • Molecular Biology of the Cell, May 2004, American Society for Cell Biology (ASCB)

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  138. A precarious balance

    Article • Current Biology, April 2004, Elsevier

    Professor John J Tyson

  139. Monitoring p53's pulse

    Article • Nature Genetics, February 2004, Springer Science + Business Media

    Professor John J Tyson

  140. Computational Cell Biology

    Article • January 2004

    Professor John J Tyson

  141. Modelling the fission yeast cell cycle

    Article • Briefings in Functional Genomics and Proteomics, January 2004, Oxford University Press (OUP)

    Professor John J Tyson

  142. Mathematical model of the morphogenesis checkpoint in budding yeast

    Article • The Journal of Cell Biology, December 2003, Rockefeller University Press

    Professor John J Tyson

  143. Modeling Regulatory Networks at Virginia Tech

    Article • OMICS A Journal of Integrative Biology, September 2003, Mary Ann Liebert Inc

    Professor John J Tyson

  144. A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos

    Article • Biophysical Chemistry, July 2003, Elsevier

    Professor John J Tyson

  145. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

    Article • Current Opinion in Cell Biology, April 2003, Elsevier

    Professor John J Tyson

  146. Checkpoints in the Cell Cycle

    Article • February 2003, Wiley

    Professor John J Tyson

  147. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts

    Article • Proceedings of the National Academy of Sciences, December 2002, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  148. The dynamics of cell cycle regulation

    Article • BioEssays, November 2002, Wiley

    Professor John J Tyson, Dr Attila Csikasz-Nagy

  149. Network dynamics and cell physiology

    Article • Nature Reviews Molecular Cell Biology, December 2001, Springer Science + Business Media

    Professor John J Tyson

  150. A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation

    Article • Biophysical Chemistry, September 2001, Elsevier

    Professor John J Tyson

  151. Regulation of the Eukaryotic Cell Cycle: Molecular Antagonism, Hysteresis, and Irreversible Transitions

    Article • Journal of Theoretical Biology, May 2001, Elsevier

    Professor John J Tyson

  152. Molecular, metabolic, and genetic control: An introduction

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, January 2001, American Institute of Physics

    Professor John J Tyson

  153. Mathematical model of the cell division cycle of fission yeast

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, January 2001, American Institute of Physics

    Professor John J Tyson

  154. Modeling the fission yeast cell cycle: Quantized cycle times in wee1 − cdc25Δ mutant cells

    Article • Proceedings of the National Academy of Sciences, July 2000, Proceedings of the National Academy of Sciences

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  155. Mathematical Model for Early Development of the Sea Urchin Embryo

    Article • Bulletin of Mathematical Biology, January 2000, Springer Science + Business Media

    Professor John J Tyson

  156. Travelling waves and static structures in a two-dimensional exactly solvable reaction-diffusion system

    Article • Journal of Physics A General Physics, November 1999, Institute of Physics Publishing

    Professor John J Tyson

  157. A Simple Model of Circadian Rhythms Based on Dimerization and Proteolysis of PER and TIM

    Article • Biophysical Journal, November 1999, Elsevier

    Professor John J Tyson

  158. Finishing the Cell Cycle

    Article • Journal of Theoretical Biology, July 1999, Elsevier

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  159. Models of cell cycle control in eukaryotes

    Article • Journal of Biotechnology, May 1999, Elsevier

    Professor John J Tyson

  160. Velocity-curvature dependence for chemical waves in the Belousov-Zhabotinsky reaction: Theoretical explanation of experimental observations

    Article • April 1999, American Physical Society (APS)

    Professor John J Tyson

  161. Multiple stationary states in the oregonator

    Article • The Journal of Chemical Physics, January 1999, American Institute of Physics

    Professor John J Tyson

  162. Bifurcation Analysis of a Model of Mitotic Control in Frog Eggs

    Article • Journal of Theoretical Biology, November 1998, Elsevier

    Professor John J Tyson

  163. Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA

    Article • Biophysical Chemistry, May 1998, Elsevier

    Professor John J Tyson

  164. Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions

    Article • Biophysical Chemistry, May 1998, Elsevier

    Dr Attila Csikasz-Nagy, Professor John J Tyson

  165. Modeling the control of DNA replication in fission yeast

    Article • Proceedings of the National Academy of Sciences, August 1997, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  166. Steady-state autowave patterns in a two-dimensional excitable medium with a band of different excitability

    Article • Physica D Nonlinear Phenomena, April 1997, Elsevier

    Professor John J Tyson

  167. A Proposal for Temperature Compensation of the Orcadian Rhythm in Drosophila Based on Dimerization of the Per Protein

    Article • Chronobiology International, January 1997, Taylor & Francis

    Professor John J Tyson

  168. Nonspiral excitation waves beyond the eikonal approximation

    Article • October 1996, American Physical Society (APS)

    Professor John J Tyson

  169. Propagation of waves through a line of discontinuity in two-dimensional excitable media: Refraction and reflection of autowaves

    Article • August 1996, American Physical Society (APS)

    Professor John J Tyson

  170. About time

    Article • Nature, March 1996, Springer Science + Business Media

    Professor John J Tyson

  171. Cellular automaton model of three-dimensional excitable media

    Article • Journal of the Chemical Society Faraday Transactions, January 1996, Royal Society of Chemistry

    Professor John J Tyson

  172. Quantitative analysis of a molecular model of mitotic control in fission yeast

    Article • Journal of Theoretical Biology, April 1995, Elsevier

    Professor John J Tyson

  173. Checkpoints in the cell cycle from a modeler’s perspective

    Article • January 1995, Springer Science + Business Media

    Professor John J Tyson

  174. A Theory of Rotating Scroll Waves in Excitable Media

    Article • January 1995, Springer Science + Business Media

    Professor John J Tyson

  175. What Everyone Should Know About the Belousov-Zhabotinsky Reaction

    Article • January 1994, Springer Science + Business Media

    Professor John J Tyson

  176. Modeling the Cell Division Cycle: M-phase Trigger, Oscillations, and Size Control

    Article • Journal of Theoretical Biology, November 1993, Elsevier

    Professor John J Tyson

  177. Law of mass action

    Article • Nature, May 1992, Springer Science + Business Media

    Professor John J Tyson

  178. Unpredictable reactions

    Article • Nature, April 1992, Springer Science + Business Media

    Professor John J Tyson

  179. The Dynamics of Scroll Waves in Excitable Media

    Article • SIAM Review, March 1992, Society for Industrial & Applied Mathematics (SIAM)

    Professor John J Tyson

  180. Third generation cellular automaton for modeling excitable media

    Article • Physica D Nonlinear Phenomena, March 1992, Elsevier

    Professor John J Tyson

  181. Diffusion and wave propagation in cellular automaton models of excitable media

    Article • Physica D Nonlinear Phenomena, March 1992, Elsevier

    Professor John J Tyson

  182. The dynamics of helical scroll waves in excitable media

    Article • Physica D Nonlinear Phenomena, October 1991, Elsevier

    Professor John J Tyson

  183. Modeling the cell division cycle: cdc2 and cyclin interactions.

    Article • Proceedings of the National Academy of Sciences, August 1991, Proceedings of the National Academy of Sciences

    Professor John J Tyson

  184. A cellular automaton model of excitable media IV. Untwisted scroll rings

    Article • Physica D Nonlinear Phenomena, June 1991, Elsevier

    Professor John J Tyson

  185. A cellular automaton model of excitable media

    Article • Physica D Nonlinear Phenomena, December 1990, Elsevier

    Professor John J Tyson

  186. A cellular automaton model of excitable media

    Article • Physica D Nonlinear Phenomena, December 1990, Elsevier

    Professor John J Tyson

  187. Experimental study of spiral waves in the cerium-catalyzed Belousov-Zhabotinskii reaction

    Article • The Journal of Physical Chemistry, November 1990, American Chemical Society (ACS)

    Professor John J Tyson

  188. Helical and circular scroll wave filaments

    Article • Physica D Nonlinear Phenomena, August 1990, Elsevier

    Professor John J Tyson

  189. Analysis of the kinetic hairpin transfer model for parvoviral DNA replication

    Article • Journal of Theoretical Biology, May 1990, Elsevier

    Professor John J Tyson

  190. A Cellular Automaton Model of Excitable Media Including Curvature and Dispersion

    Article • Science, March 1990, American Association for the Advancement of Science

    Professor John J Tyson

  191. Effects of asymmetric division on a stochastic model of the cell division cycle

    Article • Mathematical Biosciences, October 1989, Elsevier

    Professor John J Tyson

  192. A kinetic hairpin transfer model for parvoviral DNA replication

    Article • Journal of Molecular Biology, July 1989, Elsevier

    Professor John J Tyson

  193. Experimental study of the chemical waves in the cerium-catalyzed Belousov-Zhabotinskii reaction. 2. Concentration profiles

    Article • The Journal of Physical Chemistry, April 1989, American Chemical Society (ACS)

    Professor John J Tyson

  194. Cyclic-AMP waves in Dictyostelium: Specific models and general theories

    Article • January 1989, Elsevier

    Professor John J Tyson

  195. Experimental study of the chemical waves in the cerium-catalyzed Belousov-Zhabotinskii reaction. 1. Velocity of trigger waves

    Article • The Journal of Physical Chemistry, January 1989, American Chemical Society (ACS)

    Professor John J Tyson

  196. Spiral waves of cyclic amp in a model of slime mold aggregation

    Article • Physica D Nonlinear Phenomena, January 1989, Elsevier

    Professor John J Tyson

  197. The Timing of Biological Clocks Arthur T. Winfree

    Article • The Quarterly Review of Biology, December 1988, University of Chicago Press

    Professor John J Tyson

  198. When Time Breaks Down: The Three‐Dimensional Dynamics of Electrochemical Waves and Cardiac Arrhythmias

    Article • Physics Today, December 1988, American Institute of Physics

    Professor John J Tyson

  199. Singular perturbation theory of traveling waves in excitable media (a review)

    Article • Physica D Nonlinear Phenomena, December 1988, Elsevier

    Professor John J Tyson

  200. The Motion of Untwisted Untorted Scroll Waves in Belousov-Zhabotinsky Reagent

    Article • Science, March 1988, American Association for the Advancement of Science

    Professor John J Tyson

  201. Dispersion of traveling waves in the belousov-zhabotinskii reaction

    Article • Physica D Nonlinear Phenomena, February 1988, Elsevier

    Professor John J Tyson

  202. Spiral waves in a model of myocardium

    Article • Physica D Nonlinear Phenomena, November 1987, Elsevier

    Professor John J Tyson

  203. Luther's 1906 discovery and analysis of chemical waves

    Article • Journal of Chemical Education, September 1987, American Chemical Society (ACS)

    Professor John J Tyson

  204. Size control of cell division

    Article • Journal of Theoretical Biology, June 1987, Elsevier

    Professor John J Tyson

  205. A stochastic model of cell division (with application to fission yeast)

    Article • Mathematical Biosciences, June 1987, Elsevier

    Professor John J Tyson

  206. Pattern and rhythm

    Article • Nature, May 1987, Springer Science + Business Media

    Professor John J Tyson

  207. Book reviews

    Article • Bulletin of Mathematical Biology, January 1987, Springer Science + Business Media

    Professor John J Tyson

  208. Spiral waves in the Belousov-Zhabotinskii reaction

    Article • Physica D Nonlinear Phenomena, September 1986, Elsevier

    Professor John J Tyson

  209. Sloppy size control of the cell division cycle

    Article • Journal of Theoretical Biology, February 1986, Elsevier

    Professor John J Tyson

  210. Cell growth and division: a deterministic/probabilistic model of the cell cycle

    Article • Journal of Mathematical Biology, February 1986, Springer Science + Business Media

    Professor John J Tyson

  211. The PhysarumPhysarum Cell Cycle

    Article • January 1986, Springer Science + Business Media

    Professor John J Tyson

  212. Computer analysis of two-dimensional gels by a general image processing system

    Article • Electrophoresis, January 1986, Wiley

    Professor John J Tyson

  213. An improved data analysis method for interleukin 2 microassay

    Article • Computers in Biology and Medicine, January 1986, Elsevier

    Professor John J Tyson

  214. Analysis of Physarum proteins throughout the cell cycle by two-dimensional PAGE

    Article • Experimental Cell Research, December 1985, Elsevier

    Professor John J Tyson

  215. Steady-State Size Distributions in Probabilistic Models of the Cell Division Cycle

    Article • SIAM Journal on Applied Mathematics, August 1985, Society for Industrial & Applied Mathematics (SIAM)

    Professor John J Tyson

  216. The distributions of cell size and generation time in a model of the cell cycle incorporating size control and random transitions

    Article • Journal of Theoretical Biology, March 1985, Elsevier

    Professor John J Tyson

  217. The coordination of cell growth and division ? intentional or Incidental?

    Article • BioEssays, February 1985, Wiley

    Professor John J Tyson

  218. The Coordination of Cell Growth and Division: A Comparison of Models

    Article • January 1985, Springer Science + Business Media

    Professor John J Tyson

  219. Stability of the steady-state size distribution in a model of cell growth and division

    Article • Journal of Mathematical Biology, January 1985, Springer Science + Business Media

    Professor John J Tyson

  220. Evolution of eusociality in diploid species

    Article • Theoretical Population Biology, December 1984, Elsevier

    Professor John J Tyson

  221. Induction of polyploid nuclei in Physarum polycephalum by cycloheximide treatment in prophase

    Article • Experimental Cell Research, August 1984, Elsevier

    Professor John J Tyson

  222. Relaxation oscillations in the revised Oregonator

    Article • The Journal of Chemical Physics, June 1984, American Institute of Physics

    Professor John J Tyson

  223. Unstable activator models for size control of the cell cycle

    Article • Journal of Theoretical Biology, October 1983, Elsevier

    Professor John J Tyson

  224. Periodic enzyme synthesis and oscillatory repression: Why is the period of oscillation close to the cell cycle time?

    Article • Journal of Theoretical Biology, July 1983, Elsevier

    Professor John J Tyson

  225. Identification and changes in activity of five thymidine kinase forms during the cell cycle of Physarum polycephalum

    Article • Experimental Cell Research, March 1983, Elsevier

    Professor John J Tyson

  226. Scaling and reducing the Field-Koros-Noyes mechanism of the Belousov-Zhabotinskii reaction

    Article • The Journal of Physical Chemistry, July 1982, American Chemical Society (ACS)

    Professor John J Tyson

  227. Periodic Phenomena in Physarum

    Article • January 1982, Elsevier

    Professor John J Tyson

  228. On Scaling the Oregonator Equations

    Article • January 1981, Springer Science + Business Media

    Professor John J Tyson

  229. Target patterns in a realistic model of the Belousov–Zhabotinskii reaction

    Article • The Journal of Chemical Physics, September 1980, American Institute of Physics

    Professor John J Tyson

  230. Comment on ‘‘Stable limit cycles in a two‐component bimolecular reaction system’’

    Article • The Journal of Chemical Physics, February 1980, American Institute of Physics

    Professor John J Tyson

  231. Periodic enzyme synthesis: Reconsideration of the theory of oscillatory repression

    Article • Journal of Theoretical Biology, September 1979, Elsevier

    Professor John J Tyson

  232. Derepression as a model for control of the DNA-division cycle in eukaryotes

    Article • Journal of Theoretical Biology, August 1979, Elsevier

    Professor John J Tyson

  233. Control of nuclear division in Physarum polycephalum

    Article • Experimental Cell Research, March 1979, Elsevier

    Professor John J Tyson

  234. OSCILLATIONS, BISTABILITY, AND ECHO WAVES IN MODELS OF THE BELOUSOV-ZHABOTINSKII REACTION*

    Article • Annals of the New York Academy of Sciences, February 1979, Wiley

    Professor John J Tyson

  235. Is nuclear division in Physarum controlled by a continuous limit cycle oscillator?

    Article • Journal of Theoretical Biology, August 1978, Elsevier

    Professor John J Tyson

  236. The Dynamics of Feedback Control Circuits in Biochemical Pathways

    Article • January 1978, Elsevier

    Professor John J Tyson

  237. Existence of periodic solutions for negative feedback cellular control systems

    Article • Journal of Differential Equations, July 1977, Elsevier

    Professor John J Tyson

  238. Analytic representation of oscillations, excitability, and traveling waves in a realistic model of the Belousov–Zhabotinskii reaction

    Article • The Journal of Chemical Physics, February 1977, American Institute of Physics

    Professor John J Tyson

  239. The Belousov-Zhabotinskii Reaction

    Article • January 1976, Springer Science + Business Media

    Professor John J Tyson

  240. The Oregonator

    Article • January 1976, Springer Science + Business Media

    Professor John J Tyson

  241. Chemical Waves

    Article • January 1976, Springer Science + Business Media

    Professor John J Tyson

  242. Chemistry of the Belousov-Zhabotinskii Reaction

    Article • January 1976, Springer Science + Business Media

    Professor John J Tyson

  243. Classification of instabilities in chemical reaction systems

    Article • The Journal of Chemical Physics, February 1975, American Institute of Physics

    Professor John J Tyson

  244. Properties of two‐component bimolecular and trimolecular chemical reaction systems

    Article • The Journal of Chemical Physics, October 1973, American Institute of Physics

    Professor John J Tyson

  245. Semiclassical studies of planar reactive H+H2

    Article • The Journal of Chemical Physics, July 1973, American Institute of Physics

    Professor John J Tyson

  246. Some further studies of nonlinear oscillations in chemical systems

    Article • The Journal of Chemical Physics, May 1973, American Institute of Physics

    Professor John J Tyson

  247. Molecular Potential Functions Expressed in Cartesian Coordinates: Application to the Orbital Valency Force Field

    Article • The Journal of Chemical Physics, April 1971, American Institute of Physics

    Professor John J Tyson

  248. Biochemical Oscillations

    Article • Springer Science + Business Media

    Professor John J Tyson

  249. Cell Cycle Controls

    Article • Springer Science + Business Media

    Professor John J Tyson

  250. Systems biology of the yeast cell cycle engine

    Article • Springer Science + Business Media

    Professor John J Tyson