John Tyson, Ph.D. - Publications

Affiliations: 
Biology Virginia Polytechnic and State University, United States 
Area:
cell cycle modeling

141 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ahmadian M, Tyson JJ, Cao Y. A stochastic model of size control in the budding yeast cell cycle. Bmc Bioinformatics. 20: 322. PMID 31216979 DOI: 10.1186/s12859-019-2839-9  0.4
2019 Clarke R, Tyson JJ, Tan M, Baumann WT, Jin L, Xuan J, Wang Y. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers. Endocrine-Related Cancer. PMID 30965282 DOI: 10.1530/ERC-18-0309  0.68
2019 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB). Methods in Molecular Biology (Clifton, N.J.). 1945: 119-139. PMID 30945244 DOI: 10.1007/978-1-4939-9102-0_5  0.68
2019 Chen C, Whitney IP, Banerjee A, Sacristan C, Sekhri P, Kern DM, Fontan A, Kops GJPL, Tyson JJ, Cheeseman IM, Joglekar AP. Ectopic Activation of the Spindle Assembly Checkpoint Signaling Cascade Reveals Its Biochemical Design. Current Biology : Cb. 29: 104-119.e10. PMID 30595520 DOI: 10.1016/j.cub.2018.11.054  0.68
2018 Jones TC, Hoops S, Watson LT, Palmisano A, Tyson JJ, Shaffer CA. JigCell Model Connector: building large molecular network models from components. Simulation. 94: 993-1008. PMID 31303682 DOI: 10.1177/0037549717754121  0.68
2018 Battogtokh D, Tyson JJ. Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock. Biophysical Journal. 115: 2055-2066. PMID 30473017 DOI: 10.1016/j.bpj.2018.10.005  0.32
2018 Heldt FS, Lunstone R, Tyson JJ, Novák B. Dilution and titration of cell-cycle regulators may control cell size in budding yeast. Plos Computational Biology. 14: e1006548. PMID 30356259 DOI: 10.1371/journal.pcbi.1006548  0.8
2018 Weston BR, Li L, Tyson JJ. Mathematical Analysis of Cytokine-Induced Differentiation of Granulocyte-Monocyte Progenitor Cells. Frontiers in Immunology. 9: 2048. PMID 30279691 DOI: 10.3389/fimmu.2018.02048  0.88
2018 Novák B, Heldt FS, Tyson JJ. Genome Stability during Cell Proliferation: A Systems Analysis of the Molecular Mechanisms Controlling Progression through the Eukaryotic Cell Cycle. Current Opinion in Systems Biology. 9: 22-31. PMID 30221209 DOI: 10.1016/j.coisb.2018.02.004  0.8
2018 Battogtokh D, Kojima S, Tyson JJ. Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. Plos Computational Biology. 14: e1005957. PMID 29447160 DOI: 10.1371/journal.pcbi.1005957  0.32
2018 Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM, Berger B. CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. Bioinformatics (Oxford, England). PMID 29432533 DOI: 10.1093/bioinformatics/bty072  0.6
2017 Chen M, Amos B, Watson LT, Tyson J, Cao Y, Shaffer C, Trosset M, Oguz C, Kakoti G. Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29990127 DOI: 10.1109/TCBB.2017.2773083  0.68
2017 Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM. GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinformatics (Oxford, England). 33: 3134-3136. PMID 28957495 DOI: 10.1093/bioinformatics/btx382  0.6
2017 Hopkins M, Tyson JJ, Novák B. Cell cycle transitions: a common role for stoichiometric inhibitors. Molecular Biology of the Cell. PMID 28931595 DOI: 10.1091/mbc.E17-06-0349  0.8
2017 Subramanian K, Tyson JJ. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus. Results and Problems in Cell Differentiation. 61: 23-48. PMID 28409299 DOI: 10.1007/978-3-319-53150-2_2  0.36
2017 Oguz C, Watson LT, Baumann WT, Tyson JJ. Predicting network modules of cell cycle regulators using relative protein abundance statistics. Bmc Systems Biology. 11: 30. PMID 28241833 DOI: 10.1186/s12918-017-0409-1  0.68
2016 Barik D, Ball DA, Peccoud J, Tyson JJ. A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. Plos Computational Biology. 12: e1005230. PMID 27935947 DOI: 10.1371/journal.pcbi.1005230  0.76
2016 Li F, Subramanian K, Chen M, Tyson JJ, Cao Y. A stochastic spatiotemporal model of a response-regulator network in the Caulobacter crescentus cell cycle. Physical Biology. 13: 035007. PMID 27345750 DOI: 10.1088/1478-3975/13/3/035007  0.4
2016 Battogtokh D, Tyson JJ. A Bistable Switch Mechanism for Stem Cell Domain Nucleation in the Shoot Apical Meristem. Frontiers in Plant Science. 7: 674. PMID 27242874 DOI: 10.3389/fpls.2016.00674  0.32
2016 Laomettachit T, Chen KC, Baumann WT, Tyson JJ. A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks. Plos One. 11: e0153738. PMID 27187804 DOI: 10.1371/journal.pone.0153738  0.68
2015 Kraikivski P, Chen KC, Laomettachit T, Murali TM, Tyson JJ. From START to FINISH: computational analysis of cell cycle control in budding yeast. Npj Systems Biology and Applications. 1: 15016. PMID 28725464 DOI: 10.1038/npjsba.2015.16  0.6
2015 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. Bmc Systems Biology. 9: 95. PMID 26704692 DOI: 10.1186/s12918-015-0237-0  0.88
2015 Clarke R, Tyson JJ, Dixon JM. Endocrine resistance in breast cancer - An overview and update. Molecular and Cellular Endocrinology. PMID 26455641 DOI: 10.1016/j.mce.2015.09.035  0.88
2015 Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J. Experimental testing of a new integrated model of the budding yeast Start transition. Molecular Biology of the Cell. 26: 3966-84. PMID 26310445 DOI: 10.1091/mbc.E15-06-0358  0.88
2015 Tavassoly I, Parmar J, Shajahan-Haq AN, Clarke R, Baumann WT, Tyson JJ. Dynamic Modeling of the Interaction Between Autophagy and Apoptosis in Mammalian Cells. Cpt: Pharmacometrics & Systems Pharmacology. 4: 263-72. PMID 26225250 DOI: 10.1002/psp4.29  0.88
2015 Subramanian K, Paul MR, Tyson JJ. Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models. Plos Computational Biology. 11: e1004348. PMID 26186202 DOI: 10.1371/journal.pcbi.1004348  0.88
2015 Tyson JJ, Novák B. Models in biology: lessons from modeling regulation of the eukaryotic cell cycle. Bmc Biology. 13: 46. PMID 26129844 DOI: 10.1186/s12915-015-0158-9  0.88
2015 Rysavy MA, Li L, Bell EF, Das A, Hintz SR, Stoll BJ, Vohr BR, Carlo WA, Shankaran S, Walsh MC, Tyson JE, Cotten CM, Smith PB, Murray JC, Colaizy TT, et al. Between-hospital variation in treatment and outcomes in extremely preterm infants. The New England Journal of Medicine. 372: 1801-11. PMID 25946279 DOI: 10.1056/NEJMoa1410689  0.88
2015 Tyson JA, Goldberg EM, Maroof AM, Xu Q, Petros TJ, Anderson SA. Duration of culture and sonic hedgehog signaling differentially specify PV versus SST cortical interneuron fates from embryonic stem cells. Development (Cambridge, England). 142: 1267-78. PMID 25804737 DOI: 10.1242/dev.111526  0.4
2015 Carpenter D, Dhar S, Mitchell LM, Fu B, Tyson J, Shwan NA, Yang F, Thomas MG, Armour JA. Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes. Human Molecular Genetics. 24: 3472-80. PMID 25788522 DOI: 10.1093/hmg/ddv098  0.4
2015 Hong T, Oguz C, Tyson JJ. A Mathematical Framework for Understanding Four-Dimensional Heterogeneous Differentiation of [Formula: see text] T Cells. Bulletin of Mathematical Biology. 77: 1046-64. PMID 25779890 DOI: 10.1007/s11538-015-0076-6  0.88
2015 Gérard C, Tyson JJ, Coudreuse D, Novák B. Cell cycle control by a minimal Cdk network. Plos Computational Biology. 11: e1004056. PMID 25658582 DOI: 10.1371/journal.pcbi.1004056  0.8
2015 Tyson JJ, Novak B. Bistability, oscillations, and traveling waves in frog egg extracts. Bulletin of Mathematical Biology. 77: 796-816. PMID 25185750 DOI: 10.1007/s11538-014-0009-9  0.88
2015 Morris SA, Payne WA, Sami S, Wang Y, LeMaire SA, Tyson JE, Krishnamurthy R, Milewicz DM. Arterial tortuosity and change with age in young patients with aortopathy Journal of Cardiovascular Magnetic Resonance. 1-2. DOI: 10.1186/1532-429X-17-S1-P403  0.32
2014 Black HA, Khan FF, Tyson J, Al Armour J. Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus. Bmc Genomics. 15: 614. PMID 25048054 DOI: 10.1186/1471-2164-15-614  0.4
2014 Tyson JJ, Novak B. Control of cell growth, division and death: information processing in living cells. Interface Focus. 4: 20130070. PMID 24904735 DOI: 10.1098/rsfs.2013.0070  0.88
2014 Oguz C, Palmisano A, Laomettachit T, Watson LT, Baumann WT, Tyson JJ. A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of CLN2. Plos One. 9: e96726. PMID 24816736 DOI: 10.1371/journal.pone.0096726  0.88
2014 Chen C, Baumann WT, Xing J, Xu L, Clarke R, Tyson JJ. Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer. Journal of the Royal Society, Interface / the Royal Society. 11: 20140206. PMID 24806707 DOI: 10.1098/rsif.2014.0206  0.88
2014 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. Bmc Systems Biology. 8: 42. PMID 24708852 DOI: 10.1186/1752-0509-8-42  0.88
2014 Tyson JA, Anderson SA. GABAergic interneuron transplants to study development and treat disease. Trends in Neurosciences. 37: 169-77. PMID 24508416 DOI: 10.1016/j.tins.2014.01.003  0.4
2014 Wang N, Tyson J. Non-chromatographic speciation of inorganic arsenic by atomic fluorescence spectrometry with flow injection hydride generation with a tetrahydroborate-form anion-exchanger Journal of Analytical Atomic Spectrometry. 29: 665-673. DOI: 10.1039/c3ja50376c  0.48
2014 Andrew TM, Amos BD, Easterling DR, Oguz C, Baumann WT, Tyson JJ, Watson LT. Global parameter estimation for a eukaryotic cell cycle model in systems biology Simulation Series. 46: 324-331.  0.88
2013 Parmar JH, Cook KL, Shajahan-Haq AN, Clarke PA, Tavassoly I, Clarke R, Tyson JJ, Baumann WT. Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer. Interface Focus. 3: 20130012. PMID 24511377 DOI: 10.1098/rsfs.2013.0012  0.88
2013 Zhang T, Tyson JJ, Novák B. Role for regulated phosphatase activity in generating mitotic oscillations in Xenopus cell-free extracts. Proceedings of the National Academy of Sciences of the United States of America. 110: 20539-44. PMID 24297885 DOI: 10.1073/pnas.1318065110  0.88
2013 Khan FF, Carpenter D, Mitchell L, Mansouri O, Black HA, Tyson J, Armour JA. Accurate measurement of gene copy number for human alpha-defensin DEFA1A3. Bmc Genomics. 14: 719. PMID 24138543 DOI: 10.1186/1471-2164-14-719  0.4
2013 Subramanian K, Paul MR, Tyson JJ. Potential role of a bistable histidine kinase switch in the asymmetric division cycle of Caulobacter crescentus. Plos Computational Biology. 9: e1003221. PMID 24068904 DOI: 10.1371/journal.pcbi.1003221  0.88
2013 Ball DA, Adames NR, Reischmann N, Barik D, Franck CT, Tyson JJ, Peccoud J. Measurement and modeling of transcriptional noise in the cell cycle regulatory network. Cell Cycle (Georgetown, Tex.). 12: 3203-18. PMID 24013422 DOI: 10.4161/cc.26257  0.88
2013 Tyson JA, Anderson SA. The protracted maturation of human ESC-derived interneurons. Cell Cycle (Georgetown, Tex.). 12: 3129-30. PMID 24013418 DOI: 10.4161/cc.26351  0.4
2013 Chen C, Baumann WT, Clarke R, Tyson JJ. Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells. Febs Letters. 587: 3327-34. PMID 23994522 DOI: 10.1016/j.febslet.2013.08.022  0.88
2013 Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, Tyson JJ. Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. Bmc Systems Biology. 7: 53. PMID 23809412 DOI: 10.1186/1752-0509-7-53  0.88
2013 Maroof AM, Keros S, Tyson JA, Ying SW, Ganat YM, Merkle FT, Liu B, Goulburn A, Stanley EG, Elefanty AG, Widmer HR, Eggan K, Goldstein PA, Anderson SA, Studer L. Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. Cell Stem Cell. 12: 559-72. PMID 23642365 DOI: 10.1016/j.stem.2013.04.008  0.4
2013 Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-down network analysis to drive bottom-up modeling of physiological processes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 409-18. PMID 23641868 DOI: 10.1089/cmb.2012.0274  0.88
2013 Gérard C, Tyson JJ, Novák B. Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates. Biophysical Journal. 104: 1367-79. PMID 23528096 DOI: 10.1016/j.bpj.2013.02.012  0.88
2013 Verdugo A, Vinod PK, Tyson JJ, Novak B. Molecular mechanisms creating bistable switches at cell cycle transitions. Open Biology. 3: 120179. PMID 23486222 DOI: 10.1098/rsob.120179  0.88
2013 Tyson JJ, Novák B. Irreversible Transitions, Bistability and Checkpoint Controls in the Eukaryotic Cell Cycle: A Systems-Level Understanding Handbook of Systems Biology. 265-285. DOI: 10.1016/B978-0-12-385944-0.00014-9  0.88
2012 Tyson J, Armour JA. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR. Bmc Genomics. 13: 693. PMID 23231411 DOI: 10.1186/1471-2164-13-693  0.4
2012 Hong T, Xing J, Li L, Tyson JJ. A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. Bmc Systems Biology. 6: 66. PMID 22697466 DOI: 10.1186/1752-0509-6-66  0.88
2012 Fu Y, Glaros T, Zhu M, Wang P, Wu Z, Tyson JJ, Li L, Xing J. Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells. Plos Computational Biology. 8: e1002526. PMID 22615556 DOI: 10.1371/journal.pcbi.1002526  0.88
2012 Clarke R, Cook KL, Hu R, Facey CO, Tavassoly I, Schwartz JL, Baumann WT, Tyson JJ, Xuan J, Wang Y, Wärri A, Shajahan AN. Endoplasmic reticulum stress, the unfolded protein response, autophagy, and the integrated regulation of breast cancer cell fate. Cancer Research. 72: 1321-31. PMID 22422988 DOI: 10.1158/0008-5472.CAN-11-3213  0.88
2012 Hancioglu B, Tyson JJ. A mathematical model of mitotic exit in budding yeast: the role of Polo kinase. Plos One. 7: e30810. PMID 22383977 DOI: 10.1371/journal.pone.0030810  0.88
2012 Liu Z, Pu Y, Li F, Shaffer CA, Hoops S, Tyson JJ, Cao Y. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. The Journal of Chemical Physics. 136: 034105. PMID 22280742 DOI: 10.1063/1.3677190  0.88
2012 Kearns J, Tyson J. Improving the accuracy and precision of an arsenic field test kit: Increased reaction time and digital image analysis Analytical Methods. 4: 1693-1698. DOI: 10.1039/c2ay05655k  0.48
2011 Clarke R, Shajahan AN, Wang Y, Tyson JJ, Riggins RB, Weiner LM, Bauman WT, Xuan J, Zhang B, Facey C, Aiyer H, Cook K, Hickman FE, Tavassoly I, Verdugo A, et al. Endoplasmic reticulum stress, the unfolded protein response, and gene network modeling in antiestrogen resistant breast cancer. Hormone Molecular Biology and Clinical Investigation. 5: 35-44. PMID 23930139 DOI: 10.1515/hmbci.2010.073  0.68
2011 Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, Tyson JJ, Peccoud J. Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. Plos One. 6: e26272. PMID 22046265 DOI: 10.1371/journal.pone.0026272  0.88
2011 Petros TJ, Tyson JA, Anderson SA. Pluripotent stem cells for the study of CNS development. Frontiers in Molecular Neuroscience. 4: 30. PMID 22016722 DOI: 10.3389/fnmol.2011.00030  0.4
2011 Hong T, Xing J, Li L, Tyson JJ. A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. Plos Computational Biology. 7: e1002122. PMID 21829337 DOI: 10.1371/journal.pcbi.1002122  0.88
2011 Tyson JJ, Baumann WT, Chen C, Verdugo A, Tavassoly I, Wang Y, Weiner LM, Clarke R. Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nature Reviews. Cancer. 11: 523-32. PMID 21677677 DOI: 10.1038/nrc3081  0.88
2011 He E, Kapuy O, Oliveira RA, Uhlmann F, Tyson JJ, Novák B. System-level feedbacks make the anaphase switch irreversible. Proceedings of the National Academy of Sciences of the United States of America. 108: 10016-21. PMID 21617094 DOI: 10.1073/pnas.1102106108  0.88
2011 Tyson JJ, Novak B. Cell cycle: who turns the crank? Current Biology : Cb. 21: R185-7. PMID 21377093 DOI: 10.1016/j.cub.2011.01.042  0.88
2011 Ball DA, Ahn TH, Wang P, Chen KC, Cao Y, Tyson JJ, Peccoud J, Baumann WT. Stochastic exit from mitosis in budding yeast: model predictions and experimental observations. Cell Cycle (Georgetown, Tex.). 10: 999-1009. PMID 21350333 DOI: 10.4161/cc.10.6.14966  0.88
2011 Singhania R, Sramkoski RM, Jacobberger JW, Tyson JJ. A hybrid model of mammalian cell cycle regulation. Plos Computational Biology. 7: e1001077. PMID 21347318 DOI: 10.1371/journal.pcbi.1001077  0.88
2010 Barik D, Baumann WT, Paul MR, Novak B, Tyson JJ. A model of yeast cell-cycle regulation based on multisite phosphorylation. Molecular Systems Biology. 6: 405. PMID 20739927 DOI: 10.1038/msb.2010.55  0.88
2010 Novak B, Kapuy O, Domingo-Sananes MR, Tyson JJ. Regulated protein kinases and phosphatases in cell cycle decisions. Current Opinion in Cell Biology. 22: 801-8. PMID 20678910 DOI: 10.1016/j.ceb.2010.07.001  0.88
2010 Randhawa R, Shaffer CA, Tyson JJ. Model composition for macromolecular regulatory networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 278-87. PMID 20431147 DOI: 10.1109/TCBB.2008.64  0.88
2010 Tyson JJ, Novák B. Functional motifs in biochemical reaction networks. Annual Review of Physical Chemistry. 61: 219-40. PMID 20055671 DOI: 10.1146/annurev.physchem.012809.103457  0.88
2010 Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE, Gallahan D, Gatenby R, Günther U, Harms BD, ... ... Tyson J, et al. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Research. 70: 12-3. PMID 20028868 DOI: 10.1158/0008-5472.CAN-09-2676  0.88
2009 Randhawa R, Shaffer CA, Tyson JJ. Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics (Oxford, England). 25: 3289-95. PMID 19880372 DOI: 10.1093/bioinformatics/btp581  0.88
2009 Tyson JJ. In their own words: Interviews with Cell Cycle. John J. Tyson on his highly cited paper. Cell Cycle (Georgetown, Tex.). 8: 3261. PMID 19823016  0.88
2009 Su J, Zhang T, Tyson J, Li L. The interleukin-1 receptor-associated kinase M selectively inhibits the alternative, instead of the classical NFkappaB pathway. Journal of Innate Immunity. 1: 164-74. PMID 19809574 DOI: 10.1159/000158541  0.88
2009 Kapuy O, He E, López-Avilés S, Uhlmann F, Tyson JJ, Novák B. System-level feedbacks control cell cycle progression. Febs Letters. 583: 3992-8. PMID 19703449 DOI: 10.1016/j.febslet.2009.08.023  0.88
2009 Li S, Brazhnik P, Sobral B, Tyson JJ. Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus. Plos Computational Biology. 5: e1000463. PMID 19680425 DOI: 10.1371/journal.pcbi.1000463  0.88
2009 Zhang T, Brazhnik P, Tyson JJ. Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death. Biophysical Journal. 97: 415-34. PMID 19619456 DOI: 10.1016/j.bpj.2009.04.053  0.88
2009 Kapuy O, Barik D, Sananes MR, Tyson JJ, Novák B. Bistability by multiple phosphorylation of regulatory proteins. Progress in Biophysics and Molecular Biology. 100: 47-56. PMID 19523976 DOI: 10.1016/j.pbiomolbio.2009.06.004  0.88
2009 Zwolak J, Adjerid N, Bagci EZ, Tyson JJ, Sible JC. A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts. Journal of Theoretical Biology. 260: 110-20. PMID 19490919 DOI: 10.1016/j.jtbi.2009.05.018  0.88
2009 Shaffer CA, Zwolak JW, Randhawa R, Tyson JJ. Modeling molecular regulatory networks with JigCell and PET. Methods in Molecular Biology (Clifton, N.J.). 500: 81-111. PMID 19399431 DOI: 10.1007/978-1-59745-525-1_4  0.88
2009 Kar S, Baumann WT, Paul MR, Tyson JJ. Exploring the roles of noise in the eukaryotic cell cycle. Proceedings of the National Academy of Sciences of the United States of America. 106: 6471-6. PMID 19246388 DOI: 10.1073/pnas.0810034106  0.88
2009 Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ, Novák B. Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Molecular Systems Biology. 5: 236. PMID 19156128 DOI: 10.1038/msb.2008.73  0.88
2009 Ramakrishnan N, Bhalla US, Tyson JJ. Computing with proteins Computer. 42: 47-56. DOI: 10.1109/MC.2009.12  0.88
2008 Novák B, Tyson JJ. Design principles of biochemical oscillators. Nature Reviews. Molecular Cell Biology. 9: 981-91. PMID 18971947 DOI: 10.1038/nrm2530  0.88
2008 Tyson JJ, Novak B. Temporal organization of the cell cycle. Current Biology : Cb. 18: R759-R768. PMID 18786381 DOI: 10.1016/j.cub.2008.07.001  0.88
2008 Csikász-Nagy A, Novák B, Tyson JJ. Reverse engineering models of cell cycle regulation. Advances in Experimental Medicine and Biology. 641: 88-97. PMID 18783174 DOI: 10.1007/978-0-387-09794-7_7  0.88
2008 Barik D, Paul MR, Baumann WT, Cao Y, Tyson JJ. Stochastic simulation of enzyme-catalyzed reactions with disparate timescales. Biophysical Journal. 95: 3563-74. PMID 18621809 DOI: 10.1529/biophysj.108.129155  0.88
2008 Tyson JJ, Albert R, Goldbeter A, Ruoff P, Sible J. Biological switches and clocks. Journal of the Royal Society, Interface / the Royal Society. 5: S1-8. PMID 18522926 DOI: 10.1098/rsif.2008.0179.focus  0.88
2008 Li S, Brazhnik P, Sobral B, Tyson JJ. A quantitative study of the division cycle of Caulobacter crescentus stalked cells. Plos Computational Biology. 4: e9. PMID 18225942 DOI: 10.1371/journal.pcbi.0040009  0.88
2008 Csikász-Nagy A, Gyorffy B, Alt W, Tyson JJ, Novák B. Spatial controls for growth zone formation during the fission yeast cell cycle. Yeast (Chichester, England). 25: 59-69. PMID 17957823 DOI: 10.1002/yea.1571  0.88
2008 Sabouri-Ghomi M, Ciliberto A, Kar S, Novak B, Tyson JJ. Antagonism and bistability in protein interaction networks. Journal of Theoretical Biology. 250: 209-18. PMID 17950756 DOI: 10.1016/j.jtbi.2007.09.001  0.88
2008 Panning TD, Watson LT, Allen NA, Chen KC, Shaffer CA, Tyson JJ. Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle Journal of Global Optimization. 40: 719-738. DOI: 10.1007/s10898-007-9273-7  0.88
2007 Calzone L, Thieffry D, Tyson JJ, Novak B. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. Molecular Systems Biology. 3: 131. PMID 17667953 DOI: 10.1038/msb4100171  0.88
2007 Novak B, Tyson JJ, Gyorffy B, Csikasz-Nagy A. Irreversible cell-cycle transitions are due to systems-level feedback. Nature Cell Biology. 9: 724-8. PMID 17603504 DOI: 10.1038/ncb0707-724  0.88
2007 Ciliberto A, Capuani F, Tyson JJ. Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. Plos Computational Biology. 3: e45. PMID 17367203 DOI: 10.1371/journal.pcbi.0030045  0.88
2007 Csikász-Nagy A, Kapuy O, Gyorffy B, Tyson JJ, Novák B. Modeling the septation initiation network (SIN) in fission yeast cells. Current Genetics. 51: 245-55. PMID 17340144 DOI: 10.1007/s00294-007-0123-4  0.88
2007 Tyson JJ. Bringing cartoons to life. Nature. 445: 823. PMID 17314960 DOI: 10.1038/445823a  0.88
2007 Zhang T, Brazhnik P, Tyson JJ. Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle (Georgetown, Tex.). 6: 85-94. PMID 17245126  0.88
2007 Hong CI, Conrad ED, Tyson JJ. A proposal for robust temperature compensation of circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America. 104: 1195-200. PMID 17229851 DOI: 10.1073/pnas.0601378104  0.88
2007 Sible JC, Tyson JJ. Mathematical modeling as a tool for investigating cell cycle control networks. Methods (San Diego, Calif.). 41: 238-47. PMID 17189866 DOI: 10.1016/j.ymeth.2006.08.003  0.88
2007 Panning TD, Watson LT, Shaffer CA, Tyson JJ. A mathematical programming formulation for the budding yeast cell cycle Simulation. 83: 497-514. DOI: 10.1177/0037549707085075  0.88
2007 Brazhnik P, Li S, Sobral B, Tyson JJ. Computational model of the division cycle of Caulobacter crescentus Aip Conference Proceedings. 952: 219-228. DOI: 10.1063/1.2816625  0.88
2006 Vass MT, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ. The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 155-64. PMID 17048401 DOI: 10.1109/TCBB.2006.27  0.88
2006 Allen NA, Chen KC, Shaffer CA, Tyson JJ, Watson LT. Computer evaluation of network dynamics models with application to cell cycle control in budding yeast Iee Proceedings Systems Biology. 153: 13-21. PMID 16983831 DOI: 10.1049/ip-syb:20050029  0.88
2006 Tyson JJ. Another turn for p53. Molecular Systems Biology. 2: 2006.0032. PMID 16773082 DOI: 10.1038/msb4100060  0.88
2006 Battogtokh D, Aihara K, Tyson JJ. Synchronization of eukaryotic cells by periodic forcing. Physical Review Letters. 96: 148102. PMID 16712125 DOI: 10.1103/PhysRevLett.96.148102  0.88
2006 Csikász-Nagy A, Battogtokh D, Chen KC, Novák B, Tyson JJ. Analysis of a generic model of eukaryotic cell-cycle regulation. Biophysical Journal. 90: 4361-79. PMID 16581849 DOI: 10.1529/biophysj.106.081240  0.88
2006 Brazhnik P, Tyson JJ. Cell cycle control in bacteria and yeast: a case of convergent evolution? Cell Cycle (Georgetown, Tex.). 5: 522-9. PMID 16552176  0.88
2006 Battogtokh D, Tyson JJ. Periodic forcing of a mathematical model of the eukaryotic cell cycle. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 011910. PMID 16486188 DOI: 10.1103/PhysRevE.73.011910  0.88
2006 Sauro HM, Harel D, Kwiatkowska M, Shaffer CA, Uhrmacher AM, Hucka M, Mendes P, Strömback L, Tyson JJ. Challenges for modeling and simulation methods in systems biology Proceedings - Winter Simulation Conference. 1720-1730. DOI: 10.1109/WSC.2006.322948  0.88
2006 Shaffer CA, Randhawa R, Tyson JJ. The role of composition and aggregation in modeling macromolecular regulatory networks Proceedings - Winter Simulation Conference. 1628-1635. DOI: 10.1109/WSC.2006.322937  0.88
2005 Zwolak JW, Tyson JJ, Watson LT. Globally optimised parameters for a model of mitotic control in frog egg extracts. Systems Biology. 152: 81-92. PMID 17044236 DOI: 10.1049/ip-syb:20045032  0.88
2005 Ciliberto A, Lukács A, Tóth A, Tyson JJ, Novák B. Rewiring the exit from mitosis. Cell Cycle (Georgetown, Tex.). 4: 1107-12. PMID 15970669  0.88
2005 Zwolak JW, Tyson JJ, Watson LT. Parameter estimation for a mathematical model of the cell cycle in frog eggs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 48-63. PMID 15725733 DOI: 10.1089/cmb.2005.12.48  0.88
2005 Ciliberto A, Novak B, Tyson JJ. Steady states and oscillations in the p53/Mdm2 network. Cell Cycle (Georgetown, Tex.). 4: 488-93. PMID 15725723  0.88
2004 Battogtokh D, Tyson JJ. Turbulence near cyclic fold bifurcations in birhythmic media. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 026212. PMID 15447570 DOI: 10.1103/PhysRevE.70.026212  0.88
2004 Battogtokh D, Tyson JJ. Bifurcation analysis of a model of the budding yeast cell cycle. Chaos (Woodbury, N.Y.). 14: 653-61. PMID 15446975 DOI: 10.1063/1.1780011  0.88
2004 Novák B, Tyson JJ. A model for restriction point control of the mammalian cell cycle. Journal of Theoretical Biology. 230: 563-79. PMID 15363676 DOI: 10.1016/j.jtbi.2004.04.039  0.88
2004 Tyson JJ, Glass L. Arthur T. Winfree (1942-2002). Journal of Theoretical Biology. 230: 433-9. PMID 15363665 DOI: 10.1016/j.jtbi.2004.04.042  0.88
2004 Vass M, Allen N, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ. the JigCell model builder and run manager. Bioinformatics (Oxford, England). 20: 3680-1. PMID 15273159 DOI: 10.1093/bioinformatics/bth422  0.88
2004 Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell. 15: 3841-62. PMID 15169868 DOI: 10.1091/mbc.E03-11-0794  0.88
2004 Sveiczer A, Tyson JJ, Novak B. Modelling the fission yeast cell cycle. Briefings in Functional Genomics & Proteomics. 2: 298-307. PMID 15163365 DOI: 10.1093/bfgp/2.4.298  0.88
2004 Tyson JJ. A precarious balance. Current Biology : Cb. 14: R262-3. PMID 15062115 DOI: 10.1016/j.cub.2004.03.017  0.88
2004 Thornton BR, Chen KC, Cross FR, Tyson JJ, Toczyski DP. Cycling without the cyclosome: modeling a yeast strain lacking the APC. Cell Cycle (Georgetown, Tex.). 3: 629-33. PMID 15034296  0.88
2004 Tyson JJ. Monitoring p53's pulse. Nature Genetics. 36: 113-4. PMID 14752517 DOI: 10.1038/ng0204-113  0.88
2004 Zwolak JW, Tyson JJ, Watson LT. Finding all steady state solutions of chemical kinetic models Nonlinear Analysis: Real World Applications. 5: 801-814. DOI: 10.1016/j.nonrwa.2004.02.002  0.88
2004 He J, Sosonkina M, Shaffer CA, Tyson JJ, Watson LT, Zwolak JW. A hierarchical parallel scheme for global parameter estimation in systems biology Proceedings - International Parallel and Distributed Processing Symposium, Ipdps 2004 (Abstracts and Cd-Rom). 18: 571-579.  0.88
2003 Ciliberto A, Novak B, Tyson JJ. Mathematical model of the morphogenesis checkpoint in budding yeast. The Journal of Cell Biology. 163: 1243-54. PMID 14691135 DOI: 10.1083/jcb.200306139  0.88
2003 Novák B, Tyson JJ. Modelling the controls of the eukaryotic cell cycle Biochemical Society Transactions. 31: 1526-1529. PMID 14641104  0.88
2003 Allen NA, Calzone L, Chen KC, Ciliberto A, Ramakrishnan N, Shaffer CA, Sible JC, Tyson JJ, Vass MT, Watson LT, Zwolak JW. Modeling regulatory networks at Virginia Tech. Omics : a Journal of Integrative Biology. 7: 285-99. PMID 14583117 DOI: 10.1089/153623103322452404  0.88
2003 Ciliberto A, Petrus MJ, Tyson JJ, Sible JC. A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos. Biophysical Chemistry. 104: 573-89. PMID 12914904  0.52
2003 Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology. 15: 221-31. PMID 12648679  0.6
2003 Sha W, Moore J, Chen K, Lassaletta AD, Yi CS, Tyson JJ, Sible JC. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proceedings of the National Academy of Sciences of the United States of America. 100: 975-80. PMID 12509509 DOI: 10.1073/pnas.0235349100  0.88
2002 Tyson JJ, Csikasz-Nagy A, Novak B. The dynamics of cell cycle regulation. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 24: 1095-109. PMID 12447975 DOI: 10.1002/bies.10191  0.6
2001 Novak B, Pataki Z, Ciliberto A, Tyson JJ. Mathematical model of the cell division cycle of fission yeast. Chaos (Woodbury, N.Y.). 11: 277-286. PMID 12779461 DOI: 10.1063/1.1345725  0.6
2001 Tyson JJ, Mackey MC. Molecular, metabolic, and genetic control: An introduction. Chaos (Woodbury, N.Y.). 11: 81-83. PMID 12779443 DOI: 10.1063/1.1350441  0.88
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