Modeling the Budding Yeast Cell Cycle

Toth, A., Queralt, E., Uhlmann, F., and Novak, B. (2007). Mitotic exit in two dimensions. J Theor Biol 248:560-573
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Lovrics, A., Csikasz-Nagy, A., Zsely, I., Zador, J., Turanyi, T. and Novak, B. (2006). Time scale and dimension analyses of a budding yeast cell cycle model. BMC Bioinformatics 7:494.
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Queralt, E., Lehane, C., Novak, B. and Uhlmann, F. (2006). Downregulation of PP2A^Cdc55 phosphatase by separase initiates mitotic exit in budding yeast. Cell 125:1-14.
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Cross, F.R., Schroeder, L., Kruse, M. and Chen, K.C. (2005). Quantitative characterization of a mitotic cyclin threshold regulating exit from mitosis. Mol. Biol. Cell 16:2129-2138.
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Battogtokh, D. and Tyson, J. J. (2004). Bifurcation analysis of a model of the budding yeast cell cycle. Chaos 14:653-661.
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Chen, K.C., Calzone, L., Csikasz-Nagy, A., Cross, F.R., Novak, B. and Tyson, J.J. (2004). Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15:3841-3862.
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Thornton, B. R., Chen, K.C., Cross, F.R., Tyson, J.J., and Toczyski, D.P. (2004). Cycling without the cyclosome: modeling a yeast strain lacking the APC. Cell Cycle 3: 629-633.
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Ciliberto, A., Novak, B. and Tyson J.J. (2003). Mathematical model of the morphogenesis checkpoint in budding yeast. J. Cell Biol. 163:1243-1254.
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Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B. and Tyson, J.J. (2000). Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol. Biol. Cell 11:369-391.
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Ciliberto, A. and Tyson, J.J. (2000). Mathematical model for early development of the sea urchin embryo, Bull. Math. Biol. 62:37-59.
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Calzone, L., Thieffry, D., Tyson, J. J., and Novak, B. (2007). Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. Mol. Syst. Biol. 3:131-141.
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Csikasz-Nagy, A., Gyorffy, B., Alt, W., Tyson, J.J., and Novak, B. (2008). Spatial controls for growth zone formation during the fission yeast cell cycle. Yeast 25:59-69.
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Castagnetti, S., Novak, B., and Nurse, P. (2007). Microtubules offset growth site from the cell centre in fission yeast. J Cell Sci 120:2205-2213.
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Csikasz-Nagy, A., Kapuy, O., Gyorffy, B., Tyson, J. J., and Novak, B. (2007). Modeling the septation initiation network (SIN) in fission yeast cells. Curr. Genet. 51:245-255.
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Sveiczer, A., Tyson, J.J. and Novak, B. (2004). Modelling the fission yeast cell cycle. Brief. Funct. Genomics Proteomics 2:298-307.
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Novak, B., Pataki, Z., Ciliberto, A. and Tyson, J.J. (2001). Mathematical model of the cell division cycle of fission yeast. Chaos 11:277-286.
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Sveiczer, A., Tyson, J.J. and Novak, B. (2001). A stochastic molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation. Biophys. Chem. 92:1-15.
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Sveiczer, A., Csikasz-Nagy, A., Gyorffy, B., Tyson, J.J. and Novak, B. (2000). Modeling the fission yeast cell cycle: quantized cycle times in wee1^-cdc25∆ mutant cells. Proc. Natl. Acad. Sci. USA 97:7865-7870.
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Sveiczer, A., Novak, B. and Mitchison, J.M. (1999). Mitotic control in the absence of cdc25 mitotic inducer in fission yeast. J. Cell Sci. 112:1085-1092.
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Mitchison, J.M., Sveiczer, A. and Novak, B. (1998). Length growth in fission yeast: is growth exponential?--No. Microbiology 144:265-266.
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Novak, B., Csikasz-Nagy, A., Gyorffy, B., Chen, K. and Tyson, J.J. (1998). Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions Biophys. Chem. 72:185-200.
[Abstract] [Article]

Mitchison, J.M., Novak, B. and Sveiczer, A. (1997). Size control in the cell cycle. Cell Biol. Int. 21:461-463
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Novak, B. and Tyson, J.J. (1997). Modeling the control of DNA replication in fission yeast. Proc. Natl. Acad. Sci. USA 94:9147-9152.
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Sveiczer, A., Novak, B. and Mitchison, J.M. (1996). The size control of fission yeast revisited. J. Cell Sci. 109:2947-2957.
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Novak, B. and Tyson, J.J. (1995). Quantitative analysis of a molecular model of mitotic control in fission yeast. J. Theor. Biol. 173:283-305.
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Novak, B., Sveiczer, A., and Mitchison, J.M. (1993). CO2 production in cell-free extracts of fission yeast detects cell cycle changes. J. Cell Sci. 105:529-531.
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Mitchison, J.M., Creanor, J. and Novak, B. (1991). Coordation of growth and division during the cell cycle of fission yeast. In The Cell Cycle, D. Beach, B. Stillman, and J. D. Watson, eds. (Cold Spring Harbor, Cold Spring Harbor Laboratory Press), pp. 557-565.
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Hong, C. I., Conrad, E. D. and Tyson, J. J. (2007). A proposal for robust temperature compensation of circadian rhythms. Proc. Natl. Acad. Sci. U.S.A. 104:1195-1200.
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Tyson, J.J., Hong, C.I., Thron, C.D.and Novak, B. (1999). A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys. J. 77:2411-2417.
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Hong, C. I. and Tyson, J. J. (1997). A proposal for temperature compensation of the circadian rhythm in Drosophila based on dimerization of the per protein. Chronobiol. Int. 14:521-529.
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Li, S., Brazhnik, P., Sobral, B., and Tyson, J.J. (2009). Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus. PLoS Comput Biol 5: e1000463.
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Li, S., Brazhnik, P., Sorbal, B., and Tyson, J.J. (2008). A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput. Biol 4:e9.
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Brazhnik, P. and Tyson, J. J. (2006). Cell cycle control in bacteria and yeast: a case of convergent evolution? Cell Cycle 5:522-529.
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McGuinness, B.E., Anger, M., Kouznetsova, A., Gil-Bernabe, A.M., Helmhart, W., Kudo, N.R., Wuensche, A., Taylor, S., Hoog, C., Novak, B., and Nasmyth, K. (2009). Regulation of APC/C activity in oocytes by a Bub1-dependent spindle assembly checkpoint. Curr. Biol. 19: 369-380.
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Su, J., Zhang, T., Tyson, J.J., and Li, L. (2009). The interleukin-1 receptor associated kinase M selectively inhibits the alternative, instead of the classical NFkappaB pathway. J Innate Immun 1: 164-174.
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Zhang, T., Brazhnik, P., and Tyson, J.J. (2009). Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death. Biophys J. 97: 415-432.
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Zhang, T., Brazhnik, P. and Tyson, J. J. (2007). Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle 6:85-94.
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Tyson, J.J. (2006). Another turn for p53. Mol. Syst. Biol. 2:2006.0032.
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Ciliberto, A., Novak, B. and Tyson, J. J. (2005). Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 4:488-493.
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Novak, B. and Tyson, J. J. (2004). A model for restriction point control of the mammalian cell cycle. J. Theor. Biol. 230:563-579.
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Tyson, J.J. (2004). Monitoring p53's pulse. Nat. Genet. 36:113-114.
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Csikasz-Nagy, A., Kapuy, O., Toth, A., Pal, C., Jensen, L.J., Uhlmann, F., Tyson, J.J., and Novak, B. (2009). Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol. Syst. Biol. 5:236.
[Abstract] [Article]

Kapuy, O., Barik, D., Domingo Sananes, M.R., Tyson, J.J., and Novak, B. (2009). Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol June 11 Epub ahead of print
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Kapuy, O., He, E., Lopez-Avilies, S., Uhlmann, F., Tyson, J.J., and Novak, B. (2009). System-level feedbacks control cell cycle progression FEBS Lett Aug 22 Epub ahead of print.
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Tyson, J.J. (2009). In their own words: interviews with cell cycle. John Tyson on his highly cited paper. Cell Cycle 8: 3261.
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Csikasz-Nagy, A., Novak, B., and Tyson, J.J. (2008). Reverse engineering models of cell cycle regulation. Adv. Exp. Med. Biol. 641:88-97.
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Novak, B., and Tyson, J.J. (2008). Design principles of biochemical oscillators. Nature Rev. Mol. Cell Biol. 9:981-991
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Sabouri-Ghomi, M., Ciliberto, A., Kar, S., Novak, B., and Tyson, J.J. (2008). Antagonism and bistability in protein interaction networks. J Theor Biol. 250:209-218
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Tyson, J.J., and Novak, B. (2008). Temporal organization of the cell cycle. Curr. Biol. 18: R759-R768.
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Tyson, J.J., Albert, R., Goldbeter, A., Ruoff, P., and Sible, J.C. (2008). Biological switches and clocks. J R Soc Interface Aug 6; 5 Suppl. 1, S1-S8.
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Ciliberto, A., Capuani, F., and Tyson, J. J. (2007). Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput Biol 3:e45.
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Novak, B., Tyson, J. J., Gyorffy, B., and Csikasz-Nagy, A. (2007). Irreversible cell-cycle transitions are due to systems-level feedback. Nature Cell Biol 9:724-728.
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Sible, J. C. and Tyson, J. J. (2007). Mathematical modeling as a tool for investigating cell cycle control networks. Methods 41:238-247.
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Tyson, J. J. (2007). Bringing cartoons to life. Nature 445:823.
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Battogtokh, D. and Tyson, J. J. (2006) Periodic forcing of a mathematical model of the eukaryotic cell cycle. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73:011910
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Battogtokh, D., Aihara, K. and Tyson, J. J. (2006). Synchronization of eukaryotic cells by periodic forcing. Phys. Rev. Lett. 96:148102.
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Conrad, E. D. and Tyson, J. J. (2006). Modeling molecular interaction networks with nonlinear ordinary differential equations. In System Modeling in Cell Biology from Concepts to Nuts and Bolts, Z. Szallasi, J. Stelling, and V. Periwal, eds. (Cambridge, MA: MIT Press), pp. 97-123.
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Csikasz-Nagy, A., Battogtokh, D., Chen, K. C., Novak, B. and Tyson, J. J. (2006). Analysis of a generic model of eukaryotic cell cycle regulation. Biophys. J. 90:4361-4379.
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Novak, B., Chen, K.C. and Tyson, J.J. (2005). Systems biology of the yeast cell cycle engine. In Topics in Current Genetics, Vol. 13. Systems Biology: Definitions and Perspectives. L. Alberghina and H. V. Westerhoff eds. (Springer, Berlin /Heidelberg) pp. 305-324.
[Abstract] [Article]

Tyson, J. J. (2005). The coordination of cell growth and division-intentional or incidental? BioEssays 2:72-77.
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Battogtokh, D. and Tyson, J. J. (2004). Turbulence near cyclic fold bifurcations in birhythmic media. Phys. Rev. E 70:026212.
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Tyson, J. J. (2004). A precarious balance. Curr. Biol. 14:R262-263.
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Novak, B. and Tyson, J.J. (2003). Modelling the controls of the eukaryotic cell cycle. Biochem. Soc. Trans. 31:1526-1529.
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Tyson, J.J., Chen, K.C. and Novak, B. (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15:221-231.
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Fall, C.P., Marland, E.S., Wagner, J. M. and Tyson, J.J. (2002). Computational Cell Biology. (New York, Springer-Verlag).
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Novak, B., Sible, J.C.and Tyson, J.J. (2002). Checkpoints in the cell cycle. Encyclopedia of Life Sciences. London: Nature Publishing Group. http://www.els.net/   [doi:10.1038/npg.els.0001355], pp.1-8.
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Tyson J.J., Csikasz-Nagy, A. and Novak, B. (2002). The dynamics of cell cycle regulation. Bioessays 24:1095-1109.
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Tyson, J.J., Chen, K. and Novak, B. (2001). Network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2:908-916.
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Tyson, J.J. and Novak, B. (2001). Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis and irreversible transitions. J. Theor. Biol. 210:249-263.
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Tyson, J.J., Borisuk, M.T., Chen, K.and Novak, B. (2000). Analysis of complex dynamics in cell cycle regulation. In Computational Modeling of Genetic and Biochemical Networks, J. M. Bower and H. Bolouri eds. (Cambridge, MA, MIT Press), pp. 287-305.
[Abstract] [Article]

Tyson, J.J., Borisuk, M.T., Chen, K., and Novak, B. (2000). Analysis of complex dynamics in cell cycle regulation, in Computational Modeling of Genetic and Biochemical Networks, (J.M. Bower, and H. Bolouri,Eds), pp. 287-305 (Cambridge, MA, MIT Press).
[Abstract] [Article]

Novak, B., Toth, A., Csikasz-Nagy, A., Gyorffy, B., Tyson, J.J. and Nasmyth, K. (1999). Finishing the cell cycle. J. Theor. Biol. 199:223-233.
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Novak, B., Csikasz-Nagy, A., Gyorffy, B., Nasmyth, K.and Tyson, J J. (1998). Model scenarios for evolution of the eukaryotic cell cycle. Phil. Trans. R. Soc. Lond. B 353:2063-2076.
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Tyson, J.J., Chen, K.C. and Novak, B. (1997). The eukaryotic cell cycle: molecules, mechanisms and mathematical models, in Case Studies in Mathematical Modeling: Ecology, Physiology and Cell Biology. (H. G. Othmer, F. R. Adler, M. A. Lewis and J. C. Dallon Eds.) pp. 127-147 (Prentice Hall, Upper Saddle River).
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Tyson, J.J., Novak, B., Odell, G.M., Chen, K. and Thron, C.D. (1996). Chemical kinetic theory: understanding cell-cycle regulation. Trends Biochem. Sci. 21:89-96.
[Abstract] [Article]

Novak, B. and Tyson, J.J. (1995). Mathematical modeling of the cell division cycle," in Mathematical Population Dynamics: Analysis of Heterogeneity (O. Arino, D. Axelrod & M. Kimmel, Eds.) Vol. 2, pp. 155-169 (Wuerz Publ., Winnipeg).
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Tyson, J. J., Novak, B., Chen, K. and Val, J. (1995). Checkpoints in the cell cycle from a modeler's perspective. Prog. Cell Cycle Res.1:1-8.
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Novak, B. and Tyson, J.J. (1993). Modeling the cell division cycle: M-phase trigger, oscillations and size control. J. Theor. Biol. 165:101-134.
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Tyson, J.J. (1991). Modeling the cell division cycle: cdc2 and cyclin interactions.Proc. Natl. Acad. Sci. USA 88:7328-7332.
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Tyson, J.J. (1983). Unstable activator models for size control of the cell cycle. J. Theor. Biol. 104:617-631.
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Tyson, J. J. and Hannsgen, K. B. (1981). Analysis of a Deterministic/Probabilistic Model of the Cell Division Cycle, in Biomathematics and Cell Kinetics (M. Rotenberg, Ed.) pp. 167-176 (Elsevier/North Holland, Amsterdam).
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Zwolak, J.W., Adjerid, N., Bagci, E.Z., Tyson, J.J., and Sible, J.C. (2009). A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts. J Theor Biol 260: 110-120.
[Abstract] [Article]

Ciliberto, A., Lukacs, A., Toth, A.,Tyson, J. J. and Novak, B. (2005). Rewiring the exit from mitosis. Cell Cycle 4:1107-1112.
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Ciliberto, A., Petrus, M.J., Tyson, J.J. and Sible, J.C. (2003). A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos. Biophys Chem. 104:573-89.
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Sha, W., Moore, J., Chen, K., Lassaletta, A.D., Yi, C.-S., Tyson, J.J. and Sible, J.C. (2003). Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl. Acad. Sci. USA 100:975-980.
[Abstract] [Article]

Borisuk, M.T. and Tyson, J.J. (1998). Bifurcation analysis of a model of mitotic control in frog eggs. J. Theor. Biol. 195:69-85.
[Abstract] [Article]

Marlovits, G., Tyson, C.J., Novak, B. and Tyson, J.J. (1998). Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA. Biophys. Chem. 72:169-184.
[Abstract] [Article]

Novak, B. and Tyson, J.J. (1993). Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J. Cell Sci. 106:1153-1168. Highlighted by News and Views, Nature, 9 June 1994, p. 437.
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Randhawa, R., Shaffer, C.A., and Tyson, J.J. (2009). Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics, Oct 29 [Epub ahead of print].
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Shaffer, C.A., Zwolak, J.W., Randhawa, R., and Tyson, J.J. (2009). Modeling molecular regulatory networks with JigCell and PET. Methods Mol. Biol. Syst. Biol. 500: 81-111.
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Panning, T.D., Watson, L.T., Allen, N.A., Chen, K.C., Shaffer, C.A., and Tyson, J.J. (2008). Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. J Glob Optim 40:719-738.
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Randhawa, R., Shaffer, C.A., and Tyson, J.J. (2008). Model composition for macromolecular regulatory networks. IEEE/ACM Trans Comput Biol Bioinform 19 June, In press.
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Panning, T.D., Watson, L.T., Shaffer, C.A., and Tyson, J.J. (2007). A mathematical programming formulation for the budding yeast cell cycle. Simulation 8:497-514.
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Allen, N. A., Chen, K. C., Shaffer, C. A., Tyson, J. J. and Watson, L. T. (2006). Computer evaluation of network dynamics models with application to cell cycle control in budding yeast. IEE Proc Syst Biol (Stevenage) 153:13-21.
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Vass, M. T., Shaffer, C. A., Ramakrishnan, N., Watson, L. T. and Tyson, J. J. (2006). The JigCell model builder: a spreadsheet interface for creating biomedical reaction network models. IEEE/ACM Trans Comput Biol Bioinform 3:155-164.
[Abstract] [Article]

Zwolak, J.W., Tyson, J.J. and Watson, L.T. (2005). Parameter estimation for a mathematical model of the cell cycle in frog eggs. J. Comp. Biol. 12:48-63.
[Abstract] [Article]

Zwolak, J. W., Tyson, J. J. and Watson, L. T. (2005). Globally optimized parameters for a model of mitotic control in frog egg extracts. IEE Syst Biol. (Stevenage) 152:81-92.
[Abstract] [Article]

Vass, M. T., Allen, N. A., Shaffer, C. A., Ramakrishnan, N., Watson, L. T. and Tyson, J. J. (2004). The Jigcell model builder and run manager. Bioinformatics 20:3680-3681.
[Abstract] [Article]

Allen, N.A., Calzone, L., Chen, K.C., Ciliberto, A., Ramakrishnan, N., Shaffer, C.A., Sible, J.C., Tyson, J.J., Vass, M.T., Watson, L.T. and Zwolak, J.W. (2003). Modeling regulatory networks at Virginia Tech. OMICS 7:285-299.
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Kar, S., Baumann, W.T., Paul, M.R., and Tyson, J.J. (2009). Exploring the roles of noise in the eukaryotic cell cycle. Proc. Natl. Acad. Sci. USA 106:6471-6476.
[Abstract] [Article]

Barik, D., Paul, M.R., Baumann, W.T., Cao, Y., and Tyson, J.J. (2008). Stochastic simulation of enzyme-catalyzed reactions with disparate time scales. Biophys. J. 95: 3563-3574.
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