Generic Cell Cycle Model

Amon, A., Tyers, M., Futcher, B. and Nasmyth, K. (1993). Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins. Cell 74:993-1007.
[Abstract] [Article]

Ayte, J., Schweitzer, C., Zarzov, P., Nurse, P. and DeCaprio J.A. (2001). Feedback regulation of the MBF transcription factor by cyclin Cig2. Nat. Cell Biol. 3:1043-1050.
[Abstract] [Article]

Bardin, A. and Amon, A. (2001). Men and sin: what's the difference? Nat. Rev. Mol. Cell Biol. 2:815-826.
[Abstract] [Article]

Bartek, J., Bartkova, J. and Lukas, J. (1996). The retinoblastoma protein pathway and the restriction point. Curr. Opin. Cell Biol. 8, 805-814.
[Abstract] [Article]

Bartkova, J., Lukas, J. and Bartek, J. (1997). Aberrations of the G1- and G1/S-regulating genes in human cancer. Prog. Cell Cycle Res. 3, 211-220.
[Abstract] [Article]

Battogtokh, D., and J.J. Tyson. (2004) Bifurcation analysis of a model of the budding yeast cell cycle. Chaos. 14:653-661
[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]

Botchan, M. (1996). Coordinating DNA replication with cell division: Current status of the licensing concept. Proc. Natl. Acad. Sci. USA 93:9997-10000.
[Abstract] [Article]

Brewer, B.J., Chlebowicz-Sledziewska, E. and Fangman, W.L. (1984). Cell cycle phases in the unequal mother/daughter cell cycles of Saccharomyces cerevisiae. Mol. Cell. Biol. 4:2529-2531.
[Abstract] [Article]

Calzada, A., Sacristan, M., Sanchez, E. and Bueno, A. (2001). Cdc6 cooperates with Sic1 and Hct1 to inactivate mitotic cyclin-dependent kinases. Nature 412:355-358.
[Abstract] [Article]

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.
[Abstract] [Article]

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.
[Abstract] [Article]

Chow, J. P. H., Siu, W. Y., Ho, H. T. B., Ma, K. H. T., Ho, C. C. and Poon, R. Y. C. (2003). Differential contribution of inhibitory phosphorylation of CDC2 and CDK2 for unperturbed cell cycle control and DNA integrity checkpoints. Journal of Biological Chemistry 278, 40815-40828.
[Abstract] [Article]

Ciliberto, A., Novak, B. and Tyson J.J. (2003). Mathematical model of the morphogenesis checkpoint in budding yeast. J. Cell Biol. 163:1243-1254.
[Abstract] [Article]

Cohen-Fix, O. and Koshland, D. (1999). Pds1p of budding yeast has dual roles: inhibition of anaphase initiation and regulation of mitotic exit. Genes Dev. 13:1950-1959.
[Abstract] [Article]

Cross, F.R., Archambault, V., Miller, M., Klovstad, M. (2002). Testing a mathematical model of the yeast cell cycle. Mol. Biol. Cell 13:52-70.
[Abstract] [Article]

Cross, F.R. (2003). Two redundant oscillatory mechanisms in the yeast cell cycle. Dev. Cell 4:741-752.
[Abstract] [Article]

Dirick, L., Bohm, T. and Nasmyth, K. (1995). Roles and regulation of Cln/Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J. 14:4803-4813.
[Abstract] [Article]

Fall, C.P., Marland, E.S., Wagner, J. M. and Tyson, J.J. (2002). Computational Cell Biology. (New York, Springer-Verlag).
[Abstract] [Article]

Fitzpatrick, P.J., Toyn, J.H., Millar, J.B. and Johnston, L.H. (1998). DNA replication is completed in Saccharomyces cerevisiae cells that lack functional Cdc14, a dual-specificity protein phosphatase. Mol. Gen. Genet. 258:437-441.
[Abstract] [Article]

Geng, Y., Yu, Q. Y., Sicinska, E., Das, M., Schneider, J. E., Bhattacharya, S., Rideout, W. M., Bronson, R. T., Gardner, H. and Sicinski, P. (2003). Cyclin E ablation in the mouse. Cell 114, 431-443.
[Abstract] [Article]

Goldbeter, A., and Koshland D.E. Jr. (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA. 78:6840-6844.
[Abstract] [Article]

Hayles, J., Fisher, D., Woollard, A. and Nurse, P. (1994). Temporal order of S phase and mitosis in fission yeast is determined by the state of the p34cdc2 -mitotic B cyclin complex. Cell 78, 813-822.
[Abstract] [Article]

Jaspersen, S.L., Charles, J.F., Tinker-Kulberg, R.L., and Morgan, D.O. (1998). A late mitotic regulatory network controlling cyclin destruction in Saccharomyces cerevisiae. Mol. Biol. Cell 9:2803-2817.
[Abstract] [Article]

Kozar, K., Ciemerych, M. A., Rebel, V. I., Shigematsu, H., Zagozdon, A., Sicinska, E., Geng, Y., Yu, Q. Y., Bhattacharya, S., Bronson, R. T. et al. (2004). Mouse development and cell proliferation in the absence of D-cyclins. Cell 118, 477-491.
[Abstract] [Article]

Kuznetsov, Y.A. (1995) Elements of applied bifurcation theory. Springer Verlag, New York
[Abstract] [Article]

Lew, D.J. (2000). Cell-cycle checkpoints that ensure coordination between nuclear and cytoplasmic events in Saccharomyces cerevisiae. Curr. Opin. Genet. Dev. 10:47-53.
[Abstract] [Article]

Lim, H.H., Goh, P.-Y. and Surana, U. (1998). Cdc20 is essential for the cyclosome-mediated proteolysis of both Pds1 and Clb2 during M phase in budding yeast. Curr. Biol. 8:231-234.
[Abstract] [Article]

Malumbres, M., Sotillo, R., Santamaria, D., Galan, J., Cerezo, A., Ortega, S., Dubus, P. and Barbacid, M. (2004). Mammalian cells cycle without the D-type cyclin-elependent kinases Cdk4 and Cdk6. Cell 118, 493-504.
[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]

Martin-Castellanos, C., Blanco, M., de Prada, J. M. and Moreno, S. (2000). The Puc1 cyclin regulates the G1 phase of the fission yeast cell cycle in response to cell size. Mol. Biol. Cell 11, 543-54.
[Abstract] [Article]

McMillan, J. N., Longtine, M. S., Sia, R. A., Theesfeld, C. L., Bardes, E. S. G., Pringle, J. R. and Lew, D. J. (1999). The morphogenesis checkpoint in Saccharomyces cerevisiae: cell cycle control of Swe1p degradation by Hsl1p and Hsl7p. Mol. Cell. Biol. 19, 6929-6939.
[Abstract] [Article]

Nasmyth, K. and Dirick, L. (1991). The Role of SWI4 and SWI6 in the activity of G1 cyclins in yeast. Cell 66:995-1013.
[Abstract] [Article]

Nasmyth, K. (1996). At the heart of the budding yeast cell cycle. Trends Genet. 12:405-412.
[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.
[Abstract] [Article]

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.
[Abstract] [Article]

Novak, B. and Tyson, J.J. (1997). Modeling the control of DNA replication in fission yeast. Proc. Natl. Acad. Sci. USA 94:9147-9152.
[Abstract] [Article]

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]

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.
[Abstract] [Article]

Novak, B. and Tyson, J. J. (2004). A model for restriction point control of the mammalian cell cycle. Journal of Theoretical Biology 230, 563-579.
[Abstract] [Article]

Nurse, P. (1985). Cell cycle control in yeast. Trends Genet. 1, 51-55.
[Abstract] [Article]

Nurse, P. (1990) Universal control mechanism regulating onset of M-phase. Nature. 344:503-508
[Abstract] [Article]

Ortega, S., Prieto, I., Odajima, J., Martin, A., Dubus, P., Sotillo, R., Barbero, J. L., Malumbres, M. and Barbacid, M. (2003). Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice. Nature Genetics 35, 25-31.
[Abstract] [Article]

Pfleger, C.M. and Kirschner, M.W. (2000). The KEN box: an APC recognition signal distinct from the D box targeted by Cdh1. Genes Dev. 14:655-665.
[Abstract] [Article]

Richardson, H., Wittenberg, C., Cross, F.R. and Reed, S.I. (1989). An essential G1 function for cyclin-like proteins in yeast. Cell 59:1127-1133.
[Abstract] [Article]

Rudner, A.D. and Murray, A.W. (2000b). Phosphorylation by Cdc28 activates the Cdc20-dependent activity of the anaphase-promoting complex. J. Cell Biol. 149:1377-1390.
[Abstract] [Article]

Schneider, B.L., Yang, Q.-H. and Futcher, A.B. (1996). Linkage of replication to Start by the Cdk inhibitor Sic1. Science 272:560-562.
[Abstract] [Article]

Schwab, M., Lutum, A.S. and Seufert, W. (1997). Yeast Hct1 is a regulator of Clb2 cyclin proteolysis. Cell 90:683-693.
[Abstract] [Article]

Sethi, N., Monteagudo, M.C., Koshland, D., Hogan, E. and Burke, D.J. (1991). The CDC20 gene product of Saccharomyces cerevisiae, a beta-transducin homolog, is required for a subset of microtubule-dependent cellular processes. Mol. Cell. Biol. 11:5592-5602.
[Abstract] [Article]

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]

Shirayama, M., Zachariae, W., Ciosk, R. and Nasmyth, K. (1998). The Polo-like kinase Cdc5p and the WD-repeat protein Cdc20p/fizzy are regulators and substrates of the anaphase promoting complex in Saccharomyces cerevisiae. EMBO J. 17:1336-1349.
[Abstract] [Article]

Shirayama, M., Toth, A., Galova, M. and Nasmyth, K. (1999). APC(CDC20) promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5. Nature 402:203-207.
[Abstract] [Article]

Stegmeier, F., Visintin, R. and Amon, A.. (2002). Separase, polo kinase, the kinetochore protein Slk19, and Spo12 function in a network that controls Cdc14 localization during early anaphase. Cell 108:207-220.
[Abstract] [Article]

Strogatz, S.H. (1994) Nonlinear Dynamics and Chaos. Addison-Wesley Co., Reading, MA.
[Abstract] [Article]

Sveiczer, A., Novak, B. and Mitchison, J.M. (1996). The size control of fission yeast revisited. J. Cell Sci. 109:2947-2957.
[Abstract] [Article]

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.
[Abstract] [Article]

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.
[Abstract] [Article]

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.
[Abstract] [Article]

Tyson, J.J. (1991). Modeling the cell division cycle: cdc2 and cyclin interactions.Proc. Natl. Acad. Sci. USA 88:7328-7332.
[Abstract] [Article]

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.
[Abstract] [Article]

Tyson, J.J., Chen, K. and Novak, B. (2001). Network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2:908-916.
[Abstract] [Article]

Tyson J.J., Csikasz-Nagy, A. and Novak, B. (2002). The dynamics of cell cycle regulation. Bioessays 24:1095-1109.
[Abstract] [Article]

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.
[Abstract] [Article]

Visintin, R., Prinz, S. and Amon, A. (1997). CDC20 and CDH1: a family of substrate-specific activators of APC-dependent proteolysis. Science 278:460-463.
[Abstract] [Article]

Visintin, R., Craig, K., Hwang, E.S., Prinz, S., Tyers, M. and Amon, A. (1998). The phosphatase Cdc14 triggers mitotic exit by reversal of Cdk-dependent phosphorylation. Mol. Cell 2:709-718.
[Abstract] [Article]

Wasch, R. and Cross, F. (2002). APC-dependent proteolysis of the mitotic cyclin Clb2 is essential for mitotic exit. Nature 418:556-562.
[Abstract] [Article]

Zachariae, W., Schwab, M., Nasmyth, K. and Seufert, W. (1998). Control of cyclin ubiquitination by CDK-regulated binding of Hct1 to the anaphase promoting complex. Science 282:1721-1724.
[Abstract] [Article]

Zachariae, W. and Nasmyth, K. (1999). Whose end is destruction: cell division and the anaphase-promoting complex. Genes Dev. 13:2039-2058.
[Abstract] [Article]