| [1] | Morgan DO (2006) The Cell Cycle: Principles of Control, New Science Press.
|
| [2] | Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS (2010) Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res 38: D699–702.
|
| [3] | Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JE, et al. (2008) Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 453: 944–947.
|
| [4] | Coudreuse D, Nurse P (2010) Driving the cell cycle with a minimal CDK control network. Nature 468: 1074–1079.
|
| [5] | Kapuy O, He E, Lopez-Aviles S, Uhlmann F, Tyson JJ, et al. (2009) System-level feedbacks control cell cycle progression. FEBS Lett 583: 3992–3998.
|
| [6] | Novak B, Tyson JJ, Gyorffy B, Csikasz-Nagy A (2007) Irreversible cell-cycle transitions are due to systems-level feedback. Nat Cell Biol 9: 724–728.
|
| [7] | Ferrell JE Jr (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14: 140–148.
|
| [8] | Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221–231.
|
| [9] | Nurse P (1990) Universal control mechanism regulating onset of M-phase. Nature 344: 503–508.
|
| [10] | O'Farrell PH (2001) Triggering the all-or-nothing switch into mitosis. Trends Cell Biol 11: 512–519.
|
| [11] | Pomerening JR, Sontag ED, Ferrell JE Jr (2003) Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol 5: 346–351.
|
| [12] | Sha W, Moore J, Chen K, Lassaletta AD, Yi CS, et al. (2003) Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc Natl Acad Sci U S A 100: 975–980.
|
| [13] | Pomerening JR, Kim SY, Ferrell JE Jr (2005) Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Cell 122: 565–578.
|
| [14] | Deibler RW, Kirschner MW (2010) Quantitative reconstitution of mitotic CDK1 activation in somatic cell extracts. Mol Cell 37: 753–767.
|
| [15] | Lindqvist A, Rodriguez-Bravo V, Medema RH (2009) The decision to enter mitosis: feedback and redundancy in the mitotic entry network. J Cell Biol 185: 193–202.
|
| [16] | Perry JA, Kornbluth S (2007) Cdc25 and Wee1: analogous opposites? Cell Div 2: 12.
|
| [17] | Csikasz-Nagy A (2009) Computational systems biology of the cell cycle. Brief Bioinform 10: 424–434.
|
| [18] | Ferrell JE, Tsai TY, Yang Q (2011) Modeling the Cell Cycle: Why Do Certain Circuits Oscillate? Cell 144: 874–885.
|
| [19] | Tyson JJ, Novak B (2008) Temporal organization of the cell cycle. Curr Biol 18: R759–R768.
|
| [20] | Ferrell JE Jr (2008) Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses. Curr Biol 18: R244–245.
|
| [21] | Domingo-Sananes MR, Novak B (2010) Different effects of redundant feedback loops on a bistable switch. Chaos 20: 045120.
|
| [22] | Trunnell NB, Poon AC, Kim SY, Ferrell JE (2011) Ultrasensitivity in the Regulation of Cdc25C by Cdk1. Molecular cell 41: 263–274.
|
| [23] | Charvin G, Oikonomou C, Siggia ED, Cross FR (2010) Origin of irreversibility of cell cycle start in budding yeast. PLoS Biol 8: e1000284.
|
| [24] | Cross FR, Archambault V, Miller M, Klovstad M (2002) Testing a mathematical model of the yeast cell cycle. Mol Biol Cell 13: 52–70.
|
| [25] | Skotheim JM, Di Talia S, Siggia ED, Cross FR (2008) Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature 454: 291–296.
|
| [26] | Holt LJ, Krutchinsky AN, Morgan DO (2008) Positive feedback sharpens the anaphase switch. Nature 454: 353–357.
|
| [27] | Lopez-Aviles S, Kapuy O, Novak B, Uhlmann F (2009) Irreversibility of mitotic exit is the consequence of systems-level feedback. Nature 459: 592–595.
|
| [28] | Lukas J, Lukas C, Bartek J (2004) Mammalian cell cycle checkpoints: signalling pathways and their organization in space and time. DNA Repair (Amst) 3: 997–1007.
|
| [29] | Tyson JJ, Csikasz-Nagy A, Novak B (2002) The dynamics of cell cycle regulation. Bioessays 24: 1095–1109.
|
| [30] | He E, Kapuy O, Oliveira RA, Uhlmann F, Tyson JJ, et al. (2011) System-level feedbacks make the anaphase switch irreversible. Proc Natl Acad Sci U S A 108: 10016–10021.
|
| [31] | Pomerening JR (2009) Positive-feedback loops in cell cycle progression. FEBS Lett 583: 3388–3396.
|
| [32] | Dematté L, Larcher R, Palmisano A, Priami C, Romanel A (2010) Programming Biology in BlenX. In: Choi S, editor. Systems Biology for Signaling Networks. Heidelberg: Springer. pp. 777–821.
|
| [33] | Novak B, Tyson JJ (1993) Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J Cell Sci 106(Pt 4): 1153–1168.
|
| [34] | Bartek J, Lukas J (2007) DNA damage checkpoints: from initiation to recovery or adaptation. Curr Opin Cell Biol 19: 238–245.
|
| [35] | Khodjakov A, Rieder CL (2009) The nature of cell-cycle checkpoints: facts and fallacies. J Biol 8: 88.
|
| [36] | Sia RA, Herald HA, Lew DJ (1996) Cdc28 tyrosine phosphorylation and the morphogenesis checkpoint in budding yeast. Mol Biol Cell 7: 1657–1666.
|
| [37] | Rupes I (2002) Checking cell size in yeast. Trends Genet 18: 479–485.
|
| [38] | Sveiczer A, Novak B, Mitchison JM (1996) The size control of fission yeast revisited. J Cell Sci 109(Pt 12): 2947–2957.
|
| [39] | Donzelli M, Draetta GF (2003) Regulating mammalian checkpoints through Cdc25 inactivation. EMBO Rep 4: 671–677.
|
| [40] | Shirayama M, Toth A, Galova M, Nasmyth K (1999) APCCdc20 promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5. Nature 402: 203–207.
|
| [41] | Sullivan M, Uhlmann F (2003) A non-proteolytic function of separase links the onset of anaphase to mitotic exit. Nat Cell Biol 5: 249–254.
|
| [42] | Amon A (1997) Regulation of B-type cyclin proteolysis by Cdc28–associated kinases in budding yeast. The EMBO Journal 16: 2693–2702.
|
| [43] | Visintin R, Craig K, Hwang ES, Prinz S, Tyers M, et al. (1998) The phosphatase Cdc14 triggers mitotic exit by reversal of Cdk-dependent phosphorylation. Molecular cell 2: 709–718.
|
| [44] | Azzam R, Chen SL, Shou W, Mah AS, Alexandru G, et al. (2004) Phosphorylation by Cyclin B-Cdk Underlies Release of Mitotic Exit Activator Cdc14 from the Nucleolus. Science 305: 516–519.
|
| [45] | Csikász-Nagy A, Kapuy O, Gy？rffy B, Tyson J, Novák B (2007) Modeling the septation initiation network (SIN) in fission yeast cells. Current Genetics 51: 245–255.
|
| [46] | Csikasz-Nagy A, Kapuy O, Toth A, Pal C, Jensen LJ, et al. (2009) Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol Syst Biol 5: 236.
|
| [47] | Csikasz-Nagy A, Cardelli L, Soyer OS (2011) Response dynamics of phosphorelays suggest their potential utility in cell signalling. J R Soc Interface 8: 480–488.
|
| [48] | Goldbeter A (1991) A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc Natl Acad Sci U S A 88: 9107–9111.
|
| [49] | Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, et al. (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321: 126–129.
|
| [50] | Nasmyth K (2001) A Prize for Proliferation. Cell 107: 689–701.
|
| [51] | Csikasz-Nagy A, Battogtokh D, Chen KC, Novak B, Tyson JJ (2006) Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J 90: 4361–4379.
|
| [52] | Sia RA, Bardes ES, Lew DJ (1998) Control of Swe1p degradation by the morphogenesis checkpoint. EMBO J 17: 6678–6688.
|
| [53] | Enders GH (2010) Gauchos and ochos: a Wee1-Cdk tango regulating mitotic entry. Cell Div 5: 12.
|
| [54] | Novak B, Kapuy O, Domingo-Sananes MR, Tyson JJ (2010) Regulated protein kinases and phosphatases in cell cycle decisions. Curr Opin Cell Biol 22: 1–8.
|
| [55] | Boutros R, Lobjois V, Ducommun B (2007) CDC25 phosphatases in cancer cells: key players? Good targets? Nat Rev Cancer 7: 495–507.
|
| [56] | Wurzenberger C, Gerlich DW (2011) Phosphatases: providing safe passage through mitotic exit. Nat Rev Mol Cell Biol 12: 469–482.
|
| [57] | Mochida S, Ikeo S, Gannon J, Hunt T (2009) Regulated activity of PP2A-B55[delta] is crucial for controlling entry into and exit from mitosis in Xenopus egg extracts. EMBO J 28: 2777–2785.
|
| [58] | Burgess A, Vigneron S, Brioudes E, Labbé JC, Lorca T, et al. (2010) Loss of human Greatwall results in G2 arrest and multiple mitotic defects due to deregulation of the cyclin B-Cdc2/PP2A balance. Proc Natl Acad Sci U S A 107: 12564–12569.
|
| [59] | Alon U (2007) Introduction to systems biology: design principles of biological circuits. Boca Raton, FL: Chapman and Hall/CRC Press.
|
| [60] | Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588–592.
|
| [61] | Savageau MA (1998) Demand theory of gene regulation. I. Quantitative development of the theory. Genetics 149: 1665–1676.
|
| [62] | Dissmeyer N, Weimer AK, Veylder LD, Novak B, Schnittger A (2010) The regulatory network of cell-cycle progression is fundamentally different in plants versus yeast or metazoans. Plant Signal Behav 5:
|
| [63] | Lew DJ, Kornbluth S (1996) Regulatory roles of cyclin dependent kinase phosphorylation in cell cycle control. Curr Opin Cell Biol 8: 795–804.
|
| [64] | Pal G, Paraz MT, Kellogg DR (2008) Regulation of Mih1/Cdc25 by protein phosphatase 2A and casein kinase 1. J Cell Biol 180: 931–945.
|
| [65] | Maniatis T, Goodbourn S, Fischer JA (1987) Regulation of inducible and tissue-specific gene expression. Science 236: 1237–1245.
|
| [66] | Dematte L, Priami C, Romanel A (2008) The Beta Workbench: a computational tool to study the dynamics of biological systems. Brief Bioinform 9: 437–449.
|
| [67] | Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340–2361.
|
| [68] | Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387: 913–917.
|
| [69] | Ciliberto A, Novak B, Tyson JJ (2003) Mathematical model of the morphogenesis checkpoint in budding yeast. J Cell Biol 163: 1243–1254.
|
