References
- Weinberg RA. The biology of cancer 2006; London Garland Science
- Lorincz A, Carter BLA. Control of cell size at bud initiation in Saccharomyces cerevisiae. Journal of General Microbiology 1979; 113:287 - 295
- Sinclair DA, Mills K, Guarente L. Molecular mechanisms of yeast aging. Trends Biochem Sci 1998; 23:131 - 134
- Wäsch R, Cross FR. Apc-dependent proteolysis of the mitotic cyclin clb2 is essential for mitotic exit. Nature 2002; 418:556 - 562
- Cross FR. Two redundant oscillatory mechanisms in the yeast cell cycle. Dev Cell 2003; 4:741 - 752
- Lee TJ, Yao G, Bennett DC, Nevins JR, You L. Stochastic e2f activation and reconciliation of phenomenological cell cycle models. PLoS Biol 2010; 8
- Mendenhall MD, Hodge AE. Regulation of cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast saccharomyces cerevisiae. Microbiol Mol Biol Rev 1998; 62:1191 - 1243
- Zachariae W, Nasmyth K. Whose end is destruction: Cell division and the anaphase-promoting complex. Genes Dev 1999; 13:2039 - 2058
- Glotzer M, Murray AW, Kirschner MW. Cyclin is degraded by the ubiquitin pathway. Nature 1991; 349:132 - 138
- Bäumer M, Braus GH, Irniger S. Two different modes of cyclin clb2 proteolysis during mitosis in saccharomyces cerevisiae. FEBS Lett 2000; 468:142 - 148
- Schwab M, Lutum AS, Seufert W. Yeast hct1 is a regulator of clb2 cyclin proteolysis. Cell 1997; 90:683 - 693
- Visintin R, Prinz S, Amon A. Cdc20 and cdh1: A family of substrate-specific activators of apc-dependent proteolysis. Science 1997; 278:460 - 463
- Yeong FM, Lim HH, Padmashree CG, Surana U. Exit from mitosis in budding yeast: Biphasic inactivation of the cdc28-clb2 mitotic kinase and the role of cdc20. Mol Cell 2000; 5:501 - 511
- Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 2004; 15:3841 - 3862
- Gillespie D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 1976; 22:403 - 434
- Gillespie D. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977;
- Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM. Localization of ash1 mrna particles in living yeast. Mol Cell 1998; 2:437 - 445
- Cai L, Friedman N, Xie XS. Stochastic protein expression in individual cells at the single molecule level. Nature 2006; 440:358 - 362
- Ghaemmaghami S, Huh WK, Bower K, Howson R, Belle A, Dephoure N, et al. Global analysis of protein expression in yeast. Nature 2003; 425:737 - 741
- Gordon A, Colman-Lerner A, Chin T, Benjamin K, Yu R, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Meth 2007; 4:175 - 181
- Shav-Tal Y, Darzacq X, Shenoy S, Fusco D, Janicki S, Spector D, et al. Dynamics of single mmas in nuclei of living cells. Science 2004; 304:1797 - 1800
- Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Liron Y, et al. Variability and memory of protein levels in human cells. Nature 2006; 444:643 - 646
- Skotheim JM, Di Talia S, Siggia ED, Cross FR. Positive feedback of g1 cyclins ensures coherent cell cycle entry. Nature 2008; 454:291 - 296
- Xie XS, Choi PJ, Li GW, Lee NK, Lia G. Single-molecule approach to molecular biology in living bacterial cells. Ann Rev Biophys 2008; 37:417 - 444
- Zenklusen D, Larson DR, Singer RH. Single-rna counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 2008; 15:1263 - 1271
- Tyson CB, Lord PG, Wheals AE. Dependency of size of saccharomyces cerevisiae cells on growth rate. J Bacteriol 1979; 138:92 - 98
- Gardiner CW. Handbook of stochastic methods: For physics, chemistry and the natural sciences 2004; Third edition Berlin Springer-Verlag
- Goss PJE, Peccoud J. Quantitative modeling of stochastic systems in molecular biology using stochastic petri nets. Proceedings of the National Academy of Sciences of the United States of America 1998; 95:6750 - 6755
- Griffith M, Courtney T, Peccoud J, Sanders WH. Dynamic partitioning for hybrid simulation of the bistable hiv-1 transactivation network. Bioinformatics 2006; 22:2782 - 2789
- Kloeden PE, Platen E. Numerical solution of stochastic differential equations 1999; Berlin Springer-Verlag
- Lok L, Brent R. Automatic generation of cellular reaction networks with moleculizer 1.0. Nat Biotechnol 2005; 23:131 - 136
- Salis H, Sotiropoulos V, Kaznessis YN. Multiscale hy3s: Hybrid stochastic simulation for supercomputers. Bmc Bioinformatics 2006; 7:93
- Shimizu T, Bray D. Kitano H. Computational cell biology—the stochastic approach. Foundations of systems biology 2001; Cambrige, MA MIT Press 297
- Yang J, Monine MI, Faeder JR, Hlavacek WS. Kinetic monte carlo method for rule-based modeling of biochemical networks. Phys Rev E 2008; 78:31910
- Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells. Genetics 1998; 149:1633 - 1648
- Elowitz MB, Levine A, Siggia ED, Swain P. Stochastic gene expression in a single cell. Science 2002; 297:1183 - 1186
- Lo K, Denney WS, Diamond SL. Stochastic modeling of blood coagulation initiation. Pathophysiol Haemo T 2005; 34:80 - 90
- Cao Y, Gillespie D, Petzold L. The slow-scale stochastic simulation algorithm. J Chem Phys 2005;
- Cao Y, Gillespie D, Petzold L. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems. J Comput Phys 2005;
- Haseltine E, Rawlings J. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 2002;
- Rao C, Arkin A. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the gillespie algorithm. J Chem Phys 2003;
- Sabouri-Ghomi M, Ciliberto A, Kar S, Novak B, Tyson JJ. Antagonism and bistability in protein interaction networks. J Theor Biol 2008; 250:209 - 218
- Kar S, Baumann W, Paul M, Tyson J. Exploring the roles of noise in the eukaryotic cell cycle. Proc Natl Acad Sci USA 2009;
- Tyson JJ, Novak B. Regulation of the eukaryotic cell cycle: Molecular antagonism, hysteresis and irreversible transitions. J Theor Biol 2001; 210:249 - 263
- Mura I, Csikasz-Nagy A. Stochastic petri net extension of a yeast cell cycle model. J Theor Biol 2008; 254:850 - 860
- Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M. Systematic identification of pathways that couple cell growth and division in yeast. Science 2002; 297:395 - 400
- Barik D, Baumann WT, Paul MR, Novak B, Tyson JJ. A model of yeast cell cycle regulation based on multisite phosphorylation. Mol Sys Biol 2010;
- Kapuy O, Barik D, Sananes MRD, Tyson JJ, Novák B. Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol 2009; 100:47 - 56
- Raser J, O'Shea EK. Control of stochasticity in eukaryotic gene expression. Science 2004; 304:1811 - 1814
- Volfson D, Marciniak J, Blake W, Ostroff N, Tsimring L, Hasty J. Origins of extrinsic variability in eukaryotic gene expression. Nature 2006; 439:861 - 864
- Pedraza JM, Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 2008; 319:339 - 343
- Wang P. Bridging the gap between deterministic and stochastic modeling with automatic scaling and conversion 2008; Blacksburg, VA Virginia Polytechnic Institute and State University MS Thesis Computer Science
- Collett D. Modelling survival data in medical research 2003; London Chapman and Hall/CRC
- Cross FR, Archambault V, Miller M, Klovstad M. Testing a mathematical model of the yeast cell cycle. Mol Biol Cell 2002; 13:52 - 70