Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools.

[1]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[2]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[3]  B. Carter,et al.  Small-sized mutants of Saccharomyces cerevisiae. , 1980, Genetics.

[4]  M. Wigler,et al.  Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae. , 1987, Genes & development.

[5]  Michael Wigler,et al.  Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase , 1987, Cell.

[6]  L. Alberghina,et al.  Cell size modulation by CDC25 and RAS2 genes in Saccharomyces cerevisiae , 1989, Molecular and cellular biology.

[7]  M. Wigler,et al.  The NF1 locus encodes a protein functionally related to mammalian GAP and yeast IRA proteins , 1990, Cell.

[8]  A. Levitzki,et al.  Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras , 1992, Nature.

[9]  J. Thevelein.  Signal transduction in yeast , 1994, Yeast.

[10]  S. Haney,et al.  Cdc25p, the guanine nucleotide exchange factor for the Ras proteins of Saccharomyces cerevisiae, promotes exchange by stabilizing Ras in a nucleotide-free state. , 1994, The Journal of biological chemistry.

[11]  A. Wittinghofer,et al.  Kinetic analysis by fluorescence of the interaction between Ras and the catalytic domain of the guanine nucleotide exchange factor Cdc25Mm. , 1998, Biochemistry.

[12]  J. D. de Winde,et al.  Involvement of distinct G‐proteins, Gpa2 and Ras, in glucose‐ and intracellular acidification‐induced cAMP signalling in the yeast Saccharomyces cerevisiae , 1998, The EMBO journal.

[13]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[14]  J. D. de Winde,et al.  Novel sensing mechanisms and targets for the cAMP–protein kinase A pathway in the yeast Saccharomyces cerevisiae , 1999, Molecular microbiology.

[15]  P. Ma,et al.  The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling. , 1999, Molecular biology of the cell.

[16]  J. D. de Winde,et al.  Glucose‐induced cAMP signalling in yeast requires both a G‐protein coupled receptor system for extracellular glucose detection and a separable hexose kinase‐dependent sensing process , 2000, Molecular microbiology.

[17]  J. D. de Winde,et al.  Nutrient-induced signal transduction through the protein kinase A pathway and its role in the control of metabolism, stress resistance, and growth in yeast. , 2000, Enzyme and microbial technology.

[18]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[19]  E. Martegani,et al.  Role of guanine nucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae. , 2001, Biochimica et biophysica acta.

[20]  D. Gillespie.  Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .

[21]  Mike Tyers,et al.  Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast , 2002, Science.

[22]  Gheorghe Paun,et al.  Membrane Computing , 2002, Natural Computing Series.

[23]  P. Swain,et al.  Stochastic Gene Expression in a Single Cell , 2002, Science.

[24]  M. Reuss,et al.  Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae , 2003, Yeast.

[25]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[26]  Kevin Burrage,et al.  Stochastic approaches for modelling in vivo reactions , 2004, Comput. Biol. Chem..

[27]  K. Burrage,et al.  Binomial leap methods for simulating stochastic chemical kinetics. , 2004, The Journal of chemical physics.

[28]  Pawan Dhar,et al.  Modeling and simulation of biological systems with stochasticity , 2004, Silico Biol..

[29]  Enzo Martegani,et al.  Activation State of the Ras2 Protein and Glucose-induced Signaling in Saccharomyces cerevisiae* , 2004, Journal of Biological Chemistry.

[30]  Yang Cao,et al.  Sensitivity analysis of discrete stochastic systems. , 2005, Biophysical journal.

[31]  D. Vlachos,et al.  Binomial distribution based tau-leap accelerated stochastic simulation. , 2005, The Journal of chemical physics.

[32]  G. Santangelo,et al.  Glucose Signaling in Saccharomyces cerevisiae , 2006, Microbiology and Molecular Biology Reviews.

[33]  J. Derisi,et al.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.

[34]  Linda R Petzold,et al.  Efficient step size selection for the tau-leaping simulation method. , 2006, The Journal of chemical physics.

[35]  J. Hasty,et al.  Dynamics of single-cell gene expression , 2006, Molecular systems biology.

[36]  Giancarlo Mauri,et al.  Tau Leaping Stochastic Simulation Method in P Systems , 2006, Workshop on Membrane Computing.

[37]  Adam P. Arkin,et al.  Efficient stochastic sensitivity analysis of discrete event systems , 2007, J. Comput. Phys..