Modelling cellular behaviour

Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.

[1]  V. Georgiev Virology , 1955, Nature.

[2]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

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

[4]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[5]  F. Studier Relationships among different strains of T7 and among T7-related bacteriophages. , 1979, Virology.

[6]  H. Berg,et al.  Impulse responses in bacterial chemotaxis , 1982, Cell.

[7]  H. Weintraub,et al.  Expression of a single transfected cDNA converts fibroblasts to myoblasts , 1987, Cell.

[8]  K. Donner,et al.  Low retinal noise in animals with low body temperature allows high visual sensitivity , 1988, Nature.

[9]  L. Hartwell,et al.  The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. , 1988, Science.

[10]  P. O’Farrell,et al.  The roles of Drosophila cyclins A and B in mitotic control , 1990, Cell.

[11]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[12]  M. Record,et al.  Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. , 1991, Journal of molecular biology.

[13]  J. Tyson Modeling the cell division cycle: cdc2 and cyclin interactions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. Zimmerman,et al.  Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. , 1991, Journal of molecular biology.

[15]  G. Sussman,et al.  Chaotic Evolution of the Solar System , 1992, Science.

[16]  AC Tose Cell , 1993, Cell.

[17]  S. Hekimi,et al.  Mutations in the clk-1 gene of Caenorhabditis elegans affect developmental and behavioral timing. , 1995, Genetics.

[18]  P. Callaerts,et al.  Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. , 1995, Science.

[19]  B. Cairns,et al.  Signaling in the yeast pheromone response pathway: specific and high-affinity interaction of the mitogen-activated protein (MAP) kinases Kss1 and Fus3 with the upstream MAP kinase kinase Ste7 , 1996, Molecular and cellular biology.

[20]  G. Hutcheson,et al.  Technology and Economics in the Semiconductor Industry , 1996 .

[21]  D. Endy,et al.  Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7. , 1997, Biotechnology and bioengineering.

[22]  A. Arkin,et al.  Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Jeffrey C. Hall,et al.  CYCLE Is a Second bHLH-PAS Clock Protein Essential for Circadian Rhythmicity and Transcription of Drosophila period and timeless , 1998, Cell.

[24]  A. Goldbeter,et al.  A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM Proteins , 1998, Journal of biological rhythms.

[25]  D. Bray,et al.  Predicting temporal fluctuations in an intracellular signalling pathway. , 1998, Journal of theoretical biology.

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

[27]  P. D. de Boer,et al.  MinDE-Dependent Pole-to-Pole Oscillation of Division Inhibitor MinC in Escherichia coli , 1999, Journal of bacteriology.

[28]  M. Elowitz,et al.  Protein Mobility in the Cytoplasm ofEscherichia coli , 1999, Journal of bacteriology.

[29]  J. Lutkenhaus,et al.  Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE , 1999, Molecular microbiology.

[30]  Drew Endy,et al.  Toward Antiviral Strategies That Resist Viral Escape , 2000, Antimicrobial Agents and Chemotherapy.

[31]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[32]  Ralph S. Baric,et al.  Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model , 2000, Journal of Virology.

[33]  S. Leibler,et al.  Biological rhythms: Circadian clocks limited by noise , 2000, Nature.

[34]  D. Gillespie The chemical Langevin equation , 2000 .

[35]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[36]  D. Endy,et al.  Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[38]  R. Branicky,et al.  clk-1, mitochondria, and physiological rates. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[39]  Frances H. Arnold,et al.  Molecular breeding of carotenoid biosynthetic pathways , 2000, Nature Biotechnology.

[40]  W. Stemmer,et al.  Molecular breeding of viruses , 2000, Nature Genetics.