Simulating cellular dynamics through a coupled transcription, translation, metabolic model

[1]  J C Schaff,et al.  Physiological modeling with virtual cell framework. , 2000, Methods in enzymology.

[2]  Douglas B. Kell,et al.  MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems , 2001, Bioinform..

[3]  R. Larter,et al.  A theoretical basis for self-electrophoresis. , 1981, Journal of theoretical biology.

[4]  C. Martin,et al.  Positioning of the start site in the initiation of transcription by bacteriophage T7 RNA polymerase. , 1997, Journal of molecular biology.

[5]  Douglas B. Kell,et al.  Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation , 1998, Bioinform..

[6]  H. Sauro,et al.  Control by enzymes, coenzymes and conserved moieties , 1994 .

[7]  Joel R. Stiles,et al.  Monte Carlo simulation of neuro-transmitter release using MCell, a general simulator of cellular physiological processes , 1998 .

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

[9]  H. Lyman.  Mathematical biophysics: Physico-mathematical foundations of biology: N. Rashevsky. Third revised edition. Two vols. Dover, New York, 1960. Vol. I, xxvi + 488 pp. $2.50. Vol. II, xii + 462 pp. $2.50 , 1961 .

[10]  Leslie M Loew,et al.  Computational cell biology: spatiotemporal simulation of cellular events. , 2002, Annual review of biophysics and biomolecular structure.

[11]  M Hines,et al.  A program for simulation of nerve equations with branching geometries. , 1989, International journal of bio-medical computing.

[12]  H M Sauro,et al.  SCAMP: a general-purpose simulator and metabolic control analysis program , 1993, Comput. Appl. Biosci..

[13]  James C. Schaff,et al.  The Virtual Cell , 1998, Pacific Symposium on Biocomputing.

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

[15]  Masaru Tomita,et al.  The E-CELL project: towards integrative simulation of cellular processes , 2000, RECOMB '00.

[16]  L. Loew,et al.  The Virtual Cell: a software environment for computational cell biology. , 2001, Trends in biotechnology.

[17]  M. Tomita.  Whole-cell simulation: a grand challenge of the 21st century. , 2001, Trends in biotechnology.

[18]  Matthew A. Wilson,et al.  A Computer Simulation of Oscillatory Behavior in Primary Visual Cortex , 1991, Neural Computation.

[19]  Nicolas Le Novère,et al.  STOCHSIM: modelling of stochastic biomolecular processes , 2001, Bioinform..

[20]  James C. Schaff,et al.  Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell. , 2001, Chaos.

[21]  James M. Bower,et al.  Computational modeling of genetic and biochemical networks , 2001 .

[22]  Michael Marko,et al.  Topology of the Mitochondrial Inner Membrane: Dynamics and Bioenergetic Implications , 2001, IUBMB life.

[23]  B. Hess,et al.  SUBSTRATE CONTROL OF GLYCOLYTIC OSCILLATIONS , 1973 .

[24]  C. Zülicke.  Nonlinear Chemical Waves , 1994 .

[25]  R. Larter,et al.  A study of instability to electrical symmetry breaking in unicellular systems , 1982 .

[26]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[27]  Pedro Mendes,et al.  GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems , 1993, Comput. Appl. Biosci..

[28]  Peter J. Ortoleva,et al.  Geochemical Self-Organization , 1994 .

[29]  J. Reilly,et al.  Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping. , 2002, Journal of proteome research.

[30]  A. Harris.  Genes VI , 1997 .

[31]  P Mendes,et al.  Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. , 1997, Trends in biochemical sciences.

[32]  William H. Press,et al.  Numerical recipes in C , 2002 .

[33]  C. Cordeiro,et al.  In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. , 2001, European journal of biochemistry.

[34]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[35]  C. J. Morton-firth.  Stochastic simulation of cell signaling pathways , 1998 .

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

[37]  I. Prigogine,et al.  Symmetry Breaking Instabilities in Dissipative Systems. II , 1968 .

[38]  Lars Folke Olsen,et al.  Biochemical oscillations and cellular rhythms: The molecular bases of periodic and chaotic behaviour: Albert Goldbeter. Cambridge University Press, Cambridge, 1996. $99.95 (cloth), 605 + xxiv pp , 1997 .

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

[40]  R. J. Field,et al.  Oscillations and Traveling Waves in Chemical Systems , 1985 .

[41]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..