Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks
暂无分享,去创建一个
[1] G. Crabtree,et al. Cell signaling can direct either binary or graded transcriptional responses , 2001, The EMBO journal.
[2] W. Longabaugh,et al. Computational representation of developmental genetic regulatory networks. , 2005, Developmental biology.
[3] Steven J. Ruuth,et al. Implicit-explicit Runge-Kutta methods for time-dependent partial differential equations , 1997 .
[4] 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..
[5] Douglas B. Kell,et al. MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems , 2001, Bioinform..
[6] L. Hood,et al. A Genomic Regulatory Network for Development , 2002, Science.
[7] P. Guptasarma,et al. Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? , 1995, BioEssays : news and reviews in molecular, cellular and developmental biology.
[8] D. Gillespie. The chemical Langevin equation , 2000 .
[9] William H. Press,et al. Numerical recipes in C , 2002 .
[10] Hamid Bolouri,et al. A method for estimating stochastic noise in large genetic regulatory networks , 2005, Bioinform..
[11] Masaru Tomita,et al. A multi-algorithm, multi-timescale method for cell simulation , 2004, Bioinform..
[12] G. K. Ackers,et al. Quantitative model for gene regulation by lambda phage repressor. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[13] Nicolas Le Novère,et al. STOCHSIM: modelling of stochastic biomolecular processes , 2001, Bioinform..
[14] Hiroaki Kitano,et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .
[15] Upinder S. Bhalla,et al. Adaptive stochastic-deterministic chemical kinetic simulations , 2004, Bioinform..
[16] D. Gillespie. Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .
[17] D. Bray,et al. Predicting temporal fluctuations in an intracellular signalling pathway. , 1998, Journal of theoretical biology.
[18] Apirak Hoonlor,et al. Modeling biological systems using Dynetica-a simulator of dynamic networks , 2003, Bioinform..
[19] R. Rosner. Computer software , 1978, Nature.
[20] Aviv Regev,et al. Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra , 2000, Pacific Symposium on Biocomputing.
[21] J. Stoer,et al. Introduction to Numerical Analysis , 2002 .
[22] J. Dormand,et al. A family of embedded Runge-Kutta formulae , 1980 .
[23] Ertugrul M. Ozbudak,et al. Regulation of noise in the expression of a single gene , 2002, Nature Genetics.
[24] T. Kepler,et al. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.
[25] James M. Bower,et al. Computational modeling of genetic and biochemical networks , 2001 .
[26] Masaru Tomita,et al. E-CELL: software environment for whole-cell simulation , 1999, Bioinform..
[27] Mads Kærn,et al. Noise in eukaryotic gene expression , 2003, Nature.
[28] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[29] C. Rao,et al. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .
[30] P. Swain,et al. Stochastic Gene Expression in a Single Cell , 2002, Science.
[31] C. J.,et al. Predicting Temporal Fluctuations in an Intracellular Signalling Pathway , 1998 .
[32] Dennis Bray,et al. Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis , 2000, Nature Cell Biology.
[33] W. Bentley,et al. Green fluorescent protein in Saccharomyces cerevisiae: real-time studies of the GAL1 promoter. , 2000, Biotechnology and bioengineering.
[34] W. Bentley,et al. Stochastic kinetic analysis of the Escherichia coli stress circuit using σ32-targeted antisense , 2001 .
[35] Lingchong You,et al. Toward computational systems biology , 2007, Cell Biochemistry and Biophysics.
[36] James C. Schaff,et al. Numerical Approach to Fast Reactions in Reaction-Diffusion Systems , 2000 .
[37] Chris D Cox,et al. Analysis of noise in quorum sensing. , 2003, Omics : a journal of integrative biology.
[38] P de Atauri,et al. Evolution of 'design' principles in biochemical networks. , 2004, Systems biology.
[39] Igor Goryanin,et al. Mathematical simulation and analysis of cellular metabolism and regulation , 1999, Bioinform..
[40] George Marsaglia,et al. Toward a universal random number generator , 1987 .
[41] Michael A. Gibson,et al. Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .
[42] Jehoshua Bruck,et al. A probabilistic model of a prokaryotic gene and its regulation , 1999 .
[43] E. Davidson,et al. Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[44] Michael Hucka,et al. Introduction to the Systems Biology Workbench , 2003 .
[45] A. Kierzek,et al. Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. , 2004, Biophysical journal.
[46] A. Aderem,et al. Toll-like receptor-2 mediates mycobacteria-induced proinflammatory signaling in macrophages. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[47] H Matsuno,et al. Hybrid Petri net representation of gene regulatory network. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[48] A. Arkin,et al. Genetic "code": representations and dynamical models of genetic components and networks. , 2002, Annual review of genomics and human genetics.
[49] Guy L. Steele,et al. The Java Language Specification , 1996 .
[50] A. Arkin,et al. Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[51] Melvin K. Simmons,et al. Hybrid simulation of cellular behavior , 2004, Bioinform..
[52] Masao Nagasaki,et al. Genomic Object Net: I. A platform for modelling and simulating biopathways. , 2003, Applied bioinformatics.
[53] Hamid Bolouri,et al. Control of internal and external noise in genetic regulatory networks. , 2004, Journal of theoretical biology.
[54] L. Loew,et al. The Virtual Cell: a software environment for computational cell biology. , 2001, Trends in biotechnology.
[55] Corrado Priami,et al. Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..
[56] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[57] Alberto Policriti,et al. Model building and model checking for biochemical processes , 2007, Cell Biochemistry and Biophysics.
[58] Joel R. Stiles,et al. Monte Carlo simulation of neuro-transmitter release using MCell, a general simulator of cellular physiological processes , 1998 .
[59] D. Gillespie. A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .
[60] Jacky L. Snoep,et al. Web-based kinetic modelling using JWS Online , 2004, Bioinform..
[61] Christopher T. H. Baker,et al. Issues in the numerical solution of evolutionary delay differential equations , 1995, Adv. Comput. Math..
[62] Alessandro Giua,et al. Hybrid Petri Nets: a , 1996 .
[63] P J Goss,et al. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[64] Margaret Ann Shea,et al. Quantitative model for gene regulation by ? phage repressor , 1997 .
[65] Begnaud Francis Hildebrand,et al. Introduction to numerical analysis: 2nd edition , 1987 .
[66] Robert A. Bray,et al. Adult reserve stem cells and their potential for tissue engineering , 2007, Cell Biochemistry and Biophysics.
[67] Eric H Davidson,et al. New computational approaches for analysis of cis-regulatory networks. , 2002, Developmental biology.
[68] Linda R. Petzold,et al. Improved leap-size selection for accelerated stochastic simulation , 2003 .
[69] David McMillen,et al. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks , 2004, BMC Bioinformatics.
[70] Bruce E. Shapiro,et al. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations , 2003, Bioinform..
[71] A. Goldbeter,et al. Robustness of circadian rhythms with respect to molecular noise , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[72] D. A. Mcquarrie. Stochastic approach to chemical kinetics , 1967, Journal of Applied Probability.
[73] Hao Zhu,et al. Cellware-a multi-algorithmic software for computational systems biology , 2004, Bioinform..
[74] Patrick Lincoln,et al. BioSPICE: access to the most current computational tools for biologists. , 2003, Omics : a journal of integrative biology.
[75] J. Rawlings,et al. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics , 2002 .
[76] Michael Hucka,et al. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions , 2007, WWW 2007.
[77] A. Kierzek,et al. The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression* , 2001, The Journal of Biological Chemistry.
[78] Ralf Takors,et al. MMT - A Metabolic Modeling Tool for Metabolic Engineering , 2001, German Conference on Bioinformatics.
[79] M. V. Jambunathan. Some Properties of Beta and Gamma Distributions , 1954 .