Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems

PLoS Computational Biology - Tập 2 Số 8 - Trang e101
Erwin P. Gianchandani1, Jason A. Papin2, Nathan D. Price3, Andrew R. Joyce4, Bernhard Ø. Palsson3
1Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
2Dept of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
3Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
4Bioinformatics Program, University of California, San Diego, La Jolla, California, United States of America.

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2004, RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12., Nucleic Acids Res, 32, D303, 10.1093/nar/gkh140

2000, Using Bayesian networks to analyze expression data., J Comput Biol, 7, 601, 10.1089/106652700750050961

2003, Random Boolean network models and the yeast transcriptional network., Proc Natl Acad Sci U S A, 100, 14796, 10.1073/pnas.2036429100

2002, Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks., Bioinformatics, 18, 261, 10.1093/bioinformatics/18.2.261

2001, Regulation of gene expression in flux balance models of metabolism., J Theor Biol, 213, 73, 10.1006/jtbi.2001.2405

1973, Boolean formalization of genetic control circuits., J Theor Biol, 42, 563, 10.1016/0022-5193(73)90247-6

1997, Stochastic mechanisms in gene expression., Proc Natl Acad Sci U S A, 94, 814, 10.1073/pnas.94.3.814

2002, Modeling and simulation of genetic regulatory systems: A literature review., J Comput Biol, 9, 67, 10.1089/10665270252833208

2004, Integrating high-throughput and computational data elucidates bacterial networks., Nature, 429, 92, 10.1038/nature02456

2004, Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction., Proc Natl Acad Sci U S A, 101, 5934, 10.1073/pnas.0306752101

2002, Transcriptional regulatory networks in Saccharomyces cerevisiae., Science, 298, 799, 10.1126/science.1075090

2002, A genomic regulatory network for development., Science, 295, 1669, 10.1126/science.1069883

2001, Integrated genomic and proteomic analyses of a systematically perturbed metabolic network., Science, 292, 929, 10.1126/science.292.5518.929

ChvatalV 1983 Linear programming New York W. H. Freeman 478 p.

2006, Towards multidimensional genome annotation., Nat Rev Genet, 7, 130, 10.1038/nrg1769

2004, Genome-scale models of microbial cells: Evaluating the consequences of constraints., Nat Rev Microbiol, 2, 886, 10.1038/nrmicro1023

2004, Biochemistry. Completing the view of transcriptional regulation., Science, 305, 350, 10.1126/science.1101270

PalssonB 2006 Systems biology: Properties of reconstructed networks New York Cambridge University Press 322 p.

2004, Comparison of network-based pathway analysis methods., Trends Biotechnol, 22, 400, 10.1016/j.tibtech.2004.06.010

2004, Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space., J Theor Biol, 228, 437, 10.1016/j.jtbi.2004.02.006

2004, Global organization of metabolic fluxes in the bacterium Escherichia coli., Nature, 427, 839, 10.1038/nature02289

2004, Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast., Nature, 429, 661, 10.1038/nature02636

2003, Metabolic pathways in the post-genome era., Trends Biochem Sci, 28, 250, 10.1016/S0968-0004(03)00064-1

2002, Metabolic network structure determines key aspects of functionality and regulation., Nature, 420, 190, 10.1038/nature01166

2000, Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective., J Theor Biol, 203, 229, 10.1006/jtbi.2000.1073

2002, Extreme pathway analysis of human red blood cell metabolism., Biophys J, 83, 808, 10.1016/S0006-3495(02)75210-7

2004, The JAK-STAT signaling network in the human B cell: An extreme signaling pathway analysis., Biophys J, 87, 37, 10.1529/biophysj.103.029884

2002, Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis., Genome Res, 12, 760, 10.1101/gr.218002

LayDC 2003 Linear algebra and its applications Boston Addison Wesley 492 p.

2005, k-Cone analysis: Determining all candidate values for kinetic parameters on a network scale., Biophys J, 88, 1616, 10.1529/biophysj.104.050385

2004, Uniform sampling of steady state flux spaces: Means to design experiments and to interpret enzymopathies., Biophys J, 87, 2172, 10.1529/biophysj.104.043000

2005, Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet., J Biol Chem, 280, 11683, 10.1074/jbc.M409072200

2002, Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth., Nature, 420, 186, 10.1038/nature01149

2004, Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes., Nat Genet, 36, 1056, 10.1038/ng1432

2002, Extreme pathway lengths and reaction participation in genome-scale metabolic networks., Genome Res, 12, 1889, 10.1101/gr.327702

2002, Energy balance for analysis of complex metabolic networks., Biophys J, 83, 79, 10.1016/S0006-3495(02)75150-3

2005, Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli., Proc Natl Acad Sci U S A, 102, 7841, 10.1073/pnas.0500365102

2002, Network motifs in the transcriptional regulation network of Escherichia coli., Nat Genet, 31, 64, 10.1038/ng881