Integrating high-throughput and computational data elucidates bacterial networks (original) (raw)
References
Ideker, T., Galitski, T. & Hood, L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet.2, 343–372 (2001) ArticleCAS Google Scholar
Palsson, B. O. The challenges of in silico biology. Nature Biotechnol.18, 1147–1150 (2000) ArticleCAS Google Scholar
Reed, J. L., Vo, T. D., Schilling, C. H. & Palsson, B. O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol.4, R54.1–R54.12 (2003) Article Google Scholar
Bochner, B. R. New technologies to assess genotype–phenotype relationships. Nature Rev. Genet.4, 309–314 (2003) ArticleCAS Google Scholar
Glasner, J. D. et al. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res.31, 147–151 (2003) ArticleCAS Google Scholar
Forster, J., Famili, I., Palsson, B. O. & Nielsen, J. Large-scale evaluation of in silico gene knockouts in Saccharomyces cerevisiae. Omics7, 193–202 (2003) Article Google Scholar
Edwards, J. S. & Palsson, B. O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA97, 5528–5533 (2000) ArticleADSCAS Google Scholar
Covert, M. W. & Palsson, B. O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem.277, 28058–28064 (2002) ArticleCAS Google Scholar
Herrgard, M. J., Covert, M. W. & Palsson, B. O. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res.13, 2423–2434 (2003) ArticleCAS Google Scholar
Salmon, K. et al. Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J. Biol. Chem.278, 29837–29855 (2003) ArticleCAS Google Scholar
Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science292, 929–934 (2001) ArticleADSCAS Google Scholar
Compan, I. & Touati, D. Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcA. Mol. Microbiol.11, 955–964 (1994) ArticleCAS Google Scholar
Cotter, P. A., Melville, S. B., Albrecht, J. A. & Gunsalus, R. P. Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol. Microbiol.25, 605–615 (1997) ArticleCAS Google Scholar
Griffin, T. J. et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics1, 323–333 (2002) ArticleCAS Google Scholar
Reed, J. L. & Palsson, B. O. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol.185, 2692–2699 (2003) ArticleCAS Google Scholar
Edwards, J. S., Ibarra, R. U. & Palsson, B. O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnol.19, 125–130 (2001) ArticleCAS Google Scholar
Price, N. D., Papin, J. A., Schilling, C. H. & Palsson, B. O. Genome-scale microbial in silico models: the constraints-based approach. Trends. Biotechnol.21, 162–169 (2003) ArticleCAS Google Scholar
Segre, D., Vitkup, D. & Church, G. M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl Acad. Sci. USA99, 15112–15117 (2002) ArticleADSCAS Google Scholar
Burgard, A. P. & Maranas, C. D. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng.74, 364–375 (2001) ArticleCAS Google Scholar
Burgard, A. P., Vaidyaraman, S. & Maranas, C. D. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog.17, 791–797 (2001) ArticleCAS Google Scholar
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. The large-scale organization of metabolic networks. Nature407, 651–654 (2000) ArticleADSCAS Google Scholar
Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet.31, 64–68 (2002) ArticleCAS Google Scholar
Gutierrez-Rios, R. M. et al. Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res.13, 2435–2443 (2003) ArticleCAS Google Scholar
Bar-Joseph, Z. et al. Computational discovery of gene modules and regulatory networks. Nature Biotechnol.21, 1337–1342 (2003) ArticleCAS Google Scholar
Covert, M. W., Schilling, C. H. & Palsson, B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol.213, 73–88 (2001) ArticleCAS Google Scholar
Blattner, F. R. et al. The complete genome sequence of Escherichia coli K-12. Science277, 1453–1474 (1997) ArticleCAS Google Scholar
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA97, 6640–6645 (2000) ArticleADSCAS Google Scholar
Li, C. & Wong, W. H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA98, 31–36 (2001) ArticleADSCAS Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B57, 289–300 (1995) MathSciNetMATH Google Scholar