Arita M (2003) In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res 13(11):2455–66
PubMed
CrossRef
CAS
Google Scholar
Arita M (2004) The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 101(6):1543–7
PubMed
CrossRef
CAS
Google Scholar
Bailey JE (1991) Toward a science of metabolic engineering. Science 252(5013):1668–75
PubMed
CrossRef
CAS
Google Scholar
Bowers PM, Pellegrini M, Thompson MJ et al. (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 5(5):R35
PubMed
CrossRef
Google Scholar
Burden S, Lin YX, Zhang R (2005) Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences. Bioinformatics 21(5):601–7
PubMed
CrossRef
CAS
Google Scholar
Cases I, de Lorenzo V, Ouzounis CA (2003) Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 11(6):248–53
PubMed
CrossRef
CAS
Google Scholar
Caspi R, Foerster H, Fulcher CA et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 36(Database issue):D623–31
PubMed
CrossRef
CAS
Google Scholar
Chassagnole C, Letisse F, Diano A et al. (2002) Carbon flux analysis in a pantothenate overproducing Corynebacterium glutamicum strain. Mol Biol Rep 29(1–2):129–34
PubMed
CrossRef
CAS
Google Scholar
Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97(10):5528–33
PubMed
CrossRef
CAS
Google Scholar
Enault F, Suhre K, Poirot O et al. (2003) Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. Nucleic Acids Res 31(13): 3720–2
PubMed
CrossRef
CAS
Google Scholar
Feist AM, Henry CS, Reed JL et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121
PubMed
CrossRef
Google Scholar
Frazier ME, Johnson GM, Thomassen DG et al. (2003) Realizing the potential of the genome revolution: the genomes to life program. Science 300(5617):290–3
PubMed
CrossRef
CAS
Google Scholar
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M et al. (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36(Database issue):D120–4
PubMed
CrossRef
CAS
Google Scholar
Gordon L, Chervonenkis AY, Gammerman AJ et al. (2003) Sequence alignment kernel for recognition of promoter regions. Bioinformatics 19(15):1964–71
PubMed
CrossRef
CAS
Google Scholar
Jardine O, Gough J, Chothia C et al. (2002) Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Res 12(6):916–29
PubMed
CrossRef
CAS
Google Scholar
Karp PD (1997) Use of metabolic databases to guide target selection for anti-microbial drug design. Blackwell Science Ltd., Oxford, UK
Google Scholar
Karp PD (2003) The Pathway Tools software and its role in anti-microbial drug discovery. Marcel Dekker, Inc., New York
Google Scholar
Karp PD, Keseler IM, Shearer A et al. (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35(22):7577–90
PubMed
CrossRef
CAS
Google Scholar
Karp PD, Krummenacker M, Paley S et al. (1999) Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol 17(7):275–81
PubMed
CrossRef
CAS
Google Scholar
Karp PD, Ouzounis CA, Moore-Kochlacs C et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33(19):6083–9
PubMed
CrossRef
CAS
Google Scholar
Lithwick G, Margalit H (2005) Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res 33(3):1051–7
PubMed
CrossRef
CAS
Google Scholar
Ma HW, Kumar B, Ditges U et al. (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res 32(22):6643–9
PubMed
CrossRef
CAS
Google Scholar
Marcotte EM, Pellegrini M, Thompson MJ et al. (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402(6757):83–6
PubMed
CrossRef
CAS
Google Scholar
Pellegrini M, Marcotte EM, Thompson MJ et al. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96(8): 4285–8
PubMed
CrossRef
CAS
Google Scholar
Peregrin-Alvarez JM, Tsoka S, Ouzounis CA (2003) The phylogenetic extent of metabolic enzymes and pathways. Genome Res 13(3):422–7
PubMed
CrossRef
CAS
Google Scholar
Price MN, Huang KH, Alm EJ et al. (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33(3):880–92
PubMed
CrossRef
CAS
Google Scholar
Ravasz E, Somera AL, Mongru DA et al. (2002) Hierarchical organization of modularity in metabolic networks. Science 297(5586):1551–5
PubMed
CrossRef
CAS
Google Scholar
Reed JL, Palsson BO (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol 185(9):2692–9
PubMed
CrossRef
CAS
Google Scholar
Reed JL, Palsson BO (2004) Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res 14(9):1797–805
PubMed
CrossRef
CAS
Google Scholar
Reed JL, Vo TD, Schilling CH et al. (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4(9):R54
PubMed
CrossRef
Google Scholar
Rison SC, Thornton JM (2002) Pathway evolution, structurally speaking. Curr Opin Struct Biol 12(3):374–82
PubMed
CrossRef
CAS
Google Scholar
Romero PR, Karp PD (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics 20(5):709–17
PubMed
CrossRef
CAS
Google Scholar
Salgado H, Gama-Castro S, Martinez-Antonio A et al. (2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 32(Database issue):D303–6
PubMed
CrossRef
CAS
Google Scholar
Shen-Orr SS, Milo R, Mangan S et al. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31(1):64–8
PubMed
CrossRef
CAS
Google Scholar
Simeonidis E, Rison SC, Thornton JM et al. (2003) Analysis of metabolic networks using a pathway distance metric through linear programming. Metab Eng 5(3):211–9
PubMed
CrossRef
CAS
Google Scholar
Steinhauser D, Junker BH, Luedemann A et al. (2004) Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics 20(12):1928–39
PubMed
CrossRef
CAS
Google Scholar
Stephanopoulos G, Vallino JJ (1991) Network rigidity and metabolic engineering in metabolite overproduction. Science 252(5013):1675–81
PubMed
CrossRef
CAS
Google Scholar
Studholme DJ, Bentley SD, Kormanec J (2004) Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor. BMC Microbiol 4(14):14
PubMed
CrossRef
Google Scholar
Teichmann SA, Rison SC, Thornton JM et al. (2001a) The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 311(4):693–708
PubMed
CrossRef
CAS
Google Scholar
Teichmann SA, Rison SC, Thornton JM et al. (2001b) Small-molecule metabolism: an enzyme mosaic. Trends Biotechnol 19(12):482–6
PubMed
CrossRef
CAS
Google Scholar
Thanassi JA, Hartman-Neumann SL, Dougherty TJ et al. (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30(14):3152–62
PubMed
CrossRef
CAS
Google Scholar
Tomita M, Hashimoto K, Takahashi K et al. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1):72–84
PubMed
CrossRef
CAS
Google Scholar
Tsoka S, Ouzounis CA (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet 26(2):141–2
PubMed
CrossRef
CAS
Google Scholar
Tsoka S, Ouzounis CA (2001) Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Res 11(9):1503–10
PubMed
CrossRef
CAS
Google Scholar
Tweeddale H, Notley-McRobb L, Ferenci T (1999) Assessing the effect of reactive oxygen species on Escherichia coli using a metabolome approach. Redox Rep 4(5):237–41
PubMed
CrossRef
CAS
Google Scholar
Van Dien SJ, Strovas T, Lidstrom ME (2003) Quantification of central metabolic fluxes in the facultative methylotroph Methylobacterium extorquens AM1 using 13C-label tracing and mass spectrometry. Biotechnol Bioeng 84(1):45–55
PubMed
CrossRef
Google Scholar
von Mering C, Zdobnov EM, Tsoka S et al. (2003) Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA 100(26):15428–33
CrossRef
Google Scholar
Weber J, Hoffmann F, Rinas U (2002) Metabolic adaptation of Escherichia coli during temperature-induced recombinant protein production: 2. Redirection of metabolic fluxes. Biotechnol Bioeng 80(3):320–30
CrossRef
CAS
Google Scholar