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Volumn 5, Issue 3, 2009, Pages

GrowMatch: An automated method for reconciling in silico/in vivo growth predictions

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; GENES; METABOLISM; REPAIR;

EID: 63549108441     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000308     Document Type: Article
Times cited : (177)

References (49)
  • 1
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4: R54.
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 3
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14: 1298-1309.
    • (2004) Genome Res , vol.14 , pp. 1298-1309
    • Duarte, N.C.1    Herrgard, M.J.2    Palsson, B.O.3
  • 4
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3    Thiele, I.4    Mo, M.L.5
  • 5
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A 97: 5528-5533.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 6
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 7
    • 33751567092 scopus 로고    scopus 로고
    • Experimental and computational assessment of conditionally essential genes in Escherichia coli
    • Joyce AR, Reed JL, White A, Edwards R, Osterman A, et al. (2006) Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 188: 8259-8271.
    • (2006) J Bacteriol , vol.188 , pp. 8259-8271
    • Joyce, A.R.1    Reed, J.L.2    White, A.3    Edwards, R.4    Osterman, A.5
  • 8
    • 0842309871 scopus 로고    scopus 로고
    • Genomewide RNAi analysis of growth and viability in Drosophila cells
    • Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, et al. (2004) Genomewide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832-835.
    • (2004) Science , vol.303 , pp. 832-835
    • Boutros, M.1    Kiger, A.A.2    Armknecht, S.3    Kerr, K.4    Hild, M.5
  • 9
    • 0141504252 scopus 로고    scopus 로고
    • Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
    • Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185: 5673-5684.
    • (2003) J Bacteriol , vol.185 , pp. 5673-5684
    • Gerdes, S.Y.1    Scholle, M.D.2    Campbell, J.W.3    Balazsi, G.4    Ravasz, E.5
  • 10
    • 0037173615 scopus 로고    scopus 로고
    • Functional profiling of the Saccharomyces cerevisiae genome
    • Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
    • (2002) Nature , vol.418 , pp. 387-391
    • Giaever, G.1    Chu, A.M.2    Ni, L.3    Connelly, C.4    Riles, L.5
  • 13
    • 0035128859 scopus 로고    scopus 로고
    • Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi
    • Maeda I, Kohara Y, Yamamoto M, Sugimoto A (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol 11: 171-176.
    • (2001) Curr Biol , vol.11 , pp. 171-176
    • Maeda, I.1    Kohara, Y.2    Yamamoto, M.3    Sugimoto, A.4
  • 14
    • 0035940515 scopus 로고    scopus 로고
    • Comprehensive identification of conditionally essential genes in mycobacteria
    • Sassetti CM, Boyd DH, Rubin EJ (2001) Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci U S A 98: 12712-12717.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 12712-12717
    • Sassetti, C.M.1    Boyd, D.H.2    Rubin, E.J.3
  • 15
    • 27244451533 scopus 로고    scopus 로고
    • Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis
    • Song JH, Ko KS, Lee JY, Baek JY, Oh WS, et al. (2005) Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. Mol Cells 19: 365-374.
    • (2005) Mol Cells , vol.19 , pp. 365-374
    • Song, J.H.1    Ko, K.S.2    Lee, J.Y.3    Baek, J.Y.4    Oh, W.S.5
  • 16
    • 0037100683 scopus 로고    scopus 로고
    • Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae
    • Thanassi JA, Hartman-Neumann SL, Dougherty TJ, Dougherty BA, Pucci MJ (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30: 3152-3162.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3152-3162
    • Thanassi, J.A.1    Hartman-Neumann, S.L.2    Dougherty, T.J.3    Dougherty, B.A.4    Pucci, M.J.5
  • 17
    • 31544450286 scopus 로고    scopus 로고
    • Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
    • Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
  • 18
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19: 125-130.
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 19
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 20
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, 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.
    • (2007) Mol Syst Biol , vol.3 , pp. 121
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3    Krummenacker, M.4    Joyce, A.R.5
  • 23
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Satish Kumar V, Dasika MS, Maranas CD (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8: 212.
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 24
    • 33745035630 scopus 로고    scopus 로고
    • Predicting genes for orphan metabolic activities using phylogenetic profiles
    • Chen L, Vitkup D (2006) Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol 7: R17.
    • (2006) Genome Biol , vol.7
    • Chen, L.1    Vitkup, D.2
  • 25
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green ML, Karp PD (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5: 76.
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 27
    • 24744467372 scopus 로고    scopus 로고
    • Filling gaps in a metabolic network using expression information
    • Kharchenko P, Vitkup D, Church GM (2004) Filling gaps in a metabolic network using expression information. Bioinformatics 20: i178-i185.
    • (2004) Bioinformatics , vol.20
    • Kharchenko, P.1    Vitkup, D.2    Church, G.M.3
  • 28
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: A comparative genomics approach
    • Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238-251.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 29
    • 1242274402 scopus 로고    scopus 로고
    • Flux coupling analysis of genome-scale metabolic network reconstructions
    • Burgard AP, Nikolaev EV, Schilling CH, Maranas CD (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 14: 301-312.
    • (2004) Genome Res , vol.14 , pp. 301-312
    • Burgard, A.P.1    Nikolaev, E.V.2    Schilling, C.H.3    Maranas, C.D.4
  • 30
    • 38549117301 scopus 로고    scopus 로고
    • The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    • Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 36: D623-D631.
    • (2008) Nucleic Acids Res , vol.36
    • Caspi, R.1    Foerster, H.2    Fulcher, C.A.3    Kaipa, P.4    Krummenacker, M.5
  • 32
    • 33745020639 scopus 로고    scopus 로고
    • A metabolic network in the evolutionary context: Multiscale structure and modularity
    • Spirin V, Gelfand MS, Mironov AA, Mirny LA (2006) A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A 103: 8774-8779.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 8774-8779
    • Spirin, V.1    Gelfand, M.S.2    Mironov, A.A.3    Mirny, L.A.4
  • 34
    • 21144443562 scopus 로고    scopus 로고
    • Homocysteine toxicity in Escherichia coli is caused by a perturbation of branched-chain amino acid biosynthesis
    • Tuite NL, Fraser KR, O'Byrne CP (2005) Homocysteine toxicity in Escherichia coli is caused by a perturbation of branched-chain amino acid biosynthesis. J Bacteriol 187: 4362-4371.
    • (2005) J Bacteriol , vol.187 , pp. 4362-4371
    • Tuite, N.L.1    Fraser, K.R.2    O'Byrne, C.P.3
  • 35
    • 39749124901 scopus 로고    scopus 로고
    • Three factors underlying incorrect in silico predictions of essential metabolic genes
    • Becker SA, Palsson BO (2008) Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol 2: 14.
    • (2008) BMC Syst Biol , vol.2 , pp. 14
    • Becker, S.A.1    Palsson, B.O.2
  • 37
    • 0037881782 scopus 로고    scopus 로고
    • Metabolic reconstruction using shortest paths
    • Arita M (2000) Metabolic reconstruction using shortest paths. Simul Pract Theory 8: 109-125.
    • (2000) Simul Pract Theory , vol.8 , pp. 109-125
    • Arita, M.1
  • 39
    • 33751149652 scopus 로고    scopus 로고
    • Computer-assisted planning of organic syntheses: The second generation of programs
    • Ihlenfeldt WD, Gasteiger J (1996) Computer-assisted planning of organic syntheses: the second generation of programs. Angew Chem Int Ed Engl 34: 2613-2633.
    • (1996) Angew Chem Int Ed Engl , vol.34 , pp. 2613-2633
    • Ihlenfeldt, W.D.1    Gasteiger, J.2
  • 40
    • 0033423672 scopus 로고    scopus 로고
    • META 4. Prediction of the metabolism of polycyclic aromatic hydrocarbons
    • Klopman G, Tu M, Fan BT (1999) META 4. Prediction of the metabolism of polycyclic aromatic hydrocarbons. Theor Chem Acc 102: 33-38.
    • (1999) Theor Chem Acc , vol.102 , pp. 33-38
    • Klopman, G.1    Tu, M.2    Fan, B.T.3
  • 41
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A 99: 15112-15117.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 42
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A 102: 7695-7700.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 49
    • 55449113709 scopus 로고    scopus 로고
    • Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes
    • doi:10.1371/journal.pcbi.0010027
    • Ren Q, Paulsen IT (2005) Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol 1: e27. doi:10.1371/journal.pcbi.0010027.
    • (2005) PLoS Comput Biol , vol.1
    • Ren, Q.1    Paulsen, I.T.2


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