메뉴 건너뛰기




Volumn 33, Issue 6, 2017, Pages 893-900

Improving flux predictions by integrating data from multiple strains

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; ESCHERICHIA COLI; GENE INACTIVATION; GENETICS; METABOLISM; PROCEDURES; SOFTWARE; SYSTEMS BIOLOGY;

EID: 85018313020     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw706     Document Type: Article
Times cited : (6)

References (28)
  • 1
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker, S.A. and Palsson, B.O. (2008) Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol., 4, e1000082.
    • (2008) PLoS Comput. Biol. , vol.4 , pp. e1000082
    • Becker, S.A.1    Palsson, B.O.2
  • 2
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • Blazier, A.S. and Papin J.A. (2012) Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol., 3, 299.
    • (2012) Front. Physiol. , vol.3 , pp. 299
    • Blazier, A.S.1    Papin, J.A.2
  • 3
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and mycobacterium tuberculosis
    • Chandrasekaran, S. and Price, N.D. (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A., 107, 17845-17850.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 4
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang, R.L. et al. (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput. Biol., 6, e1000938.
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000938
    • Chang, R.L.1
  • 5
    • 70049110173 scopus 로고    scopus 로고
    • Interpreting expression data with metabolic flux models: Predicting mycobacterium tuberculosis mycolic acid production
    • Colijn, C. et al. (2009) Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol., 5, e1000489.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000489
    • Colijn, C.1
  • 6
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards J.S. et al. (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
  • 7
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • Fong, S.S. and Palsson, B. (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet., 36, 1056-1058.
    • (2004) Nat. Genet. , vol.36 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.2
  • 8
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra, R.U. et al. (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
  • 9
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E
    • Ishii, N. et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 316, 593-597.
    • (2007) Coli to Perturbations. Science , vol.316 , pp. 593-597
    • Ishii, N.1
  • 10
    • 79951536020 scopus 로고    scopus 로고
    • Functional integration of a metabolic network model and expression data without arbitrary thresholding
    • Jensen, P.A. and Papin, J.A. (2011) Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics, 27, 541-547.
    • (2011) Bioinformatics , vol.27 , pp. 541-547
    • Jensen, P.A.1    Papin, J.A.2
  • 11
    • 78751556862 scopus 로고    scopus 로고
    • Integrative genome-scale metabolic analysis of vibrio vulnificus for drug targeting and discovery
    • Kim, H.U. et al. (2011) Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol. Syst. Biol., 7, 460.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 460
    • Kim, H.U.1
  • 12
    • 84866539049 scopus 로고    scopus 로고
    • RELATCH: Relative Optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
    • Kim, J. and Reed, J.L. (2012) RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biol., 13, R78.
    • (2012) Genome Biol. , vol.13 , pp. R78
    • Kim, J.1    Reed, J.L.2
  • 13
    • 84884386184 scopus 로고    scopus 로고
    • COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis
    • Leighty, R.W. and Antoniewicz, M.R. (2013) COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis. Metab. Eng., 20, 49-55.
    • (2013) Metab. Eng. , vol.20 , pp. 49-55
    • Leighty, R.W.1    Antoniewicz, M.R.2
  • 15
    • 84973335042 scopus 로고    scopus 로고
    • Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism
    • Long, C.P. et al. (2016) Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism. Metab. Eng., 37, 102-113.
    • (2016) Metab. Eng. , vol.37 , pp. 102-113
    • Long, C.P.1
  • 16
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado, D. and Herrgård, M. (2014) Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput. Biol., 10, e1003580.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003580
    • Machado, D.1    Herrgård, M.2
  • 17
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan, R. and Schilling, C.H. (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng., 5, 264-276.
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 18
    • 84964043843 scopus 로고    scopus 로고
    • In silico constraint-based strain optimization methods: The quest for optimal cell factories
    • Maia, P. et al. (2016) In silico constraint-based strain optimization methods: the quest for optimal cell factories. Microbiol. Mol. Biol. Rev., 80, 45-67.
    • (2016) Microbiol. Mol. Biol. Rev. , vol.80 , pp. 45-67
    • Maia, P.1
  • 19
    • 84941915231 scopus 로고    scopus 로고
    • Flux balance analysis with objective function defined by proteomics data - Metabolism of mycobacterium tuberculosis exposed to mefloquine
    • Montezano, D. et al. (2015) Flux balance analysis with objective function defined by proteomics data - metabolism of Mycobacterium tuberculosis exposed to mefloquine. PLoS One, 10, e0134014.
    • (2015) PLoS One , vol.10 , pp. e0134014
    • Montezano, D.1
  • 20
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
    • Orth, J.D. et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol. Syst. Biol., 7, 535.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 535
    • Orth, J.D.1
  • 21
    • 0021383728 scopus 로고
    • Equations and calculations for fermentations of butyric acid bacteria
    • Papoutsakis, E.T. (1984) Equations and calculations for fermentations of butyric acid bacteria. Biotechnol. Bioeng., 26, 174-187.
    • (1984) Biotechnol. Bioeng. , vol.26 , pp. 174-187
    • Papoutsakis, E.T.1
  • 22
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed, J.L. et al. (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol., 4, R54.
    • (2003) Genome Biol. , vol.4 , pp. R54
    • Reed, J.L.1
  • 23
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz, R. et al. (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol., 3, 119.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 119
    • Schuetz, R.1
  • 24
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of Optimality in natural and perturbed metabolic networks
    • Segrè, D. et al. (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
    • Segrè, D.1
  • 25
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • Shlomi, T. et al. (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
  • 26
    • 66749182798 scopus 로고    scopus 로고
    • (13)C-based metabolic flux analysis
    • Zamboni, N. et al. (2009) (13)C-based metabolic flux analysis. Nat. Protoc., 4, 878-892.
    • (2009) Nat. Protoc. , vol.4 , pp. 878-892
    • Zamboni, N.1
  • 27
    • 84941279254 scopus 로고    scopus 로고
    • CeCaFDB: A curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics
    • Zhang, Z. et al. (2015) CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. Nucleic Acids Res., 43, D549-D557.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D549-D557
    • Zhang, Z.1
  • 28
    • 79951745716 scopus 로고    scopus 로고
    • IMAT: An integrative metabolic analysis tool
    • Zur, H. et al. (2010) iMAT: an integrative metabolic analysis tool. Bioinformatics, 26, 3140-3142.
    • (2010) Bioinformatics , vol.26 , pp. 3140-3142
    • Zur, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.