메뉴 건너뛰기




Volumn 31, Issue 13, 2015, Pages 2159-2165

CycleFreeFlux: Efficient removal of thermodynamically infeasible loops from flux distributions

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; METABOLIC FLUX ANALYSIS; METABOLISM; PROCEDURES; THERMODYNAMICS;

EID: 84936791945     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv096     Document Type: Article
Times cited : (45)

References (26)
  • 1
    • 84881477852 scopus 로고    scopus 로고
    • A latent capacity for evolutionary innovation through exaptation in metabolic systems
    • Barve,A. and Wagner,A. (2013) A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature, 500, 203-206.
    • (2013) Nature , vol.500 , pp. 203-206
    • Barve, A.1    Wagner, A.2
  • 2
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • Beard,D.A. et al. (2002) Energy balance for analysis of complex metabolic networks. Biophys. J., 83, 79-86.
    • (2002) Biophys. J. , vol.83 , pp. 79-86
    • Beard, D.A.1
  • 3
    • 78049304837 scopus 로고    scopus 로고
    • Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    • Bordel,S. et al. (2010) Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput. Biol., 6, e1000859.
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000859
    • Bordel, S.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
    • 84988350465 scopus 로고    scopus 로고
    • Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks
    • De Martino,D. et al. (2013) Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks. Metabolites, 3, 946-966.
    • (2013) Metabolites , vol.3 , pp. 946-966
    • De Martino, D.1
  • 7
    • 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,A.M. 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
  • 8
    • 84887364569 scopus 로고    scopus 로고
    • Sybil-Efficient constraint-based modelling in R
    • Gelius-Dietrich,G. et al. (2013) sybil-Efficient constraint-based modelling in R. BMC Syst. Biol., 7, 125.
    • (2013) BMC Syst. Biol. , vol.7 , pp. 125
    • Gelius-Dietrich, G.1
  • 9
    • 3242795003 scopus 로고    scopus 로고
    • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
    • Holzhütter,H.-G. (2004) The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Federation Eur. Biochem. Soc. J., 271, 2905-2922.
    • (2004) Federation Eur. Biochem. Soc. J. , vol.271 , pp. 2905-2922
    • Holzhütter, H.-G.1
  • 10
    • 77955141026 scopus 로고    scopus 로고
    • Omic data from evolved E. Coli are consistent with computed optimal growth from genome-scale models
    • Lewis,N. E. et al. (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.Mol. Syst. Biol., 6, 390.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 390
    • Lewis, N.E.1
  • 11
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis,N.E. et al. (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol., 10, 291-305.
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 291-305
    • Lewis, N.E.1
  • 12
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan,R. and Schilling,C. (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.2
  • 13
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast
    • Mo,M.L. et al. (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol., 3, 37.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 37
    • Mo, M.L.1
  • 14
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth,J.D. et al. (2010) What is flux balance analysis? Nat. Biotechnol., 28, 245-248.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 245-248
    • Orth, J.D.1
  • 15
    • 28444475529 scopus 로고    scopus 로고
    • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    • Pál,C. et al. (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet., 37, 1372-1375.
    • (2005) Nat. Genet. , vol.37 , pp. 1372-1375
    • Pál, C.1
  • 16
    • 33646182934 scopus 로고    scopus 로고
    • An integrated view of protein evolution
    • Pál,C. et al. (2006) An integrated view of protein evolution. Nat. Rev. Genet., 7, 337-348.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 337-348
    • Pál, C.1
  • 17
    • 77956419824 scopus 로고    scopus 로고
    • Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network
    • Plata,G. et al. (2010) Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol. Syst. Biol., 6, 408.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 408
    • Plata, G.1
  • 18
    • 0036840340 scopus 로고    scopus 로고
    • Extreme pathways and Kirchhoff's second law
    • Price,N.D. et al. (2002) Extreme pathways and Kirchhoff's second law. Biophys. J., 83, 2879-2882.
    • (2002) Biophys. J. , vol.83 , pp. 2879-2882
    • Price, N.D.1
  • 20
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Database
    • Schellenberger,J. et al. (2010) BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Database. BMC Bioinformatics, 11, 213.
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1
  • 21
    • 79551676901 scopus 로고    scopus 로고
    • Elimination of thermodynamically infeasible loops in steady-state metabolic models
    • Schellenberger,J. et al. (2011) Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys. J., 100, 544-553.
    • (2011) Biophys. J. , vol.100 , pp. 544-553
    • Schellenberger, J.1
  • 22
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathwayoriented perspective
    • Schilling,C.H. et al. (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathwayoriented perspective. J. Theor. Biol., 203, 229-248.
    • (2000) J. Theor. Biol. , vol.203 , pp. 229-248
    • Schilling, C.H.1
  • 23
    • 84860487758 scopus 로고    scopus 로고
    • Multidimensional Optimality of Microbial Metabolism
    • Schuetz,R. et al. (2012) Multidimensional Optimality of Microbial Metabolism. Science, 336, 601-604.
    • (2012) Science , vol.336 , pp. 601-604
    • Schuetz, R.1
  • 24
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster,S. and Hilgetag,C. (1994) On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst., 2, 165-182.
    • (1994) J. Biol. Syst. , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 25
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • Schuster,S. et al. (2008) Is maximization of molar yield in metabolic networks favoured by evolution? J. Theor. Biol., 252, 497-504.
    • (2008) J. Theor. Biol. , vol.252 , pp. 497-504
    • Schuster, S.1
  • 26
    • 48249155053 scopus 로고    scopus 로고
    • Exhaustive identification of steady state cycles in large stoichiometric networks
    • Wright,J. and Wagner,A. (2008) Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Systems Biol., 2, 61.
    • (2008) BMC Systems Biol. , vol.2 , pp. 61
    • Wright, J.1    Wagner, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.