메뉴 건너뛰기




Volumn 161, Issue 5, 2015, Pages 971-987

Using genome-scale models to predict biological capabilities

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE SEQUENCE; GENOMICS; HUMAN; METABOLIC ENGINEERING; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; BIOLOGICAL MODEL; COMPUTER SIMULATION; ESCHERICHIA COLI; GENETICS; PROCEDURES; PROTEIN PROTEIN INTERACTION; SYSTEMS BIOLOGY; THERMOTOGA MARITIMA; YEAST;

EID: 84930227327     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.05.019     Document Type: Review
Times cited : (531)

References (99)
  • 1
    • 84875788751 scopus 로고    scopus 로고
    • Engineering microbial chemical factories to produce renewable "biomonomers"
    • J. Adkins, S. Pugh, R. McKenna, and D.R. Nielsen Engineering microbial chemical factories to produce renewable "biomonomers" Front Microbiol 3 2012 313
    • (2012) Front Microbiol , vol.3 , pp. 313
    • Adkins, J.1    Pugh, S.2    McKenna, R.3    Nielsen, D.R.4
  • 2
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • R. Agren, S. Bordel, A. Mardinoglu, N. Pornputtapong, I. Nookaew, and J. Nielsen Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT PLoS Comput. Biol. 8 2012 e1002518
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002518
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 3
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • R. Agren, L. Liu, S. Shoaie, W. Vongsangnak, I. Nookaew, and J. Nielsen The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum PLoS Comput. Biol. 9 2013 e1002980
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002980
    • Agren, R.1    Liu, L.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 4
    • 78349239648 scopus 로고    scopus 로고
    • An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models
    • D. Barua, J. Kim, and J.L. Reed An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models PLoS Comput. Biol. 6 2010 e1000970
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000970
    • Barua, D.1    Kim, J.2    Reed, J.L.3
  • 5
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • S.A. Becker, and B.O. Palsson Context-specific metabolic networks are consistent with experiments PLoS Comput. Biol. 4 2008 e1000082
    • (2008) PLoS Comput. Biol. , vol.4 , pp. e1000082
    • Becker, S.A.1    Palsson, B.O.2
  • 6
    • 34547887655 scopus 로고    scopus 로고
    • Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
    • Q.K. Beg, A. Vazquez, J. Ernst, M.A. de Menezes, Z. Bar-Joseph, A.L. Barabási, and Z.N. Oltvai Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity Proc. Natl. Acad. Sci. USA 104 2007 12663 12668
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12663-12668
    • Beg, Q.K.1    Vazquez, A.2    Ernst, J.3    De Menezes, M.A.4    Bar-Joseph, Z.5    Barabási, A.L.6    Oltvai, Z.N.7
  • 7
    • 77958537509 scopus 로고    scopus 로고
    • Insight into human alveolar macrophage and M. Tuberculosis interactions via metabolic reconstructions
    • A. Bordbar, N.E. Lewis, J. Schellenberger, B.O. Palsson, and N. Jamshidi Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions Mol. Syst. Biol. 6 2010 422
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 422
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.O.4    Jamshidi, N.5
  • 8
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • A. Bordbar, J.M. Monk, Z.A. King, and B.O. Palsson Constraint-based models predict metabolic and associated cellular functions Nat. Rev. Genet. 15 2014 107 120
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 9
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • A.P. Burgard, P. Pharkya, and C.D. Maranas Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 84 2003 647 657
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 10
    • 84907350970 scopus 로고    scopus 로고
    • Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
    • M.A. Campodonico, B.A. Andrews, J.A. Asenjo, B.O. Palsson, and A.M. Feist Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path Metab. Eng. 25 2014 140 158
    • (2014) Metab. Eng. , vol.25 , pp. 140-158
    • Campodonico, M.A.1    Andrews, B.A.2    Asenjo, J.A.3    Palsson, B.O.4    Feist, A.M.5
  • 11
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • S. Chandrasekaran, and N.D. Price Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis Proc. Natl. Acad. Sci. USA 107 2010 17845 17850
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 12
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • R.L. Chang, L. Xie, L. Xie, P.E. Bourne, and B. Palsson Drug off-target effects predicted using structural analysis in the context of a metabolic network model PLoS Comput. Biol. 6 2010 e1000938
    • (2010) PLoS Comput. Biol. , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.5
  • 13
    • 84878756325 scopus 로고    scopus 로고
    • Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli
    • R.L. Chang, K. Andrews, D. Kim, Z. Li, A. Godzik, and B.O. Palsson Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli Science 340 2013 1220 1223
    • (2013) Science , vol.340 , pp. 1220-1223
    • Chang, R.L.1    Andrews, K.2    Kim, D.3    Li, Z.4    Godzik, A.5    Palsson, B.O.6
  • 14
    • 84885147536 scopus 로고    scopus 로고
    • Antibacterial mechanisms identified through structural systems pharmacology
    • R.L. Chang, L. Xie, P.E. Bourne, and B.O. Palsson Antibacterial mechanisms identified through structural systems pharmacology BMC Syst. Biol. 7 2013 102
    • (2013) BMC Syst. Biol. , vol.7 , pp. 102
    • Chang, R.L.1    Xie, L.2    Bourne, P.E.3    Palsson, B.O.4
  • 15
    • 84861165967 scopus 로고    scopus 로고
    • Are we ready for genome-scale modeling in plants?
    • E. Collakova, J.Y. Yen, and R.S. Senger Are we ready for genome-scale modeling in plants? Plant Sci. 191-192 2012 53 70
    • (2012) Plant Sci. , vol.191-192 , pp. 53-70
    • Collakova, E.1    Yen, J.Y.2    Senger, R.S.3
  • 16
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • M.W. Covert, E.M. Knight, J.L. Reed, M.J. Herrgard, and B.O. Palsson Integrating high-throughput and computational data elucidates bacterial networks Nature 429 2004 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
  • 17
    • 84860405978 scopus 로고    scopus 로고
    • Mathematical models of cell factories: Moving towards the core of industrial biotechnology
    • M. Cvijovic, S. Bordel, and J. Nielsen Mathematical models of cell factories: moving towards the core of industrial biotechnology Microb. Biotechnol. 4 2011 572 584
    • (2011) Microb. Biotechnol. , vol.4 , pp. 572-584
    • Cvijovic, M.1    Bordel, S.2    Nielsen, J.3
  • 19
  • 20
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • J.S. Edwards, and B.O. Palsson Systems properties of the Haemophilus influenzae Rd metabolic genotype J. Biol. Chem. 274 1999 17410 17416
    • (1999) J. Biol. Chem. , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.O.2
  • 21
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • J.S. Edwards, and B.O. Palsson The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities Proc. Natl. Acad. Sci. USA 97 2000 5528 5533
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 22
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • J.S. Edwards, R.U. Ibarra, and B.O. Palsson In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat. Biotechnol. 19 2001 125 130
    • (2001) Nat. Biotechnol. , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 23
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • A.M. Feist, and B.O. Palsson The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli Nat. Biotechnol. 26 2008 659 667
    • (2008) Nat. Biotechnol. , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 25
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • S.S. Fong, and B.O. Palsson Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes Nat. Genet. 36 2004 1056 1058
    • (2004) Nat. Genet. , vol.36 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.O.2
  • 26
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • S.S. Fong, A.R. Joyce, and B.O. Palsson Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states Genome Res. 15 2005 1365 1372
    • (2005) Genome Res. , vol.15 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.O.3
  • 27
    • 84876321687 scopus 로고    scopus 로고
    • Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant
    • N.L. Fong, J.A. Lerman, I. Lam, B.O. Palsson, and P. Charusanti Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant FEMS Microbiol. Lett. 342 2013 62 69
    • (2013) FEMS Microbiol. Lett. , vol.342 , pp. 62-69
    • Fong, N.L.1    Lerman, J.A.2    Lam, I.3    Palsson, B.O.4    Charusanti, P.5
  • 32
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • R.U. Ibarra, J.S. Edwards, and B.O. Palsson Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 420 2002 186 189
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 33
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • L. Jerby, T. Shlomi, and E. Ruppin Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism Mol. Syst. Biol. 6 2010 401
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 39
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • N. Klitgord, and D. Segrè Environments that induce synthetic microbial ecosystems PLoS Comput. Biol. 6 2010 e1001002
    • (2010) PLoS Comput. Biol. , vol.6
    • Klitgord, N.1    Segrè, D.2
  • 41
    • 84881110826 scopus 로고    scopus 로고
    • Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
    • R. Levy, and E. Borenstein Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules Proc. Natl. Acad. Sci. USA 110 2013 12804 12809
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 12804-12809
    • Levy, R.1    Borenstein, E.2
  • 44
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • N.E. Lewis, H. Nagarajan, and B.O. Palsson Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Nat. Rev. Microbiol. 10 2012 291 305
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 45
    • 84907272917 scopus 로고    scopus 로고
    • Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
    • J.K. Liu, E.J. O'Brien, J.A. Lerman, K. Zengler, B.O. Palsson, and A.M. Feist Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale BMC Syst. Biol. 8 2014 110
    • (2014) BMC Syst. Biol. , vol.8 , pp. 110
    • Liu, J.K.1    O'Brien, E.J.2    Lerman, J.A.3    Zengler, K.4    Palsson, B.O.5    Feist, A.M.6
  • 46
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • R. Mahadevan, and C.H. Schilling The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Metab. Eng. 5 2003 264 276
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 47
    • 84879002382 scopus 로고    scopus 로고
    • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • D. McCloskey, B.O. Palsson, and A.M. Feist Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli Mol. Syst. Biol. 9 2013 661
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 661
    • McCloskey, D.1    Palsson, B.O.2    Feist, A.M.3
  • 48
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast
    • M.L. Mo, B.O. Palsson, and M.J. Herrgård Connecting extracellular metabolomic measurements to intracellular flux states in yeast BMC Syst. Biol. 3 2009 37
    • (2009) BMC Syst. Biol. , vol.3 , pp. 37
    • Mo, M.L.1    Palsson, B.O.2    Herrgård, M.J.3
  • 49
    • 84903287056 scopus 로고    scopus 로고
    • Genetics. Predicting microbial growth
    • J. Monk, and B.O. Palsson Genetics. Predicting microbial growth Science 344 2014 1448 1449
    • (2014) Science , vol.344 , pp. 1448-1449
    • Monk, J.1    Palsson, B.O.2
  • 50
    • 84900303762 scopus 로고    scopus 로고
    • Optimizing genome-scale network reconstructions
    • J. Monk, J. Nogales, and B.O. Palsson Optimizing genome-scale network reconstructions Nat. Biotechnol. 32 2014 447 452
    • (2014) Nat. Biotechnol. , vol.32 , pp. 447-452
    • Monk, J.1    Nogales, J.2    Palsson, B.O.3
  • 51
    • 84888371682 scopus 로고    scopus 로고
    • Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
    • H. Nagarajan, M. Embree, A.E. Rotaru, P.M. Shrestha, A.M. Feist, B.O. Palsson, D.R. Lovley, and K. Zengler Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association Nat. Commun. 4 2013 2809
    • (2013) Nat. Commun. , vol.4 , pp. 2809
    • Nagarajan, H.1    Embree, M.2    Rotaru, A.E.3    Shrestha, P.M.4    Feist, A.M.5    Palsson, B.O.6    Lovley, D.R.7    Zengler, K.8
  • 56
    • 84920923824 scopus 로고    scopus 로고
    • Computing the functional proteome: Recent progress and future prospects for genome-scale models
    • E.J. O'Brien, and B.O. Palsson Computing the functional proteome: recent progress and future prospects for genome-scale models Curr. Opin. Biotechnol. 34C 2015 125 134
    • (2015) Curr. Opin. Biotechnol. , vol.34 C , pp. 125-134
    • O'Brien, E.J.1    Palsson, B.O.2
  • 57
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • E.J. O'Brien, J.A. Lerman, R.L. Chang, D.R. Hyduke, and B.O. Palsson Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction Mol. Syst. Biol. 9 2013 693
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 693
    • O'Brien, E.J.1    Lerman, J.A.2    Chang, R.L.3    Hyduke, D.R.4    Palsson, B.O.5
  • 58
  • 59
    • 79953649492 scopus 로고    scopus 로고
    • Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis
    • M.A. Oberhardt, J. Puchałka, V.A. Martins dos Santos, and J.A. Papin Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis PLoS Comput. Biol. 7 2011 e1001116
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1001116
    • Oberhardt, M.A.1    Puchałka, J.2    Martins Dos Santos, V.A.3    Papin, J.A.4
  • 60
    • 78651335279 scopus 로고    scopus 로고
    • Systematizing the generation of missing metabolic knowledge
    • J.D. Orth, and B.O. Palsson Systematizing the generation of missing metabolic knowledge Biotechnol. Bioeng. 107 2010 403 412
    • (2010) Biotechnol. Bioeng. , vol.107 , pp. 403-412
    • Orth, J.D.1    Palsson, B.O.2
  • 61
    • 78651335279 scopus 로고    scopus 로고
    • Systematizing the generation of missing metabolic knowledge
    • J.D. Orth, and B.O. Palsson Systematizing the generation of missing metabolic knowledge Biotechnol. Bioeng. 107 2010 403 412
    • (2010) Biotechnol. Bioeng. , vol.107 , pp. 403-412
    • Orth, J.D.1    Palsson, B.O.2
  • 63
    • 84876789665 scopus 로고    scopus 로고
    • Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
    • T. Österlund, I. Nookaew, S. Bordel, and J. Nielsen Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling BMC Syst. Biol. 7 2013 36
    • (2013) BMC Syst. Biol. , vol.7 , pp. 36
    • Österlund, T.1    Nookaew, I.2    Bordel, S.3    Nielsen, J.4
  • 64
    • 0033764285 scopus 로고    scopus 로고
    • The challenges of in silico biology
    • B. Palsson The challenges of in silico biology Nat. Biotechnol. 18 2000 1147 1150
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1147-1150
    • Palsson, B.1
  • 65
    • 84922623948 scopus 로고    scopus 로고
    • Long-term phenotypic evolution of bacteria
    • G. Plata, C.S. Henry, and D. Vitkup Long-term phenotypic evolution of bacteria Nature 517 2015 369 372
    • (2015) Nature , vol.517 , pp. 369-372
    • Plata, G.1    Henry, C.S.2    Vitkup, D.3
  • 66
    • 77954590959 scopus 로고    scopus 로고
    • OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions
    • S. Ranganathan, P.F. Suthers, and C.D. Maranas OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions PLoS Comput. Biol. 6 2010 e1000744
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000744
    • Ranganathan, S.1    Suthers, P.F.2    Maranas, C.D.3
  • 67
    • 84866128045 scopus 로고    scopus 로고
    • Shrinking the metabolic solution space using experimental datasets
    • J.L. Reed Shrinking the metabolic solution space using experimental datasets PLoS Comput. Biol. 8 2012 e1002662
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002662
    • Reed, J.L.1
  • 68
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • J.L. Reed, and B.O. Palsson Thirteen years of building constraint-based in silico models of Escherichia coli J. Bacteriol. 185 2003 2692 2699
    • (2003) J. Bacteriol. , vol.185 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.O.2
  • 70
    • 80053375237 scopus 로고    scopus 로고
    • The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    • O. Rolfsson, B.O. Palsson, and I. Thiele The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions BMC Syst. Biol. 5 2011 155
    • (2011) BMC Syst. Biol. , vol.5 , pp. 155
    • Rolfsson, O.1    Palsson, B.O.2    Thiele, I.3
  • 71
    • 80053375237 scopus 로고    scopus 로고
    • The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    • O. Rolfsson, B.O. Palsson, and I. Thiele The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions BMC Syst. Biol. 5 2011 155
    • (2011) BMC Syst. Biol. , vol.5 , pp. 155
    • Rolfsson, O.1    Palsson, B.O.2    Thiele, I.3
  • 72
    • 69849084132 scopus 로고    scopus 로고
    • Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
    • T.D. Scheibe, R. Mahadevan, Y. Fang, S. Garg, P.E. Long, and D.R. Lovley Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation Microb. Biotechnol. 2 2009 274 286
    • (2009) Microb. Biotechnol. , vol.2 , pp. 274-286
    • Scheibe, T.D.1    Mahadevan, R.2    Fang, Y.3    Garg, S.4    Long, P.E.5    Lovley, D.R.6
  • 73
    • 65549092780 scopus 로고    scopus 로고
    • Use of randomized sampling for analysis of metabolic networks
    • J. Schellenberger, and B.O. Palsson Use of randomized sampling for analysis of metabolic networks J. Biol. Chem. 284 2009 5457 5461
    • (2009) J. Biol. Chem. , vol.284 , pp. 5457-5461
    • Schellenberger, J.1    Palsson, B.O.2
  • 74
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    • J. Schellenberger, J.O. Park, T.M. Conrad, and B.O. Palsson BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions BMC Bioinformatics 11 2010 213
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.O.4
  • 77
    • 84890092837 scopus 로고    scopus 로고
    • GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data
    • B.J. Schmidt, A. Ebrahim, T.O. Metz, J.N. Adkins, B.O. Palsson, and D.R. Hyduke GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data Bioinformatics 29 2013 2900 2908
    • (2013) Bioinformatics , vol.29 , pp. 2900-2908
    • Schmidt, B.J.1    Ebrahim, A.2    Metz, T.O.3    Adkins, J.N.4    Palsson, B.O.5    Hyduke, D.R.6
  • 78
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • R. Schuetz, L. Kuepfer, and U. Sauer Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol. Syst. Biol. 3 2007 119
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 83
    • 84880860962 scopus 로고    scopus 로고
    • Robust flux balance analysis of multiscale biochemical reaction networks
    • Y. Sun, R.M. Fleming, I. Thiele, and M.A. Saunders Robust flux balance analysis of multiscale biochemical reaction networks BMC Bioinformatics 14 2013 240
    • (2013) BMC Bioinformatics , vol.14 , pp. 240
    • Sun, Y.1    Fleming, R.M.2    Thiele, I.3    Saunders, M.A.4
  • 84
    • 84856038703 scopus 로고    scopus 로고
    • The SuBliMinaL Toolbox: Automating steps in the reconstruction of metabolic networks
    • N. Swainston, K. Smallbone, P. Mendes, D. Kell, and N. Paton The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks J. Integr. Bioinform. 8 2011 186
    • (2011) J. Integr. Bioinform. , vol.8 , pp. 186
    • Swainston, N.1    Smallbone, K.2    Mendes, P.3    Kell, D.4    Paton, N.5
  • 86
    • 79251610629 scopus 로고    scopus 로고
    • Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments
    • N. Tepper, and T. Shlomi Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments PLoS ONE 6 2011 e16274
    • (2011) PLoS ONE , vol.6 , pp. e16274
    • Tepper, N.1    Shlomi, T.2
  • 87
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • I. Thiele, and B.O. Palsson A protocol for generating a high-quality genome-scale metabolic reconstruction Nat. Protoc. 5 2010 93 121
    • (2010) Nat. Protoc. , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 88
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization
    • I. Thiele, N. Jamshidi, R.M. Fleming, and B.O. Palsson Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization PLoS Comput. Biol. 5 2009 e1000312
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000312
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.3    Palsson, B.O.4
  • 89
    • 77952774546 scopus 로고    scopus 로고
    • Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
    • I. Thiele, R.M. Fleming, A. Bordbar, J. Schellenberger, and B.O. Palsson Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery Biophys. J. 98 2010 2072 2081
    • (2010) Biophys. J. , vol.98 , pp. 2072-2081
    • Thiele, I.1    Fleming, R.M.2    Bordbar, A.3    Schellenberger, J.4    Palsson, B.O.5
  • 90
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. Coli and its application to the evolution of codon usage
    • I. Thiele, R.M. Fleming, R. Que, A. Bordbar, D. Diep, and B.O. Palsson Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage PLoS ONE 7 2012 e45635
    • (2012) PLoS ONE , vol.7 , pp. e45635
    • Thiele, I.1    Fleming, R.M.2    Que, R.3    Bordbar, A.4    Diep, D.5    Palsson, B.O.6
  • 92
    • 79960126760 scopus 로고    scopus 로고
    • RBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
    • S.G. Thorleifsson, and I. Thiele rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks Bioinformatics 27 2011 2009 2010
    • (2011) Bioinformatics , vol.27 , pp. 2009-2010
    • Thorleifsson, S.G.1    Thiele, I.2
  • 94
    • 77956415336 scopus 로고    scopus 로고
    • Emergent cooperation in microbial metabolism
    • E.H. Wintermute, and P.A. Silver Emergent cooperation in microbial metabolism Mol. Syst. Biol. 6 2010 407
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 407
    • Wintermute, E.H.1    Silver, P.A.2
  • 98
    • 78751584992 scopus 로고    scopus 로고
    • Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
    • K. Zhuang, M. Izallalen, P. Mouser, H. Richter, C. Risso, R. Mahadevan, and D.R. Lovley Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments ISME J. 5 2011 305 316
    • (2011) ISME J. , vol.5 , pp. 305-316
    • Zhuang, K.1    Izallalen, M.2    Mouser, P.3    Richter, H.4    Risso, C.5    Mahadevan, R.6    Lovley, D.R.7
  • 99
    • 79959610766 scopus 로고    scopus 로고
    • Economics of membrane occupancy and respiro-fermentation
    • K. Zhuang, G.N. Vemuri, and R. Mahadevan Economics of membrane occupancy and respiro-fermentation Mol. Syst. Biol. 7 2011 500
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 500
    • Zhuang, K.1    Vemuri, G.N.2    Mahadevan, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.