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Volumn 42, Issue 3, 2015, Pages 339-348

Applications of genome-scale metabolic network model in metabolic engineering

Author keywords

Gene amplification prediction; Gene knock out prediction; Genome scale metabolic network; Integrated genome scale model; Metabolic pathway prediction; Systems metabolic engineering

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; BIOSYNTHESIS; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METABOLIC ENGINEERING; METABOLISM; PROCEDURES;

EID: 84925485244     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-014-1554-9     Document Type: Article
Times cited : (77)

References (95)
  • 1
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • COI: 1:CAS:528:DC%2BC3sXlvVamurw%3D, PID: 23555215
    • Agren R, Liu LM, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol 9(3):e1002980
    • (2013) PLoS Comput Biol , vol.9 , Issue.3 , pp. 1002980
    • Agren, R.1    Liu, L.M.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 2
    • 18844392599 scopus 로고    scopus 로고
    • Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
    • COI: 1:CAS:528:DC%2BD2MXktVKgtbg%3D, PID: 15885614
    • Alper H, Jin YS, Moxley JF, Stephanopoulos G (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 7(3):155–164
    • (2005) Metab Eng , vol.7 , Issue.3 , pp. 155-164
    • Alper, H.1    Jin, Y.S.2    Moxley, J.F.3    Stephanopoulos, G.4
  • 3
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • Anna SB, Jason AP (2012) Integration of expression data in genome-scale metabolic network reconstructions. Front Physiol 3:299
    • (2012) Front Physiol , vol.3 , pp. 299
    • Anna, S.B.1    Jason, A.P.2
  • 4
    • 79960029354 scopus 로고    scopus 로고
    • GLAMM: genome-linked application for metabolic maps
    • COI: 1:CAS:528:DC%2BC3MXosVOnu7s%3D, PID: 21624891
    • Bates JT, Chivian D, Arkin AP (2011) GLAMM: genome-linked application for metabolic maps. Nucleic Acids Res 39:W400–W405
    • (2011) Nucleic Acids Res , vol.39 , pp. W400-W405
    • Bates, J.T.1    Chivian, D.2    Arkin, A.P.3
  • 5
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • PID: 18483554
    • Becker SA, Palsson BØ (2008) Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 4(5):e1000082
    • (2008) PLoS Comput Biol , vol.4 , Issue.5 , pp. 1000082
    • Becker, S.A.1    Palsson, B.Ø.2
  • 7
    • 84860998236 scopus 로고    scopus 로고
    • Inferring carbon sources from gene expression profiles using metabolic flux models
    • COI: 1:CAS:528:DC%2BC38XnvFWqtbY%3D, PID: 22606312
    • Brandes A, Lun DS, Ip K, Zucker J, Colijn C, Weiner B, Galagan JE (2012) Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS One 7(5):e36947
    • (2012) PLoS One , vol.7 , Issue.5 , pp. 36947
    • Brandes, A.1    Lun, D.S.2    Ip, K.3    Zucker, J.4    Colijn, C.5    Weiner, B.6    Galagan, J.E.7
  • 10
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • COI: 1:CAS:528:DC%2BD3sXptFWmsL0%3D, PID: 14595777
    • Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6):647–657
    • (2003) Biotechnol Bioeng , vol.84 , Issue.6 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 11
    • 79961116083 scopus 로고    scopus 로고
    • A retrosynthetic biology approach to metabolic pathway design for therapeutic production
    • Carbonell P, Planson AG, Fichera D, Faulon JL (2011) A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol 5:112
    • (2011) BMC Syst Biol , vol.5 , pp. 112
    • Carbonell, P.1    Planson, A.G.2    Fichera, D.3    Faulon, J.L.4
  • 13
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • COI: 1:CAS:528:DC%2BC3cXhtlartb3O, PID: 20876091
    • Chandrasekaran S, Price ND (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci USA 107(41):17845–17850
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.41 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 14
    • 77953329895 scopus 로고    scopus 로고
    • Prediction of novel synthetic pathways for the production of desired chemicals
    • PID: 20346180
    • Cho A, Yun H, Park JH, Lee SY, Park S (2010) Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol 4:35
    • (2010) BMC Syst Biol , vol.4 , pp. 35
    • Cho, A.1    Yun, H.2    Park, J.H.3    Lee, S.Y.4    Park, S.5
  • 15
    • 77952265112 scopus 로고    scopus 로고
    • In silico identification of gene amplification targets for improvement of lycopene production
    • COI: 1:CAS:528:DC%2BC3cXmsF2ltL0%3D, PID: 20348305
    • Choi HS, Lee SY, Kim TY, Woo HM (2010) In silico identification of gene amplification targets for improvement of lycopene production. Appl Environ Microbiol 76(10):3097–3105
    • (2010) Appl Environ Microbiol , vol.76 , Issue.10 , pp. 3097-3105
    • Choi, H.S.1    Lee, S.Y.2    Kim, T.Y.3    Woo, H.M.4
  • 16
    • 84895756673 scopus 로고    scopus 로고
    • k-OptForce: integrating kinetics with flux balance analysis for strain design
    • PID: 24586136
    • Chowdhury A, Zomorrodi AR, Maranas CD, Beard DA (2014) k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol 10(2):e1003487
    • (2014) PLoS Comput Biol , vol.10 , Issue.2 , pp. 1003487
    • Chowdhury, A.1    Zomorrodi, A.R.2    Maranas, C.D.3    Beard, D.A.4
  • 17
    • 74549189330 scopus 로고    scopus 로고
    • Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network
    • PID: 20021680
    • Chung BKS, Lee DY (2009) Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. BMC Syst Biol 3:117
    • (2009) BMC Syst Biol , vol.3 , pp. 117
    • Chung, B.K.S.1    Lee, D.Y.2
  • 19
    • 84870689618 scopus 로고    scopus 로고
    • Temporal expression-based analysis of metabolism
    • COI: 1:CAS:528:DC%2BC38XhvVKqsLnM, PID: 23209390
    • Collins SB, Reznik E, Segre D (2012) Temporal expression-based analysis of metabolism. PLoS Comput Biol 8(11):e1002781
    • (2012) PLoS Comput Biol , vol.8 , Issue.11 , pp. 1002781
    • Collins, S.B.1    Reznik, E.2    Segre, D.3
  • 20
    • 84877118199 scopus 로고    scopus 로고
    • Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering
    • COI: 1:CAS:528:DC%2BC3sXmsVeit7s%3D, PID: 23703951
    • Cotten C, Reed JL (2013) Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnol J 8(5):595–604
    • (2013) Biotechnol J , vol.8 , Issue.5 , pp. 595-604
    • Cotten, C.1    Reed, J.L.2
  • 22
    • 52649136124 scopus 로고    scopus 로고
    • Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae
    • COI: 1:CAS:528:DC%2BD1cXhtFCqt7nJ
    • Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG (2008) Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae. Appl Environ Microb 74(18):5809–5816
    • (2008) Appl Environ Microb , vol.74 , Issue.18 , pp. 5809-5816
    • Dikicioglu, D.1    Pir, P.2    Onsan, Z.I.3    Ulgen, K.O.4    Kirdar, B.5    Oliver, S.G.6
  • 23
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities
    • COI: 1:CAS:528:DC%2BD3cXjsVWms7g%3D, PID: 10805808
    • Edwards JS, Palsson BØ (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97(10):5528–5533
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.10 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.Ø.2
  • 27
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • COI: 1:CAS:528:DC%2BD3sXhtlCrsLo%3D, PID: 12566402
    • Forster J, Famili I, Fu P, Palsson BØ, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13(2):244–253
    • (2003) Genome Res , vol.13 , Issue.2 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.Ø.4    Nielsen, J.5
  • 28
    • 77952585143 scopus 로고    scopus 로고
    • CASOP: a computational approach for strain optimization aiming at high productivity
    • PID: 20303369
    • Hadicke O, Klamt S (2010) CASOP: a computational approach for strain optimization aiming at high productivity. J Biotechnol 147(2):88–101
    • (2010) J Biotechnol , vol.147 , Issue.2 , pp. 88-101
    • Hadicke, O.1    Klamt, S.2
  • 30
    • 84861744439 scopus 로고    scopus 로고
    • Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
    • PID: 22663945
    • Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP (2012) Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 6:55
    • (2012) BMC Syst Biol , vol.6 , pp. 55
    • Heavner, B.D.1    Smallbone, K.2    Barker, B.3    Mendes, P.4    Walker, L.P.5
  • 31
    • 67650573077 scopus 로고    scopus 로고
    • iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
    • PID: 19555510
    • Henry CS, Zinner JF, Cohoon MP, Stevens RL (2009) iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10(6):R69
    • (2009) Genome Biol , vol.10 , Issue.6 , pp. R69
    • Henry, C.S.1    Zinner, J.F.2    Cohoon, M.P.3    Stevens, R.L.4
  • 32
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • COI: 1:CAS:528:DC%2BC3cXhtVyiu73M, PID: 20802497
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28(9):977–982
    • (2010) Nat Biotechnol , vol.28 , Issue.9 , pp. 977-982
    • Henry, C.S.1    DeJongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 33
    • 84881540727 scopus 로고    scopus 로고
    • Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism
    • Hnin WA, Susan AH, Larry PW (2013) Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism. Ind Biotechnol 9(4):215–228
    • (2013) Ind Biotechnol , vol.9 , Issue.4 , pp. 215-228
    • Hnin, W.A.1    Susan, A.H.2    Larry, P.W.3
  • 34
    • 84872093417 scopus 로고    scopus 로고
    • Analysis of omics data with genome-scale models of metabolism
    • COI: 1:CAS:528:DC%2BC3sXhsFShtg%3D%3D, PID: 23247105
    • Hyduke DR, Lewis NE, Palsson BØ (2013) Analysis of omics data with genome-scale models of metabolism. Mol BioSyst 9(2):167–174
    • (2013) Mol BioSyst , vol.9 , Issue.2 , pp. 167-174
    • Hyduke, D.R.1    Lewis, N.E.2    Palsson, B.Ø.3
  • 37
    • 80053175304 scopus 로고    scopus 로고
    • TIGER: toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
    • COI: 1:CAS:528:DC%2BC3MXhtlWjsb7O, PID: 21943338
    • Jensen PA, Lutz KA, Papin JA (2011) TIGER: toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 5:147
    • (2011) BMC Syst Biol , vol.5 , pp. 147
    • Jensen, P.A.1    Lutz, K.A.2    Papin, J.A.3
  • 38
    • 79951536020 scopus 로고    scopus 로고
    • Functional integration of a metabolic network model and expression data without arbitrary thresholding
    • COI: 1:CAS:528:DC%2BC3MXitVWgsb4%3D, PID: 21172910
    • Jensen PA, Papin JA (2011) Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 27(4):541–547
    • (2011) Bioinformatics , vol.27 , Issue.4 , pp. 541-547
    • Jensen, P.A.1    Papin, J.A.2
  • 39
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • PID: 20823844
    • Jerby L, Shlomi T, Ruppin E (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 6:401
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 40
    • 84890290025 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
    • COI: 1:CAS:528:DC%2BC3sXhvFKmsL3K, PID: 24277855
    • Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ (2013) Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci USA 110(50):20338–20343
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.50 , pp. 20338-20343
    • Monk, J.M.1    Charusanti, P.2    Aziz, R.K.3    Lerman, J.A.4    Premyodhin, N.5    Orth, J.D.6    Feist, A.M.7    Palsson, B.Ø.8
  • 41
    • 73949094856 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers
    • COI: 1:CAS:528:DC%2BD1MXhsVymtrrK, PID: 19937727
    • Jung YK, Kim TY, Park SJ, Lee SY (2010) Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers. Biotechnol Bioeng 105(1):161–171
    • (2010) Biotechnol Bioeng , vol.105 , Issue.1 , pp. 161-171
    • Jung, Y.K.1    Kim, T.Y.2    Park, S.J.3    Lee, S.Y.4
  • 43
    • 84883808938 scopus 로고    scopus 로고
    • Flux-coupled genes and their use in metabolic flux analysis
    • COI: 1:CAS:528:DC%2BC3sXkt1Kmu7w%3D, PID: 23420780
    • Kim HU, Kim WJ, Lee SY (2013) Flux-coupled genes and their use in metabolic flux analysis. Biotechnol J 8(9):1035–1042
    • (2013) Biotechnol J , vol.8 , Issue.9 , pp. 1035-1042
    • Kim, H.U.1    Kim, W.J.2    Lee, S.Y.3
  • 44
    • 77951552860 scopus 로고    scopus 로고
    • OptORF: optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
    • PID: 20426856
    • Kim J, Reed JL (2010) OptORF: optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol 4:53
    • (2010) BMC Syst Biol , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 45
    • 84866539049 scopus 로고    scopus 로고
    • RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
    • PID: 23013597
    • Kim J, Reed JL (2012) RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biol 13(9):R78
    • (2012) Genome Biol , vol.13 , Issue.9 , pp. R78
    • Kim, J.1    Reed, J.L.2
  • 46
    • 34447296697 scopus 로고    scopus 로고
    • Genome-scale analysis of Mannheimia succiniciproducens metabolism
    • COI: 1:CAS:528:DC%2BD2sXms1aktb4%3D, PID: 17405177
    • Kim TY, Kim HU, Park JM, Song H, Kim JS, Lee SY (2007) Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol Bioeng 97(4):657–671
    • (2007) Biotechnol Bioeng , vol.97 , Issue.4 , pp. 657-671
    • Kim, T.Y.1    Kim, H.U.2    Park, J.M.3    Song, H.4    Kim, J.S.5    Lee, S.Y.6
  • 47
    • 84891614139 scopus 로고    scopus 로고
    • Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement
    • Lakshmanan M, Chung BKS, Liu CC, Kim SW, Lee DY (2013) Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement. J Bioinf Comput Biol 11(6):1343006
    • (2013) J Bioinf Comput Biol , vol.11 , Issue.6 , pp. 1343006
    • Lakshmanan, M.1    Chung, B.K.S.2    Liu, C.C.3    Kim, S.W.4    Lee, D.Y.5
  • 48
    • 51849115840 scopus 로고    scopus 로고
    • Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
    • COI: 1:CAS:528:DC%2BD1cXhtFWls7jO, PID: 18758767
    • Lee J, Yun H, Feist AM, Palsson BØ, Lee SY (2008) Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 80(5):849–862
    • (2008) Appl Microbiol Biotechnol , vol.80 , Issue.5 , pp. 849-862
    • Lee, J.1    Yun, H.2    Feist, A.M.3    Palsson, B.Ø.4    Lee, S.Y.5
  • 49
    • 78549287163 scopus 로고    scopus 로고
    • The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies
    • COI: 1:CAS:528:DC%2BC3cXhsFKjsr7N, PID: 21092328
    • Lee KY, Park JM, Kim TY, Yun H, Lee SY (2010) The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact 9:94
    • (2010) Microb Cell Fact , vol.9 , pp. 94
    • Lee, K.Y.1    Park, J.M.2    Kim, T.Y.3    Yun, H.4    Lee, S.Y.5
  • 51
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • PID: 24084808
    • Lerman JA, Chang RL, Hyduke DR (2013) Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9:693
    • (2013) Mol Syst Biol , vol.9 , pp. 693
    • Lerman, J.A.1    Chang, R.L.2    Hyduke, D.R.3
  • 52
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • COI: 1:CAS:528:DC%2BC38XislyntLw%3D, PID: 22367118
    • Lewis NE, Nagarajan H, Palsson BØ (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10(4):291–305
    • (2012) Nat Rev Microbiol , vol.10 , Issue.4 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.Ø.3
  • 54
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • PID: 24762745
    • Machado D, Herrgard M (2014) Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol 10(4):e1003580
    • (2014) PLoS Comput Biol , vol.10 , Issue.4 , pp. 1003580
    • Machado, D.1    Herrgard, M.2
  • 55
    • 74549189949 scopus 로고    scopus 로고
    • Flux design: in silico design of cell factories based on correlation of pathway fluxes to desired properties
    • PID: 20035624
    • Melzer G, Esfandabadi ME, Franco-Lara E, Wittmann C (2009) Flux design: in silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 3:120
    • (2009) BMC Syst Biol , vol.3 , pp. 120
    • Melzer, G.1    Esfandabadi, M.E.2    Franco-Lara, E.3    Wittmann, C.4
  • 56
    • 84907350970 scopus 로고    scopus 로고
    • Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
    • COI: 1:CAS:528:DC%2BC2cXht1OqsLvL, PID: 25080239
    • Campodonico MA, Andrews BA, Asenjo JA, Palsson BØ, Feist AM (2014) Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 25:140–158
    • (2014) Metab Eng , vol.25 , pp. 140-158
    • Campodonico, M.A.1    Andrews, B.A.2    Asenjo, J.A.3    Palsson, B.Ø.4    Feist, A.M.5
  • 57
    • 80051641411 scopus 로고    scopus 로고
    • Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
    • COI: 1:CAS:528:DC%2BC3MXhtFKms7jL, PID: 21846360
    • Milne CB, Eddy JA, Raju R, Ardekani S, Kim P-J, Senger RS, Jin Y-S, Blaschek HP, Price ND (2011) Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol 5:130
    • (2011) BMC Syst Biol , vol.5 , pp. 130
    • Milne, C.B.1    Eddy, J.A.2    Raju, R.3    Ardekani, S.4    Kim, P.-J.5    Senger, R.S.6    Jin, Y.-S.7    Blaschek, H.P.8    Price, N.D.9
  • 58
    • 84900303762 scopus 로고    scopus 로고
    • Optimizing genome-scale network reconstructions
    • COI: 1:CAS:528:DC%2BC2cXns1Wqtrs%3D, PID: 24811519
    • Monk J, Nogales J, Palsson BØ (2014) Optimizing genome-scale network reconstructions. Nat Biotechnol 32(5):447–452
    • (2014) Nat Biotechnol , vol.32 , Issue.5 , pp. 447-452
    • Monk, J.1    Nogales, J.2    Palsson, B.Ø.3
  • 60
    • 84870398009 scopus 로고    scopus 로고
    • Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach
    • COI: 1:CAS:528:DC%2BC3sXjsVaks7g%3D, PID: 23216785
    • Navid A, Almaas E (2012) Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach. BMC Syst Biol 6:150
    • (2012) BMC Syst Biol , vol.6 , pp. 150
    • Navid, A.1    Almaas, E.2
  • 62
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
    • PID: 21988831
    • Orth JD, Conrad TM, Na J, Lerman JA (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    Conrad, T.M.2    Na, J.3    Lerman, J.A.4
  • 63
    • 84876789665 scopus 로고    scopus 로고
    • Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
    • PID: 23631471
    • Österlund T, Nookaew I, Bordel S (2013) Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst Biol 7:36
    • (2013) BMC Syst Biol , vol.7 , pp. 36
    • Österlund, T.1    Nookaew, I.2    Bordel, S.3
  • 64
    • 34249934691 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation
    • COI: 1:CAS:528:DC%2BD2sXmtFCitrc%3D, PID: 17463081
    • Park JH, Lee KH, Kim TY, Lee SY (2007) Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci USA 104(19):7797–7802
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.19 , pp. 7797-7802
    • Park, J.H.1    Lee, K.H.2    Kim, T.Y.3    Lee, S.Y.4
  • 65
    • 84865075156 scopus 로고    scopus 로고
    • Flux variability scanning based on enforced objective flux for identifying gene amplification targets
    • PID: 22909053
    • Park JM, Park HM, Kim WJ, Kim HU, Kim TY, Lee SY (2012) Flux variability scanning based on enforced objective flux for identifying gene amplification targets. BMC Syst Biol 6:106
    • (2012) BMC Syst Biol , vol.6 , pp. 106
    • Park, J.M.1    Park, H.M.2    Kim, W.J.3    Kim, H.U.4    Kim, T.Y.5    Lee, S.Y.6
  • 66
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Forster J, Nielsen J (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform 6:308
    • (2005) BMC Bioinform , vol.6 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Forster, J.3    Nielsen, J.4
  • 67
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: a computational framework for redesign of microbial production systems
    • COI: 1:CAS:528:DC%2BD2cXpvVCiu74%3D, PID: 15520298
    • Pharkya P, Burgard AP, Maranas CD (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14(11):2367–2376
    • (2004) Genome Res , vol.14 , Issue.11 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 68
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
    • COI: 1:CAS:528:DC%2BD28XhsFKlug%3D%3D, PID: 16199194
    • Pharkya P, Maranas CD (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8(1):1–13
    • (2006) Metab Eng , vol.8 , Issue.1 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 70
    • 67449096729 scopus 로고    scopus 로고
    • Flux balance analysis of biological systems: applications and challenges
    • COI: 1:CAS:528:DC%2BD1MXnsFajsr4%3D, PID: 19287049
    • Raman K, Chandra N (2009) Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 10(4):435–449
    • (2009) Brief Bioinform , vol.10 , Issue.4 , pp. 435-449
    • Raman, K.1    Chandra, N.2
  • 71
    • 77954732846 scopus 로고    scopus 로고
    • Microbial 1-butanol production: identification of non-native production routes and in silico engineering interventions
    • COI: 1:CAS:528:DC%2BC3cXptV2hurY%3D, PID: 20665644
    • Ranganathan S, Maranas CD (2010) Microbial 1-butanol production: identification of non-native production routes and in silico engineering interventions. Biotechnol J 5(7):716–725
    • (2010) Biotechnol J , vol.5 , Issue.7 , pp. 716-725
    • Ranganathan, S.1    Maranas, C.D.2
  • 72
    • 77954590959 scopus 로고    scopus 로고
    • OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions
    • PID: 20419153
    • Ranganathan S, Suthers PF, Maranas CD (2010) OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol 6(4):e1000744
    • (2010) PLoS Comput Biol , vol.6 , Issue.4 , pp. 1000744
    • Ranganathan, S.1    Suthers, P.F.2    Maranas, C.D.3
  • 74
    • 54949140438 scopus 로고    scopus 로고
    • DESHARKY: automatic design of metabolic pathways for optimal cell growth
    • COI: 1:CAS:528:DC%2BD1cXht12gtbrI, PID: 18776195
    • Rodrigo G, Carrera J, Prather KJ, Jaramillo A (2008) DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24(21):2554–2556
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2554-2556
    • Rodrigo, G.1    Carrera, J.2    Prather, K.J.3    Jaramillo, A.4
  • 75
    • 84875977583 scopus 로고    scopus 로고
    • Inferring metabolic states in uncharacterized environments using gene-expression measurements
    • COI: 1:CAS:528:DC%2BC3sXlvVamurg%3D, PID: 23555222
    • Rossell S, Huynen MA, Notebaart RA (2013) Inferring metabolic states in uncharacterized environments using gene-expression measurements. PLoS Comput Biol 9(3):e1002988
    • (2013) PLoS Comput Biol , vol.9 , Issue.3 , pp. 1002988
    • Rossell, S.1    Huynen, M.A.2    Notebaart, R.A.3
  • 76
    • 84890092837 scopus 로고    scopus 로고
    • 3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
    • COI: 1:CAS:528:DC%2BC3sXhslWnsb7P, PID: 23975765
    • 3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 29(22):2900–2908
    • (2013) Bioinformatics , vol.29 , Issue.22 , pp. 2900-2908
    • Schmidt, B.J.1    Ebrahim, A.2    Metz, T.O.3    Adkins, J.N.4    Palsson, B.Ø.5    Hyduke, D.R.6
  • 77
    • 84860487758 scopus 로고    scopus 로고
    • Multidimensional optimality of microbial metabolism
    • COI: 1:CAS:528:DC%2BC38Xmt1Gntr4%3D, PID: 22556256
    • Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U (2012) Multidimensional optimality of microbial metabolism. Science 336(6081):601–604
    • (2012) Science , vol.336 , Issue.6081 , pp. 601-604
    • Schuetz, R.1    Zamboni, N.2    Zampieri, M.3    Heinemann, M.4    Sauer, U.5
  • 78
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • COI: 1:CAS:528:DC%2BD38Xpt1yru7Y%3D, PID: 12415116
    • Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99(23):15112–15117
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.23 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 79
    • 84862784156 scopus 로고    scopus 로고
    • Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture
    • COI: 1:CAS:528:DC%2BC38XhsVyhs7Y%3D, PID: 22252269
    • Selvarasu S, Ho YS, Chong WPK, Wong NSC, Yusufi FNK, Lee YY, Yap MGS, Lee D-Y (2012) Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture. Biotechnol Bioeng 109(6):1415–1429
    • (2012) Biotechnol Bioeng , vol.109 , Issue.6 , pp. 1415-1429
    • Selvarasu, S.1    Ho, Y.S.2    Chong, W.P.K.3    Wong, N.S.C.4    Yusufi, F.N.K.5    Lee, Y.Y.6    Yap, M.G.S.7    Lee, D.-Y.8
  • 80
    • 69249154275 scopus 로고    scopus 로고
    • Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum
    • PID: 19646286
    • Shinfuku Y, Sorpitiporn N, Sono M, Furusawa C, Hirasawa T, Shimizu H (2009) Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum. Microb Cell Fact 8:43
    • (2009) Microb Cell Fact , vol.8 , pp. 43
    • Shinfuku, Y.1    Sorpitiporn, N.2    Sono, M.3    Furusawa, C.4    Hirasawa, T.5    Shimizu, H.6
  • 81
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • COI: 1:CAS:528:DC%2BD2MXkslOms7o%3D, PID: 15897462
    • Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102(21):7695–7700
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.21 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 82
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissue-specific metabolism
    • COI: 1:CAS:528:DC%2BD1cXhtVygtLrF, PID: 18711341
    • Shlomi T, Cabili MN, Herrgard MJ, Palsson BØ, Ruppin E (2008) Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 26(9):1003–1010
    • (2008) Nat Biotechnol , vol.26 , Issue.9 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgard, M.J.3    Palsson, B.Ø.4    Ruppin, E.5
  • 83
    • 77954743150 scopus 로고    scopus 로고
    • Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production
    • COI: 1:CAS:528:DC%2BC3cXptV2hur8%3D, PID: 20503221
    • Sohn SB, Graf AB, Kim TY, Gasser B, Maurer M, Ferrer P, Mattanovich D, Lee SY (2010) Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol J 5(7):705–715
    • (2010) Biotechnol J , vol.5 , Issue.7 , pp. 705-715
    • Sohn, S.B.1    Graf, A.B.2    Kim, T.Y.3    Gasser, B.4    Maurer, M.5    Ferrer, P.6    Mattanovich, D.7    Lee, S.Y.8
  • 84
    • 84878409603 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of fumaric acid
    • COI: 1:CAS:528:DC%2BC3sXjtlanu7o%3D, PID: 23436277
    • Song CW, Kim DI, Choi S, Jang JW, Lee SY (2013) Metabolic engineering of Escherichia coli for the production of fumaric acid. Biotechnol Bioeng 110(7):2025–2034
    • (2013) Biotechnol Bioeng , vol.110 , Issue.7 , pp. 2025-2034
    • Song, C.W.1    Kim, D.I.2    Choi, S.3    Jang, J.W.4    Lee, S.Y.5
  • 85
    • 84856038703 scopus 로고    scopus 로고
    • The SuBliMinaL toolbox: automating steps in the reconstruction of metabolic networks
    • PID: 22095399
    • Swainston N, Smallbone K, Mendes P, Kell DB, Paton NW (2011) The SuBliMinaL toolbox: automating steps in the reconstruction of metabolic networks. J Integr Bioinform 8:186
    • (2011) J Integr Bioinform , vol.8 , pp. 186
    • Swainston, N.1    Smallbone, K.2    Mendes, P.3    Kell, D.B.4    Paton, N.W.5
  • 86
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
    • COI: 1:CAS:528:DC%2BC3cXhvF2qu7c%3D, PID: 20031969
    • Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26(4):536–543
    • (2010) Bioinformatics , vol.26 , Issue.4 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 87
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • COI: 1:CAS:528:DC%2BC3cXks12hsA%3D%3D, PID: 20057383
    • Thiele I, Palsson BØ (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5(1):93–121
    • (2010) Nat Protoc , vol.5 , Issue.1 , pp. 93-121
    • Thiele, I.1    Palsson, B.Ø.2
  • 89
    • 84874020311 scopus 로고    scopus 로고
    • Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli
    • PID: 23194026
    • Topfer N, Jozefczuk S, Nikoloski Z (2012) Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Syst Biol 6:148
    • (2012) BMC Syst Biol , vol.6 , pp. 148
    • Topfer, N.1    Jozefczuk, S.2    Nikoloski, Z.3
  • 91
    • 84877141897 scopus 로고    scopus 로고
    • Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production
    • COI: 1:CAS:528:DC%2BC3sXmsVejtrw%3D, PID: 23613453
    • Vu TT, Hill EA, Kucek LA, Konopka AE, Beliaev AS, Reed JL (2013) Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production. Biotechnol J 8(5):619–630
    • (2013) Biotechnol J , vol.8 , Issue.5 , pp. 619-630
    • Vu, T.T.1    Hill, E.A.2    Kucek, L.A.3    Konopka, A.E.4    Beliaev, A.S.5    Reed, J.L.6
  • 92
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • PID: 23234303
    • Wang YL, Eddy JA, Price ND (2012) Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 6:153
    • (2012) BMC Syst Biol , vol.6 , pp. 153
    • Wang, Y.L.1    Eddy, J.A.2    Price, N.D.3
  • 93
    • 79955145774 scopus 로고    scopus 로고
    • EMILiO: a fast algorithm for genome-scale strain design
    • COI: 1:CAS:528:DC%2BC3MXltFems78%3D, PID: 21414417
    • Yang L, Cluett WR, Mahadevan R (2011) EMILiO: a fast algorithm for genome-scale strain design. Metab Eng 13(3):272–281
    • (2011) Metab Eng , vol.13 , Issue.3 , pp. 272-281
    • Yang, L.1    Cluett, W.R.2    Mahadevan, R.3
  • 95
    • 84881496214 scopus 로고    scopus 로고
    • Optimizing cofactor specificity of oxidoreductase enzymes for the generation of microbial production strains—OptSwap
    • Zachary AK, Adam MF (2013) Optimizing cofactor specificity of oxidoreductase enzymes for the generation of microbial production strains—OptSwap. Ind Biotechnol 9(4):236–246
    • (2013) Ind Biotechnol , vol.9 , Issue.4 , pp. 236-246
    • Zachary, A.K.1    Adam, M.F.2


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