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Volumn 29, Issue 1, 2014, Pages 34-38

Refining metabolic models and accounting for regulatory effects

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING; REPAIR;

EID: 84896051852     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.02.009     Document Type: Review
Times cited : (16)

References (50)
  • 1
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I., Palsson B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 3
    • 84891635463 scopus 로고    scopus 로고
    • Software platforms to facilitate reconstructing genome-scale metabolic networks
    • Hamilton J.J., Reed J.L. Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ Microbiol 2013, 16:49-59.
    • (2013) Environ Microbiol , vol.16 , pp. 49-59
    • Hamilton, J.J.1    Reed, J.L.2
  • 4
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis N.E., Nagarajan H., Palsson B.O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012, 10:291-305.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 6
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • Agren R., Liu L., Shoaie S., Vongsangnak W., Nookaew I., Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol 2013, 9:e1002980.
    • (2013) PLoS Comput Biol , vol.9
    • Agren, R.1    Liu, L.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 7
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • Kuepfer L., Sauer U., Blank L.M. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15:1421-1430.
    • (2005) Genome Res , vol.15 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 11
    • 84870941105 scopus 로고    scopus 로고
    • FOCAL: an experimental design tool for systematizing metabolic discoveries and model development
    • Tervo C.J., Reed J.L. FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol 2012, 13:R116.
    • (2012) Genome Biol , vol.13
    • Tervo, C.J.1    Reed, J.L.2
  • 13
    • 84870053320 scopus 로고    scopus 로고
    • MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
    • Vitkin E., Shlomi T. MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. Genome Biol 2012, 13:R111.
    • (2012) Genome Biol , vol.13
    • Vitkin, E.1    Shlomi, T.2
  • 14
    • 63549108441 scopus 로고    scopus 로고
    • GrowMatch: an automated method for reconciling in silico/in vivo growth predictions
    • Kumar V.S., Maranas C.D. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 2009, 5:e1000308.
    • (2009) PLoS Comput Biol , vol.5
    • Kumar, V.S.1    Maranas, C.D.2
  • 15
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Satish Kumar V., Dasika M.S., Maranas C.D. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 2007, 8:212.
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 16
    • 84862159261 scopus 로고    scopus 로고
    • Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
    • Orth J.D., Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol 2012, 6:30.
    • (2012) BMC Syst Biol , vol.6 , pp. 30
    • Orth, J.D.1    Palsson, B.2
  • 17
    • 69249102097 scopus 로고    scopus 로고
    • Genome-scale gene/reaction essentiality and synthetic lethality analysis
    • Suthers P.F., Zomorrodi A., Maranas C.D. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol 2009, 5:301.
    • (2009) Mol Syst Biol , vol.5 , pp. 301
    • Suthers, P.F.1    Zomorrodi, A.2    Maranas, C.D.3
  • 18
    • 78650595350 scopus 로고    scopus 로고
    • Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data
    • Zomorrodi A.R., Maranas C.D. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol 2010, 4:178.
    • (2010) BMC Syst Biol , vol.4 , pp. 178
    • Zomorrodi, A.R.1    Maranas, C.D.2
  • 19
    • 84870256513 scopus 로고    scopus 로고
    • Global probabilistic annotation of metabolic networks enables enzyme discovery
    • Plata G., Fuhrer T., Hsiao T.L., Sauer U., Vitkup D. Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol 2012, 8:848-854.
    • (2012) Nat Chem Biol , vol.8 , pp. 848-854
    • Plata, G.1    Fuhrer, T.2    Hsiao, T.L.3    Sauer, U.4    Vitkup, D.5
  • 20
    • 33746660425 scopus 로고    scopus 로고
    • Identification of genome-scale metabolic network models using experimentally measured flux profiles
    • Herrgard M.J., Fong S.S., Palsson B.O. Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2006, 2:e72.
    • (2006) PLoS Comput Biol , vol.2
    • Herrgard, M.J.1    Fong, S.S.2    Palsson, B.O.3
  • 21
    • 84891959604 scopus 로고    scopus 로고
    • BioMog: a computational framework for the de novo generation or modification of essential biomass components
    • Tervo C.J., Reed J.L. BioMog: a computational framework for the de novo generation or modification of essential biomass components. PLoS One 2013, 8:e81322.
    • (2013) PLoS One , vol.8
    • Tervo, C.J.1    Reed, J.L.2
  • 22
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert M.W., Knight E.M., Reed J.L., Herrgard M.J., Palsson B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 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
  • 23
    • 33745178476 scopus 로고    scopus 로고
    • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
    • Herrgard M.J., Lee B.S., Portnoy V., Palsson B.O. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res 2006, 16:627-635.
    • (2006) Genome Res , vol.16 , pp. 627-635
    • Herrgard, M.J.1    Lee, B.S.2    Portnoy, V.3    Palsson, B.O.4
  • 24
    • 0037008673 scopus 로고    scopus 로고
    • Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    • Covert M.W., Palsson B.O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 2002, 277:28058-28064.
    • (2002) J Biol Chem , vol.277 , pp. 28058-28064
    • Covert, M.W.1    Palsson, B.O.2
  • 25
    • 78349239648 scopus 로고    scopus 로고
    • An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models
    • Barua D., Kim J., Reed J.L. An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol 2010, 6:e1000970.
    • (2010) PLoS Comput Biol , vol.6
    • Barua, D.1    Kim, J.2    Reed, J.L.3
  • 26
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran S., Price N.D. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010, 107:17845-17850.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 29
    • 38549162091 scopus 로고    scopus 로고
    • DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    • Database issue
    • Sierro N., Makita Y., de Hoon M., Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008, 36(Database issue):D93-D96.
    • (2008) Nucleic Acids Res , vol.36
    • Sierro, N.1    Makita, Y.2    de Hoon, M.3    Nakai, K.4
  • 30
    • 84875521674 scopus 로고    scopus 로고
    • RegTransBase-a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
    • Cipriano M.J., Novichkov P.N., Kazakov A.E., Rodionov D.A., Arkin A.P., Gelfand M.S., Dubchak I. RegTransBase-a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 2013, 14:213.
    • (2013) BMC Genomics , vol.14 , pp. 213
    • Cipriano, M.J.1    Novichkov, P.N.2    Kazakov, A.E.3    Rodionov, D.A.4    Arkin, A.P.5    Gelfand, M.S.6    Dubchak, I.7
  • 31
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 2008, 9:326-332.
    • (2008) Brief Bioinform , vol.9 , pp. 326-332
    • Wingender, E.1
  • 34
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
    • Thiele I., Fleming R.M., Que R., Bordbar A., Diep D., Palsson B.O. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One 2012, 7:e45635.
    • (2012) PLoS One , vol.7
    • Thiele, I.1    Fleming, R.M.2    Que, R.3    Bordbar, A.4    Diep, D.5    Palsson, B.O.6
  • 35
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • O'Brien E.J., Lerman J.A., Chang R.L., Hyduke D.R., Palsson B.O. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 2013, 9:693.
    • (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
  • 38
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker S.A., Palsson B.O. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 2008, 4:e1000082.
    • (2008) PLoS Comput Biol , vol.4
    • Becker, S.A.1    Palsson, B.O.2
  • 40
    • 79951536020 scopus 로고    scopus 로고
    • Functional integration of a metabolic network model and expression data without arbitrary thresholding
    • Jensen P.A., Papin J.A. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 2011, 27:541-547.
    • (2011) Bioinformatics , vol.27 , pp. 541-547
    • Jensen, P.A.1    Papin, J.A.2
  • 42
    • 84856015478 scopus 로고    scopus 로고
    • Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
    • Mintz-Oron S., Meir S., Malitsky S., Ruppin E., Aharoni A., Shlomi T. Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci U S A 2012, 109:339-344.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 339-344
    • Mintz-Oron, S.1    Meir, S.2    Malitsky, S.3    Ruppin, E.4    Aharoni, A.5    Shlomi, T.6
  • 44
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • Jerby L., Shlomi T., Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010, 6:401.
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 47
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • Agren R., Bordel S., Mardinoglu A., Pornputtapong N., Nookaew I., Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 2012, 8:e1002518.
    • (2012) PLoS Comput Biol , vol.8
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 48
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang Y., Eddy J.A., Price N.D. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 2012, 6:153.
    • (2012) BMC Syst Biol , vol.6 , pp. 153
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 50
    • 84883389182 scopus 로고    scopus 로고
    • Understanding the interactions between bacteria in the human gut through metabolic modeling
    • Shoaie S., Karlsson F., Mardinoglu A., Nookaew I., Bordel S., Nielsen J. Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci Rep 2013, 3:2532.
    • (2013) Sci Rep , vol.3 , pp. 2532
    • Shoaie, S.1    Karlsson, F.2    Mardinoglu, A.3    Nookaew, I.4    Bordel, S.5    Nielsen, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.