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Volumn 5, Issue , 2011, Pages

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES;

EID: 80053175304     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-147     Document Type: Article
Times cited : (92)

References (27)
  • 1
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • 2795471, 19888215
    • Oberhardt MA, Palsson B, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009, 5:320. 2795471, 19888215.
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.2    Papin, J.A.3
  • 2
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • 10.1002/bit.10803, 14595777
    • Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84(6):647-57. 10.1002/bit.10803, 14595777.
    • (2003) Biotechnol Bioeng , vol.84 , Issue.6 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 3
    • 77957837882 scopus 로고    scopus 로고
    • Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection
    • 10.1128/JB.00900-10, 2950489, 20709898
    • Oberhardt MA, Goldberg JB, Hogardt M, Papin JA. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 2010, 192(20):5534-48. 10.1128/JB.00900-10, 2950489, 20709898.
    • (2010) J Bacteriol , vol.192 , Issue.20 , pp. 5534-5548
    • Oberhardt, M.A.1    Goldberg, J.B.2    Hogardt, M.3    Papin, J.A.4
  • 4
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • 10.1371/journal.pcbi.1001002, 2987903, 21124952
    • Klitgord N, Segrè D. Environments that induce synthetic microbial ecosystems. PLoS Comput Biol 2010, 6(11):e1001002. 10.1371/journal.pcbi.1001002, 2987903, 21124952.
    • (2010) PLoS Comput Biol , vol.6 , Issue.11
    • Klitgord, N.1    Segrè, D.2
  • 5
    • 77954699812 scopus 로고    scopus 로고
    • Metabolic systems analysis to advance algal biotechnology
    • 10.1002/biot.201000129, 20665641
    • Schmidt BJ, Lin-Schmidt X, Chamberlin A, Salehi-Ashtiani K, Papin JA. Metabolic systems analysis to advance algal biotechnology. Biotechnol J 2010, 5(7):660-70. 10.1002/biot.201000129, 20665641.
    • (2010) Biotechnol J , vol.5 , Issue.7 , pp. 660-670
    • Schmidt, B.J.1    Lin-Schmidt, X.2    Chamberlin, A.3    Salehi-Ashtiani, K.4    Papin, J.A.5
  • 7
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • 10.1038/nbt.1614, 3108565, 20212490
    • Orth JD, Thiele I, Palsson B. What is flux balance analysis?. Nat Biotechnol 2010, 28(3):245-8. 10.1038/nbt.1614, 3108565, 20212490.
    • (2010) Nat Biotechnol , vol.28 , Issue.3 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.3
  • 8
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • 10.1016/j.mib.2010.03.003, 2912156, 20430689
    • Feist AM, Palsson BO. The biomass objective function. Curr Opin Microbiol 2010, 13(3):344-349. 10.1016/j.mib.2010.03.003, 2912156, 20430689.
    • (2010) Curr Opin Microbiol , vol.13 , Issue.3 , pp. 344-349
    • Feist, A.M.1    Palsson, B.O.2
  • 9
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • 10.1101/gr.2250904, 442145, 15197165
    • Duarte NC, Herrgård MJ, Palsson B. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004, 14(7):1298-309. 10.1101/gr.2250904, 442145, 15197165.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1298-1309
    • Duarte, N.C.1    Herrgård, M.J.2    Palsson, B.3
  • 10
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • 1865583, 17437026
    • Shlomi T, Eisenberg Y, Sharan R, Ruppin E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 2007, 3:101. 1865583, 17437026.
    • (2007) Mol Syst Biol , vol.3 , pp. 101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 11
    • 77951552860 scopus 로고    scopus 로고
    • OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
    • 10.1186/1752-0509-4-53, 2887412, 20426856
    • Kim J, Reed JL. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol 2010, 4:53. 10.1186/1752-0509-4-53, 2887412, 20426856.
    • (2010) BMC Syst Biol , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 12
    • 79951536020 scopus 로고    scopus 로고
    • Functional integration of a metabolic network model and expression data without arbitrary thresholding
    • 10.1093/bioinformatics/btq702, 21172910
    • Jensen PA, Papin JA. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 2011, 27(4):541-7. 10.1093/bioinformatics/btq702, 21172910.
    • (2011) Bioinformatics , vol.27 , Issue.4 , pp. 541-547
    • Jensen, P.A.1    Papin, J.A.2
  • 13
    • 78349239648 scopus 로고    scopus 로고
    • An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models
    • 10.1371/journal.pcbi.1000970, 2965739, 21060853
    • Barua D, Kim J, Reed JL. An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol 2010, 6(10):e1000970. 10.1371/journal.pcbi.1000970, 2965739, 21060853.
    • (2010) PLoS Comput Biol , vol.6 , Issue.10
    • Barua, D.1    Kim, J.2    Reed, J.L.3
  • 14
    • 69249102097 scopus 로고    scopus 로고
    • Genome-scale gene/reaction essentiality and synthetic lethality analysis
    • 2736653, 19690570
    • Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol 2009, 5:301. 2736653, 19690570.
    • (2009) Mol Syst Biol , vol.5 , pp. 301
    • Suthers, P.F.1    Zomorrodi, A.2    Maranas, C.D.3
  • 15
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • 10.1038/nature02456, 15129285
    • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429(6987):92-6. 10.1038/nature02456, 15129285.
    • (2004) Nature , vol.429 , Issue.6987 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 16
    • 33745178476 scopus 로고    scopus 로고
    • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
    • 10.1101/gr.4083206, 1457053, 16606697
    • Herrgård MJ, Lee BS, Portnoy V, Palsson B. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res 2006, 16(5):627-35. 10.1101/gr.4083206, 1457053, 16606697.
    • (2006) Genome Res , vol.16 , Issue.5 , pp. 627-635
    • Herrgård, M.J.1    Lee, B.S.2    Portnoy, V.3    Palsson, B.4
  • 17
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • 10.1006/jtbi.2001.2405, 11708855
    • Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. J Theor Biol 2001, 213:73-88. 10.1006/jtbi.2001.2405, 11708855.
    • (2001) J Theor Biol , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.3
  • 18
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • 10.1186/1752-0509-1-2, 1847467, 17408509
    • Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007, 1:2. 10.1186/1752-0509-1-2, 1847467, 17408509.
    • (2007) BMC Syst Biol , vol.1 , pp. 2
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 20
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • 10.1038/nprot.2007.99, 17406635
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson B, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2(3):727-38. 10.1038/nprot.2007.99, 17406635.
    • (2007) Nat Protoc , vol.2 , Issue.3 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.5    Herrgard, M.J.6
  • 22
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • 10.1016/j.ymben.2003.09.002, 14642354
    • Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003, 5(4):264-276. 10.1016/j.ymben.2003.09.002, 14642354.
    • (2003) Metab Eng , vol.5 , Issue.4 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 23
    • 77957117220 scopus 로고    scopus 로고
    • Computationally efficient flux variability analysis
    • 10.1186/1471-2105-11-489, 2963619, 20920235
    • Gudmundsson S, Thiele I. Computationally efficient flux variability analysis. BMC Bioinformatics 2010, 11:489. 10.1186/1471-2105-11-489, 2963619, 20920235.
    • (2010) BMC Bioinformatics , vol.11 , pp. 489
    • Gudmundsson, S.1    Thiele, I.2
  • 24
    • 33748049119 scopus 로고    scopus 로고
    • Matrix formalism to describe functional states of transcriptional regulatory systems
    • 10.1371/journal.pcbi.0020101, 1534074, 16895435
    • Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2006, 2(8):e101. 10.1371/journal.pcbi.0020101, 1534074, 16895435.
    • (2006) PLoS Comput Biol , vol.2 , Issue.8
    • Gianchandani, E.P.1    Papin, J.A.2    Price, N.D.3    Joyce, A.R.4    Palsson, B.O.5
  • 25
    • 0026598738 scopus 로고
    • Multiple regulatory elements control expression of the gene encoding the Saccharomyces cerevisiae cytochrome P450, lanosterol 14 alpha-demethylase (ERG11)
    • Turi TG, Loper JC. Multiple regulatory elements control expression of the gene encoding the Saccharomyces cerevisiae cytochrome P450, lanosterol 14 alpha-demethylase (ERG11). J Biol Chem 1992, 267(3):2046-2056.
    • (1992) J Biol Chem , vol.267 , Issue.3 , pp. 2046-2056
    • Turi, T.G.1    Loper, J.C.2
  • 26
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • 10.1371/journal.pcbi.1000082, 2366062, 18483554
    • Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 2008, 4(5):e1000082. 10.1371/journal.pcbi.1000082, 2366062, 18483554.
    • (2008) PLoS Comput Biol , vol.4 , Issue.5
    • Becker, S.A.1    Palsson, B.O.2
  • 27
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissue-specific metabolism
    • 10.1038/nbt.1487, 18711341
    • Shlomi T, Cabili MN, Herrgård MJ, Palsson B, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26(9):1003-10. 10.1038/nbt.1487, 18711341.
    • (2008) Nat Biotechnol , vol.26 , Issue.9 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgård, M.J.3    Palsson, B.4    Ruppin, E.5


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