메뉴 건너뛰기




Volumn 4, Issue , 2010, Pages

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

EID: 77951552860     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-53     Document Type: Article
Times cited : (190)

References (55)
  • 1
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • 10.1038/ng1432, 15448692
    • Fong SS, Palsson B. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004, 36:1056-1058. 10.1038/ng1432, 15448692.
    • (2004) Nat Genet , vol.36 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.2
  • 2
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • 10.1073/pnas.232349399, 137552, 12415116
    • Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99:15112-15117. 10.1073/pnas.232349399, 137552, 12415116.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 15112-15117
    • Segrè, D.1    Vitkup, D.2    Church, G.M.3
  • 3
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • 10.1073/pnas.0406346102, 1140402, 15897462
    • Shlomi T, Berkman O, Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 2005, 102:7695-7700. 10.1073/pnas.0406346102, 1140402, 15897462.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 4
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • 10.1038/msb4100162, 1949037, 17625511
    • Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:119. 10.1038/msb4100162, 1949037, 17625511.
    • (2007) Mol Syst Biol , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 5
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: A computational framework for redesign of microbial production systems
    • 10.1101/gr.2872004, 525696, 15520298
    • Pharkya P, Burgard AP, Maranas CD. OptStrain: A computational framework for redesign of microbial production systems. Genome Res 2004, 14:2367-2376. 10.1101/gr.2872004, 525696, 15520298.
    • (2004) Genome Res , vol.14 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 6
    • 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
    • 10.1073/pnas.0702609104, 1857225, 17463081
    • Park JH, Lee KH, Kim TY, Lee SY. 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 2007, 104:7797-7802. 10.1073/pnas.0702609104, 1857225, 17463081.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 7797-7802
    • Park, J.H.1    Lee, K.H.2    Kim, T.Y.3    Lee, S.Y.4
  • 7
    • 22844452835 scopus 로고    scopus 로고
    • Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets
    • 10.1038/nbt1083, 15821729
    • Alper H, Miyaoku K, Stephanopoulos G. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 2005, 23:612-616. 10.1038/nbt1083, 15821729.
    • (2005) Nat Biotechnol , vol.23 , pp. 612-616
    • Alper, H.1    Miyaoku, K.2    Stephanopoulos, G.3
  • 8
    • 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, 84:647-657. 10.1002/bit.10803, 14595777.
    • (2003) Biotechnol Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 10
    • 77954087740 scopus 로고    scopus 로고
    • Methods and organisms for the growth-coupled production of succinate
    • WO/2007/030830
    • Burgard AP, Van Dien SJ. Methods and organisms for the growth-coupled production of succinate. Patent 2007, WO/2007/030830.
    • (2007) Patent
    • Burgard, A.P.1    Van Dien, S.J.2
  • 11
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • 10.1186/1471-2105-6-308, 1327682, 16375763
    • Patil K, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, 6:308. 10.1186/1471-2105-6-308, 1327682, 16375763.
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.1    Rocha, I.2    Forster, J.3    Nielsen, J.4
  • 12
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
    • 10.1016/j.ymben.2005.08.003, 16199194
    • Pharkya P, Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 2006, 8:1-13. 10.1016/j.ymben.2005.08.003, 16199194.
    • (2006) Metab Eng , vol.8 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 14
    • 0037008673 scopus 로고    scopus 로고
    • Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    • 10.1074/jbc.M201691200, 12006566
    • Covert MW, Palsson B. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 2002, 277:28058-28064. 10.1074/jbc.M201691200, 12006566.
    • (2002) J Biol Chem , vol.277 , pp. 28058-28064
    • Covert, M.W.1    Palsson, B.2
  • 15
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • 10.1038/msb4100141, 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. 10.1038/msb4100141, 1865583, 17437026.
    • (2007) Mol Syst Biol , vol.3 , pp. 101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 16
    • 67650872959 scopus 로고    scopus 로고
    • Functional states of the genome-scale Escherichia Coli transcriptional regulatory system
    • 10.1371/journal.pcbi.1000403, 2685017, 19503608
    • Gianchandani EP, Joyce AR, Palsson B, Papin JA. Functional states of the genome-scale Escherichia Coli transcriptional regulatory system. PLoS Comput Biol 2009, 5:e1000403. 10.1371/journal.pcbi.1000403, 2685017, 19503608.
    • (2009) PLoS Comput Biol , vol.5
    • Gianchandani, E.P.1    Joyce, A.R.2    Palsson, B.3    Papin, J.A.4
  • 17
    • 69249102097 scopus 로고    scopus 로고
    • Genome-scale gene/reaction essentiality and synthetic lethality analysis
    • 10.1038/msb.2009.56, 2736653, 19690570
    • Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol 2009, 5:301. 10.1038/msb.2009.56, 2736653, 19690570.
    • (2009) Mol Syst Biol , vol.5 , pp. 301
    • Suthers, P.F.1    Zomorrodi, A.2    Maranas, C.D.3
  • 18
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • 10.1186/gb-2003-4-9-r54, 193654, 12952533
    • Reed JL, Vo TD, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.4
  • 19
    • 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 B. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96. 10.1038/nature02456, 15129285.
    • (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.5
  • 20
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • 10.1038/nature06450, 18172501
    • Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89. 10.1038/nature06450, 18172501.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 21
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
    • 201879, 7986045
    • Varma A, Palsson B. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60:3724-3731. 201879, 7986045.
    • (1994) Appl Environ Microbiol , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.2
  • 22
    • 0028131269 scopus 로고
    • An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth
    • 196835, 7928977
    • Zhao G, Winkler ME. An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. J Bacteriol 1994, 176:6134-6138. 196835, 7928977.
    • (1994) J Bacteriol , vol.176 , pp. 6134-6138
    • Zhao, G.1    Winkler, M.E.2
  • 23
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • 10.1038/msb4100155, 1911197, 17593909
    • Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3:121. 10.1038/msb4100155, 1911197, 17593909.
    • (2007) Mol Syst Biol , vol.3 , pp. 121
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3    Krummenacker, M.4    Joyce, A.R.5    Karp, P.D.6    Broadbelt, L.J.7    Hatzimanikatis, V.8    Palsson, B.9
  • 26
    • 33947357776 scopus 로고    scopus 로고
    • Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes
    • 10.1128/AEM.02456-06, 1828829, 17259366
    • Kim Y, Ingram LO, Shanmugam KT. Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes. Appl Environ Microbiol 2007, 73:1766-1771. 10.1128/AEM.02456-06, 1828829, 17259366.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 1766-1771
    • Kim, Y.1    Ingram, L.O.2    Shanmugam, K.T.3
  • 27
    • 0029975820 scopus 로고    scopus 로고
    • Stabilization of pet operon plasmids and ethanol production in Escherichia coli strains lacking lactate dehydrogenase and pyruvate formate-lyase activities
    • 168284, 8953729
    • Hespell RB, Wyckoff H, Dien BS, Bothast RJ. Stabilization of pet operon plasmids and ethanol production in Escherichia coli strains lacking lactate dehydrogenase and pyruvate formate-lyase activities. Appl Environ Microbiol 1996, 62:4594-4597. 168284, 8953729.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 4594-4597
    • Hespell, R.B.1    Wyckoff, H.2    Dien, B.S.3    Bothast, R.J.4
  • 28
    • 2442545374 scopus 로고    scopus 로고
    • The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli
    • 10.1007/s00253-003-1499-9, 14673546
    • Zhu J, Shimizu K. The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli. Appl Microbiol Biotechnol 2004, 64:367-375. 10.1007/s00253-003-1499-9, 14673546.
    • (2004) Appl Microbiol Biotechnol , vol.64 , pp. 367-375
    • Zhu, J.1    Shimizu, K.2
  • 29
    • 15944366483 scopus 로고    scopus 로고
    • Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses
    • 10.1002/bit.20381, 15669087
    • Levanon SS, San K-Y, Bennett GN. Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol Bioeng 2005, 89:556-564. 10.1002/bit.20381, 15669087.
    • (2005) Biotechnol Bioeng , vol.89 , pp. 556-564
    • Levanon, S.S.1    San, K.-Y.2    Bennett, G.N.3
  • 30
    • 44349173795 scopus 로고    scopus 로고
    • Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12
    • 10.1128/JB.00104-08, 2395023, 18375566
    • Kim Y, Ingram LO, Shanmugam KT. Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12. J Bacteriol 2008, 190:3851-3858. 10.1128/JB.00104-08, 2395023, 18375566.
    • (2008) J Bacteriol , vol.190 , pp. 3851-3858
    • Kim, Y.1    Ingram, L.O.2    Shanmugam, K.T.3
  • 31
    • 0037560068 scopus 로고    scopus 로고
    • The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli
    • 10.1007/s00253-003-1234-6, 12835924
    • Tomar A, Eiteman MA, Altman E. The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli. Appl Microbiol Biotechnol 2003, 62:76-82. 10.1007/s00253-003-1234-6, 12835924.
    • (2003) Appl Microbiol Biotechnol , vol.62 , pp. 76-82
    • Tomar, A.1    Eiteman, M.A.2    Altman, E.3
  • 32
    • 1442306213 scopus 로고    scopus 로고
    • Engineering Escherichia coli for efficient conversion of glucose to pyruvate
    • 10.1073/pnas.0308171100, 356934, 14982993
    • Causey TB, Shanmugam KT, Yomano LP, Ingram LO. Engineering Escherichia coli for efficient conversion of glucose to pyruvate. Proc Natl Acad Sci USA 2004, 101:2235-2240. 10.1073/pnas.0308171100, 356934, 14982993.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 2235-2240
    • Causey, T.B.1    Shanmugam, K.T.2    Yomano, L.P.3    Ingram, L.O.4
  • 33
    • 16344391449 scopus 로고    scopus 로고
    • Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate
    • Dittrich CR, Vadali RV, Bennett GN, San K-Y. Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate. Biotechnol Progr 2005, 21:627-631.
    • (2005) Biotechnol Progr , vol.21 , pp. 627-631
    • Dittrich, C.R.1    Vadali, R.V.2    Bennett, G.N.3    San, K.-Y.4
  • 34
    • 0031691147 scopus 로고    scopus 로고
    • Methylglyoxal production in bacteria: suicide or survival?
    • 10.1007/s002030050635, 9732434
    • Ferguson GP, Tötemeyer S, MacLean MJ, Booth IR. Methylglyoxal production in bacteria: suicide or survival?. Arch Microbiol 1998, 170:209-218. 10.1007/s002030050635, 9732434.
    • (1998) Arch Microbiol , vol.170 , pp. 209-218
    • Ferguson, G.P.1    Tötemeyer, S.2    MacLean, M.J.3    Booth, I.R.4
  • 35
    • 26844512919 scopus 로고    scopus 로고
    • Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system
    • 10.1186/1475-2859-4-14, 1156936, 15904518
    • Gosset G. Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system. Microb Cell Fact 2005, 4:14. 10.1186/1475-2859-4-14, 1156936, 15904518.
    • (2005) Microb Cell Fact , vol.4 , pp. 14
    • Gosset, G.1
  • 36
    • 0028129875 scopus 로고
    • Why does Escherichia coli have two primary pathways for synthesis of glutamate?
    • 196288, 7913929
    • Helling RB. Why does Escherichia coli have two primary pathways for synthesis of glutamate?. J Bacteriol 1994, 176:4664-4668. 196288, 7913929.
    • (1994) J Bacteriol , vol.176 , pp. 4664-4668
    • Helling, R.B.1
  • 37
    • 45749137679 scopus 로고    scopus 로고
    • Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
    • 10.1128/AEM.02708-07, 2446564, 18424547
    • Trinh CT, Unrean P, Srienc F. Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses. Appl Environ Microbiol 2008, 74:3634-3643. 10.1128/AEM.02708-07, 2446564, 18424547.
    • (2008) Appl Environ Microbiol , vol.74 , pp. 3634-3643
    • Trinh, C.T.1    Unrean, P.2    Srienc, F.3
  • 39
    • 0142152457 scopus 로고    scopus 로고
    • Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model
    • 10.1128/JB.185.21.6400-6408.2003, 219384, 14563875
    • Fong SS, Marciniak JY, Palsson B. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol 2003, 185:6400-6408. 10.1128/JB.185.21.6400-6408.2003, 219384, 14563875.
    • (2003) J Bacteriol , vol.185 , pp. 6400-6408
    • Fong, S.S.1    Marciniak, J.Y.2    Palsson, B.3
  • 40
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • 10.1101/gr.3832305, 1240078, 16204189
    • Fong SS, Joyce AR, Palsson B. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 2005, 15:1365-1372. 10.1101/gr.3832305, 1240078, 16204189.
    • (2005) Genome Res , vol.15 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.3
  • 41
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • 10.1126/science.1081900, 12843395
    • Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301:102-105. 10.1126/science.1081900, 12843395.
    • (2003) Science , vol.301 , pp. 102-105
    • Gardner, T.S.1    di Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 42
    • 70049110173 scopus 로고    scopus 로고
    • Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
    • 10.1371/journal.pcbi.1000489, 2726785, 19714220
    • Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol 2009, 5:e1000489. 10.1371/journal.pcbi.1000489, 2726785, 19714220.
    • (2009) PLoS Comput Biol , vol.5
    • Colijn, C.1    Brandes, A.2    Zucker, J.3    Lun, D.S.4    Weiner, B.5    Farhat, M.R.6    Cheng, T.Y.7    Moody, D.B.8    Murray, M.9    Galagan, J.E.10
  • 43
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissue-specific metabolism
    • 10.1038/nbt.1487, 18711341
    • Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26:1003-1010. 10.1038/nbt.1487, 18711341.
    • (2008) Nat Biotechnol , vol.26 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgard, M.J.3    Palsson, B.O.4    Ruppin, E.5
  • 45
    • 70449592325 scopus 로고    scopus 로고
    • Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
    • 10.1016/j.ymben.2009.07.001, 19619667
    • Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 2009, 11:328-334. 10.1016/j.ymben.2009.07.001, 19619667.
    • (2009) Metab Eng , vol.11 , pp. 328-334
    • Asadollahi, M.A.1    Maury, J.2    Patil, K.R.3    Schalk, M.4    Clark, A.5    Nielsen, J.6
  • 46
    • 34548219522 scopus 로고    scopus 로고
    • Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    • 10.1021/cr068309+, 2643304, 17636889
    • Rodionov DA. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 2007, 107:3467-3497. 10.1021/cr068309+, 2643304, 17636889.
    • (2007) Chem Rev , vol.107 , pp. 3467-3497
    • Rodionov, D.A.1
  • 47
    • 33646920070 scopus 로고    scopus 로고
    • Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach
    • 10.1371/journal.pcbi.0020052, 1463018,1463018, 16710450
    • Barrett CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol 2006, 2:e52. 10.1371/journal.pcbi.0020052, 1463018,1463018, 16710450.
    • (2006) PLoS Comput Biol , vol.2
    • Barrett, C.L.1    Palsson, B.O.2
  • 48
    • 34548499877 scopus 로고    scopus 로고
    • Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
    • 10.1186/1471-2105-8-293, 1964768, 17683642
    • Rodriguez-Penagos C, Salgado H, Martinez-Flores I, Collado-Vides J. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 2007, 8:293. 10.1186/1471-2105-8-293, 1964768, 17683642.
    • (2007) BMC Bioinformatics , vol.8 , pp. 293
    • Rodriguez-Penagos, C.1    Salgado, H.2    Martinez-Flores, I.3    Collado-Vides, J.4
  • 49
    • 62649125796 scopus 로고    scopus 로고
    • Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms
    • 10.1186/1752-0509-3-8, 2653031, 19146695
    • Baumbach J, Rahmann S, Tauch A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol 2009, 3:8. 10.1186/1752-0509-3-8, 2653031, 19146695.
    • (2009) BMC Syst Biol , vol.3 , pp. 8
    • Baumbach, J.1    Rahmann, S.2    Tauch, A.3
  • 50
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • 10.1371/journal.pbio.0050008, 1764438,1764438, 17214507
    • Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5:e8. 10.1371/journal.pbio.0050008, 1764438,1764438, 17214507.
    • (2007) PLoS Biol , vol.5
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6    Kasif, S.7    Collins, J.J.8    Gardner, T.S.9
  • 51
    • 67249157808 scopus 로고    scopus 로고
    • Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
    • 10.1093/nar/gkp248, 2691844, 19383880
    • Zhang S, Xu M, Li S, Su Z. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res 2009, 37:e72. 10.1093/nar/gkp248, 2691844, 19383880.
    • (2009) Nucleic Acids Res , vol.37
    • Zhang, S.1    Xu, M.2    Li, S.3    Su, Z.4
  • 52
    • 28444484981 scopus 로고    scopus 로고
    • Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
    • 10.1073/pnas.0505147102, 1297658, 16301543
    • Wang T, Stormo GD. Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci USA 2005, 102:17400-17405. 10.1073/pnas.0505147102, 1297658, 16301543.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 17400-17405
    • Wang, T.1    Stormo, G.D.2
  • 53
    • 0346328227 scopus 로고    scopus 로고
    • Metabolic engineering for drug discovery and development
    • 10.1038/nrd1256, 14654799
    • Khosla C, Keasling JD. Metabolic engineering for drug discovery and development. Nat Rev Drug Discov 2003, 2:1019-1025. 10.1038/nrd1256, 14654799.
    • (2003) Nat Rev Drug Discov , vol.2 , pp. 1019-1025
    • Khosla, C.1    Keasling, J.D.2
  • 54
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • 10.1038/nbt1401, 18536691
    • Feist AM, Palsson B. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-667. 10.1038/nbt1401, 18536691.
    • (2008) Nat Biotechnol , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.2
  • 55
    • 70349281876 scopus 로고    scopus 로고
    • Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?
    • 10.1038/nrmicro2186, 19756010
    • Alper H, Stephanopoulos G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?. Nat Rev Microbiol 2009, 7:715-723. 10.1038/nrmicro2186, 19756010.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 715-723
    • Alper, H.1    Stephanopoulos, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.