{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T08:32:23Z","timestamp":1771057943691,"version":"3.50.1"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,4,28]],"date-time":"2010-04-28T00:00:00Z","timestamp":1272412800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1752-0509-4-53","type":"journal-article","created":{"date-parts":[[2010,4,28]],"date-time":"2010-04-28T18:15:49Z","timestamp":1272478549000},"source":"Crossref","is-referenced-by-count":188,"title":["OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains"],"prefix":"10.1186","volume":"4","author":[{"given":"Joonhoon","family":"Kim","sequence":"first","affiliation":[]},{"given":"Jennifer L","family":"Reed","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,4,28]]},"reference":[{"key":"442_CR1","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1038\/ng1432","volume":"36","author":"SS Fong","year":"2004","unstructured":"Fong SS, Palsson B\u00d8: Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet. 2004, 36: 1056-1058. 10.1038\/ng1432","journal-title":"Nat Genet"},{"key":"442_CR2","doi-asserted-by":"publisher","first-page":"15112","DOI":"10.1073\/pnas.232349399","volume":"99","author":"D Segr\u00e8","year":"2002","unstructured":"Segr\u00e8 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","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR3","doi-asserted-by":"publisher","first-page":"7695","DOI":"10.1073\/pnas.0406346102","volume":"102","author":"T Shlomi","year":"2005","unstructured":"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","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR4","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/msb4100162","volume":"3","author":"R Schuetz","year":"2007","unstructured":"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","journal-title":"Mol Syst Biol"},{"key":"442_CR5","doi-asserted-by":"publisher","first-page":"2367","DOI":"10.1101\/gr.2872004","volume":"14","author":"P Pharkya","year":"2004","unstructured":"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","journal-title":"Genome Res"},{"key":"442_CR6","doi-asserted-by":"publisher","first-page":"7797","DOI":"10.1073\/pnas.0702609104","volume":"104","author":"JH Park","year":"2007","unstructured":"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","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR7","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nbt1083","volume":"23","author":"H Alper","year":"2005","unstructured":"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","journal-title":"Nat Biotechnol"},{"key":"442_CR8","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1002\/bit.10803","volume":"84","author":"AP Burgard","year":"2003","unstructured":"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","journal-title":"Biotechnol Bioeng"},{"key":"442_CR9","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1002\/bit.20542","volume":"91","author":"SS Fong","year":"2005","unstructured":"Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson B\u00d8: In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng. 2005, 91: 643-648. 10.1002\/bit.20542","journal-title":"Biotechnol Bioeng"},{"key":"442_CR10","volume-title":"Patent","author":"AP Burgard","year":"2007","unstructured":"Burgard AP, Van Dien SJ: Methods and organisms for the growth-coupled production of succinate. Patent. 2007,WO\/2007\/030830,"},{"key":"442_CR11","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1186\/1471-2105-6-308","volume":"6","author":"K Patil","year":"2005","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"442_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ymben.2005.08.003","volume":"8","author":"P Pharkya","year":"2006","unstructured":"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","journal-title":"Metab Eng"},{"key":"442_CR13","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1038\/msb.2009.57","volume":"5","author":"DS Lun","year":"2009","unstructured":"Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM: Large-scale identification of genetic design strategies using local search. Mol Syst Biol. 2009, 5: 296- 10.1038\/msb.2009.57","journal-title":"Mol Syst Biol"},{"key":"442_CR14","doi-asserted-by":"publisher","first-page":"28058","DOI":"10.1074\/jbc.M201691200","volume":"277","author":"MW Covert","year":"2002","unstructured":"Covert MW, Palsson B\u00d8: Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem. 2002, 277: 28058-28064. 10.1074\/jbc.M201691200","journal-title":"J Biol Chem"},{"key":"442_CR15","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/msb4100141","volume":"3","author":"T Shlomi","year":"2007","unstructured":"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","journal-title":"Mol Syst Biol"},{"key":"442_CR16","doi-asserted-by":"publisher","first-page":"e1000403","DOI":"10.1371\/journal.pcbi.1000403","volume":"5","author":"EP Gianchandani","year":"2009","unstructured":"Gianchandani EP, Joyce AR, Palsson B\u00d8, Papin JA: Functional states of the genome-scale Escherichia Coli transcriptional regulatory system. PLoS Comput Biol. 2009, 5: e1000403- 10.1371\/journal.pcbi.1000403","journal-title":"PLoS Comput Biol"},{"key":"442_CR17","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/msb.2009.56","volume":"5","author":"PF Suthers","year":"2009","unstructured":"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","journal-title":"Mol Syst Biol"},{"key":"442_CR18","doi-asserted-by":"publisher","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","volume":"4","author":"JL Reed","year":"2003","unstructured":"Reed JL, Vo TD, Schilling CH, Palsson B\u00d8: An expanded genome-scale model of Escherichia coli K-12 (i JR904 GSM\/GPR). Genome Biol. 2003, 4: R54- 10.1186\/gb-2003-4-9-r54","journal-title":"Genome Biol"},{"key":"442_CR19","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/nature02456","volume":"429","author":"MW Covert","year":"2004","unstructured":"Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson B\u00d8: Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004, 429: 92-96. 10.1038\/nature02456","journal-title":"Nature"},{"key":"442_CR20","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1038\/nature06450","volume":"451","author":"S Atsumi","year":"2008","unstructured":"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","journal-title":"Nature"},{"key":"442_CR21","doi-asserted-by":"crossref","first-page":"3724","DOI":"10.1128\/AEM.60.10.3724-3731.1994","volume":"60","author":"A Varma","year":"1994","unstructured":"Varma A, Palsson B\u00d8: 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.","journal-title":"Appl Environ Microbiol"},{"key":"442_CR22","doi-asserted-by":"crossref","first-page":"6134","DOI":"10.1128\/jb.176.19.6134-6138.1994","volume":"176","author":"G Zhao","year":"1994","unstructured":"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.","journal-title":"J Bacteriol"},{"key":"442_CR23","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/msb4100155","volume":"3","author":"AM Feist","year":"2007","unstructured":"Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B\u00d8: 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","journal-title":"Mol Syst Biol"},{"key":"442_CR24","doi-asserted-by":"publisher","first-page":"8259","DOI":"10.1128\/JB.00740-06","volume":"188","author":"AR Joyce","year":"2006","unstructured":"Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson B\u00d8, Agarwalla S: Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol. 2006, 188: 8259-8271. 10.1128\/JB.00740-06","journal-title":"J Bacteriol"},{"key":"442_CR25","volume-title":"Mol Syst Biol","author":"T Baba","year":"2006","unstructured":"Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006, 2: 10.1038\/msb4100050. 2006.0008,"},{"key":"442_CR26","doi-asserted-by":"publisher","first-page":"1766","DOI":"10.1128\/AEM.02456-06","volume":"73","author":"Y Kim","year":"2007","unstructured":"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","journal-title":"Appl Environ Microbiol"},{"key":"442_CR27","doi-asserted-by":"crossref","first-page":"4594","DOI":"10.1128\/AEM.62.12.4594-4597.1996","volume":"62","author":"RB Hespell","year":"1996","unstructured":"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.","journal-title":"Appl Environ Microbiol"},{"key":"442_CR28","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1007\/s00253-003-1499-9","volume":"64","author":"J Zhu","year":"2004","unstructured":"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","journal-title":"Appl Microbiol Biotechnol"},{"key":"442_CR29","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1002\/bit.20381","volume":"89","author":"SS Levanon","year":"2005","unstructured":"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","journal-title":"Biotechnol Bioeng"},{"key":"442_CR30","doi-asserted-by":"publisher","first-page":"3851","DOI":"10.1128\/JB.00104-08","volume":"190","author":"Y Kim","year":"2008","unstructured":"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","journal-title":"J Bacteriol"},{"key":"442_CR31","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1007\/s00253-003-1234-6","volume":"62","author":"A Tomar","year":"2003","unstructured":"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","journal-title":"Appl Microbiol Biotechnol"},{"key":"442_CR32","doi-asserted-by":"publisher","first-page":"2235","DOI":"10.1073\/pnas.0308171100","volume":"101","author":"TB Causey","year":"2004","unstructured":"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","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR33","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1021\/bp049730r","volume":"21","author":"CR Dittrich","year":"2005","unstructured":"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. 10.1021\/bp049730r.","journal-title":"Biotechnol Progr"},{"key":"442_CR34","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s002030050635","volume":"170","author":"GP Ferguson","year":"1998","unstructured":"Ferguson GP, T\u00f6temeyer S, MacLean MJ, Booth IR: Methylglyoxal production in bacteria: suicide or survival?. Arch Microbiol. 1998, 170: 209-218. 10.1007\/s002030050635","journal-title":"Arch Microbiol"},{"key":"442_CR35","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1475-2859-4-14","volume":"4","author":"G Gosset","year":"2005","unstructured":"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","journal-title":"Microb Cell Fact"},{"key":"442_CR36","doi-asserted-by":"crossref","first-page":"4664","DOI":"10.1128\/jb.176.15.4664-4668.1994","volume":"176","author":"RB Helling","year":"1994","unstructured":"Helling RB: Why does Escherichia coli have two primary pathways for synthesis of glutamate?. J Bacteriol. 1994, 176: 4664-4668.","journal-title":"J Bacteriol"},{"key":"442_CR37","doi-asserted-by":"publisher","first-page":"3634","DOI":"10.1128\/AEM.02708-07","volume":"74","author":"CT Trinh","year":"2008","unstructured":"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","journal-title":"Appl Environ Microbiol"},{"key":"442_CR38","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1038\/ng1906","volume":"38","author":"CD Herring","year":"2006","unstructured":"Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, Boom van den D, Cantor CR, Palsson BO: Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 2006, 38: 1406-1412. 10.1038\/ng1906","journal-title":"Nat Genet"},{"key":"442_CR39","doi-asserted-by":"publisher","first-page":"6400","DOI":"10.1128\/JB.185.21.6400-6408.2003","volume":"185","author":"SS Fong","year":"2003","unstructured":"Fong SS, Marciniak JY, Palsson B\u00d8: 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","journal-title":"J Bacteriol"},{"key":"442_CR40","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1101\/gr.3832305","volume":"15","author":"SS Fong","year":"2005","unstructured":"Fong SS, Joyce AR, Palsson B\u00d8: 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","journal-title":"Genome Res"},{"key":"442_CR41","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.1081900","volume":"301","author":"TS Gardner","year":"2003","unstructured":"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","journal-title":"Science"},{"key":"442_CR42","doi-asserted-by":"publisher","first-page":"e1000489","DOI":"10.1371\/journal.pcbi.1000489","volume":"5","author":"C Colijn","year":"2009","unstructured":"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","journal-title":"PLoS Comput Biol"},{"key":"442_CR43","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1038\/nbt.1487","volume":"26","author":"T Shlomi","year":"2008","unstructured":"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","journal-title":"Nat Biotechnol"},{"key":"442_CR44","doi-asserted-by":"publisher","first-page":"6477","DOI":"10.1073\/pnas.0811091106","volume":"106","author":"JF Moxley","year":"2009","unstructured":"Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci USA. 2009, 106: 6477-6482. 10.1073\/pnas.0811091106","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR45","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/j.ymben.2009.07.001","volume":"11","author":"MA Asadollahi","year":"2009","unstructured":"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","journal-title":"Metab Eng"},{"key":"442_CR46","doi-asserted-by":"publisher","first-page":"3467","DOI":"10.1021\/cr068309+","volume":"107","author":"DA Rodionov","year":"2007","unstructured":"Rodionov DA: Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev. 2007, 107: 3467-3497. 10.1021\/cr068309+","journal-title":"Chem Rev"},{"key":"442_CR47","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1371\/journal.pcbi.0020052","volume":"2","author":"CL Barrett","year":"2006","unstructured":"Barrett CL, Palsson BO: Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol. 2006, 2: e52- 10.1371\/journal.pcbi.0020052","journal-title":"PLoS Comput Biol"},{"key":"442_CR48","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1186\/1471-2105-8-293","volume":"8","author":"C Rodriguez-Penagos","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"442_CR49","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1752-0509-3-8","volume":"3","author":"J Baumbach","year":"2009","unstructured":"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","journal-title":"BMC Syst Biol"},{"key":"442_CR50","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"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","journal-title":"PLoS Biol"},{"key":"442_CR51","doi-asserted-by":"publisher","first-page":"e72","DOI":"10.1093\/nar\/gkp248","volume":"37","author":"S Zhang","year":"2009","unstructured":"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","journal-title":"Nucleic Acids Res"},{"key":"442_CR52","doi-asserted-by":"publisher","first-page":"17400","DOI":"10.1073\/pnas.0505147102","volume":"102","author":"T Wang","year":"2005","unstructured":"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","journal-title":"Proc Natl Acad Sci USA"},{"key":"442_CR53","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1038\/nrd1256","volume":"2","author":"C Khosla","year":"2003","unstructured":"Khosla C, Keasling JD: Metabolic engineering for drug discovery and development. Nat Rev Drug Discov. 2003, 2: 1019-1025. 10.1038\/nrd1256","journal-title":"Nat Rev Drug Discov"},{"key":"442_CR54","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/nbt1401","volume":"26","author":"AM Feist","year":"2008","unstructured":"Feist AM, Palsson B\u00d8: The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol. 2008, 26: 659-667. 10.1038\/nbt1401","journal-title":"Nat Biotechnol"},{"key":"442_CR55","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/nrmicro2186","volume":"7","author":"H Alper","year":"2009","unstructured":"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","journal-title":"Nat Rev Microbiol"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-53.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-4-53\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-53.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T02:43:43Z","timestamp":1591238623000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-53"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,28]]},"references-count":55,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["442"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-53","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,28]]},"article-number":"53"}}