{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T22:24:30Z","timestamp":1775773470563,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-016-1412-z","type":"journal-article","created":{"date-parts":[[2017,1,3]],"date-time":"2017-01-03T12:10:05Z","timestamp":1483445405000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks"],"prefix":"10.1186","volume":"18","author":[{"given":"Annika","family":"R\u00f6hl","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Bockmayr","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,1,3]]},"reference":[{"issue":"5","key":"1412_CR1","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1016\/j.cell.2015.05.019","volume":"161","author":"EJ O\u2019Brien","year":"2015","unstructured":"O\u2019Brien EJ, Monk JM, Palsson BO. Using genome-scale models to predict biological capabilities. Cell. 2015; 161(5):971\u201387.","journal-title":"Cell"},{"issue":"4","key":"1412_CR2","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nrmicro2737","volume":"10","author":"NE Lewis","year":"2012","unstructured":"Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012; 10(4):291\u2013305.","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"1412_CR3","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1142\/S0218339094000131","volume":"2","author":"S Schuster","year":"1994","unstructured":"Schuster S, Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst. 1994; 2(2):165\u201382.","journal-title":"J Biol Syst"},{"issue":"2","key":"1412_CR4","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1093\/bioinformatics\/btg395","volume":"20","author":"S Klamt","year":"2004","unstructured":"Klamt S, Gilles ED. Minimal cut sets in biochemical reaction networks. Bioinformatics. 2004; 20(2):226\u201334.","journal-title":"Bioinformatics"},{"issue":"1","key":"1412_CR5","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s12918-015-0191-x","volume":"9","author":"P Erdrich","year":"2015","unstructured":"Erdrich P, Steuer R, Klamt S. An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Syst Biol. 2015; 9(1):48.","journal-title":"BMC Syst Biol"},{"issue":"3","key":"1412_CR6","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1093\/bioinformatics\/15.3.251","volume":"15","author":"T Pfeiffer","year":"1999","unstructured":"Pfeiffer T, Sanchez-Valdenebro I, Nu J, Montero F, Schuster S. METATOOL: for studying metabolic networks. Bioinformatics. 1999; 15(3):251\u20137.","journal-title":"Bioinformatics"},{"issue":"4","key":"1412_CR7","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","volume":"5","author":"R Mahadevan","year":"2003","unstructured":"Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003; 5(4):264\u201376.","journal-title":"Metab Eng"},{"issue":"1","key":"1412_CR8","doi-asserted-by":"crossref","first-page":"e1003424","DOI":"10.1371\/journal.pcbi.1003424","volume":"10","author":"N Vlassis","year":"2014","unstructured":"Vlassis N, Pacheco MP, Sauter T. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput Biol. 2014; 10(1):e1003424.","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"1412_CR9","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1021\/bp0100880","volume":"17","author":"AP Burgard","year":"2001","unstructured":"Burgard AP, Vaidyaraman S, Maranas CD. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol Prog. 2001; 17(5):791\u20137.","journal-title":"Biotechnol Prog"},{"issue":"28","key":"1412_CR10","first-page":"1","volume":"8","author":"S Jonnalagadda","year":"2014","unstructured":"Jonnalagadda S, Srinivasan R. An efficient graph theory based method to identify every minimal reaction set in a metabolic network. BMC Syst Biol. 2014; 8(28):1.","journal-title":"BMC Syst Biol"},{"issue":"6","key":"1412_CR11","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1021\/bp0000712","volume":"16","author":"JS Edwards","year":"2000","unstructured":"Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog. 2000; 16(6):927\u201339.","journal-title":"Biotechnol Prog"},{"issue":"23","key":"1412_CR12","doi-asserted-by":"crossref","first-page":"15112","DOI":"10.1073\/pnas.232349399","volume":"99","author":"D Segre","year":"2002","unstructured":"Segre D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA. 2002; 99(23):15112\u20137.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"1412_CR13","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1049\/sb:20045004","volume":"1","author":"T Wilhelm","year":"2004","unstructured":"Wilhelm T, Behre J, Schuster S. Analysis of structural robustness of metabolic networks. Syst Biol. 2004; 1(1):114\u201320.","journal-title":"Syst Biol"},{"issue":"3","key":"1412_CR14","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.jtbi.2007.09.043","volume":"252","author":"J Behre","year":"2008","unstructured":"Behre J, Wilhelm T, von Kamp A, Ruppin E, Schuster S. Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol. 2008; 252(3):433\u201341.","journal-title":"J Theor Biol"},{"issue":"1","key":"1412_CR15","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.biosystems.2008.06.015","volume":"95","author":"V Acuna","year":"2009","unstructured":"Acuna V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot MF, Stougie L. Modes and cuts in metabolic networks: complexity and algorithms. Biosystems. 2009; 95(1):51\u201360.","journal-title":"Biosystems"},{"issue":"6","key":"1412_CR16","doi-asserted-by":"crossref","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(6):647\u201357.","journal-title":"Biotechnol Bioeng"},{"issue":"3","key":"1412_CR17","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1089\/cmb.2007.0229","volume":"15","author":"UU Haus","year":"2008","unstructured":"Haus UU, Klamt S, Stephen T. Computing knock-out strategies in metabolic networks. J Comput Biol. 2008; 15(3):259\u201368.","journal-title":"J Comput Biol"},{"key":"1412_CR18","doi-asserted-by":"crossref","first-page":"240","DOI":"10.4018\/978-1-4666-1785-8.ch014","volume":"1","author":"T Tamura","year":"2012","unstructured":"Tamura T, Takemoto K, Akutsu T. Finding minimum reaction cuts of metabolic networks under a Boolean model using integer programming and feedback vertex sets. Comput Knowl Disco Bioinformatics Res. 2012; 1:240\u2013258.","journal-title":"Comput Knowl Disco Bioinformatics Res"},{"issue":"2","key":"1412_CR19","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1101\/gr.1926504","volume":"14","author":"AP Burgard","year":"2004","unstructured":"Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004; 14(2):301\u201312.","journal-title":"Genome Res"},{"issue":"1","key":"1412_CR20","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/1471-2105-13-57","volume":"13","author":"A Larhlimi","year":"2012","unstructured":"Larhlimi A, David L, Selbig J, Bockmayr A. F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. BMC Bioinforma. 2012; 13(1):57.","journal-title":"BMC Bioinforma"},{"key":"1412_CR21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13015-014-0028-y","volume":"10","author":"Y Goldstein","year":"2015","unstructured":"Goldstein Y, Bockmayr A. Double and multiple knockout simulations for genome-scale metabolic network reconstructions. Algorithm Mol Biol. 2015; 10:1.","journal-title":"Algorithm Mol Biol"},{"key":"1412_CR22","unstructured":"R\u00f6hl A, Goldstein Y, Bockmayr A. EFM-Recorder - faster elementary mode enumeration via reaction coupling order. In: Strasbourg Spring School on Advances in Systems and Synthetic Biology: 2015. p. 91\u2013100."},{"key":"1412_CR23","unstructured":"CPLEX. http:\/\/www-01.ibm.com\/software\/commerce\/optimization\/cplex-optimizer\/ ."},{"key":"1412_CR24","unstructured":"BiGG Models. http:\/\/bigg.ucsd.edu\/ ."},{"key":"1412_CR25","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.biosystems.2010.09.011","volume":"103","author":"SA Marashi","year":"2011","unstructured":"Marashi SA, Bockmayr A. Flux coupling analysis of metabolic networks is sensitive to missing reactions. BioSystems. 2011; 103:57\u201366.","journal-title":"BioSystems"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1412-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,17]],"date-time":"2019-09-17T03:43:47Z","timestamp":1568691827000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1412-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,3]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1412"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1412-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,3]]},"article-number":"2"}}