{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T08:04:09Z","timestamp":1761293049465},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,7,30]],"date-time":"2013-07-30T00:00:00Z","timestamp":1375142400000},"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 Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1471-2105-14-240","type":"journal-article","created":{"date-parts":[[2013,7,30]],"date-time":"2013-07-30T14:14:10Z","timestamp":1375193650000},"source":"Crossref","is-referenced-by-count":20,"title":["Robust flux balance analysis of multiscale biochemical reaction networks"],"prefix":"10.1186","volume":"14","author":[{"given":"Yuekai","family":"Sun","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronan MT","family":"Fleming","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ines","family":"Thiele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael A","family":"Saunders","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,7,30]]},"reference":[{"issue":"3","key":"5997_CR1","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nbt.1614","volume":"28","author":"JD Orth","year":"2010","unstructured":"Orth JD, Thiele I, Palsson B\u00d8: What is flux balance analysis?. Nat Biotechnol. 2010, 28 (3): 245-248. 10.1038\/nbt.1614.","journal-title":"Nat Biotechnol"},{"issue":"9","key":"5997_CR2","doi-asserted-by":"publisher","first-page":"e45635","DOI":"10.1371\/journal.pone.0045635","volume":"7","author":"I Thiele","year":"2012","unstructured":"Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson B\u00d8: Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One. 2012, 7 (9): e45635-10.1371\/journal.pone.0045635.","journal-title":"PLoS One"},{"issue":"10","key":"5997_CR3","doi-asserted-by":"publisher","first-page":"2072","DOI":"10.1016\/j.bpj.2010.01.060","volume":"98","author":"I Thiele","year":"2010","unstructured":"Thiele I, Fleming RMT, Bordbar A, Schellenberger J, Palsson B\u00d8: Functional characterization of alternate optimal solutions of Escherichia coli\u2019s transcriptional and translational machinery. Biophys J. 2010, 98 (10): 2072-2081. 10.1016\/j.bpj.2010.01.060.","journal-title":"Biophys J"},{"key":"5997_CR4","unstructured":"CPLEX mathematical programming solver. [\n                    http:\/\/www-01.ibm.com\/software\/integration\/optimization\/cplex-optimizer\/\n                    \n                  ]"},{"key":"5997_CR5","unstructured":"Gurobi mathematical programming solver. [\n                    http:\/\/www.gurobi.com\/\n                    \n                  ]"},{"key":"5997_CR6","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1007\/s10589-011-9420-4","volume":"52","author":"J Elble","year":"2012","unstructured":"Elble J, Sahinidis N: Scaling linear optimization problems prior to application of the simplex method. Comput Optimization Appl. 2012, 52: 345-371. 10.1007\/s10589-011-9420-4.","journal-title":"Comput Optimization Appl"},{"issue":"3","key":"5997_CR7","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1137\/080724885","volume":"20","author":"J Albersmeyer","year":"2010","unstructured":"Albersmeyer J, Diehl M: The lifted Newton method and its application in optimization. SIAM J Optim. 2010, 20 (3): 1655-1684. 10.1137\/080724885.","journal-title":"SIAM J Optim"},{"key":"5997_CR8","unstructured":"Gouveia J, Parrilo PA, Thomas R: Lifts of convex sets and cone factorizations. ArXiv:1111.3164 2011"},{"issue":"2","key":"5997_CR9","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1145\/321386.321394","volume":"14","author":"CB Moler","year":"1967","unstructured":"Moler CB: Iterative refinement in floating point. J ACM. 1967, 14 (2): 316-321. 10.1145\/321386.321394.","journal-title":"J ACM"},{"key":"5997_CR10","doi-asserted-by":"publisher","DOI":"10.1145\/2442829.2442858","volume-title":"Improving the accuracy of linear programming solvers with iterative refinement","author":"A Gleixner","year":"2012","unstructured":"Gleixner A, Steffy D, Wolter K: Improving the accuracy of linear programming solvers with iterative refinement. ZIB-Report 12-19, Zuse Institute Berlin 2012"},{"key":"5997_CR11","volume-title":"Presented at INFORMS Annual Meeting, Pittsburgh, PA","author":"MA Saunders","year":"2006","unstructured":"Saunders MA, Tenenblat L: The Zoom strategy for accelerating and warm-starting interior methods. Presented at INFORMS Annual Meeting, Pittsburgh, PA. Nov 5-8, 2006, [\n                    http:\/\/www.stanford.edu\/group\/SOL\/talks\/saunders-tenenblat-INFORMS2006.pdf\n                    \n                  ]"},{"issue":"9","key":"5997_CR12","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1038\/nprot.2011.308","volume":"6","author":"J Schellenberger","year":"2011","unstructured":"Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, et al: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protoc. 2011, 6 (9): 1290-1307. 10.1038\/nprot.2011.308. [\n                    http:\/\/github.com\/opencobra\n                    \n                  ]","journal-title":"Nature Protoc"},{"key":"5997_CR13","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1137\/S0036144504446096","volume":"47","author":"PE Gill","year":"2005","unstructured":"Gill PE, Murray W, Saunders MA: SNOPT: An SQP algorithm for large-scale constrained optimization. SIAM Review. 2005, 47: 99-131. 10.1137\/S0036144504446096. [SIGEST article]","journal-title":"SIAM Review"},{"issue":"4","key":"5997_CR14","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/S0022-5193(05)80161-4","volume":"154","author":"JM Savinell","year":"1992","unstructured":"Savinell JM, Palsson B\u00d8: Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J Theor Biol. 1992, 154 (4): 421-454. 10.1016\/S0022-5193(05)80161-4.","journal-title":"J Theor Biol"},{"key":"5997_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/msb4100155","volume":"3","author":"A Feist","year":"2007","unstructured":"Feist A, Henry C, Reed J, Krummenacker M, Joyce A, Karp P, Broadbelt L, 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: 1-18.","journal-title":"Mol Syst Biol"},{"issue":"1","key":"5997_CR16","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.copbio.2012.10.001","volume":"21","author":"I Thiele","year":"2012","unstructured":"Thiele I, Heinken A, Fleming RMT: A systems biology approach to studying the role of microbes in human health. Curr Opin Biotechnol. 2012, 21 (1): 4-12.","journal-title":"Curr Opin Biotechnol"},{"key":"5997_CR17","first-page":"104","volume-title":"Proceedings of the 15th international conference on Integer Programming and Combinatorial Optimization, IPCO\u201911","author":"W Cook","year":"2011","unstructured":"Cook W, Koch T, Daniel E, Wolter K: An exact rational mixed-integer programming solver. Proceedings of the 15th international conference on Integer Programming and Combinatorial Optimization, IPCO\u201911. 2011, Berlin, Heidelberg: Springer-Verlag, 104-116. [\n                    http:\/\/dl.acm.org\/citation.cfm?id=2018167\n                    \n                  ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-240.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-240\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-240.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T05:45:49Z","timestamp":1548135949000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-240"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,7,30]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5997"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-240","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,7,30]]},"article-number":"240"}}