{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T19:20:02Z","timestamp":1782501602455,"version":"3.54.5"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2014,1,16]],"date-time":"2014-01-16T00:00:00Z","timestamp":1389830400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003424","type":"journal-article","created":{"date-parts":[[2014,1,16]],"date-time":"2014-01-16T16:10:18Z","timestamp":1389888618000},"page":"e1003424","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":249,"title":["Fast Reconstruction of Compact Context-Specific Metabolic Network Models"],"prefix":"10.1371","volume":"10","author":[{"given":"Nikos","family":"Vlassis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Pires","family":"Pacheco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Sauter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,1,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1016\/j.cell.2012.02.032","article-title":"Cellular metabolism and disease: what do metabolic outliers teach us?","volume":"148","author":"RJ DeBerardinis","year":"2012","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","unstructured":"Pourfar M, Niethammer M, Eidelberg D (2013) Metabolic networks in Parkinson&apos;s disease. In: Grimaldi G, Manto M, editors, Mechanisms and Emerging Therapies in Tremor Disorders, Springer New York, Contemporary Clinical Neuroscience. pp. 403\u2013415. doi:10.1007\/978-1-4614-4027-7 22. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/dx.doi.org\/10.1007\/978-1-4614-4027-7\" xlink:type=\"simple\">http:\/\/dx.doi.org\/10.1007\/978-1-4614-4027-7<\/ext-link> 22.","DOI":"10.1007\/978-1-4614-4027-7"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.copbio.2012.11.001","article-title":"Profiling metabolic networks to study cancer metabolism","volume":"24","author":"K Hiller","year":"2013","journal-title":"Current Opinion in Biotechnology"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1073\/pnas.0610772104","article-title":"Global reconstruction of the human metabolic network based on genomic and bibliomic data","volume":"104","author":"NC Duarte","year":"2007","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1186\/1471-2105-11-393","article-title":"Compartmentalization of the Edinburgh human metabolic network","volume":"11","author":"T Hao","year":"2010","journal-title":"BMC bioinformatics"},{"key":"ref6","article-title":"A community-driven global reconstruction of human metabolism","author":"I Thiele","year":"2013","journal-title":"Nature biotechnology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"I Thiele","year":"2010","journal-title":"Nature protocols"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e1000082","DOI":"10.1371\/journal.pcbi.1000082","article-title":"Context-specific metabolic networks are consistent with experiments","volume":"4","author":"SA Becker","year":"2008","journal-title":"PLoS computational biology"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1039\/b915913b","article-title":"An integrative approach towards completing genome-scale metabolic networks","volume":"5","author":"N Christian","year":"2009","journal-title":"Mol BioSyst"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/msb.2010.56","article-title":"Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism","volume":"6","author":"L Jerby","year":"2010","journal-title":"Molecular Systems Biology"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e1000938","DOI":"10.1371\/journal.pcbi.1000938","article-title":"Drug off-target effects predicted using structural analysis in the context of a metabolic network model","volume":"6","author":"RL Chang","year":"2010","journal-title":"PLoS Computational Biology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1038\/nbt.1711","article-title":"Large-scale in silico modeling of metabolic interactions between cell types in the human brain","volume":"28","author":"NE Lewis","year":"2010","journal-title":"Nature biotechnology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e1002518","DOI":"10.1371\/journal.pcbi.1002518","article-title":"Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT","volume":"8","author":"R Agren","year":"2012","journal-title":"PLoS Computational Biology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/msb.2011.35","article-title":"Predicting selective drug targets in cancer through metabolic networks","volume":"7","author":"O Folger","year":"2011","journal-title":"Molecular systems biology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1038\/msb.2012.21","article-title":"Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation","volume":"8","author":"A Bordbar","year":"2012","journal-title":"Molecular Systems Biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nbt.1487","article-title":"Network-based prediction of human tissue-specific metabolism","volume":"26","author":"T Shlomi","year":"2008","journal-title":"Nature biotechnology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"17845","DOI":"10.1073\/pnas.1005139107","article-title":"Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis","volume":"107","author":"S Chandrasekaran","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1093\/bioinformatics\/btq702","article-title":"Functional integration of a metabolic network model and expression data without arbitrary thresholding","volume":"27","author":"PA Jensen","year":"2011","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1142\/S0218339094000131","article-title":"On elementary flux modes in biochemical reaction systems at steady state","volume":"2","author":"S Schuster","year":"1994","journal-title":"Journal of Biological Systems"},{"key":"ref20","doi-asserted-by":"crossref","unstructured":"Stephanopoulos G, Aristidou AA, Nielsen J (1998) Metabolic engineering: principles and methodologies. San Diego: Academic Press.","DOI":"10.1016\/B978-012666260-3\/50002-9"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/nrmicro1023","article-title":"Genome-scale models of microbial cells: evaluating the consequences of constraints","volume":"2","author":"ND Price","year":"2004","journal-title":"Nature Reviews Microbiology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/1471-2105-5-175","article-title":"Computation of elementary modes: a unifying framework and the new binary approach","volume":"5","author":"J Gagneur","year":"2004","journal-title":"BMC bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.jtbi.2011.09.029","article-title":"A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks","volume":"292","author":"RMT Fleming","year":"2012","journal-title":"Journal of Theoretical Biology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"299","DOI":"10.3389\/fphys.2012.00299","article-title":"Integration of expression data in genome-scale metabolic network reconstructions","volume":"3","author":"AS Blazier","year":"2012","journal-title":"Frontiers in Physiology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/msb.2011.65","article-title":"A comprehensive genome-scale reconstruction of Escherichia coli metabolism","volume":"7","author":"JD Orth","year":"2011","journal-title":"Molecular systems biology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1752-0509-6-153","article-title":"Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE","volume":"6","author":"Y Wang","year":"2012","journal-title":"BMC Systems Biology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.biosystems.2008.06.015","article-title":"Modes and cuts in metabolic networks: Complexity and algorithms","volume":"95","author":"V Acu\u00f1a","year":"2009","journal-title":"Biosystems"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","article-title":"The effects of alternate optimal solutions in constraint-based genome-scale metabolic models","volume":"5","author":"R Mahadevan","year":"2003","journal-title":"Metabolic engineering"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nprot.2011.308","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0","volume":"6","author":"J Schellenberger","year":"2011","journal-title":"Nat Protoc"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1186\/1471-2105-11-489","article-title":"Computationally efficient flux variability analysis","volume":"11","author":"S Gudmundsson","year":"2010","journal-title":"BMC bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","unstructured":"Boyd S, Vandenberghe L (2004) Convex Optimization. Cambridge, UK: Cambridge University Press.","DOI":"10.1017\/CBO9780511804441"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e1003126","DOI":"10.1371\/journal.pcbi.1003126","article-title":"Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM","volume":"9","author":"JM Dreyfuss","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1287\/moor.4.3.233","article-title":"A greedy heuristic for the set-covering problem","volume":"4","author":"V Chv\u00e1tal","year":"1979","journal-title":"Mathematics of operations research"},{"key":"ref34","doi-asserted-by":"crossref","unstructured":"Julius AA, Imielinski M, Pappas GJ (2008) Metabolic networks analysis using convex optimization. In: 47th IEEE Conference on Decision and Control. pp. 762\u2013767.","DOI":"10.1109\/CDC.2008.4739111"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1093\/bioinformatics\/btq602","article-title":"iMAT: an integrative metabolic analysis tool","volume":"26","author":"H Zur","year":"2010","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"R111","DOI":"10.1186\/gb-2012-13-11-r111","article-title":"MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks","volume":"13","author":"E Vitkin","year":"2012","journal-title":"Genome biology"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/1752-0509-4-178","article-title":"Improving the iMM904 S.cerevisiae metabolic model using essentiality and synthetic lethality data","volume":"4","author":"AR Zomorrodi","year":"2010","journal-title":"BMC systems biology"},{"key":"ref38","doi-asserted-by":"crossref","unstructured":"Orth JD, Fleming RMT, Palsson B\u00d8 (2010) Reconstruction and use of microbial metabolic networks: the core <italic>Escherichia coli<\/italic> metabolic model as an educational guide. In: B\u00f6ck A, Curtiss III R, Kaper JB, Karp PD, Neidhardt FC, <etal>et al<\/etal>.., editors, <italic>Escherichia coli<\/italic> and Salmonella: Cellular and Molecular Biology, Washington, DC: ASM Press. doi:10.1128\/ecosal.10.2.1.","DOI":"10.1128\/ecosal.10.2.1"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"8021","DOI":"10.1073\/pnas.140082197","article-title":"In vivo urea cycle flux distinguishes and correlates with phenotypic severity in disorders of the urea cycle","volume":"97","author":"B Lee","year":"2000","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"5572","DOI":"10.1158\/1078-0432.CCR-12-1856","article-title":"Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling","volume":"18","author":"L Jerby","year":"2012","journal-title":"Clinical Cancer Research"},{"key":"ref41","first-page":"750","article-title":"The completeness of molecular biology","volume":"20","author":"HJ Morowitz","year":"1984","journal-title":"Israel journal of medical sciences"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"10004","DOI":"10.1073\/pnas.93.19.10004","article-title":"The minimal cell genome: \u201con being the right size\u201d","volume":"93","author":"J Maniloff","year":"1996","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1006\/jmbi.1996.0479","article-title":"Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure","volume":"261","author":"J Suckow","year":"1996","journal-title":"Journal of molecular biology"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003424","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T14:23:30Z","timestamp":1565101410000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003424"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,1,16]]},"references-count":43,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,1,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003424","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,16]]}}}