{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:06:55Z","timestamp":1740143215936,"version":"3.37.3"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2016,8,26]],"date-time":"2016-08-26T00:00:00Z","timestamp":1472169600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["SystemsX.ch RTD MetaNetX"],"award-info":[{"award-number":["SystemsX.ch RTD MetaNetX"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sixth Framework Programme (BE)","award":["SystemTB"],"award-info":[{"award-number":["SystemTB"]}]},{"DOI":"10.13039\/501100004965","name":"Sixth Framework Programme","doi-asserted-by":"publisher","award":["INFECT"],"award-info":[{"award-number":["INFECT"]}],"id":[{"id":"10.13039\/501100004965","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005085","type":"journal-article","created":{"date-parts":[[2016,8,26]],"date-time":"2016-08-26T17:33:11Z","timestamp":1472232791000},"page":"e1005085","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Efficient Reconstruction of Predictive Consensus Metabolic Network Models"],"prefix":"10.1371","volume":"12","author":[{"given":"Ruben G. A.","family":"van Heck","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathias","family":"Ganter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vitor A. P.","family":"Martins dos Santos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joerg","family":"Stelling","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,8,26]]},"reference":[{"key":"ref1","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":"ref2","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms4006","article-title":"Predicting network functions with nested patterns","volume":"5","author":"M Ganter","year":"2014","journal-title":"Nature communications"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"28791","DOI":"10.1074\/jbc.M703759200","article-title":"Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data","volume":"282","author":"Y-K Oh","year":"2007","journal-title":"Journal of Biological Chemistry"},{"key":"ref4","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":"ref5","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":"ref6","doi-asserted-by":"crossref","first-page":"e1000489","DOI":"10.1371\/journal.pcbi.1000489","article-title":"Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production","volume":"5","author":"C Colijn","year":"2009","journal-title":"PLoS computational biology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"R89","DOI":"10.1186\/gb-2007-8-5-r89","article-title":"GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism","volume":"8","author":"DJV Beste","year":"2007","journal-title":"Genome biology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e1000210","DOI":"10.1371\/journal.pcbi.1000210","article-title":"Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology","volume":"4","author":"J Puchalka","year":"2008","journal-title":"PLoS computational biology"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"20338","DOI":"10.1073\/pnas.1307797110","article-title":"Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments","volume":"110","author":"JM Monk","year":"2013","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e1001116","DOI":"10.1371\/journal.pcbi.1001116","article-title":"Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis","volume":"7","author":"MA Oberhardt","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1128\/JB.00997-13","article-title":"Comparative metabolic systems analysis of pathogenic Burkholderia","volume":"196","author":"JA Bartell","year":"2014","journal-title":"Journal of bacteriology"},{"key":"ref12","doi-asserted-by":"crossref","DOI":"10.1155\/2014\/416289","article-title":"Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences?","volume":"2014","author":"P Babaei","year":"2014","journal-title":"The Scientific World Journal"},{"key":"ref13","doi-asserted-by":"crossref","DOI":"10.1038\/msb.2010.60","article-title":"Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network","volume":"6","author":"G Plata","year":"2010","journal-title":"Molecular systems biology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1752-0509-1-26","article-title":"Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets","volume":"1","author":"N Jamshidi","year":"2007","journal-title":"BMC systems biology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nchembio.580","article-title":"Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol","volume":"7","author":"H Yim","year":"2011","journal-title":"Nature chemical biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nrg3643","article-title":"Constraint-based models predict metabolic and associated cellular functions","volume":"15","author":"A Bordbar","year":"2014","journal-title":"Nature Reviews Genetics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/nrg1769","article-title":"Towards multidimensional genome annotation","volume":"7","author":"JL Reed","year":"2006","journal-title":"Nature Reviews Genetics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/1752-0509-5-165","article-title":"Critical assessment of human metabolic pathway databases: a stepping stone for future integration","volume":"5","author":"MD Stobbe","year":"2011","journal-title":"BMC systems biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2983","DOI":"10.1093\/bioinformatics\/btp535","article-title":"A dictionary to identify small molecules and drugs in free text","volume":"25","author":"KM Hettne","year":"2009","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/nbt1492","article-title":"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology","volume":"26","author":"MJ Herrg\u00e5rd","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/1752-0509-4-114","article-title":"Integration of metabolic databases for the reconstruction of genome-scale metabolic networks","volume":"4","author":"K Radrich","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref22","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100155","article-title":"A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information","volume":"3","author":"AM Feist","year":"2007","journal-title":"Molecular systems biology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2105-13-6","article-title":"MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases","volume":"13","author":"A Kumar","year":"2012","journal-title":"BMC bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/nbt.2488","article-title":"A community-driven global reconstruction of human metabolism","volume":"31","author":"I Thiele","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.smim.2014.09.013","article-title":"Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets","volume":"26","author":"RA Rienksma","year":"2014","journal-title":"Semin Immunol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1038\/nbt.2870","article-title":"Optimizing genome-scale network reconstructions","volume":"32","author":"J Monk","year":"2014","journal-title":"Nat Biotechnol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1752-0509-5-8","article-title":"A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2","volume":"5","author":"I Thiele","year":"2011","journal-title":"BMC systems biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1089\/ind.2013.0013","article-title":"Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism","volume":"9","author":"HW Aung","year":"2013","journal-title":"Industrial Biotechnology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"r6","DOI":"10.1186\/gb-2012-13-1-r6","article-title":"MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis","volume":"13","author":"L Chindelevitch","year":"2012","journal-title":"Genome Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1752-0509-7-50","article-title":"Consensus and conflict cards for metabolic pathway databases","volume":"7","author":"MD Stobbe","year":"2013","journal-title":"BMC Syst Biol"},{"key":"ref31","article-title":"Reconciliation of metabolites and biochemical reactions for metabolic networks","author":"T Bernard","year":"2012","journal-title":"Briefings in bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"M Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1752-0509-2-79","article-title":"A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory","volume":"2","author":"J Nogales","year":"2008","journal-title":"BMC systems biology"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000308","article-title":"GrowMatch: An Automated Method for Reconciling In Silico\/In Vivo Growth Predictions","volume":"5","author":"VS Kumar","year":"2009","journal-title":"Plos Computational Biology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"BW Matthews","year":"1975","journal-title":"Biochimica et Biophysica Acta (BBA)-Protein Structure"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"R69","DOI":"10.1186\/gb-2009-10-6-r69","article-title":"iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations","volume":"10","author":"CS Henry","year":"2009","journal-title":"Genome Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/1752-0509-3-37","article-title":"Connecting extracellular metabolomic measurements to intracellular flux states in yeast","volume":"3","author":"ML Mo","year":"2009","journal-title":"BMC Syst Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1101\/gr.3992505","article-title":"Metabolic functions of duplicate genes in Saccharomyces cerevisiae","volume":"15","author":"L Kuepfer","year":"2005","journal-title":"Genome Res"},{"key":"ref39","article-title":"fastGapFill: Efficient gap filling in metabolic networks","volume":"321","author":"I Thiele","year":"2014","journal-title":"Bioinformatics: btu"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/bts317","article-title":"An integrated open framework for thermodynamics of reactions that combines accuracy and coverage","volume":"28","author":"E Noor","year":"2012","journal-title":"Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"i247","DOI":"10.1093\/bioinformatics\/btp209","article-title":"Network-based prediction of metabolic enzymes' subcellular localization","volume":"25","author":"S Mintz-Oron","year":"2009","journal-title":"Bioinformatics"},{"key":"ref42","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 computational biology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1038\/nbt.1672","article-title":"High-throughput generation, optimization and analysis of genome-scale metabolic models","volume":"28","author":"CS Henry","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref44","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":"ref45","unstructured":"The MathWorks I MATLAB. Natick, Massachusetts, United States."},{"key":"ref46","unstructured":"Gurobi Optimization I (2015) Gurobi Optimizer Reference Manual."},{"key":"ref47","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btt036","article-title":"MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks","volume":"29","author":"M Ganter","year":"2013","journal-title":"Bioinformatics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1752-0509-2-71","article-title":"The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism","volume":"2","author":"I Nookaew","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1101\/gr.2250904","article-title":"Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model","volume":"14","author":"NC Duarte","year":"2004","journal-title":"Genome Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1111\/j.1462-2920.2010.02166.x","article-title":"Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library","volume":"12","author":"MA Molina-Henares","year":"2010","journal-title":"Environmental Microbiology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1046\/j.1365-2958.2003.03425.x","article-title":"Genes required for mycobacterial growth defined by high density mutagenesis","volume":"48","author":"CM Sassetti","year":"2003","journal-title":"Molecular microbiology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005085","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,19]],"date-time":"2024-06-19T02:39:45Z","timestamp":1718764785000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005085"}},"subtitle":[],"editor":[{"given":"Jennifer L.","family":"Reed","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,8,26]]},"references-count":51,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2016,8,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005085","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2016,8,26]]}}}