{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T07:18:47Z","timestamp":1767943127526,"version":"3.49.0"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"3","content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1001116","type":"journal-article","created":{"date-parts":[[2011,3,31]],"date-time":"2011-03-31T20:15:01Z","timestamp":1301602501000},"page":"e1001116","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":113,"title":["Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis"],"prefix":"10.1371","volume":"7","author":[{"given":"Matthew A.","family":"Oberhardt","sequence":"first","affiliation":[]},{"given":"Jacek","family":"Pucha\u0142ka","sequence":"additional","affiliation":[]},{"given":"V\u00edtor A. P.","family":"Martins dos Santos","sequence":"additional","affiliation":[]},{"given":"Jason A.","family":"Papin","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,3,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/nrmicro1949","article-title":"Reconstruction of biochemical networks in microorganisms.","volume":"7","author":"AM Feist","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/msb.2009.77","article-title":"Applications of genome-scale metabolic reconstructions.","volume":"5","author":"MA Oberhardt","year":"2009","journal-title":"Mol Syst Biol"},{"key":"ref3","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":"Nat Protoc"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/msb.2010.15","article-title":"Reconstruction annotation jamborees: a community approach to systems biology.","volume":"6","author":"I Thiele","year":"2010","journal-title":"Mol Syst Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1097\/MOP.0b013e3280123a5d","article-title":"Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients.","volume":"19","author":"TS Murray","year":"2007","journal-title":"Curr Opin Pediatr"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1128\/CMR.4.1.35","article-title":"Microbiology of airway disease in patients with cystic fibrosis.","volume":"4","author":"PH Gilligan","year":"1991","journal-title":"Clin Microbiol Rev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.medmal.2005.10.007","article-title":"Targeting mechanisms of Pseudomonas aeruginosa pathogenesis.","volume":"36","author":"E Kipnis","year":"2006","journal-title":"Med Mal Infect"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1046\/j.1462-2920.2002.00366.x","article-title":"Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.","volume":"4","author":"KE Nelson","year":"2002","journal-title":"Environ Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1111\/j.1574-6976.2008.00135.x","article-title":"Regulation of virulence and antibiotic resistance by two-component regulatory systems in Pseudomonas aeruginosa.","volume":"33","author":"WJ Gooderham","year":"2009","journal-title":"FEMS Microbiol Rev"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.tim.2005.05.011","article-title":"Modulation of lung epithelial functions by Pseudomonas aeruginosa.","volume":"13","author":"GW Lau","year":"2005","journal-title":"Trends Microbiol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1007\/s002530000443","article-title":"Pseudomonas aeruginosa rhamnolipids: biosynthesis and potential applications.","volume":"54","author":"RM Maier","year":"2000","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1111\/j.1462-2920.2004.00734.x","article-title":"Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440.","volume":"6","author":"VA Dos Santos","year":"2004","journal-title":"Environ Microbiol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1128\/JB.01583-07","article-title":"Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.","volume":"190","author":"MA Oberhardt","year":"2008","journal-title":"J Bacteriol"},{"key":"ref14","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 Comput Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","article-title":"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM\/GPR).","volume":"4","author":"JL Reed","year":"2003","journal-title":"Genome Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nbt.1614","article-title":"What is flux balance analysis?","volume":"28","author":"JD Orth","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"S Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref18","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":"Nat Rev Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"D338","DOI":"10.1093\/nar\/gki047","article-title":"Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.","volume":"33","author":"GL Winsor","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref20","first-page":"261","article-title":"Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa.","volume":"15","author":"J King","year":"2009","journal-title":"J Endotoxin Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/35023079","article-title":"Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen.","volume":"406","author":"CK Stover","year":"2000","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e1000211","DOI":"10.1371\/journal.pgen.1000211","article-title":"High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes.","volume":"4","author":"DA Johnson","year":"2008","journal-title":"PLoS Genet"},{"key":"ref23","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":"Proc Natl Acad Sci U S A"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-2911(06)52001-6","article-title":"Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa.","volume":"52","author":"HD Williams","year":"2007","journal-title":"Adv Microb Physiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.ijmm.2006.01.043","article-title":"Impact of quorum sensing on fitness of Pseudomonas aeruginosa.","volume":"296","author":"K Heurlier","year":"2006","journal-title":"Int J Med Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"6454","DOI":"10.1128\/JB.183.21.6454-6465.2001","article-title":"Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1.","volume":"183","author":"DV Mavrodi","year":"2001","journal-title":"J Bacteriol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1007\/s00253-005-0150-3","article-title":"Production of rhamnolipids by Pseudomonas aeruginosa.","volume":"68","author":"G Soberon-Chavez","year":"2005","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/s00253-008-1728-3","article-title":"Induction of ortho- and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes.","volume":"81","author":"B Cao","year":"2008","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1007\/s10532-008-9190-6","article-title":"Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes.","volume":"19","author":"R Piskonen","year":"2008","journal-title":"Biodegradation"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1111\/j.1574-6968.2006.00285.x","article-title":"Inducible uptake and metabolism of glucose by the phosphorylative pathway in Pseudomonas putida CSV86.","volume":"259","author":"A Basu","year":"2006","journal-title":"FEMS Microbiol Lett"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1101\/gr.186501","article-title":"Phenotype microarrays for high-throughput phenotypic testing and assay of gene function.","volume":"11","author":"BR Bochner","year":"2001","journal-title":"Genome Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"14339","DOI":"10.1073\/pnas.2036282100","article-title":"Comprehensive transposon mutant library of Pseudomonas aeruginosa.","volume":"100","author":"MA Jacobs","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1101\/gr.3513905","article-title":"Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes.","volume":"15","author":"S Lewenza","year":"2005","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"5534","DOI":"10.1128\/JB.00900-10","article-title":"Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection.","volume":"192","author":"MA Oberhardt","year":"2010","journal-title":"J Bacteriol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1021\/bp049877i","article-title":"Correlation of denitrification-accepted fraction of electrons with NAD(P)H fluorescence for Pseudomonas aeruginosa performing simultaneous denitrification and respiration at extremely low dissolved oxygen conditions.","volume":"20","author":"F Chen","year":"2004","journal-title":"Biotechnol Prog"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"4596","DOI":"10.1128\/JB.186.14.4596-4604.2004","article-title":"Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation.","volume":"186","author":"M Eschbach","year":"2004","journal-title":"J Bacteriol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1111\/j.1462-2920.2010.02253.x","article-title":"How Pseudomonas aeruginosa adapts to various environments: a metabolomic approach.","volume":"12","author":"E Frimmersdorf","year":"2010","journal-title":"Environ Microbiol"},{"key":"ref38","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 Syst Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1002\/biot.201000124","article-title":"In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival.","volume":"5","author":"SB Sohn","year":"2010","journal-title":"Biotechnol J"},{"key":"ref40","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 Herrgard","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.","volume":"33","author":"R Overbeek","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1097\/CCM.0b013e31819ff137","article-title":"Pseudomonas aeruginosa virulence and therapy: evolving translational strategies.","volume":"37","author":"JL Veesenmeyer","year":"2009","journal-title":"Crit Care Med"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e8842","DOI":"10.1371\/journal.pone.0008842","article-title":"Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7.","volume":"5","author":"PH Roy","year":"2010","journal-title":"PLoS One"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1128\/IAI.00621-09","article-title":"The pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to virulence of Pseudomonas aeruginosa strain PA14.","volume":"78","author":"EM Harrison","year":"2010","journal-title":"Infect Immun"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.jhin.2006.08.009","article-title":"Pseudomonas aeruginosa and Pseudomonas putida outbreak associated with contaminated water outlets in an oncohaematology paediatric unit.","volume":"65","author":"C Aumeran","year":"2007","journal-title":"J Hosp Infect"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.mrfmmm.2009.10.015","article-title":"Molecular characterization of Rif(r) mutations in Pseudomonas aeruginosa and Pseudomonas putida.","volume":"683","author":"T Jatsenko","year":"2010","journal-title":"Mutat Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1093\/jxb\/erh176","article-title":"The role of soil microbes in plant sulphur nutrition.","volume":"55","author":"MA Kertesz","year":"2004","journal-title":"J Exp Bot"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"6743","DOI":"10.1128\/JB.00889-07","article-title":"Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa.","volume":"189","author":"T Tralau","year":"2007","journal-title":"J Bacteriol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1046\/j.1432-1327.1999.00941.x","article-title":"Proteome mapping, mass spectrometric sequencing and reverse transcription-PCR for characterization of the sulfate starvation-induced response in Pseudomonas aeruginosa PAO1.","volume":"266","author":"M Quadroni","year":"1999","journal-title":"Eur J Biochem"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"R90","DOI":"10.1186\/gb-2006-7-10-r90","article-title":"Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.","volume":"7","author":"DG Lee","year":"2006","journal-title":"Genome Biol"},{"key":"ref51","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":"YK Oh","year":"2007","journal-title":"J Biol Chem"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"4678","DOI":"10.1073\/pnas.0730515100","article-title":"Essential Bacillus subtilis genes.","volume":"100","author":"K Kobayashi","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1093\/bib\/bbl007","article-title":"Flux balance analysis in the era of metabolomics.","volume":"7","author":"JM Lee","year":"2006","journal-title":"Brief Bioinform"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nprot.2007.99","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.","volume":"2","author":"S Becker","year":"2007","journal-title":"Nat Protoc"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T20:50:23Z","timestamp":1540327823000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001116"}},"subtitle":[],"editor":[{"given":"Philip E.","family":"Bourne","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,3,31]]},"references-count":54,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2011,3,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1001116","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,3,31]]}}}