{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T23:02:24Z","timestamp":1777071744146,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007562","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T00:00:00Z","timestamp":1578268800000}}],"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2019,12,20]],"date-time":"2019-12-20T00:00:00Z","timestamp":1576800000000},"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.1007562","type":"journal-article","created":{"date-parts":[[2019,12,20]],"date-time":"2019-12-20T13:31:32Z","timestamp":1576848692000},"page":"e1007562","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection"],"prefix":"10.1371","volume":"15","author":[{"given":"Jinyuan","family":"Yan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henri","family":"Estanbouli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Liao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6818-9688","authenticated-orcid":true,"given":"Wook","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3895-8949","authenticated-orcid":true,"given":"Jonathan M.","family":"Monk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rayees","family":"Rahman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mini","family":"Kamboj","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernhard O.","family":"Palsson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4585-1872","authenticated-orcid":true,"given":"Weigang","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3592-1689","authenticated-orcid":true,"given":"Joao B.","family":"Xavier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,12,20]]},"reference":[{"key":"pcbi.1007562.ref001","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/S1473-3099(18)30605-4","article-title":"Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis","volume":"19","author":"A Cassini","year":"2019","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1007562.ref002","first-page":"277","article-title":"The antibiotic resistance crisis: part 1: causes and threats","volume":"40","author":"CL Ventola","year":"2015","journal-title":"P T"},{"key":"pcbi.1007562.ref003","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nrg3351","article-title":"Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance","volume":"14","author":"AC Palmer","year":"2013","journal-title":"Nat Rev Genet"},{"key":"pcbi.1007562.ref004","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1128\/MMBR.00016-10","article-title":"Origins and evolution of antibiotic resistance","volume":"74","author":"J Davies","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"key":"pcbi.1007562.ref005","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1177\/003335490712200205","article-title":"Estimating health care-associated infections and deaths in U.S. hospitals, 2002","volume":"122","author":"RM Klevens","year":"2007","journal-title":"Public Health Rep"},{"key":"pcbi.1007562.ref006","doi-asserted-by":"crossref","first-page":"8487","DOI":"10.1073\/pnas.0602138103","article-title":"Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients","volume":"103","author":"EE Smith","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007562.ref007","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/416740a","article-title":"Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation","volume":"416","author":"E Drenkard","year":"2002","journal-title":"Nature"},{"issue":"Suppl 4","key":"pcbi.1007562.ref008","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1111\/j.1469-0691.2005.01161.x","article-title":"Treatment and control of severe infections caused by multiresistant Pseudomonas aeruginosa","volume":"11","author":"GM Rossolini","year":"2005","journal-title":"Clin Microbiol Infect"},{"key":"pcbi.1007562.ref009","first-page":"78","article-title":"Antibiotic selection in the treatment of acute invasive infections by Pseudomonas aeruginosa: Guidelines by the Spanish Society of Chemotherapy","volume":"31","author":"J Mensa","year":"2018","journal-title":"Rev Esp Quimioter"},{"key":"pcbi.1007562.ref010","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1086\/322604","article-title":"Evolution, incidence, and susceptibility of bacterial bloodstream isolates from 519 bone marrow transplant patients","volume":"33","author":"BA Collin","year":"2001","journal-title":"Clin Infect Dis"},{"key":"pcbi.1007562.ref011","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/0002-9343(85)90196-2","article-title":"Aztreonam: the first monobactam","volume":"78","author":"RB Sykes","year":"1985","journal-title":"Am J Med"},{"key":"pcbi.1007562.ref012","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nrd3170","article-title":"Inhaled aztreonam","volume":"9","author":"BP O\u2019Sullivan","year":"2010","journal-title":"Nat Rev Drug Discov"},{"key":"pcbi.1007562.ref013","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00517-17","article-title":"Evolved Aztreonam Resistance Is Multifactorial and Can Produce Hypervirulence in Pseudomonas aeruginosa","volume":"8","author":"P Jorth","year":"2017","journal-title":"MBio"},{"key":"pcbi.1007562.ref014","doi-asserted-by":"crossref","first-page":"e1005677","DOI":"10.1371\/journal.pcbi.1005677","article-title":"Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network","volume":"13","author":"J Yan","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007562.ref015","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1128\/AAC.49.5.1782-1786.2005","article-title":"Mutations in PA3574 (nalD) lead to increased MexAB-OprM expression and multidrug resistance in laboratory and clinical isolates of Pseudomonas aeruginosa","volume":"49","author":"ML Sobel","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"key":"pcbi.1007562.ref016","article-title":"Mutations in NalC induce MexAB-OprM overexpression resulting in high level of aztreonam resistance in environmental isolates of Pseudomonas aeruginosa","volume":"363","author":"VS Braz","year":"2016","journal-title":"FEMS Microbiol Lett"},{"key":"pcbi.1007562.ref017","doi-asserted-by":"crossref","first-page":"e32684","DOI":"10.1371\/journal.pone.0032684","article-title":"Pentachlorophenol induction of the Pseudomonas aeruginosa mexAB-oprM efflux operon: involvement of repressors NalC and MexR and the antirepressor ArmR","volume":"7","author":"LM Starr","year":"2012","journal-title":"PLoS One"},{"key":"pcbi.1007562.ref018","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center","volume":"45","author":"AR Wattam","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007562.ref019","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1084\/jem.20112408","article-title":"Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation","volume":"209","author":"RR Jenq","year":"2012","journal-title":"J Exp Med"},{"key":"pcbi.1007562.ref020","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1182\/blood-2014-02-554725","article-title":"The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation","volume":"124","author":"Y Taur","year":"2014","journal-title":"Blood"},{"key":"pcbi.1007562.ref021","article-title":"Adaptive evolution within the gut microbiome of individual people","author":"S Zhao","year":"2017","journal-title":"BioRxiv"},{"key":"pcbi.1007562.ref022","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":"pcbi.1007562.ref023","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.cell.2017.12.012","article-title":"Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections","volume":"172","author":"L Imamovic","year":"2018","journal-title":"Cell"},{"key":"pcbi.1007562.ref024","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression Shrinkage and Selection via the Lasso","volume":"58","author":"R Tibshirani","year":"1996","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"key":"pcbi.1007562.ref025","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/jac\/dkf210","article-title":"Molecular characterization of SPM-1, a novel metallo-beta-lactamase isolated in Latin America: report from the SENTRY antimicrobial surveillance programme","volume":"50","author":"MA Toleman","year":"2002","journal-title":"J Antimicrob Chemother"},{"key":"pcbi.1007562.ref026","doi-asserted-by":"crossref","first-page":"3322","DOI":"10.1128\/AAC.44.12.3322-3327.2000","article-title":"Substrate specificities of MexAB-OprM, MexCD-OprJ, and MexXY-OprM efflux pumps in Pseudomonas aeruginosa","volume":"44","author":"N Masuda","journal-title":"Antimicrob Agents Chemother"},{"key":"pcbi.1007562.ref027","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1128\/AAC.48.3.843-851.2004","article-title":"Selection of an antibiotic-hypersusceptible mutant of Pseudomonas aeruginosa: identification of the GlmR transcriptional regulator","volume":"48","author":"J Ramos-Aires","journal-title":"Antimicrob Agents Chemother"},{"key":"pcbi.1007562.ref028","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1111\/mmi.13346","article-title":"Novobiocin binding to NalD induces the expression of the MexAB-OprM pump in Pseudomonas aeruginosa","volume":"100","author":"W Chen","year":"2016","journal-title":"Mol Microbiol"},{"key":"pcbi.1007562.ref029","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1128\/AAC.39.9.1948","article-title":"Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa","volume":"39","author":"XZ Li","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"pcbi.1007562.ref030","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1016\/j.celrep.2017.07.062","article-title":"Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria","volume":"20","author":"PA Jensen","year":"2017","journal-title":"Cell Rep"},{"key":"pcbi.1007562.ref031","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 Comput Biol"},{"key":"pcbi.1007562.ref032","article-title":"Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness","author":"J Nogales","year":"2017","journal-title":"BioRxiv."},{"key":"pcbi.1007562.ref033","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1126\/science.1217405","article-title":"Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space","volume":"336","author":"O Shoval","year":"2012","journal-title":"Science (80-)"},{"key":"pcbi.1007562.ref034","doi-asserted-by":"crossref","first-page":"2776","DOI":"10.3389\/fmicb.2018.02776","article-title":"Metabolic Analyses Revealed Time-Dependent Synergistic Killing by Colistin and Aztreonam Combination Against Multidrug-Resistant Acinetobacter baumannii","volume":"9","author":"M-L Han","year":"2018","journal-title":"Front Microbiol"},{"key":"pcbi.1007562.ref035","doi-asserted-by":"crossref","first-page":"E5125","DOI":"10.1073\/pnas.1717525115","article-title":"Pseudomonas aeruginosa transcriptome during human infection","volume":"115","author":"DM Cornforth","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007562.ref036","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/cid\/cis580","article-title":"Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation","volume":"55","author":"Y Taur","year":"2012","journal-title":"Clin Infect Dis"},{"key":"pcbi.1007562.ref037","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1038\/s41591-018-0202-8","article-title":"Precision identification of diverse bloodstream pathogens in the gut microbiome","volume":"24","author":"FB Tamburini","year":"2018","journal-title":"Nat Med"},{"key":"pcbi.1007562.ref038","doi-asserted-by":"crossref","first-page":"e1003617","DOI":"10.1371\/journal.pgen.1003617","article-title":"Bacterial adaptation through loss of function","volume":"9","author":"AK Hottes","year":"2013","journal-title":"PLoS Genet"},{"key":"pcbi.1007562.ref039","doi-asserted-by":"crossref","first-page":"e00981","DOI":"10.1128\/mBio.00981-15","article-title":"Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung","volume":"6","author":"J Diaz Caballero","year":"2015","journal-title":"MBio"},{"key":"pcbi.1007562.ref040","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.vetmic.2015.03.002","article-title":"A naturally occurring prfA truncation in a Listeria monocytogenes field strain contributes to reduced replication and cell-to-cell spread","volume":"179","author":"S Rupp","year":"2015","journal-title":"Vet Microbiol"},{"key":"pcbi.1007562.ref041","doi-asserted-by":"crossref","first-page":"e00969","DOI":"10.1128\/mBio.00969-14","article-title":"Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity","volume":"5","author":"C B\u00e9cavin","year":"2014","journal-title":"MBio"},{"key":"pcbi.1007562.ref042","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1111\/mmi.12682","article-title":"Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element","volume":"93","author":"MA Benson","year":"2014","journal-title":"Mol Microbiol"},{"key":"pcbi.1007562.ref043","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1111\/mmi.13584","article-title":"Regulatory gene mutation: a driving force behind group a Streptococcus strain- and serotype-specific variation","volume":"103","author":"P Sarkar","year":"2017","journal-title":"Mol Microbiol"},{"key":"pcbi.1007562.ref044","doi-asserted-by":"crossref","first-page":"e95936","DOI":"10.1371\/journal.pone.0095936","article-title":"A gacS deletion in Pseudomonas aeruginosa cystic fibrosis isolate CHA shapes its virulence","volume":"9","author":"KM Sall","year":"2014","journal-title":"PLoS One"},{"key":"pcbi.1007562.ref045","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1093\/infdis\/jiw402","article-title":"Interplay Between Antibiotic Resistance and Virulence During Disease Promoted by Multidrug-Resistant Bacteria","volume":"215","author":"E Geisinger","year":"2017","journal-title":"J Infect Dis"},{"key":"pcbi.1007562.ref046","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":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007562.ref047","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 Comput Biol"},{"key":"pcbi.1007562.ref048","doi-asserted-by":"crossref","first-page":"3706","DOI":"10.1038\/s41598-017-03416-2","article-title":"Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections","volume":"7","author":"L Presta","year":"2017","journal-title":"Sci Rep"},{"key":"pcbi.1007562.ref049","article-title":"Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa","volume":"7","author":"Y Zhu","year":"2018","journal-title":"Gigascience"},{"key":"pcbi.1007562.ref050","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.cels.2018.12.002","article-title":"Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa","volume":"8","author":"LJ Dunphy","journal-title":"Cell Syst"},{"key":"pcbi.1007562.ref051","doi-asserted-by":"crossref","first-page":"e44637","DOI":"10.1371\/journal.pone.0044637","article-title":"Novel targets of the CbrAB\/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa","volume":"7","author":"E Sonnleitner","year":"2012","journal-title":"PLoS One"},{"key":"pcbi.1007562.ref052","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.3389\/fmicb.2018.02709","article-title":"Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa","volume":"9","author":"P Pusic","year":"2018","journal-title":"Front Microbiol"},{"key":"pcbi.1007562.ref053","doi-asserted-by":"crossref","first-page":"3196","DOI":"10.1111\/j.1462-2920.2010.02292.x","article-title":"The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa","volume":"12","author":"JF Linares","year":"2010","journal-title":"Environ Microbiol"},{"key":"pcbi.1007562.ref054","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1128\/JB.00911-10","article-title":"The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa","volume":"193","author":"ATY Yeung","year":"2011","journal-title":"J Bacteriol"},{"issue":"Pt 1","key":"pcbi.1007562.ref055","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1099\/00221287-141-1-133","article-title":"The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system","volume":"141","author":"AC Ghrist","year":"1995","journal-title":"Microbiology (Reading, Engl)"},{"key":"pcbi.1007562.ref056","doi-asserted-by":"crossref","first-page":"8079","DOI":"10.1128\/JB.01138-07","article-title":"Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum","volume":"189","author":"KL Palmer","year":"2007","journal-title":"J Bacteriol"},{"key":"pcbi.1007562.ref057","doi-asserted-by":"crossref","first-page":"230","DOI":"10.3389\/fcimb.2018.00230","article-title":"The pseudomonas quinolone signal (PQS): not just for quorum sensing anymore","volume":"8","author":"J Lin","year":"2018","journal-title":"Front Cell Infect Microbiol"},{"key":"pcbi.1007562.ref058","doi-asserted-by":"crossref","first-page":"e1000166","DOI":"10.1371\/journal.ppat.1000166","article-title":"The pseudomonas quinolone signal (PQS) balances life and death in Pseudomonas aeruginosa populations","volume":"4","author":"S H\u00e4ussler","year":"2008","journal-title":"PLoS Pathog"},{"key":"pcbi.1007562.ref059","doi-asserted-by":"crossref","first-page":"25920","DOI":"10.1074\/jbc.M115.687749","article-title":"Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways","volume":"290","author":"PI Nikel","year":"2015","journal-title":"J Biol Chem"},{"key":"pcbi.1007562.ref060","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.mib.2017.10.029","article-title":"Metabolic-flux dependent regulation of microbial physiology","volume":"42","author":"A Litsios","year":"2018","journal-title":"Curr Opin Microbiol"},{"key":"pcbi.1007562.ref061","doi-asserted-by":"crossref","first-page":"3377","DOI":"10.1128\/JB.06379-11","article-title":"The Entner-Doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of Vibrio cholerae","volume":"194","author":"T Patra","year":"2012","journal-title":"J Bacteriol"},{"key":"pcbi.1007562.ref062","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf2786","article-title":"Systems-level analysis of mechanisms regulating yeast metabolic flux","volume":"354","author":"SR Hackett","year":"2016","journal-title":"Science (80-)"},{"key":"pcbi.1007562.ref063","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/msb.2013.66","article-title":"Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis","volume":"9","author":"V Chubukov","year":"2013","journal-title":"Mol Syst Biol"},{"key":"pcbi.1007562.ref064","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007562.ref065","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":"pcbi.1007562.ref066","doi-asserted-by":"crossref","first-page":"e1003580","DOI":"10.1371\/journal.pcbi.1003580","article-title":"Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism","volume":"10","author":"D Machado","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007562.ref067","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1752-0509-7-74","article-title":"COBRApy: COnstraints-Based Reconstruction and Analysis for Python","volume":"7","author":"A Ebrahim","year":"2013","journal-title":"BMC Syst Biol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007562","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T00:00:00Z","timestamp":1578268800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T13:35:28Z","timestamp":1578317728000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007562"}},"subtitle":[],"editor":[{"given":"Kiran Raosaheb","family":"Patil","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,12,20]]},"references-count":67,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2019,12,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007562","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1007562","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12,20]]}}}