{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:54:29Z","timestamp":1778226869036,"version":"3.51.4"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2015,11,30]],"date-time":"2015-11-30T00:00:00Z","timestamp":1448841600000},"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.1004543","type":"journal-article","created":{"date-parts":[[2015,11,30]],"date-time":"2015-11-30T13:51:40Z","timestamp":1448891500000},"page":"e1004543","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":70,"title":["Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis"],"prefix":"10.1371","volume":"11","author":[{"given":"Shuyi","family":"Ma","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle J.","family":"Minch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tige R.","family":"Rustad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Hobbs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suk-Lin","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David R.","family":"Sherman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan D.","family":"Price","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,11,30]]},"reference":[{"key":"ref1","article-title":"World Health Organization","year":"2010"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"87s","DOI":"10.1183\/09031936.02.00309102","article-title":"Tuberculosis therapy: past, present and future","volume":"36","author":"MD Iseman","year":"2002","journal-title":"Eur Respir J Suppl"},{"issue":"3","key":"ref3","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.tim.2011.12.004","article-title":"A metabolic network approach for the identification and prioritization of antimicrobial drug targets","volume":"20","author":"AK Chavali","year":"2012","journal-title":"Trends Microbiol"},{"issue":"13","key":"ref4","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1101\/gad.1325605","article-title":"Constructing transcriptional regulatory networks","volume":"19","author":"A Blais","year":"2005","journal-title":"Genes Dev"},{"issue":"10","key":"ref5","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/nrm2503","article-title":"Modelling and analysis of gene regulatory networks","volume":"9","author":"G Karlebach","year":"2008","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/msb4100162","article-title":"Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli","volume":"3","author":"R Schuetz","year":"2007","journal-title":"Mol Syst Biol"},{"issue":"5","key":"ref7","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"},{"issue":"4","key":"ref8","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"},{"issue":"9","key":"ref9","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":"Nat Biotechnol"},{"issue":"24","key":"ref10","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"},{"issue":"8","key":"ref11","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"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1006\/jtbi.2001.2405","article-title":"Regulation of gene expression in flux balance models of metabolism","volume":"213","author":"MW Covert","year":"2001","journal-title":"J Theor Biol"},{"issue":"31","key":"ref13","doi-asserted-by":"crossref","first-page":"28058","DOI":"10.1074\/jbc.M201691200","article-title":"Transcriptional regulation in constraints-based metabolic models of Escherichia coli","volume":"277","author":"MW Covert","year":"2002","journal-title":"J Biol Chem"},{"issue":"6987","key":"ref14","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/nature02456","article-title":"Integrating high-throughput and computational data elucidates bacterial networks","volume":"429","author":"MW Covert","year":"2004","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/msb4100141","article-title":"A genome-scale computational study of the interplay between transcriptional regulation and metabolism","volume":"3","author":"T Shlomi","year":"2007","journal-title":"Mol Syst Biol"},{"issue":"41","key":"ref16","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 U S A"},{"key":"ref17","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 Syst Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/msb.2008.63","article-title":"The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest","volume":"4","author":"G Balazsi","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"5829","DOI":"10.1038\/ncomms6829","article-title":"The DNA-binding network of Mycobacterium tuberculosis","volume":"6","author":"KJ Minch","year":"2015","journal-title":"Nat Commun"},{"issue":"5","key":"ref20","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":"DJ Beste","year":"2007","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/1752-0509-4-160","article-title":"Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis","volume":"4","author":"X Fang","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref22","article-title":"Edinburgh","author":"S Kalapanulak","year":"2009"},{"issue":"9","key":"ref23","doi-asserted-by":"crossref","first-page":"e75913","DOI":"10.1371\/journal.pone.0075913","article-title":"Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex","volume":"8","author":"EK Lofthouse","year":"2013","journal-title":"PLoS One"},{"issue":"4","key":"ref24","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.tube.2010.03.010","article-title":"TB database 2010: overview and update","volume":"90","author":"JE Galagan","year":"2010","journal-title":"Tuberculosis (Edinb)"},{"issue":"Database issue","key":"ref25","doi-asserted-by":"crossref","first-page":"D499","DOI":"10.1093\/nar\/gkn652","article-title":"TB database: an integrated platform for tuberculosis research","volume":"37","author":"TB Reddy","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"ref26","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1186\/s13059-014-0502-3","article-title":"Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network","volume":"15","author":"TR Rustad","year":"2014","journal-title":"Genome Biol"},{"issue":"9","key":"ref27","doi-asserted-by":"crossref","first-page":"e1002251","DOI":"10.1371\/journal.ppat.1002251","article-title":"High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism","volume":"7","author":"JE Griffin","year":"2011","journal-title":"PLoS Pathog"},{"issue":"9","key":"ref28","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"},{"issue":"9","key":"ref29","doi-asserted-by":"crossref","first-page":"e75245","DOI":"10.1371\/journal.pone.0075245","article-title":"Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis","volume":"8","author":"TR Ioerger","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"ref30","doi-asserted-by":"crossref","first-page":"e1502","DOI":"10.1371\/journal.pone.0001502","article-title":"The enduring hypoxic response of Mycobacterium tuberculosis","volume":"3","author":"TR Rustad","year":"2008","journal-title":"PLoS One"},{"issue":"5","key":"ref31","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1128\/AAC.41.5.1004","article-title":"Microplate alamar blue assay versus BACTEC 460 system for high-throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium","volume":"41","author":"L Collins","year":"1997","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"ref32","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":"SA Becker","year":"2007","journal-title":"Nat Protoc"},{"issue":"2","key":"ref33","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"},{"issue":"8","key":"ref34","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1086\/651452","article-title":"Attenuation of Mycobacterium tuberculosis functionally disrupted in a fatty acyl-coenzyme A synthetase gene fadD5","volume":"201","author":"KY Dunphy","year":"2010","journal-title":"J Infect Dis"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1128\/JB.185.1.142-147.2003","article-title":"Growth of mycobacteria on carbon monoxide and methanol","volume":"185","author":"SW Park","year":"2003","journal-title":"J Bacteriol"},{"issue":"31","key":"ref36","doi-asserted-by":"crossref","first-page":"9058","DOI":"10.1021\/bi700688x","article-title":"Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase","volume":"46","author":"X Yang","year":"2007","journal-title":"Biochemistry"},{"issue":"Unit 10A","key":"ref37","first-page":"1","article-title":"Laboratory maintenance of Mycobacterium tuberculosis","volume":"Chapter 10","author":"MH Larsen","year":"2007","journal-title":"Curr Protoc Microbiol"},{"key":"ref38","article-title":"R: A Language and Environment for Statistical Computing","year":"2014"},{"key":"ref39","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4614-7138-7","article-title":"An Introduction to Statistical Learning: with Applications in R","author":"G James","year":"2013"},{"key":"ref40","article-title":"cvTools: Cross-validation tools for regression models","author":"A Alfons","year":"2012"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004543","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T22:32:18Z","timestamp":1567377138000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004543"}},"subtitle":[],"editor":[{"given":"Jorg","family":"Stelling","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,11,30]]},"references-count":40,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2015,11,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004543","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,11,30]]}}}