{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:49:34Z","timestamp":1767178174056,"version":"build-2238731810"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T00:00:00Z","timestamp":1421280000000},"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.1004028","type":"journal-article","created":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T15:47:04Z","timestamp":1421336824000},"page":"e1004028","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data"],"prefix":"10.1371","volume":"11","author":[{"given":"Diana","family":"Stefan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Corinne","family":"Pinel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phane","family":"Pinhal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eugenio","family":"Cinquemani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Geiselmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hidde","family":"de Jong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,1,15]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100120","article-title":"How to infer gene networks from expression profiles","volume":"3","author":"M Bansal","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1111\/j.1742-4658.2008.06844.x","article-title":"Systems biology: parameter estimation for biochemical models","volume":"276","author":"M Ashyraliyev","year":"2009","journal-title":"FEBS J"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg3244","article-title":"Studying and modelling dynamic biological processes using time-series gene expression data","volume":"13","author":"Z Bar-Joseph","year":"2012","journal-title":"Nat Rev Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nrmicro2419","article-title":"Advantages and limitations of current network inference methods","volume":"8","author":"R de Smet","year":"2010","journal-title":"Nat Rev Microbiol"},{"key":"ref5","first-page":"86","article-title":"Reverse engineering and identification in systems biology: strategies, perspectives and challenges","volume":"96","author":"M Hecker","year":"2009","journal-title":"Biosystems"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/nmeth.2016","article-title":"Wisdom of crowds for robust gene network inference","volume":"9","author":"D Marbach","year":"2012","journal-title":"Nat Methods"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"20130505","DOI":"10.1098\/rsif.2013.0505","article-title":"Reverse engineering and identification in systems biology: strategies, perspectives and challenges","volume":"11","author":"A Villaverde","year":"2014","journal-title":"J R Soc Interface"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nbt1270","article-title":"Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation","volume":"25","author":"P Lu","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1126\/science.1188308","article-title":"Quantifying <italic>E. coli<\/italic> proteome and transcriptome with single-molecule sensitivity in single cells","volume":"329","author":"Y Taniguchi","year":"2010","journal-title":"Science"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"9697","DOI":"10.1073\/pnas.112318199","article-title":"Global analysis of mRNA decay and abundance in <italic>Escherichia coli<\/italic> at single-gene resolution using two-color fluorescent DNA microarrays","volume":"99","author":"J Bernstein","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"4125","DOI":"10.1016\/S0021-9258(19)85642-9","article-title":"The relative rates of protein synthesis and degradation in a growing culture of <italic>Escherichia coli<\/italic>","volume":"255","author":"K Larrabee","year":"1980","journal-title":"J Biol Chem"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1016\/S0021-9258(19)85924-0","article-title":"Metabolism of individual proteins in exponentially growing <italic>Escherichia coli<\/italic>","volume":"255","author":"R Mosteller","year":"1980","journal-title":"J Biol Chem"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"3966","DOI":"10.1016\/j.febslet.2009.10.036","article-title":"Correlation of mRNA and protein in complex biological samples","volume":"583","author":"T Maier","year":"2009","journal-title":"FEBS Lett"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nature11835","article-title":"A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis","volume":"494","author":"P Picotti","year":"2013","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1074\/mcp.M113.032672","article-title":"Mass spectrometry-based workflow for accurate quantification of <italic>E. coli<\/italic> enzymes: how proteomics can play a key role in metabolic engineering","volume":"13","author":"M Trauchessec","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1016\/j.cell.2009.12.001","article-title":"Growth rate-dependent global effects on gene expression in bacteria","volume":"139","author":"S Klumpp","year":"2009","journal-title":"Cell"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1038\/msb.2012.70","article-title":"Shared control of gene expression in bacteria by transcription factors and global physiology of the cell","volume":"9","author":"S Berthoumieux","year":"2013","journal-title":"Mol Syst Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/msb.2013.14","article-title":"Dissecting specific and global transcriptional regulation of bacterial gene expression","volume":"9","author":"L Gerosa","year":"2013","journal-title":"Mol Syst Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/msb.2013.59","article-title":"Promoters maintain their relative activity levels under different growth conditions","volume":"9","author":"L Keren","year":"2013","journal-title":"Mol Syst Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"R107","DOI":"10.1186\/gb-2006-7-11-r107","article-title":"Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in <italic>Saccharomyces cerevisiae<\/italic>","volume":"7","author":"B Regenberg","year":"2006","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.cell.2012.10.012","article-title":"Revisiting global gene expression analysis","volume":"151","author":"J Lov\u00e9n","year":"2012","journal-title":"Cell"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1152\/physrev.00038.2009","article-title":"Fluorescent proteins and their applications in imaging living cells and tissues","volume":"90","author":"D Chudakov","year":"2010","journal-title":"Physiol Rev"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"10555","DOI":"10.1073\/pnas.152046799","article-title":"Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics","volume":"99","author":"M Ronen","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/35002125","article-title":"A synthetic oscillatory network of transcriptional regulators","volume":"403","author":"M Elowitz","year":"2000","journal-title":"Nature"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1752-0509-4-55","article-title":"Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria","volume":"4","author":"H de Jong","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1006\/jmbi.1999.3056","article-title":"Activities of constitutive promoters in <italic>Escherichia coli<\/italic>","volume":"292","author":"S Liang","year":"1999","journal-title":"J Mol Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2080","DOI":"10.1126\/science.1058758","article-title":"Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria","volume":"292","author":"S Kalir","year":"2001","journal-title":"Science"},{"key":"ref28","first-page":"12345","article-title":"Flagella and motility","author":"R Macnab","year":"1996"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nrmicro1887","article-title":"Coordinating assembly of a bacterial macromolecular machine","volume":"6","author":"F Chevance","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"ref30","first-page":"110329","article-title":"Chemotaxis","author":"R Macnab","year":"1996"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/nrm1524","article-title":"Making sense of it all: bacterial chemotaxis","volume":"5","author":"G Wadhams","year":"2004","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1128\/jb.172.2.741-747.1990","article-title":"Transcriptional analysis of the flagellar regulon of <italic>Salmonella typhimurium<\/italic>","volume":"172","author":"K Kutsukake","year":"1990","journal-title":"J Bacteriol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"D583","DOI":"10.1093\/nar\/gkq1143","article-title":"EcoCyc: a comprehensive database of <italic>Escherichia coli<\/italic> biology","volume":"39","author":"I Keseler","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"4560","DOI":"10.3390\/ijms14034560","article-title":"Small regulatory RNAs in the control of motility and biofilm formation in <italic>E. coli<\/italic> and <italic>Salmonella<\/italic>","volume":"14","author":"F Mika","year":"2013","journal-title":"Int J Mol Sci"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e154","DOI":"10.1371\/journal.pgen.0030154","article-title":"A comprehensive genetic characterization of bacterial motility","volume":"3","author":"H Girgis","year":"2007","journal-title":"PLoS Genet"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1099\/00221287-46-2-175","article-title":"The effect of environmental conditions on the motility of <italic>Escherichia coli<\/italic>","volume":"46","author":"J Adler","year":"1967","journal-title":"J Gen Microbiol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"7500","DOI":"10.1128\/JB.181.24.7500-7508.1999","article-title":"Multiple control of flagellum biosynthesis in <italic>Escherichia coli<\/italic>: Role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the <italic>flhDC<\/italic> master operon","volume":"181","author":"O Soutourina","year":"1999","journal-title":"J Bacteriol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1128\/MMBR.64.4.694-708.2000","article-title":"Coupling of flagellar gene expression to flagellar assembly in <italic>Salmonella enterica<\/italic> serovar typhimurium and <italic>Escherichia coli<\/italic>","volume":"64","author":"G Chilcott","year":"2000","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1016\/j.cell.2004.05.010","article-title":"Using a quantitative blueprint to reprogram the dynamics of the flagella gene network","volume":"117","author":"S Kalir","year":"2004","journal-title":"Cell"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1128\/JB.00938-13","article-title":"Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of <italic>Escherichia coli<\/italic> biofilm formation","volume":"196","author":"O Dudin","year":"2014","journal-title":"J Bacteriol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"7006","DOI":"10.1128\/jb.175.21.7006-7015.1993","article-title":"Transcription from two promoters and autoregulation contribute to the control of expression of the <italic>Salmonella typhimurium<\/italic> flagellar regulatory gene <italic>flgM<\/italic>","volume":"175","author":"K Gillen","year":"1993","journal-title":"J Bacteriol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1093\/bioinformatics\/btq120","article-title":"Identification of genetic network dynamics with unate structure","volume":"26","author":"R Porreca","year":"2010","journal-title":"Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/S0006-3495(03)74970-4","article-title":"Fluctuations and slow variables in genetic networks","volume":"84","author":"R Bundschuh","year":"2003","journal-title":"Biophys J"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.jmb.2008.09.079","article-title":"Molecular titration and ultrasensitivity in regulatory networks","volume":"384","author":"N Buchler","year":"2008","journal-title":"J Mol Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"32840","DOI":"10.1287\/ijoc.1060.0175","article-title":"Scatter search and local NLP solvers: A multistart framework for global optimization","volume":"19","author":"Z Ugray","year":"2007","journal-title":"INFORMS J Comput"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1007\/s00285-012-0614-x","article-title":"On the identifiability of metabolic network models","volume":"67","author":"S Berthoumieux","year":"2013","journal-title":"J Math Biol"},{"key":"ref47","first-page":"1553","article-title":"Modulation of chemical composition and other parameters of the cell by growth rate","author":"H Bremer","year":"1996"},{"key":"ref48","article-title":"Control of Macromolecular Synthesis: A Study of DNA, RNA and Protein Synthesis in Bacteria","author":"O Maal\u00f8e","year":"1966"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"20245","DOI":"10.1073\/pnas.0804953105","article-title":"Growth-rate-dependent partitioning of RNA polymerases in bacteria","volume":"105","author":"S Klumpp","year":"2008","journal-title":"Proc Nat Acad Sci USA"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/JB.130.1.212-222.1977","article-title":"Physiological regulation of a decontrolled <italic>lac<\/italic> operon","volume":"130","author":"B Wanner","year":"1977","journal-title":"J Bacteriol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1101\/gad.380406","article-title":"The flagellar-specific transcription factor, <italic>\u03c3<\/italic><sup>28<\/sup>, is the type III secretion chaperone for the flagellar-specific anti-<italic>\u03c3<\/italic><sup>28<\/sup> factor FlgM","volume":"20","author":"P Aldridge","year":"2006","journal-title":"Genes Dev"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1111\/j.1365-2958.2007.05770.x","article-title":"Cellular levels and activity of the flagellar sigma factor FliA of <italic>Escherichia coli<\/italic> are controlled by FlgM-modulated proteolysis","volume":"65","author":"C Barembruch","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1046\/j.1365-2958.2000.02081.x","article-title":"Completion of the hook-basal body complex of the <italic>Salmonella typhimurium<\/italic> flagellum is coupled to FlgM secretion and <italic>fliC<\/italic> transcription","volume":"37","author":"J Karlinsey","year":"2000","journal-title":"Mol Microbiol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"5384","DOI":"10.1128\/JB.180.20.5384-5397.1998","article-title":"Flk couples <italic>flgM<\/italic> translation to flagellar ring assembly in <italic>Salmonella typhimurium<\/italic>","volume":"180","author":"J Karlinsey","year":"1998","journal-title":"J Bacteriol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"6286","DOI":"10.1073\/pnas.0913357107","article-title":"Revealing strengths and weaknesses of methods for gene network inference","volume":"107","author":"D Marbach","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.copbio.2011.04.014","article-title":"Bacterial growth laws and their applications","volume":"22","author":"M Scott","year":"2011","journal-title":"Curr Opin Biotechnol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1128\/MMBR.68.4.639-668.2004","article-title":"Control of rRNA synthesis in <italic>Escherichia coli<\/italic>: a systems biology approach","volume":"68","author":"P Dennis","year":"2004","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/nrmicro1088","article-title":"DNA supercoiling\u2014a global transcriptional regulator for enterobacterial growth?","volume":"3","author":"A Travers","year":"2005","journal-title":"Nat Rev Microbiol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/1752-0509-2-64","article-title":"Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data","volume":"2","author":"Z Huang","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"6752","DOI":"10.1128\/JB.183.23.6752-6762.2001","article-title":"Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria","volume":"183","author":"J Leveau","year":"2001","journal-title":"J Bacteriol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1529\/biophysj.107.122200","article-title":"Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters","volume":"94","author":"X Wang","year":"2008","journal-title":"Biophys J"},{"key":"ref62","first-page":"137","article-title":"Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria","volume":"49","author":"S Subramanian","year":"1996","journal-title":"J Bacteriol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"13004","DOI":"10.1073\/pnas.0605420103","article-title":"Quantification of protein half-lives in the budding yeast proteome","volume":"103","author":"A Belle","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref64","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100050","article-title":"Construction of <italic>Escherichia coli<\/italic> K-12 in-frame, single-gene knockout mutants: the Keio collection","volume":"2","author":"T Baba","year":"2006","journal-title":"Mol Syst Biol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nmeth895","article-title":"A comprehensive library of fluorescent transcriptional reporters for <italic>Escherichia coli<\/italic>","volume":"3","author":"A Zaslaver","year":"2006","journal-title":"Nat Methods"},{"key":"ref66","article-title":"Experiments in Molecular Genetics","author":"J Miller","year":"1972"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.jbiotec.2005.11.014","article-title":"Absolute and relative QPCR quantification of plasmid copy number in <italic>Escherichia coli<\/italic>","volume":"123","author":"C Lee","year":"2004","journal-title":"J Biotechnol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005402","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T00:00:00Z","timestamp":1488931200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004028","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,26]],"date-time":"2022-04-26T18:10:12Z","timestamp":1650996612000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004028"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,1,15]]},"references-count":67,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2015,1,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004028","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,15]]}}}