{"id":"https://openalex.org/W1992009029","doi":"https://doi.org/10.1371/journal.pcbi.1004028","title":"Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data","display_name":"Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data","publication_year":2015,"publication_date":"2015-01-15","ids":{"openalex":"https://openalex.org/W1992009029","doi":"https://doi.org/10.1371/journal.pcbi.1004028","mag":"1992009029","pmid":"https://pubmed.ncbi.nlm.nih.gov/25590141"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004028","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004028","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004028&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004028&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079861951","display_name":"Diana Stefan","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I177483745","display_name":"Universit\u00e9 Joseph Fourier","ror":"https://ror.org/02aj0kh94","country_code":"FR","type":"education","lineage":["https://openalex.org/I177483745"]},{"id":"https://openalex.org/I4210113150","display_name":"Laboratoire Interdisciplinaire de Physique","ror":"https://ror.org/023n9q531","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210113150","https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Diana Stefan","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","institution_ids":["https://openalex.org/I177483745","https://openalex.org/I4210113150","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","institution_ids":["https://openalex.org/I4210113150"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109710268","display_name":"Corinne Pinel","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I177483745","display_name":"Universit\u00e9 Joseph Fourier","ror":"https://ror.org/02aj0kh94","country_code":"FR","type":"education","lineage":["https://openalex.org/I177483745"]},{"id":"https://openalex.org/I4210113150","display_name":"Laboratoire Interdisciplinaire de Physique","ror":"https://ror.org/023n9q531","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210113150","https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Corinne Pinel","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","institution_ids":["https://openalex.org/I177483745","https://openalex.org/I4210113150","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","institution_ids":["https://openalex.org/I4210113150"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024943883","display_name":"St\u00e9phane Pinhal","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I177483745","display_name":"Universit\u00e9 Joseph Fourier","ror":"https://ror.org/02aj0kh94","country_code":"FR","type":"education","lineage":["https://openalex.org/I177483745"]},{"id":"https://openalex.org/I4210113150","display_name":"Laboratoire Interdisciplinaire de Physique","ror":"https://ror.org/023n9q531","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210113150","https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phane Pinhal","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","institution_ids":["https://openalex.org/I177483745","https://openalex.org/I4210113150","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","institution_ids":["https://openalex.org/I4210113150"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010375183","display_name":"Eugenio Cinquemani","orcid":"https://orcid.org/0000-0003-3353-6525"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eugenio Cinquemani","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068981088","display_name":"Johannes Geiselmann","orcid":"https://orcid.org/0000-0002-1329-7558"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I177483745","display_name":"Universit\u00e9 Joseph Fourier","ror":"https://ror.org/02aj0kh94","country_code":"FR","type":"education","lineage":["https://openalex.org/I177483745"]},{"id":"https://openalex.org/I4210113150","display_name":"Laboratoire Interdisciplinaire de Physique","ror":"https://ror.org/023n9q531","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210113150","https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Johannes Geiselmann","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France; Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Universit\u00e9 Joseph Fourier, Grenoble, France","institution_ids":["https://openalex.org/I177483745","https://openalex.org/I4210113150","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]},{"raw_affiliation_string":"LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","institution_ids":["https://openalex.org/I4210113150"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054406248","display_name":"Hidde de Jong","orcid":"https://orcid.org/0000-0002-2226-650X"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hidde de Jong","raw_affiliation_strings":["INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Grenoble - Rh\u00f4ne-Alpes, Grenoble, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2002,"currency":"EUR","value_usd":2159},"fwci":2.9288,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.91187456,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"1","first_page":"e1004028","last_page":"e1004028"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6827191710472107},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6383578777313232},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6377473473548889},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5490701794624329},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.48785853385925293},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.476053923368454},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4530952572822571},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.44372496008872986},{"id":"https://openalex.org/keywords/bacterial-transcription","display_name":"Bacterial transcription","score":0.4403515160083771},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3447161316871643},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.31984376907348633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2997303605079651},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27424755692481995},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14747074246406555}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6827191710472107},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6383578777313232},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6377473473548889},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5490701794624329},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.48785853385925293},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.476053923368454},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4530952572822571},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.44372496008872986},{"id":"https://openalex.org/C26261996","wikidata":"https://www.wikidata.org/wiki/Q2382392","display_name":"Bacterial transcription","level":5,"score":0.4403515160083771},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3447161316871643},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.31984376907348633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2997303605079651},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27424755692481995},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14747074246406555}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012808","descriptor_name":"Sigma Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017930","descriptor_name":"Genes, Reporter","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004028","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004028","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004028&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25590141","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25590141","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:figshare.com:article/1290353","is_oa":true,"landing_page_url":null,"pdf_url":"https://figshare.com/articles/dataset/_Inference_of_Quantitative_Models_of_Bacterial_Promoters_from_Time_Series_Reporter_Gene_Data_/1290353","source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:HAL:hal-01097632v1","is_oa":false,"landing_page_url":"https://inria.hal.science/hal-01097632","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2015, 11 (1), pp.e1004028. ⟨10.1371/journal.pcbi.1004028⟩","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:7634114449a24ea790d3bc53da0c50da","is_oa":true,"landing_page_url":"https://doaj.org/article/7634114449a24ea790d3bc53da0c50da","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 1, p e1004028 (2015)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4295839","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4295839","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004028","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004028","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004028&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5103729303","display_name":"Eteindre et rallumer la machinerie d'expression g\u00e9nique chez les bact\u00e9ries: de mod\u00e8les math\u00e9matiques aux applications biotechnologiques","funder_award_id":"ANR-11-BINF-0005","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320313934","display_name":"Institut national de recherche en informatique et en automatique (INRIA)","ror":"https://ror.org/02kvxyf05"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1992009029.pdf","grobid_xml":"https://content.openalex.org/works/W1992009029.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W19761145","https://openalex.org/W208046272","https://openalex.org/W1509329028","https://openalex.org/W1541504929","https://openalex.org/W1546783991","https://openalex.org/W1563663197","https://openalex.org/W1645305843","https://openalex.org/W1841558112","https://openalex.org/W1886048099","https://openalex.org/W1910544225","https://openalex.org/W1963522244","https://openalex.org/W1977389772","https://openalex.org/W1996264210","https://openalex.org/W2010420771","https://openalex.org/W2016097940","https://openalex.org/W2021246213","https://openalex.org/W2025166348","https://openalex.org/W2038186289","https://openalex.org/W2038540528","https://openalex.org/W2042493870","https://openalex.org/W2048073472","https://openalex.org/W2053460598","https://openalex.org/W2057266064","https://openalex.org/W2057746324","https://openalex.org/W2064441783","https://openalex.org/W2065096062","https://openalex.org/W2065479717","https://openalex.org/W2078635599","https://openalex.org/W2101058428","https://openalex.org/W2101762601","https://openalex.org/W2105129830","https://openalex.org/W2109281577","https://openalex.org/W2109384743","https://openalex.org/W2111484165","https://openalex.org/W2111967267","https://openalex.org/W2114435056","https://openalex.org/W2115108153","https://openalex.org/W2115606218","https://openalex.org/W2115955060","https://openalex.org/W2123374042","https://openalex.org/W2123425265","https://openalex.org/W2124227685","https://openalex.org/W2128605063","https://openalex.org/W2130665506","https://openalex.org/W2130863397","https://openalex.org/W2133068979","https://openalex.org/W2134440848","https://openalex.org/W2137325336","https://openalex.org/W2139414608","https://openalex.org/W2139915240","https://openalex.org/W2144533552","https://openalex.org/W2144738674","https://openalex.org/W2145633829","https://openalex.org/W2147109452","https://openalex.org/W2148342439","https://openalex.org/W2152630555","https://openalex.org/W2152910833","https://openalex.org/W2153481137","https://openalex.org/W2157603268","https://openalex.org/W2161782181","https://openalex.org/W2161922735","https://openalex.org/W2163833586","https://openalex.org/W2166744717","https://openalex.org/W2167898143","https://openalex.org/W2292299839","https://openalex.org/W6632620185","https://openalex.org/W6696783150"],"related_works":["https://openalex.org/W2949927938","https://openalex.org/W2029387041","https://openalex.org/W2135896045","https://openalex.org/W2581702729","https://openalex.org/W2010571965","https://openalex.org/W2032799661","https://openalex.org/W2002709996","https://openalex.org/W2884256268","https://openalex.org/W2131025197","https://openalex.org/W3128451840"],"abstract_inverted_index":{"The":[0,33,244],"inference":[1],"of":[2,8,24,35,53,65,93,128,134,150,157,176,179,190,196,229,265,271,280,288,296],"regulatory":[3,266],"interactions":[4],"and":[5,19,31,84,98,115,130,137,145,170,226,263,284,290],"quantitative":[6],"models":[7,129,178,198],"gene":[9,73,95,180,231],"regulation":[10,287],"from":[11,200],"time-series":[12,255],"transcriptomics":[13,58],"data":[14,257],"has":[15],"been":[16],"extensively":[17],"studied":[18],"applied":[20],"to":[21,62,77,81,213,258],"a":[22,126],"range":[23],"problems":[25],"in":[26,57,72,90,107,142,146,153,219,240,247],"drug":[27],"discovery,":[28],"cancer":[29],"research,":[30],"biotechnology.":[32],"application":[34],"existing":[36],"methods":[37],"is":[38,250],"commonly":[39],"based":[40],"on":[41,44],"implicit":[42],"assumptions":[43,110,192],"the":[45,51,69,91,94,117,132,148,154,158,188,194,197,201,227,230,241,261,269,272,278,285,294],"biological":[46],"processes":[47],"under":[48],"study.":[49],"First,":[50],"measurements":[52],"mRNA":[54],"abundance":[55],"obtained":[56],"experiments":[59],"are":[60,75,103,111,211],"taken":[61],"be":[63,78,214],"representative":[64],"protein":[66,168,221],"concentrations.":[67],"Second,":[68],"observed":[70],"changes":[71,89],"expression":[74,96,232],"assumed":[76],"solely":[79],"due":[80],"transcription":[82],"factors":[83],"other":[85,99],"specific":[86],"regulators,":[87],"while":[88],"activity":[92,149,228],"machinery":[97,233],"global":[100,171,281],"physiological":[101,172,282],"effects":[102,173,283],"neglected.":[104],"While":[105],"convenient":[106],"practice,":[108],"these":[109,164,209],"often":[112],"not":[113],"valid":[114],"bias":[116,136,189],"reverse":[118],"engineering":[119],"process.":[120],"Here":[121],"we":[122,166,204],"systematically":[123],"investigate,":[124],"using":[125,254],"combination":[127],"experiments,":[131],"importance":[133,279],"this":[135,248],"possible":[138],"corrections.":[139],"We":[140],"measure":[141],"real":[143],"time":[144],"vivo":[147],"genes":[151],"involved":[152],"FliA-FlgM":[155,242,273],"module":[156],"E.":[159],"coli":[160],"motility":[161],"network.":[162],"From":[163],"data,":[165],"estimate":[167],"concentrations":[169,222],"by":[174,206],"means":[175],"kinetic":[177],"expression.":[181],"Our":[182],"results":[183,276],"indicate":[184],"that":[185,208],"correcting":[186],"for":[187,217,293],"commonly-made":[191],"improves":[193],"quality":[195],"inferred":[199],"data.":[202],"Moreover,":[203],"show":[205],"simulation":[207],"improvements":[210],"expected":[212],"even":[215],"stronger":[216],"systems":[218],"which":[220],"have":[223],"longer":[224],"half-lives":[225,292],"varies":[234],"more":[235],"strongly":[236],"across":[237],"conditions":[238],"than":[239],"module.":[243],"approach":[245],"proposed":[246],"study":[249],"broadly":[251],"applicable":[252],"when":[253],"transcriptome":[256],"learn":[259],"about":[260],"structure":[262],"dynamics":[264,295],"networks.":[267],"In":[268],"case":[270],"module,":[274],"our":[275],"demonstrate":[277],"active":[286],"FliA":[289],"FlgM":[291],"FliA-dependent":[297],"promoters.":[298]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}