{"id":"https://openalex.org/W2046417832","doi":"https://doi.org/10.1371/journal.pcbi.1000614","title":"Model of Transcriptional Activation by MarA in Escherichia coli","display_name":"Model of Transcriptional Activation by MarA in Escherichia coli","publication_year":2009,"publication_date":"2009-12-18","ids":{"openalex":"https://openalex.org/W2046417832","doi":"https://doi.org/10.1371/journal.pcbi.1000614","mag":"2046417832","pmid":"https://pubmed.ncbi.nlm.nih.gov/20019803"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000614","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1000614","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114374642","display_name":"Michael E. Wall","orcid":"https://orcid.org/0000-0003-1000-688X"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael E. Wall","raw_affiliation_strings":["Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. mewall@lanl.gov","Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. mewall@lanl.gov","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056526975","display_name":"David A. Markowitz","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David A. Markowitz","raw_affiliation_strings":["Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023066104","display_name":"Judah L. Rosner","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210090567","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210090567"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Judah L. Rosner","raw_affiliation_strings":["Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210090567","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103475524","display_name":"Robert G. Martin","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210090567","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210090567"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert G. Martin","raw_affiliation_strings":["Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210090567","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5114374642"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3446,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.82459214,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"12","first_page":"e1000614","last_page":"e1000614"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9998000264167786,"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":0.9998000264167786,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9975000023841858,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9973999857902527,"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/regulon","display_name":"Regulon","score":0.9717215299606323},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6439533233642578},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.6344079375267029},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.6200501918792725},{"id":"https://openalex.org/keywords/rna-polymerase","display_name":"RNA polymerase","score":0.5400320887565613},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.507000207901001},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.49848079681396484},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4759109616279602},{"id":"https://openalex.org/keywords/polymerase","display_name":"Polymerase","score":0.44853076338768005},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3907841444015503},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.3601452708244324},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.3183632493019104},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.19252601265907288}],"concepts":[{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.9717215299606323},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6439533233642578},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.6344079375267029},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.6200501918792725},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.5400320887565613},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.507000207901001},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49848079681396484},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4759109616279602},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.44853076338768005},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3907841444015503},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.3601452708244324},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.3183632493019104},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.19252601265907288},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013482","descriptor_name":"Superoxide Dismutase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013482","descriptor_name":"Superoxide Dismutase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013482","descriptor_name":"Superoxide Dismutase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1000614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000614","pdf_url":null,"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:20019803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20019803","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:info:ark/67531/metadc927889","is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc927889/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000614","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000614","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:96ee336dc6d24aba842173806a7f8510","is_oa":true,"landing_page_url":"https://doaj.org/article/96ee336dc6d24aba842173806a7f8510","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 5, Iss 12, p e1000614 (2009)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1894807","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2787020","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/145359","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Model_of_Transcriptional_Activation_by_MarA_in_Escherichia_coli_/145359","pdf_url":null,"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:osti.gov:956506","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/956506","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000614","pdf_url":null,"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/G254211665","display_name":null,"funder_award_id":"DE-FG02-97ER2530","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4879360136","display_name":null,"funder_award_id":"FG02-97ER25308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5219260752","display_name":null,"funder_award_id":"DE-FG","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7039840861","display_name":null,"funder_award_id":"DE-FG02-97ER25308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7186324567","display_name":null,"funder_award_id":"DE-FG02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8684078510","display_name":null,"funder_award_id":"DE-FG02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1492819466","https://openalex.org/W1590950559","https://openalex.org/W1936237469","https://openalex.org/W1957843310","https://openalex.org/W1971696785","https://openalex.org/W1982204394","https://openalex.org/W1987137450","https://openalex.org/W2009875303","https://openalex.org/W2019460535","https://openalex.org/W2022891974","https://openalex.org/W2023368756","https://openalex.org/W2023491365","https://openalex.org/W2039751039","https://openalex.org/W2040388235","https://openalex.org/W2049725457","https://openalex.org/W2056728270","https://openalex.org/W2081162288","https://openalex.org/W2087234479","https://openalex.org/W2087903802","https://openalex.org/W2087950896","https://openalex.org/W2091437986","https://openalex.org/W2108078368","https://openalex.org/W2110699703","https://openalex.org/W2110823478","https://openalex.org/W2134548479","https://openalex.org/W2137508075","https://openalex.org/W2139004845","https://openalex.org/W2140841500","https://openalex.org/W2143920302","https://openalex.org/W2144347639","https://openalex.org/W2144524717","https://openalex.org/W2152927202","https://openalex.org/W2157937275","https://openalex.org/W2163999241","https://openalex.org/W2169135201","https://openalex.org/W2171047744","https://openalex.org/W2171662523","https://openalex.org/W2179084493","https://openalex.org/W2500798221"],"related_works":["https://openalex.org/W2155710417","https://openalex.org/W1513616826","https://openalex.org/W1982204394","https://openalex.org/W3129718514","https://openalex.org/W2119300214","https://openalex.org/W2140899665","https://openalex.org/W2086884639","https://openalex.org/W2371175271","https://openalex.org/W2005166450","https://openalex.org/W1969906365"],"abstract_inverted_index":{"The":[0,116,154],"AraC":[1],"family":[2],"transcription":[3,83,101],"factor":[4,84],"MarA":[5,61,111,159],"activates":[6],"approximately":[7],"40":[8],"genes":[9],"(the":[10],"marA/soxS/rob":[11,35],"regulon)":[12],"of":[13,22,28,34,48,53,60,70,77,113,122,127,138,149,184,197,239,241,266],"the":[14,46,51,58,105,120,125,130,136,147,150,181,202,237],"Escherichia":[15],"coli":[16,204,271],"chromosome":[17],"resulting":[18],"in":[19,39,80,174,217,255,269],"different":[20],"levels":[21],"resistance":[23],"to":[24,31,45,63,107,180,227,247,261],"a":[25,40,74,82,172,224,242,253],"wide":[26],"array":[27],"antibiotics":[29],"and":[30,92,129,133,166,201,220,244,272],"superoxides.":[32],"Activation":[33],"regulon":[36,243],"promoters":[37],"occurs":[38],"well-defined":[41],"order":[42,52,126,137,238],"with":[43,100,192],"respect":[44],"level":[47],"MarA;":[49],"however,":[50],"activation":[54,79,128,139,168,185,209,240,250],"does":[55],"not":[56],"parallel":[57],"strength":[59,148],"binding":[62,165,213,257],"promoter":[64,114],"sequences.":[65],"To":[66],"understand":[67],"this":[68],"lack":[69,121],"correspondence,":[71],"we":[72,259],"developed":[73],"computational":[75],"model":[76,106,117,183,230],"transcriptional":[78],"which":[81,177,258],"either":[85,93],"increases":[86],"or":[87,95],"decreases":[88],"RNA":[89],"polymerase":[90,164,175,200,212,256],"binding,":[91,176],"accelerates":[94],"retards":[96],"post-binding":[97],"events":[98],"associated":[99],"initiation.":[102],"We":[103,206],"used":[104],"analyze":[108],"data":[109],"characterizing":[110],"regulation":[112,219,268],"activity.":[115],"clearly":[118],"explains":[119],"correspondence":[123],"between":[124,199],"MarA-DNA":[131],"affinity":[132],"indicates":[134],"that":[135,158,167,208,249],"can":[140,160,169],"only":[141],"be":[142,262],"predicted":[143],"using":[144],"information":[145],"about":[146],"full":[151],"MarA-polymerase-DNA":[152],"interaction.":[153],"analysis":[155],"further":[156],"suggests":[157],"activate":[161],"without":[162],"increasing":[163],"even":[170],"involve":[171,252],"decrease":[173,254],"is":[178],"opposite":[179],"textbook":[182],"by":[186],"recruitment.":[187],"These":[188],"findings":[189],"are":[190],"consistent":[191],"published":[193],"chromatin":[194],"immunoprecipitation":[195],"assays":[196],"interactions":[198],"E.":[203,270],"chromosome.":[205],"find":[207],"involving":[210],"decreased":[211],"yields":[214,231],"lower":[215],"latency":[216],"gene":[218,267],"therefore":[221],"might":[222,251],"confer":[223],"competitive":[225],"advantage":[226],"cells.":[228],"Our":[229],"insights":[232],"into":[233],"requirements":[234],"for":[235],"predicting":[236],"enables":[245],"us":[246],"suggest":[248],"expect":[260],"an":[263],"important":[264],"theme":[265],"beyond.":[273]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}