{"id":"https://openalex.org/W2169721219","doi":"https://doi.org/10.1371/journal.pcbi.1003595","title":"Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli","display_name":"Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli","publication_year":2014,"publication_date":"2014-04-24","ids":{"openalex":"https://openalex.org/W2169721219","doi":"https://doi.org/10.1371/journal.pcbi.1003595","mag":"2169721219","pmid":"https://pubmed.ncbi.nlm.nih.gov/24763195"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003595","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003595","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003595&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.1003595&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055076167","display_name":"Hao Bai","orcid":"https://orcid.org/0000-0002-5253-2194"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hao Bai","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040062325","display_name":"Matthew D. Rolfe","orcid":null},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Matthew D. Rolfe","raw_affiliation_strings":["Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100395314","display_name":"Wenjing Jia","orcid":"https://orcid.org/0000-0002-0940-3338"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Wenjing Jia","raw_affiliation_strings":["Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100981400","display_name":"Simon Coakley","orcid":null},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Simon Coakley","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008614222","display_name":"Robert K. Poole","orcid":"https://orcid.org/0000-0002-4664-6689"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robert K. Poole","raw_affiliation_strings":["Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042328891","display_name":"Jeffrey Green","orcid":"https://orcid.org/0000-0002-9070-3361"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jeffrey Green","raw_affiliation_strings":["Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031576868","display_name":"Mike Holcombe","orcid":null},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mike Holcombe","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5008614222","https://openalex.org/A5031576868","https://openalex.org/A5040062325","https://openalex.org/A5042328891","https://openalex.org/A5055076167","https://openalex.org/A5100395314","https://openalex.org/A5100981400"],"corresponding_institution_ids":["https://openalex.org/I91136226"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6317,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.85472662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"4","first_page":"e1003595","last_page":"e1003595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9957000017166138,"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/escherichia-coli","display_name":"Escherichia coli","score":0.8153988122940063},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.6055728793144226},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5475538372993469},{"id":"https://openalex.org/keywords/chemostat","display_name":"Chemostat","score":0.5466488003730774},{"id":"https://openalex.org/keywords/cytoplasm","display_name":"Cytoplasm","score":0.5318422317504883},{"id":"https://openalex.org/keywords/derepression","display_name":"Derepression","score":0.4876154959201813},{"id":"https://openalex.org/keywords/psychological-repression","display_name":"Psychological repression","score":0.47667765617370605},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.46691301465034485},{"id":"https://openalex.org/keywords/nucleoid","display_name":"Nucleoid","score":0.46422621607780457},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43943536281585693},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4382026195526123},{"id":"https://openalex.org/keywords/cell-membrane","display_name":"Cell membrane","score":0.4245557487010956},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.4212776720523834},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4207509160041809},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3976944386959076},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3904007375240326},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.300589382648468},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.27673786878585815},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17404502630233765}],"concepts":[{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.8153988122940063},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.6055728793144226},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5475538372993469},{"id":"https://openalex.org/C125111812","wikidata":"https://www.wikidata.org/wiki/Q902311","display_name":"Chemostat","level":3,"score":0.5466488003730774},{"id":"https://openalex.org/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"score":0.5318422317504883},{"id":"https://openalex.org/C73766848","wikidata":"https://www.wikidata.org/wiki/Q5262529","display_name":"Derepression","level":5,"score":0.4876154959201813},{"id":"https://openalex.org/C186310378","wikidata":"https://www.wikidata.org/wiki/Q941796","display_name":"Psychological repression","level":4,"score":0.47667765617370605},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.46691301465034485},{"id":"https://openalex.org/C53642103","wikidata":"https://www.wikidata.org/wiki/Q459485","display_name":"Nucleoid","level":4,"score":0.46422621607780457},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43943536281585693},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4382026195526123},{"id":"https://openalex.org/C2778106830","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Cell membrane","level":3,"score":0.4245557487010956},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.4212776720523834},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4207509160041809},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3976944386959076},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3904007375240326},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.300589382648468},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.27673786878585815},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17404502630233765},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010100","descriptor_name":"Oxygen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010100","descriptor_name":"Oxygen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010100","descriptor_name":"Oxygen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1003595","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003595","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003595&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:24763195","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24763195","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:eprints.whiterose.ac.uk:78897","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003595","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003595","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:0b3fc402414a4fb18dc229db31fb1b0b","is_oa":true,"landing_page_url":"https://doaj.org/article/0b3fc402414a4fb18dc229db31fb1b0b","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 10, Iss 4, p e1003595 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2979349","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3998891","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":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1006874","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Agent_Based_Modeling_of_Oxygen_Responsive_Transcription_Factors_in_Escherichia_coli_/1006874","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:pubmedcentral.nih.gov:3998891","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3998891","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1003595","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003595","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003595&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":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2818506492","display_name":null,"funder_award_id":"BB/I004122/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6121431995","display_name":null,"funder_award_id":"EP/I030654/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169721219.pdf","grobid_xml":"https://content.openalex.org/works/W2169721219.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1531704802","https://openalex.org/W1962430074","https://openalex.org/W1969870476","https://openalex.org/W1971602185","https://openalex.org/W1975818668","https://openalex.org/W1987005877","https://openalex.org/W2007961478","https://openalex.org/W2008604062","https://openalex.org/W2027068064","https://openalex.org/W2028775627","https://openalex.org/W2037097058","https://openalex.org/W2037957900","https://openalex.org/W2038470803","https://openalex.org/W2049328674","https://openalex.org/W2061133366","https://openalex.org/W2066363284","https://openalex.org/W2069888431","https://openalex.org/W2076854043","https://openalex.org/W2082363762","https://openalex.org/W2087503372","https://openalex.org/W2090911869","https://openalex.org/W2104372310","https://openalex.org/W2106650488","https://openalex.org/W2106773811","https://openalex.org/W2124677924","https://openalex.org/W2138457121","https://openalex.org/W2150618302","https://openalex.org/W2157488040","https://openalex.org/W2158718811","https://openalex.org/W2159682622","https://openalex.org/W2159883877","https://openalex.org/W2163973179","https://openalex.org/W2167208367","https://openalex.org/W2174691349","https://openalex.org/W4244151339","https://openalex.org/W4245245389","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2117627298","https://openalex.org/W1837413175","https://openalex.org/W66909360","https://openalex.org/W2416757430","https://openalex.org/W2422338521","https://openalex.org/W1760704814","https://openalex.org/W1976238592","https://openalex.org/W1972038116","https://openalex.org/W24265121","https://openalex.org/W1580368581"],"abstract_inverted_index":{"In":[0,129],"the":[1,6,69,72,75,79,109,114,119,126,142,152,208,219,222,238,242],"presence":[2],"of":[3,71,121,146,155,172,210,216,227,233,248],"oxygen":[4],"(O2)":[5],"model":[7,199],"bacterium":[8],"Escherichia":[9],"coli":[10,62,150,196],"is":[11,38,45,241],"able":[12,39],"to":[13,40,139,212],"conserve":[14],"energy":[15],"by":[16,86,108,148,221],"aerobic":[17],"respiration.":[18],"Two":[19],"major":[20],"terminal":[21,77,110,177,223],"oxidases":[22,111,178,224],"are":[23,84,179,189,203],"involved":[24],"in":[25,125,191,245],"this":[26,130],"process":[27],"-":[28],"Cyo":[29],"has":[30,49,103,136],"a":[31,50,192],"relatively":[32],"low":[33],"affinity":[34,52],"for":[35,53],"O2":[36,54,67,94,100,147,217,228],"but":[37,55],"pump":[41,58],"protons":[42],"and":[43,81,96,123,144,151,157,176,184,187,225],"hence":[44],"energetically":[46],"efficient;":[47],"Cyd":[48],"high":[51],"does":[56],"not":[57],"protons.":[59],"When":[60],"E.":[61,149,195],"encounters":[63],"environments":[64],"with":[65,229],"different":[66],"availabilities,":[68],"expression":[70],"genes":[73],"encoding":[74],"alternative":[76],"oxidases,":[78],"cydAB":[80],"cyoABCDE":[82],"operons,":[83],"regulated":[85],"two":[87,204],"O2-responsive":[88],"transcription":[89,174],"factors,":[90],"ArcA":[91,122,156],"(an":[92],"indirect":[93],"sensor)":[95],"FNR":[97,124,158,211,234],"(a":[98],"direct":[99],"sensor).":[101],"It":[102],"been":[104,137],"suggested":[105,236],"that":[106,201,206,237],"O2-consumption":[107],"located":[112],"at":[113,218],"cytoplasmic":[115,230],"membrane":[116,220],"significantly":[117],"affects":[118],"activities":[120,159],"bacterial":[127],"nucleoid.":[128],"study,":[131],"an":[132],"agent-based":[133],"modeling":[134],"approach":[135],"taken":[138],"spatially":[140],"simulate":[141],"uptake":[143],"consumption":[145,215],"consequent":[153],"modulation":[154],"based":[160],"on":[161],"experimental":[162],"data":[163],"obtained":[164],"from":[165],"highly":[166],"controlled":[167],"chemostat":[168],"cultures.":[169],"The":[170,198],"molecules":[171],"O2,":[173,213],"factors":[175],"treated":[180],"as":[181],"individual":[182],"agents":[183],"their":[185],"behaviors":[186],"interactions":[188],"imitated":[190],"simulated":[193],"3-D":[194],"cell.":[197],"implies":[200],"there":[202],"barriers":[205],"dampen":[207],"response":[209],"i.e.":[214],"reaction":[226],"FNR.":[231],"Analysis":[232],"variants":[235],"monomer-dimer":[239],"transition":[240],"key":[243],"step":[244],"FNR-mediated":[246],"repression":[247],"gene":[249],"expression.":[250]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
