{"id":"https://openalex.org/W3091901779","doi":"https://doi.org/10.1093/nar/gkaa810","title":"iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning","display_name":"iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning","publication_year":2020,"publication_date":"2020-09-15","ids":{"openalex":"https://openalex.org/W3091901779","doi":"https://doi.org/10.1093/nar/gkaa810","mag":"3091901779","pmid":"https://pubmed.ncbi.nlm.nih.gov/33045728"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkaa810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa810","pdf_url":"https://academic.oup.com/nar/article-pdf/49/D1/D112/35364090/gkaa810.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/49/D1/D112/35364090/gkaa810.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091471112","display_name":"Kevin Rychel","orcid":"https://orcid.org/0000-0002-4769-2804"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Rychel","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0002-4769-2804","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110715415","display_name":"Katherine Decker","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine Decker","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047222181","display_name":"Anand V. Sastry","orcid":"https://orcid.org/0000-0002-8293-3909"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anand V Sastry","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0002-8293-3909","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073232270","display_name":"Patrick V. Phaneuf","orcid":"https://orcid.org/0000-0002-4122-6589"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick V Phaneuf","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0002-4122-6589","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018695597","display_name":"Saugat Poudel","orcid":"https://orcid.org/0000-0002-3732-2463"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saugat Poudel","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","US"],"is_corresponding":true,"raw_author_name":"Bernhard O Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-2357-6785","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I36258959","https://openalex.org/I96673099"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.5359,"has_fulltext":true,"cited_by_count":137,"citation_normalized_percentile":{"value":0.9616099,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"49","issue":"D1","first_page":"D112","last_page":"D120"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9944000244140625,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.993399977684021,"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/biology","display_name":"Biology","score":0.8639008402824402},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.783335268497467},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6297279000282288},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.629636287689209},{"id":"https://openalex.org/keywords/bacillus-subtilis","display_name":"Bacillus subtilis","score":0.4679231643676758},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.46642404794692993},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.43662604689598083},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4198918342590332},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4124619960784912},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.37733182311058044},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3262821435928345},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.15529689192771912}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8639008402824402},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.783335268497467},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6297279000282288},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.629636287689209},{"id":"https://openalex.org/C2777272437","wikidata":"https://www.wikidata.org/wiki/Q131238","display_name":"Bacillus subtilis","level":3,"score":0.4679231643676758},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.46642404794692993},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.43662604689598083},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4198918342590332},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4124619960784912},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.37733182311058044},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3262821435928345},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.15529689192771912}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkaa810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa810","pdf_url":"https://academic.oup.com/nar/article-pdf/49/D1/D112/35364090/gkaa810.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:33045728","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33045728","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7778901","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7778901","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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9sb2q961","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9sb2q961","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Nucleic Acids Research, vol 49, iss D1","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkaa810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkaa810","pdf_url":"https://academic.oup.com/nar/article-pdf/49/D1/D112/35364090/gkaa810.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5417901379","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G6160741424","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320323153","funder_display_name":"Danmarks Tekniske Universitet"},{"id":"https://openalex.org/G7701966108","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3091901779.pdf","grobid_xml":"https://content.openalex.org/works/W3091901779.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1673310716","https://openalex.org/W1946555313","https://openalex.org/W1952553890","https://openalex.org/W1975107026","https://openalex.org/W1977407898","https://openalex.org/W2036492728","https://openalex.org/W2043399591","https://openalex.org/W2077460182","https://openalex.org/W2078202582","https://openalex.org/W2078355959","https://openalex.org/W2099741732","https://openalex.org/W2101234009","https://openalex.org/W2116041602","https://openalex.org/W2118258530","https://openalex.org/W2123649031","https://openalex.org/W2123861597","https://openalex.org/W2141224535","https://openalex.org/W2142284828","https://openalex.org/W2159703006","https://openalex.org/W2179438025","https://openalex.org/W2560707317","https://openalex.org/W2753215236","https://openalex.org/W2762699776","https://openalex.org/W2770806876","https://openalex.org/W2791975541","https://openalex.org/W2804799006","https://openalex.org/W2900007277","https://openalex.org/W2900566045","https://openalex.org/W2933601491","https://openalex.org/W2952405827","https://openalex.org/W2954205175","https://openalex.org/W2971832717","https://openalex.org/W2981438196","https://openalex.org/W2990783874","https://openalex.org/W2993166334","https://openalex.org/W2997591727","https://openalex.org/W3018903834","https://openalex.org/W3021320798","https://openalex.org/W3039562686","https://openalex.org/W3044812170","https://openalex.org/W3113079090","https://openalex.org/W3128033315","https://openalex.org/W6637131181","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2010571965","https://openalex.org/W2912720016","https://openalex.org/W2002709996","https://openalex.org/W4387092964","https://openalex.org/W2103471012","https://openalex.org/W2966064480","https://openalex.org/W2115810854","https://openalex.org/W2380236774","https://openalex.org/W4317476908","https://openalex.org/W2620422757"],"abstract_inverted_index":{"Independent":[0],"component":[1],"analysis":[2],"(ICA)":[3],"of":[4,26,58,72,130,146,150,156,168],"bacterial":[5],"transcriptomes":[6],"has":[7,108],"emerged":[8],"as":[9],"a":[10,24,51,70],"powerful":[11],"tool":[12],"for":[13],"obtaining":[14],"co-regulated,":[15],"independently-modulated":[16],"gene":[17,107,135],"sets":[18,136],"(iModulons),":[19],"inferring":[20],"their":[21,30,138],"activities":[22],"across":[23],"range":[25],"conditions,":[27],"and":[28,38,91,106,115,120,137,153,161,177,183],"enabling":[29],"association":[31],"to":[32,62,143,187],"known":[33],"genetic":[34,162],"regulators.":[35],"By":[36],"grouping":[37],"analyzing":[39],"genes":[40],"based":[41],"on":[42],"observations":[43],"from":[44,77,87],"big":[45],"data":[46],"alone,":[47],"iModulons":[48,98],"can":[49,184],"provide":[50],"novel":[52],"perspective":[53],"into":[54],"how":[55],"the":[56,59,88,96,154],"composition":[57],"transcriptome":[60],"adapts":[61],"environmental":[63],"conditions.":[64],"Here,":[65],"we":[66],"present":[67],"iModulonDB":[68,169],"(imodulondb.org),":[69],"knowledgebase":[71],"prokaryotic":[73],"transcriptional":[74],"regulation":[75],"computed":[76],"high-quality":[78],"transcriptomic":[79],"datasets":[80],"using":[81],"ICA.":[82],"Users":[83],"select":[84],"an":[85],"organism":[86],"home":[89],"page":[90],"then":[92],"search":[93],"or":[94],"browse":[95],"curated":[97],"that":[99],"make":[100],"up":[101],"its":[102,109],"transcriptome.":[103],"Each":[104],"iModulon":[105],"own":[110],"interactive":[111],"dashboard,":[112],"featuring":[113],"plots":[114],"tables":[116],"with":[117,133,180],"clickable,":[118],"hoverable,":[119],"downloadable":[121],"features.":[122],"This":[123],"site":[124],"enhances":[125],"research":[126],"by":[127],"presenting":[128],"scientists":[129],"all":[131],"backgrounds":[132],"co-expressed":[134],"activity":[139],"levels,":[140],"which":[141],"lead":[142],"improved":[144],"understanding":[145],"regulator-gene":[147],"relationships,":[148],"discovery":[149],"transcription":[151],"factors,":[152],"elucidation":[155],"unexpected":[157],"relationships":[158],"between":[159],"conditions":[160],"regulatory":[163],"activity.":[164],"The":[165],"current":[166],"release":[167],"covers":[170],"three":[171],"organisms":[172],"(Escherichia":[173],"coli,":[174],"Staphylococcus":[175],"aureus":[176],"Bacillus":[178],"subtilis)":[179],"204":[181],"iModulons,":[182],"be":[185],"expanded":[186],"cover":[188],"many":[189],"additional":[190],"organisms.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":30},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":31},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}