{"id":"https://openalex.org/W4403678800","doi":"https://doi.org/10.1371/journal.pcbi.1012546","title":"iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia","display_name":"iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia","publication_year":2024,"publication_date":"2024-10-23","ids":{"openalex":"https://openalex.org/W4403678800","doi":"https://doi.org/10.1371/journal.pcbi.1012546","pmid":"https://pubmed.ncbi.nlm.nih.gov/39441835"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012546","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012546","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.1012546","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8293-3909","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052601120","display_name":"Yuan Yuan","orcid":"https://orcid.org/0000-0002-9509-9167"},"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":"Yuan Yuan","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","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, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","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, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001633366","display_name":"Reo Yoo","orcid":"https://orcid.org/0000-0002-0658-5084"},"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":"Reo Yoo","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012946533","display_name":"Cameron Lamoureux","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":"Cameron R. Lamoureux","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034741432","display_name":"Gaoyuan Li","orcid":"https://orcid.org/0009-0003-4392-0966"},"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":"Gaoyuan Li","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079505672","display_name":"Jeffrey T. A. Burrows","orcid":"https://orcid.org/0000-0001-6595-8736"},"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":"Joshua T. Burrows","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026417613","display_name":"Siddharth Chauhan","orcid":"https://orcid.org/0000-0001-6674-895X"},"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":"Siddharth Chauhan","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6674-895X","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046266224","display_name":"Zachary B. Haiman","orcid":"https://orcid.org/0000-0001-6175-5050"},"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":"Zachary B. Haiman","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044108012","display_name":"Tahani Al Bulushi","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":"Tahani Al Bulushi","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090742414","display_name":"Yara Seif","orcid":"https://orcid.org/0000-0001-8813-5679"},"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":"Yara Seif","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","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":false,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, United States of America","Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070567302","display_name":"Daniel C. Zielinski","orcid":"https://orcid.org/0000-0001-6452-483X"},"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":"Daniel C. Zielinski","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6452-483X","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":14,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":17.0254,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.99127423,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"20","issue":"10","first_page":"e1012546","last_page":"e1012546"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9911999702453613,"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/computational-biology","display_name":"Computational biology","score":0.5495778322219849},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5014593601226807},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.49187541007995605},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3923204839229584},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37827855348587036},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3314898908138275},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3187512159347534},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29926797747612},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08447098731994629}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5495778322219849},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5014593601226807},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.49187541007995605},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3923204839229584},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37827855348587036},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3314898908138275},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3187512159347534},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29926797747612},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08447098731994629}],"mesh":[{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1012546","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012546","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:39441835","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39441835","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:pubmedcentral.nih.gov:11534266","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11534266","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11534266/pdf/pcbi.1012546.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:012b0c0d41224b3b907edb195e4abdcc","is_oa":false,"landing_page_url":"https://doaj.org/article/012b0c0d41224b3b907edb195e4abdcc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 10, p e1012546 (2024)","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/43f957c5-0191-49f3-ae89-e14723225508","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/43f957c5-0191-49f3-ae89-e14723225508","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Sastry , A V , Yuan , Y , Poudel , S , Rychel , K , Yoo , R , Lamoureux , C R , Li , G , Burrows , J T , Chauhan , S , Haiman , Z B , Bulushi , T A , Seif , Y , Palsson , B O &amp; Zielinski , D C 2024 , ' iModulonMiner and PyModulon : Software for unsupervised mining of gene expression compendia ' , PLOS Computational Biology , vol. 20 , no. 10 , e1012546 . https://doi.org/10.1371/journal.pcbi.1012546","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012546","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012546","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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G177594769","display_name":null,"funder_award_id":"NNF20CC0035580","funder_id":"https://openalex.org/F4320323153","funder_display_name":"Danmarks Tekniske Universitet"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7042228497","display_name":null,"funder_award_id":"NNF20CC0035580","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7361212524","display_name":null,"funder_award_id":"NNF20CC0035580","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G7368046788","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","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/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"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1595287493","https://openalex.org/W1977407898","https://openalex.org/W1985723784","https://openalex.org/W2026096252","https://openalex.org/W2037562549","https://openalex.org/W2068858902","https://openalex.org/W2077460182","https://openalex.org/W2084821192","https://openalex.org/W2099741732","https://openalex.org/W2124985265","https://openalex.org/W2137586531","https://openalex.org/W2138207763","https://openalex.org/W2141224535","https://openalex.org/W2165446840","https://openalex.org/W2169456326","https://openalex.org/W2432815617","https://openalex.org/W2579294549","https://openalex.org/W2592811885","https://openalex.org/W2605897695","https://openalex.org/W2623066228","https://openalex.org/W2735897797","https://openalex.org/W2791975541","https://openalex.org/W2803576222","https://openalex.org/W2906064383","https://openalex.org/W2907094739","https://openalex.org/W2931264270","https://openalex.org/W2933601491","https://openalex.org/W2951215318","https://openalex.org/W2953067954","https://openalex.org/W2973374494","https://openalex.org/W2981438196","https://openalex.org/W2990783874","https://openalex.org/W2993166334","https://openalex.org/W2997591727","https://openalex.org/W3006653136","https://openalex.org/W3012560802","https://openalex.org/W3012668557","https://openalex.org/W3027038786","https://openalex.org/W3039562686","https://openalex.org/W3091901779","https://openalex.org/W3113079090","https://openalex.org/W3128033315","https://openalex.org/W3135309465","https://openalex.org/W3147358936","https://openalex.org/W3154566182","https://openalex.org/W3165877358","https://openalex.org/W3208712063","https://openalex.org/W4220802959","https://openalex.org/W4225272203","https://openalex.org/W4225610651","https://openalex.org/W4307840050","https://openalex.org/W4379508890","https://openalex.org/W4379537119","https://openalex.org/W4386209534","https://openalex.org/W4390662514","https://openalex.org/W4391096681","https://openalex.org/W4391786588","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2131250617","https://openalex.org/W4233034052","https://openalex.org/W2371030422","https://openalex.org/W4366601060","https://openalex.org/W2364878181","https://openalex.org/W2803323662","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"Public":[0],"gene":[1,72],"expression":[2],"databases":[3],"are":[4,126],"a":[5,20,37,56,89,137,147,174],"rapidly":[6],"expanding":[7],"resource":[8],"of":[9,29,52,70,100,122,136,177],"organism":[10,58],"responses":[11],"to":[12,25,43,84,95,153,169,172],"diverse":[13,170],"perturbations,":[14],"presenting":[15],"both":[16],"an":[17],"opportunity":[18],"and":[19,48,133,156,183],"challenge":[21],"for":[22,55,116],"bioinformatics":[23],"workflows":[24],"extract":[26],"actionable":[27],"knowledge":[28],"transcription":[30,118,131],"regulatory":[31,114,180],"network":[32,181],"function.":[33],"Here,":[34],"we":[35,91,112],"introduce":[36],"five-step":[38],"computational":[39],"pipeline,":[40,161],"called":[41,78],"iModulonMiner,":[42],"compile,":[44],"process,":[45],"curate,":[46],"analyze,":[47],"characterize":[49],"the":[50,67,97],"totality":[51],"RNA-seq":[53,107],"data":[54],"given":[57],"or":[59],"cell":[60],"type.":[61],"This":[62],"workflow":[63,94],"is":[64],"centered":[65],"around":[66],"data-driven":[68],"computation":[69],"co-regulated":[71],"sets":[73],"using":[74,103],"Independent":[75],"Component":[76],"Analysis,":[77],"iModulons,":[79],"which":[80],"have":[81,85],"been":[82],"shown":[83],"broad":[86],"applications.":[87],"As":[88],"demonstration,":[90],"applied":[92,168],"this":[93,110],"generate":[96],"iModulon":[98],"structure":[99,182],"Bacillus":[101],"subtilis":[102],"all":[104],"high-quality,":[105],"publicly-available":[106],"data.":[108],"Using":[109],"structure,":[111],"predicted":[113,134],"interactions":[115],"multiple":[117],"factors,":[119,132],"identified":[120],"groups":[121],"co-expressed":[123],"genes":[124],"that":[125],"putatively":[127],"regulated":[128],"by":[129],"undiscovered":[130],"properties":[135],"recently":[138],"discovered":[139],"single-subunit":[140],"phage":[141],"RNA":[142],"polymerase.":[143],"We":[144],"also":[145],"present":[146],"Python":[148],"package,":[149],"PyModulon,":[150],"with":[151],"functions":[152],"characterize,":[154],"visualize,":[155],"explore":[157],"computed":[158],"iModulons.":[159],"The":[160],"available":[162],"at":[163],"https://github.com/SBRG/iModulonMiner,":[164],"can":[165],"be":[166],"readily":[167],"organisms":[171],"gain":[173],"rapid":[175],"understanding":[176],"their":[178],"transcriptional":[179],"condition-specific":[184],"activity.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
