{"id":"https://openalex.org/W3096841710","doi":"https://doi.org/10.1093/bioinformatics/btaa947","title":"Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data","display_name":"Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data","publication_year":2020,"publication_date":"2020-10-27","ids":{"openalex":"https://openalex.org/W3096841710","doi":"https://doi.org/10.1093/bioinformatics/btaa947","mag":"3096841710","pmid":"https://pubmed.ncbi.nlm.nih.gov/33135076"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa947","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa947","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/9/1234/38575203/btaa947.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/9/1234/38575203/btaa947.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088991858","display_name":"Z. Cynthia","orcid":"https://orcid.org/0000-0001-6706-2466"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cynthia Z Ma","raw_affiliation_strings":["Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 63110, USA","Department of Computer Science and Engineering, Washington University , St. Louis, MO 63130, USA"],"affiliations":[{"raw_affiliation_string":"Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 63110, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , St. Louis, MO 63130, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010345611","display_name":"Michael R. Brent","orcid":"https://orcid.org/0000-0002-8689-0299"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael R Brent","raw_affiliation_strings":["Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 63110, USA","Department of Computer Science and Engineering, Washington University , St. Louis, MO 63130, USA","Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110, USA"],"affiliations":[{"raw_affiliation_string":"Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 63110, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University , St. Louis, MO 63130, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110, USA","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010345611"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.4465,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.91391563,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"9","first_page":"1234","last_page":"1245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9081000089645386,"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"}},"topics":[{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9081000089645386,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49671727418899536},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4820359945297241},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4615919589996338},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.446592777967453},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4354175925254822},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37796705961227417},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36569491028785706},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33675631880760193}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49671727418899536},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4820359945297241},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4615919589996338},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.446592777967453},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4354175925254822},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37796705961227417},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36569491028785706},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33675631880760193}],"mesh":[{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa947","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa947","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/9/1234/38575203/btaa947.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33135076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33135076","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:digitalcommons.wustl.edu:oa_4-1770","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/oa_4/779","pdf_url":null,"source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"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":"2020-Current year OA Pubs","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8189679","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8189679","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa947","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa947","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/9/1234/38575203/btaa947.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G3575971994","display_name":null,"funder_award_id":"AI087794","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6773853611","display_name":null,"funder_award_id":"GM129126","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3096841710.pdf","grobid_xml":"https://content.openalex.org/works/W3096841710.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1582471009","https://openalex.org/W1614045200","https://openalex.org/W1753000577","https://openalex.org/W1971470015","https://openalex.org/W1981331174","https://openalex.org/W1984000968","https://openalex.org/W1994267372","https://openalex.org/W1996783999","https://openalex.org/W2010532309","https://openalex.org/W2013620058","https://openalex.org/W2019312328","https://openalex.org/W2030436997","https://openalex.org/W2032627751","https://openalex.org/W2058333934","https://openalex.org/W2068000365","https://openalex.org/W2069645361","https://openalex.org/W2071852157","https://openalex.org/W2080498142","https://openalex.org/W2089062027","https://openalex.org/W2089691349","https://openalex.org/W2096139934","https://openalex.org/W2099922553","https://openalex.org/W2100485294","https://openalex.org/W2107209294","https://openalex.org/W2115260093","https://openalex.org/W2119445257","https://openalex.org/W2122761711","https://openalex.org/W2128644645","https://openalex.org/W2128648326","https://openalex.org/W2129151536","https://openalex.org/W2130215066","https://openalex.org/W2133376865","https://openalex.org/W2133914326","https://openalex.org/W2137799805","https://openalex.org/W2140952049","https://openalex.org/W2142433578","https://openalex.org/W2144710927","https://openalex.org/W2144882991","https://openalex.org/W2147703218","https://openalex.org/W2150584810","https://openalex.org/W2152014285","https://openalex.org/W2153208554","https://openalex.org/W2155465020","https://openalex.org/W2160064408","https://openalex.org/W2161942543","https://openalex.org/W2166303358","https://openalex.org/W2168175751","https://openalex.org/W2170567460","https://openalex.org/W2178240050","https://openalex.org/W2205662772","https://openalex.org/W2282198798","https://openalex.org/W2472255748","https://openalex.org/W2528622855","https://openalex.org/W2530630735","https://openalex.org/W2606236050","https://openalex.org/W2772692099","https://openalex.org/W2776546488","https://openalex.org/W2789609639","https://openalex.org/W2798124328","https://openalex.org/W2800927494","https://openalex.org/W2887611308","https://openalex.org/W2939185749","https://openalex.org/W2946173685","https://openalex.org/W2950199998","https://openalex.org/W2954393006","https://openalex.org/W2964090523","https://openalex.org/W2964315448","https://openalex.org/W3006349006","https://openalex.org/W3011348378","https://openalex.org/W3016236341"],"related_works":["https://openalex.org/W2803323662","https://openalex.org/W2052655934","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2023641020","https://openalex.org/W2017047508"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}