{"id":"https://openalex.org/W2099807710","doi":"https://doi.org/10.1093/bioinformatics/bti388","title":"Inferring genetic regulatory logic from expression data","display_name":"Inferring genetic regulatory logic from expression data","publication_year":2005,"publication_date":"2005-03-22","ids":{"openalex":"https://openalex.org/W2099807710","doi":"https://doi.org/10.1093/bioinformatics/bti388","mag":"2099807710","pmid":"https://pubmed.ncbi.nlm.nih.gov/15784747"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2706/833535/bti388.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2706/833535/bti388.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074079692","display_name":"Svetlana Bulashevska","orcid":"https://orcid.org/0000-0002-8802-5602"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"S. Bulashevska","raw_affiliation_strings":["Division Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. s.bulashevska@dkfz.de","Division 'Theoretical Bioinformatics', German Cancer Research Center  Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Division Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. s.bulashevska@dkfz.de","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Division 'Theoretical Bioinformatics', German Cancer Research Center  Im Neuenheimer Feld 280, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044191947","display_name":"Roland Eils","orcid":"https://orcid.org/0000-0002-0034-4036"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"R. Eils","raw_affiliation_strings":["Division 'Theoretical Bioinformatics', German Cancer Research Center  Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Division 'Theoretical Bioinformatics', German Cancer Research Center  Im Neuenheimer Feld 280, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074079692"],"corresponding_institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"],"apc_list":null,"apc_paid":null,"fwci":2.8305,"has_fulltext":false,"cited_by_count":62,"citation_normalized_percentile":{"value":0.90788101,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"11","first_page":"2706","last_page":"2713"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9984999895095825,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9984999895095825,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976000189781189,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996999979019165,"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/computer-science","display_name":"Computer science","score":0.6358456015586853},{"id":"https://openalex.org/keywords/genetic-data","display_name":"Genetic data","score":0.550757646560669},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5208302736282349},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5067921280860901},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5031060576438904},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.46729472279548645},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.44953563809394836},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4416591227054596},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.4286220073699951},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.42264240980148315},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4073200523853302},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38570815324783325},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2710258960723877},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23980507254600525},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.0749121904373169}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6358456015586853},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.550757646560669},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5208302736282349},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5067921280860901},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5031060576438904},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.46729472279548645},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.44953563809394836},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4416591227054596},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.4286220073699951},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42264240980148315},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4073200523853302},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38570815324783325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2710258960723877},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23980507254600525},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0749121904373169},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2706/833535/bti388.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15784747","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15784747","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2706/833535/bti388.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099807710.pdf","grobid_xml":"https://content.openalex.org/works/W2099807710.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1481919380","https://openalex.org/W1486016120","https://openalex.org/W1528905581","https://openalex.org/W1557900165","https://openalex.org/W1563726162","https://openalex.org/W1582614941","https://openalex.org/W1592590442","https://openalex.org/W1603353793","https://openalex.org/W1620545569","https://openalex.org/W1634005169","https://openalex.org/W1746680969","https://openalex.org/W1851004085","https://openalex.org/W1872619067","https://openalex.org/W1921637172","https://openalex.org/W1926693308","https://openalex.org/W2020999234","https://openalex.org/W2045656233","https://openalex.org/W2081999679","https://openalex.org/W2093976733","https://openalex.org/W2094414211","https://openalex.org/W2095436574","https://openalex.org/W2097973787","https://openalex.org/W2101736851","https://openalex.org/W2103453943","https://openalex.org/W2104267885","https://openalex.org/W2105518356","https://openalex.org/W2108020239","https://openalex.org/W2108420379","https://openalex.org/W2112821758","https://openalex.org/W2117591156","https://openalex.org/W2130416410","https://openalex.org/W2133401281","https://openalex.org/W2136549265","https://openalex.org/W2142460132","https://openalex.org/W2148534890","https://openalex.org/W2156685011","https://openalex.org/W2160256138","https://openalex.org/W2160533336","https://openalex.org/W2169690805","https://openalex.org/W2171265988","https://openalex.org/W2611370172","https://openalex.org/W3008617006","https://openalex.org/W3015463134","https://openalex.org/W3146404850"],"related_works":["https://openalex.org/W2012610719","https://openalex.org/W1987909119","https://openalex.org/W2009699504","https://openalex.org/W4237728685","https://openalex.org/W235411870","https://openalex.org/W2122780970","https://openalex.org/W4306666682","https://openalex.org/W2021132264","https://openalex.org/W2385436307","https://openalex.org/W1602316262"],"abstract_inverted_index":{"We":[0,33,52],"propose":[1,34],"a":[2,10,19,35],"model":[3,40],"for":[4,37],"genetic":[5],"regulatory":[6],"interactions,":[7],"which":[8],"has":[9],"biologically":[11],"motivated":[12],"Boolean":[13],"logic":[14],"semantics,":[15],"but":[16],"is":[17,23],"of":[18,60],"probabilistic":[20],"nature,":[21],"and":[22,31,48,66],"hence":[24],"able":[25],"to":[26],"confront":[27],"noisy":[28],"biological":[29,73],"processes":[30],"data.":[32],"method":[36,55],"learning":[38],"the":[39,45,61],"from":[41],"data":[42,59],"based":[43],"on":[44],"Bayesian":[46],"approach":[47],"utilizing":[49],"Gibbs":[50],"sampling.":[51],"tested":[53],"our":[54],"with":[56,72],"previously":[57],"published":[58],"Saccharomyces":[62],"cerevisiae":[63],"cell":[64],"cycle":[65],"found":[67],"relations":[68],"between":[69],"genes":[70],"consistent":[71],"knowledge.":[74]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}