{"id":"https://openalex.org/W2153208554","doi":"https://doi.org/10.1093/bioinformatics/bth941","title":"Inferring quantitative models of regulatory networks from expression data","display_name":"Inferring quantitative models of regulatory networks from expression data","publication_year":2004,"publication_date":"2004-07-19","ids":{"openalex":"https://openalex.org/W2153208554","doi":"https://doi.org/10.1093/bioinformatics/bth941","mag":"2153208554","pmid":"https://pubmed.ncbi.nlm.nih.gov/15262806"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth941","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth941","pdf_url":null,"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":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","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010737438","display_name":"Iftach Nachman","orcid":"https://orcid.org/0000-0002-4667-0398"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"I. Nachman","raw_affiliation_strings":["School of Computer Science & Engineering, Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & Engineering, Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004067604","display_name":"Aviv Regev","orcid":"https://orcid.org/0000-0003-3293-3158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Regev","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5076999649","display_name":"Nir Friedman","orcid":"https://orcid.org/0000-0002-9678-3550"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"N. Friedman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010737438"],"corresponding_institution_ids":["https://openalex.org/I197251160"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.5615,"has_fulltext":false,"cited_by_count":201,"citation_normalized_percentile":{"value":0.98621749,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"suppl_1","first_page":"i248","last_page":"i256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991000294685364,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965000152587891,"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":0.7036325931549072},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5941028594970703},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5693857669830322},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5573757290840149},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5474338531494141},{"id":"https://openalex.org/keywords/regulator","display_name":"Regulator","score":0.4749051332473755},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4446479082107544},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4421786963939667},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4415239095687866},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42065492272377014},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.25644081830978394},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23634889721870422},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2181667983531952},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1198190450668335}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7036325931549072},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5941028594970703},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5693857669830322},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5573757290840149},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5474338531494141},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.4749051332473755},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4446479082107544},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4421786963939667},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4415239095687866},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42065492272377014},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25644081830978394},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23634889721870422},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2181667983531952},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1198190450668335},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth941","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth941","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15262806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15262806","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:CiteSeerX.psu:10.1.1.194.5395","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.194.5395","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://leibniz.cs.huji.ac.il/tr/acc/2004/HUJI-CSE-LTR-2004-17_ismb04.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1557270760","https://openalex.org/W1872596602","https://openalex.org/W1896341954","https://openalex.org/W1978319180","https://openalex.org/W1987079970","https://openalex.org/W1996264210","https://openalex.org/W2065458745","https://openalex.org/W2069645361","https://openalex.org/W2073506826","https://openalex.org/W2100603120","https://openalex.org/W2103453943","https://openalex.org/W2107817133","https://openalex.org/W2108579152","https://openalex.org/W2110699703","https://openalex.org/W2122055675","https://openalex.org/W2126602684","https://openalex.org/W2129531837","https://openalex.org/W2135000328","https://openalex.org/W2139083403","https://openalex.org/W2139956963","https://openalex.org/W2143784594","https://openalex.org/W2149579404","https://openalex.org/W2151098983","https://openalex.org/W2168175751","https://openalex.org/W2170778160","https://openalex.org/W2611370172","https://openalex.org/W2611831635"],"related_works":["https://openalex.org/W2354064740","https://openalex.org/W2389923937","https://openalex.org/W2380273283","https://openalex.org/W2386858378","https://openalex.org/W2347280302","https://openalex.org/W2369640577","https://openalex.org/W1849276116","https://openalex.org/W2363047424","https://openalex.org/W1571263303","https://openalex.org/W2389443558"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genetic":[1],"networks":[2],"regulate":[3],"key":[4],"processes":[5],"in":[6],"living":[7],"cells.":[8],"Various":[9],"methods":[10,66],"have":[11],"been":[12],"suggested":[13],"to":[14,115,150],"reconstruct":[15,152],"network":[16,155],"architecture":[17],"from":[18,70,118,156],"gene":[19,62,71],"expression":[20,72,116],"data.":[21],"However,":[22],"most":[23],"approaches":[24],"are":[25,45],"based":[26],"on":[27],"qualitative":[28],"models":[29,60],"that":[30,44,97,108,122],"provide":[31],"only":[32],"rough":[33],"approximations":[34],"of":[35,52,61,77,105],"the":[36,41,49,75,94,102,126,134,153],"underlying":[37],"events,":[38],"and":[39,64,90,101,120,146],"lack":[40],"quantitative":[42,87],"aspects":[43],"critical":[46],"for":[47,67],"understanding":[48],"proper":[50],"function":[51],"biomolecular":[53],"systems.":[54],"RESULTS:":[55],"We":[56,111,138],"present":[57],"fine-grained":[58],"dynamical":[59],"transcription":[63,88],"develop":[65],"reconstructing":[68],"them":[69],"data":[73],"within":[74],"framework":[76],"a":[78,141],"generative":[79],"probabilistic":[80],"model.":[81],"Unlike":[82],"previous":[83],"works,":[84],"we":[85,123],"employ":[86],"rates,":[89,100],"simultaneously":[91],"estimate":[92],"both":[93],"kinetic":[95],"parameters":[96],"govern":[98],"these":[99],"activity":[103,129],"levels":[104],"unobserved":[106],"regulators":[107],"control":[109],"them.":[110],"apply":[112],"our":[113],"approach":[114],"datasets":[117],"yeast":[119],"show":[121],"can":[124],"learn":[125],"unknown":[127],"regulator":[128],"profiles,":[130],"as":[131,133],"well":[132],"binding":[135],"affinity":[136],"parameters.":[137],"also":[139],"introduce":[140],"novel":[142],"structure":[143],"learning":[144],"algorithm,":[145],"demonstrate":[147],"its":[148],"power":[149],"accurately":[151],"regulatory":[154],"those":[157],"datasets.":[158]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
