{"id":"https://openalex.org/W2317013263","doi":"https://doi.org/10.1109/embc.2014.6944690","title":"A Model-based approach to transcription regulatory network reconstruction from time-course gene expression data","display_name":"A Model-based approach to transcription regulatory network reconstruction from time-course gene expression data","publication_year":2014,"publication_date":"2014-08-01","ids":{"openalex":"https://openalex.org/W2317013263","doi":"https://doi.org/10.1109/embc.2014.6944690","mag":"2317013263","pmid":"https://pubmed.ncbi.nlm.nih.gov/25571058"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2014.6944690","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2014.6944690","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","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/A5112225751","display_name":"Hong Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Hu","raw_affiliation_strings":["Department of Bioengineering (MC563), University of Illinois at Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering (MC563), University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025440962","display_name":"Yang Dai","orcid":"https://orcid.org/0000-0002-7638-849X"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Dai","raw_affiliation_strings":["Department of Bioengineering (MC563), University of Illinois at Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering (MC563), University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I39422238"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"58","issue":null,"first_page":"4767","last_page":"4770"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9993000030517578,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9993000030517578,"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/T10604","display_name":"RNA Research and Splicing","score":0.9951000213623047,"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":0.9943000078201294,"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":0.7157137989997864},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5988978743553162},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5927549600601196},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5849587321281433},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5316477417945862},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.4763874411582947},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4698554277420044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45726877450942993},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.44054940342903137},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3968712091445923},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3070785403251648}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7157137989997864},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5988978743553162},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5927549600601196},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5849587321281433},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5316477417945862},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.4763874411582947},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4698554277420044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45726877450942993},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.44054940342903137},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3968712091445923},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3070785403251648},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004958","descriptor_name":"Estradiol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004958","descriptor_name":"Estradiol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004958","descriptor_name":"Estradiol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D004967","descriptor_name":"Estrogens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":"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":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc.2014.6944690","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2014.6944690","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-article"},{"id":"pmid:25571058","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25571058","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1554745858","https://openalex.org/W1775295994","https://openalex.org/W1963672021","https://openalex.org/W1965021143","https://openalex.org/W1987122345","https://openalex.org/W1988393300","https://openalex.org/W2015416439","https://openalex.org/W2021786299","https://openalex.org/W2051533392","https://openalex.org/W2059699217","https://openalex.org/W2069645361","https://openalex.org/W2070212927","https://openalex.org/W2071278881","https://openalex.org/W2074703985","https://openalex.org/W2081303346","https://openalex.org/W2084620487","https://openalex.org/W2086802511","https://openalex.org/W2122342005","https://openalex.org/W2126122040","https://openalex.org/W2129795133","https://openalex.org/W2135046866","https://openalex.org/W2144738674","https://openalex.org/W2149769193","https://openalex.org/W2151945801","https://openalex.org/W2162870748"],"related_works":["https://openalex.org/W2134744955","https://openalex.org/W2010571965","https://openalex.org/W2002709996","https://openalex.org/W3128451840","https://openalex.org/W4387092964","https://openalex.org/W2103471012","https://openalex.org/W2966064480","https://openalex.org/W2115810854","https://openalex.org/W2380236774","https://openalex.org/W4291672717"],"abstract_inverted_index":{"Time-course":[0],"gene":[1,77,92,129],"expression":[2,78,130],"profiling":[3],"provides":[4],"valuable":[5],"data":[6],"on":[7,32,95,132],"dynamic":[8,27],"behavior":[9],"of":[10,17,47,55,73,98,104,124,138],"cellular":[11],"responses":[12],"to":[13,59,67,114,127],"external":[14],"stimulation.":[15],"Investigation":[16],"transcription":[18],"factors":[19],"(TFs)":[20],"that":[21,142],"regulate":[22],"co-expressed":[23,105],"genes":[24],"in":[25,49,101,135],"a":[26,45,64,128,136],"process":[28],"can":[29],"reveal":[30],"insights":[31],"the":[33,38,52,69,111,117,143],"underlying":[34],"molecular":[35],"mechanisms.":[36],"As":[37],"ChIP-seq":[39],"technology":[40],"is":[41],"only":[42],"suitable":[43],"for":[44,86,116],"fraction":[46],"TFs":[48,57,74],"mammalian":[50],"organisms,":[51],"computational":[53,96],"identification":[54],"relevant":[56],"remains":[58],"be":[60],"critical.":[61],"We":[62],"propose":[63],"regression-based":[65],"model":[66,108],"infer":[68],"functional":[70],"binding":[71,99],"sites":[72,100],"from":[75],"time-course":[76],"profiles.":[79],"Our":[80,107],"approach":[81],"incorporates":[82],"an":[83],"association":[84],"strength":[85],"each":[87],"potential":[88],"TF":[89],"and":[90],"target":[91],"pair":[93],"based":[94],"analysis":[97],"promoter":[102],"sequences":[103],"genes.":[106],"further":[109],"uses":[110],"Lasso-penalized":[112],"technique":[113],"search":[115],"most":[118],"informative":[119],"TF-target":[120],"pairs.":[121],"The":[122],"application":[123],"our":[125],"method":[126],"study":[131],"E2-induced":[133],"apoptosis":[134],"variant":[137],"MCF-7":[139],"cells":[140],"revealed":[141],"findings":[144],"are":[145],"biologically":[146],"meaningful.":[147]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}