{"id":"https://openalex.org/W2136988691","doi":"https://doi.org/10.1093/bioinformatics/bth463","title":"A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data","display_name":"A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data","publication_year":2004,"publication_date":"2004-08-12","ids":{"openalex":"https://openalex.org/W2136988691","doi":"https://doi.org/10.1093/bioinformatics/bth463","mag":"2136988691","pmid":"https://pubmed.ncbi.nlm.nih.gov/15308537"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth463","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth463","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/A5079318932","display_name":"Min Zou","orcid":"https://orcid.org/0000-0003-3066-4812"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Min Zou","raw_affiliation_strings":["Department of Medicine, 5841 South Maryland Avenue, University of Chicago, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, 5841 South Maryland Avenue, University of Chicago, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006194387","display_name":"Suzanne D. Conzen","orcid":"https://orcid.org/0000-0003-1750-5868"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne D. Conzen","raw_affiliation_strings":["Department of Medicine, 5841 South Maryland Avenue, University of Chicago, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, 5841 South Maryland Avenue, University of Chicago, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079318932"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":9.1645,"has_fulltext":false,"cited_by_count":598,"citation_normalized_percentile":{"value":0.98780249,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"21","issue":"1","first_page":"71","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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":0.9983000159263611,"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":0.9961000084877014,"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/dynamic-bayesian-network","display_name":"Dynamic Bayesian network","score":0.9320152401924133},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6696792244911194},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.609328031539917},{"id":"https://openalex.org/keywords/time-point","display_name":"Time point","score":0.5944450497627258},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.5437594056129456},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4869571626186371},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.47791868448257446},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4306565821170807},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3981545865535736},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3896009624004364},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35779693722724915},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34249550104141235},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32889264822006226},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2776014804840088},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22530609369277954},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15971335768699646}],"concepts":[{"id":"https://openalex.org/C82142266","wikidata":"https://www.wikidata.org/wiki/Q3456604","display_name":"Dynamic Bayesian network","level":3,"score":0.9320152401924133},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6696792244911194},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.609328031539917},{"id":"https://openalex.org/C2779466056","wikidata":"https://www.wikidata.org/wiki/Q107630651","display_name":"Time point","level":2,"score":0.5944450497627258},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.5437594056129456},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4869571626186371},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.47791868448257446},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4306565821170807},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3981545865535736},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3896009624004364},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35779693722724915},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34249550104141235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32889264822006226},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2776014804840088},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22530609369277954},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15971335768699646},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C107038049","wikidata":"https://www.wikidata.org/wiki/Q35986","display_name":"Aesthetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"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":"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":"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":"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":"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/bth463","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth463","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:15308537","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15308537","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":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309149","display_name":"Entertainment Industry Foundation","ror":"https://ror.org/01dmpb598"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W2073506826","https://openalex.org/W2090554117","https://openalex.org/W2099189600","https://openalex.org/W2108579152","https://openalex.org/W2121995533","https://openalex.org/W2142460132","https://openalex.org/W2151098983"],"related_works":["https://openalex.org/W2544242547","https://openalex.org/W3128072696","https://openalex.org/W2119218276","https://openalex.org/W2369018153","https://openalex.org/W2530648058","https://openalex.org/W1604786655","https://openalex.org/W2957822107","https://openalex.org/W2386937658","https://openalex.org/W2124007391","https://openalex.org/W1965576512"],"abstract_inverted_index":{"In":[0],"this":[1,128],"paper,":[2],"we":[3,64],"present":[4],"a":[5,77],"DBN-based":[6],"approach":[7,24,111,129],"with":[8,16,31,134,143],"increased":[9],"accuracy":[10,104,137],"and":[11,57,81,138],"reduced":[12,139],"computational":[13,140],"time":[14,67,90,99,141],"compared":[15,142],"existing":[17,144],"DBN":[18,145],"methods.":[19],"Unlike":[20],"previous":[21],"methods,":[22],"our":[23],"limits":[25],"potential":[26,55,83],"regulators":[27,56],"to":[28,43,50,86],"those":[29],"genes":[30],"either":[32],"earlier":[33],"or":[34,39],"simultaneous":[35],"expression":[36,75,116],"changes":[37],"(up-":[38],"down-regulation)":[40],"in":[41,73],"relation":[42],"their":[44],"target":[45,84],"genes.":[46,95],"This":[47,96],"allows":[48],"us":[49],"limit":[51],"the":[52,60,66,70,74,88,103,120],"number":[53],"of":[54,76,98,105],"consequently":[58],"reduce":[59],"search":[61],"space.":[62],"Furthermore,":[63],"use":[65],"difference":[68],"between":[69,92],"initial":[71],"change":[72],"given":[78],"regulator":[79],"gene":[80,85,107],"its":[82],"estimate":[87],"transcriptional":[89],"lag":[91,100],"these":[93],"two":[94],"method":[97],"estimation":[101],"increases":[102],"predicting":[106],"regulatory":[108,132],"networks.":[109],"Our":[110],"is":[112],"evaluated":[113],"using":[114],"time-series":[115],"data":[117],"measured":[118],"during":[119],"yeast":[121],"cell":[122],"cycle.":[123],"The":[124],"results":[125],"demonstrate":[126],"that":[127],"can":[130],"predict":[131],"networks":[133],"significantly":[135],"improved":[136],"approaches.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":25},{"year":2018,"cited_by_count":28},{"year":2017,"cited_by_count":30},{"year":2016,"cited_by_count":37},{"year":2015,"cited_by_count":32},{"year":2014,"cited_by_count":33},{"year":2013,"cited_by_count":29},{"year":2012,"cited_by_count":30}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
