{"id":"https://openalex.org/W2054416990","doi":"https://doi.org/10.1089/10665270252935403","title":"Context-Specific Bayesian Clustering for Gene Expression Data","display_name":"Context-Specific Bayesian Clustering for Gene Expression Data","publication_year":2002,"publication_date":"2002-04-01","ids":{"openalex":"https://openalex.org/W2054416990","doi":"https://doi.org/10.1089/10665270252935403","mag":"2054416990","pmid":"https://pubmed.ncbi.nlm.nih.gov/12015876"},"language":"en","primary_location":{"id":"doi:10.1089/10665270252935403","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270252935403","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","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/A5040287362","display_name":"Yoseph Barash","orcid":"https://orcid.org/0000-0003-3005-5048"},"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":"Yoseph Barash","raw_affiliation_strings":["School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076999649","display_name":"Nir Friedman","orcid":"https://orcid.org/0000-0002-9678-3550"},"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":false,"raw_author_name":"Nir Friedman","raw_affiliation_strings":["School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel","institution_ids":["https://openalex.org/I197251160"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5040287362"],"corresponding_institution_ids":["https://openalex.org/I197251160"],"apc_list":null,"apc_paid":null,"fwci":5.1559,"has_fulltext":false,"cited_by_count":105,"citation_normalized_percentile":{"value":0.96370709,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"9","issue":"2","first_page":"169","last_page":"191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T10885","display_name":"Gene expression and cancer classification","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9936000108718872,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9900000095367432,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6741116642951965},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5950038433074951},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5674279928207397},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5339431166648865},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.49186110496520996},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.4577641785144806},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4367210566997528},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4219720959663391},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.4200163781642914},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40928930044174194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3990800380706787},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3885190188884735},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3802034854888916},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3259422183036804},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2443457841873169},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.14000174403190613}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6741116642951965},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5950038433074951},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5674279928207397},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5339431166648865},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.49186110496520996},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.4577641785144806},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4367210566997528},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4219720959663391},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.4200163781642914},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40928930044174194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3990800380706787},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3885190188884735},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3802034854888916},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3259422183036804},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2443457841873169},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.14000174403190613}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1089/10665270252935403","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270252935403","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:12015876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12015876","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.19.915","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.915","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/2002/HUJI-CSE-LTR-2002-5_BF1Full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.24.2003","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.24.2003","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.huji.ac.il/~nir/Papers/BF1Full.ps","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.33.2450","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.33.2450","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://robotics.stanford.edu/people/nir/Papers/BF1.ps.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.463.2820","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.463.2820","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.csim.scu.edu.tw/~chiang/course/Msthesis/Epaper/p12-barash.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.75.1819","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.75.1819","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://robotics.stanford.edu/~nir/Papers/BF1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1523680690","https://openalex.org/W1524704912","https://openalex.org/W1544444076","https://openalex.org/W1549994062","https://openalex.org/W1566045017","https://openalex.org/W1567331820","https://openalex.org/W1586476557","https://openalex.org/W1615454278","https://openalex.org/W1817561967","https://openalex.org/W1864566053","https://openalex.org/W1906182963","https://openalex.org/W1998300401","https://openalex.org/W2006258746","https://openalex.org/W2049633694","https://openalex.org/W2054658115","https://openalex.org/W2060406328","https://openalex.org/W2064879068","https://openalex.org/W2084908610","https://openalex.org/W2099111195","https://openalex.org/W2099600000","https://openalex.org/W2103453943","https://openalex.org/W2109970232","https://openalex.org/W2126185296","https://openalex.org/W2127190318","https://openalex.org/W2131510173","https://openalex.org/W2132434674","https://openalex.org/W2135000328","https://openalex.org/W2137683543","https://openalex.org/W2137786672","https://openalex.org/W2140115103","https://openalex.org/W2140611547","https://openalex.org/W2142890842","https://openalex.org/W2154664365","https://openalex.org/W2168157737","https://openalex.org/W2168175751","https://openalex.org/W2169929748","https://openalex.org/W3022603917","https://openalex.org/W3150555252","https://openalex.org/W4246925013"],"related_works":["https://openalex.org/W2494523064","https://openalex.org/W2943623134","https://openalex.org/W2215759665","https://openalex.org/W2960358116","https://openalex.org/W2002739602","https://openalex.org/W2345647014","https://openalex.org/W2201192772","https://openalex.org/W3136891595","https://openalex.org/W2535030201","https://openalex.org/W1964819397"],"abstract_inverted_index":{"The":[0],"recent":[1],"growth":[2],"in":[3,37,74,175],"genomic":[4,53],"data":[5,147,154,172],"and":[6,44,52,67,87,107,113,155],"measurements":[7],"of":[8,32,47,62,68,71,84,96,103,167],"genome-wide":[9],"expression":[10,69,88,177],"patterns":[11,89],"allows":[12],"us":[13,91],"to":[14,18,92,108,137,170],"apply":[15],"computational":[16],"tools":[17],"examine":[19],"gene":[20,73,176],"regulation":[21],"by":[22],"transcription":[23,42,63],"factors.":[24],"In":[25],"this":[26],"work,":[27],"we":[28,125,163],"present":[29],"a":[30,56,72,75,80,117,127,134,138],"class":[31],"mathematical":[33],"models":[34,122],"that":[35,131],"help":[36],"understanding":[38],"the":[39,59,94,97,101,157,165,168],"connections":[40],"between":[41],"factors":[43],"functional":[45],"classes":[46],"genes":[48,98],"based":[49,99],"on":[50,100,145,151],"genetic":[51],"data.":[54,178],"Such":[55],"model":[57,83,135],"represents":[58],"joint":[60],"distribution":[61],"factor":[64],"binding":[65,85,105,111],"sites":[66,86,106,112],"levels":[70],"unified":[76],"probabilistic":[77],"model.":[78],"Learning":[79],"combined":[81],"probability":[82],"enables":[90],"improve":[93],"clustering":[95],"discovery":[102],"putative":[104],"detect":[109],"which":[110],"experiments":[114],"best":[115],"characterize":[116],"cluster.":[118],"To":[119],"learn":[120],"such":[121],"from":[123],"data,":[124],"introduce":[126],"new":[128],"search":[129],"method":[130,144,169],"rapidly":[132],"learns":[133],"according":[136],"Bayesian":[139],"score.":[140],"We":[141],"evaluate":[142],"our":[143],"synthetic":[146],"as":[148,150],"well":[149],"real":[152],"life":[153],"analyze":[156],"biological":[158],"insights":[159],"it":[160],"provides.":[161],"Finally,":[162],"demonstrate":[164],"applicability":[166],"other":[171],"analysis":[173],"problems":[174]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
