{"id":"https://openalex.org/W2018740085","doi":"https://doi.org/10.1145/974614.974637","title":"Probabilistic discovery of overlapping cellular processes and their regulation","display_name":"Probabilistic discovery of overlapping cellular processes and their regulation","publication_year":2004,"publication_date":"2004-01-01","ids":{"openalex":"https://openalex.org/W2018740085","doi":"https://doi.org/10.1145/974614.974637","mag":"2018740085"},"language":"en","primary_location":{"id":"doi:10.1145/974614.974637","doi":"https://doi.org/10.1145/974614.974637","is_oa":false,"landing_page_url":"https://doi.org/10.1145/974614.974637","pdf_url":null,"source":{"id":"https://openalex.org/S4306420791","display_name":"Research in Computational Molecular Biology","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"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/A5063708781","display_name":"Alexis J. Battle","orcid":"https://orcid.org/0000-0002-5287-627X","observed_orcids":["https://orcid.org/0000-0002-5287-627X"]},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexis Battle","raw_affiliation_strings":["Stanford University, Stanford, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012450539","display_name":"Eran Segal","orcid":"https://orcid.org/0000-0002-6859-1164","observed_orcids":["https://orcid.org/0000-0002-6859-1164","https://orcid.org/0000-0003-4064-767X"]},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eran Segal","raw_affiliation_strings":["Stanford University, Stanford, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051658526","display_name":"Daphne Koller","orcid":"https://orcid.org/0000-0002-2361-6479","observed_orcids":["https://orcid.org/0000-0002-2361-6479","https://orcid.org/0009-0007-1645-951X"]},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daphne Koller","raw_affiliation_strings":["Stanford University, Stanford, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":4.1015,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.93212571,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"167","last_page":"176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9940999746322632,"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":0.9940999746322632,"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":0.003000000026077032,"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":0.0006000000284984708,"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/gene-expression-regulation","display_name":"gene expression regulation","score":0.8709999918937683},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.6669999957084656},{"id":"https://openalex.org/keywords/probabilistic-models","display_name":"probabilistic models","score":0.7269999980926514},{"id":"https://openalex.org/keywords/gene-expression-data","display_name":"gene expression data","score":0.6079999804496765},{"id":"https://openalex.org/keywords/regulatory-network-inference","display_name":"regulatory network inference","score":0.546999990940094},{"id":"https://openalex.org/keywords/gene-function-annotation","display_name":"gene function annotation","score":0.40400001406669617},{"id":"https://openalex.org/keywords/regulatory-programs","display_name":"regulatory programs","score":0.375},{"id":"https://openalex.org/keywords/genome-wide-gene-expression","display_name":"genome-wide gene expression","score":0.5619999766349792}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6365355849266052},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5824356079101562},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.571469783782959},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.552899956703186},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5399354696273804},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5203656554222107},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5158442854881287},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.49893760681152344},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4815412163734436},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46856310963630676},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4636026620864868},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.41064202785491943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3203319311141968},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2683075964450836},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23062923550605774},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2254715859889984},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/974614.974637","doi":"https://doi.org/10.1145/974614.974637","is_oa":false,"landing_page_url":"https://doi.org/10.1145/974614.974637","pdf_url":null,"source":{"id":"https://openalex.org/S4306420791","display_name":"Research in Computational Molecular Biology","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.128.5600","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.128.5600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://ai.stanford.edu/~koller/Papers/Battle+al:RECOMB04.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.373.2793","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.373.2793","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/~koller/Papers/Battle+al:JCB05.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.92.6899","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.92.6899","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://ai.stanford.edu/~serafim/CS374_2004/Papers/Battle_RegulatoryMProcesses.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1493217831","https://openalex.org/W1557726990","https://openalex.org/W1566045017","https://openalex.org/W1594031697","https://openalex.org/W1769824028","https://openalex.org/W1987079970","https://openalex.org/W2000284082","https://openalex.org/W2005382543","https://openalex.org/W2010315317","https://openalex.org/W2046320066","https://openalex.org/W2049633694","https://openalex.org/W2093766978","https://openalex.org/W2100603120","https://openalex.org/W2103017472","https://openalex.org/W2103453943","https://openalex.org/W2104877015","https://openalex.org/W2110111529","https://openalex.org/W2126602684","https://openalex.org/W2136107412","https://openalex.org/W2137683543","https://openalex.org/W2140115103","https://openalex.org/W2146264532","https://openalex.org/W2148541040","https://openalex.org/W2150926065","https://openalex.org/W2154664365","https://openalex.org/W2158128075","https://openalex.org/W2159080219","https://openalex.org/W2162735386","https://openalex.org/W2167190345","https://openalex.org/W2341059552","https://openalex.org/W2569199996","https://openalex.org/W3021022378","https://openalex.org/W3085162807","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W7098669972","https://openalex.org/W2004022680","https://openalex.org/W2133572196","https://openalex.org/W1978469373","https://openalex.org/W2399943572","https://openalex.org/W1967124272","https://openalex.org/W7095558967","https://openalex.org/W2031584019","https://openalex.org/W937657080","https://openalex.org/W2084171381"],"abstract_inverted_index":{"Many":[0],"of":[1,50,56,71,94,112,139,149,180],"the":[2,13,37,54,62,92,137,146,170,177],"functions":[3],"carried":[4],"out":[5],"by":[6,124,134],"a":[7,46,86],"living":[8],"cell":[9],"are":[10,20,24,167],"regulated":[11],"at":[12],"transcriptional":[14,39],"level,":[15],"to":[16,27,35,79,101,121,159],"ensure":[17],"that":[18,75,166],"genes":[19,78,140,157],"expressed":[21],"when":[22],"they":[23],"needed.":[25],"Thus,":[26],"understand":[28,36],"biological":[29,59],"processes,":[30,83],"it":[31],"is":[32,74],"thus":[33,84],"necessary":[34],"cell's":[38],"network.":[40],"In":[41],"this":[42,103],"paper,":[43],"we":[44,76],"propose":[45],"novel":[47,174],"probabilistic":[48],"model":[49,90,104],"gene":[51,95,113],"regulation":[52],"for":[53,91],"task":[55],"identifying":[57],"overlapping":[58,142],"processes":[60,144],"and":[61,127,145,172],"regulatory":[63,147,164,178],"mechanism":[64],"controlling":[65],"their":[66],"activation.":[67],"A":[68],"key":[69],"feature":[70],"our":[72,119,153],"approach":[73],"allow":[77],"participate":[80],"in":[81,169],"multiple":[82],"providing":[85],"more":[87],"biologically":[88],"plausible":[89],"process":[93],"regulation.":[96],"We":[97,117],"present":[98],"an":[99],"algorithm":[100],"learn":[102],"automatically":[105],"from":[106],"data,":[107],"using":[108],"only":[109],"genome-wide":[110],"measurements":[111],"expression":[114],"as":[115],"input.":[116],"compare":[118],"results":[120],"those":[122],"obtained":[123],"other":[125],"approaches,":[126],"show":[128],"significant":[129],"benefits":[130],"can":[131],"be":[132],"gained":[133],"modeling":[135],"both":[136],"organization":[138],"into":[141],"cellular":[143],"programs":[148],"these":[150],"processes.":[151],"Moreover,":[152],"method":[154],"successfully":[155],"grouped":[156],"known":[158,168],"function":[160],"together,":[161],"recovered":[162],"many":[163],"relationships":[165],"literature,":[171],"suggested":[173],"hypotheses":[175],"regarding":[176],"role":[179],"previously":[181],"uncharacterized":[182],"proteins.":[183]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2016-06-24T00:00:00"}
