{"id":"https://openalex.org/W1562282953","doi":"https://doi.org/10.1109/csb.2003.1227361","title":"A rule-based framework for gene regulation pathways discovery","display_name":"A rule-based framework for gene regulation pathways discovery","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W1562282953","doi":"https://doi.org/10.1109/csb.2003.1227361","mag":"1562282953"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227361","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227361","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/15004202","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081814379","display_name":"Bartek Wilczy\u0144ski","orcid":"https://orcid.org/0000-0002-8134-0589"},"institutions":[{"id":"https://openalex.org/I47996466","display_name":"University of Warmia and Mazury in Olsztyn","ror":"https://ror.org/05s4feg49","country_code":"PL","type":"education","lineage":["https://openalex.org/I47996466"]},{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["PL","US"],"is_corresponding":true,"raw_author_name":"B. Wilczynski","raw_affiliation_strings":["Lawrence Livermore National Laboratories, Livermore, CA, USA","University of Warmia and Mazury, Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratories, Livermore, CA, USA","institution_ids":["https://openalex.org/I1282311441"]},{"raw_affiliation_string":"University of Warmia and Mazury, Warsaw, Poland","institution_ids":["https://openalex.org/I47996466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022568938","display_name":"Torgeir R. Hvidsten","orcid":"https://orcid.org/0000-0001-6097-2539"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Hvidsten","raw_affiliation_strings":["Lawrence Livermore National Laboratories, Livermore, CA, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratories, Livermore, CA, USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046112262","display_name":"Andriy Kryshtafovych","orcid":"https://orcid.org/0000-0001-5066-7178"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Kryshtafovych","raw_affiliation_strings":["Lawrence Livermore National Laboratories, Livermore, CA, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratories, Livermore, CA, USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082905763","display_name":"Lisa Stubbs","orcid":"https://orcid.org/0000-0002-9556-1972"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. Stubbs","raw_affiliation_strings":["Lawrence Livermore National Laboratories, Livermore, CA, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratories, Livermore, CA, USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"J. Komorowski","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala, Sweden","institution_ids":["https://openalex.org/I223464139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074974770","display_name":"Krzysztof Fidelis","orcid":"https://orcid.org/0000-0002-8061-412X"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Fidelis","raw_affiliation_strings":["Lawrence Livermore National Laboratories, Livermore, CA, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratories, Livermore, CA, USA","institution_ids":["https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5081814379"],"corresponding_institution_ids":["https://openalex.org/I1282311441","https://openalex.org/I47996466"],"apc_list":null,"apc_paid":null,"fwci":0.1206,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.46631966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"9","issue":null,"first_page":"435","last_page":"436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9779000282287598,"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":0.9779000282287598,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9668999910354614,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.963699996471405,"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","display_name":"Gene","score":0.6321324706077576},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5943346619606018},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.539766788482666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5331968665122986},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5204018354415894},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.5057134628295898},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.48443153500556946},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.44325020909309387},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3736215829849243},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35675889253616333},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3321242332458496},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.15594539046287537}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6321324706077576},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5943346619606018},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.539766788482666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5331968665122986},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5204018354415894},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.5057134628295898},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.48443153500556946},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.44325020909309387},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3736215829849243},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35675889253616333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3321242332458496},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.15594539046287537},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/csb.2003.1227361","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227361","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},{"id":"pmh:info:ark/67531/metadc1407864","is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc1407864/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Computer Society Bioinformatics Conference, Stanford, CA, Aug 11 - Aug 14, 2003","raw_type":"Article"},{"id":"pmh:oai:osti.gov:15004202","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/15004202","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:15004202","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/15004202","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1557923305","https://openalex.org/W2017200304","https://openalex.org/W2077609634","https://openalex.org/W2125508747","https://openalex.org/W6633188799"],"related_works":["https://openalex.org/W1576021314","https://openalex.org/W3151254369","https://openalex.org/W2613929436","https://openalex.org/W68078148","https://openalex.org/W2347793859","https://openalex.org/W46113340","https://openalex.org/W2536763320","https://openalex.org/W2125854412","https://openalex.org/W2016183850","https://openalex.org/W2129550547"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,35,45,58],"novel":[3],"approach":[4],"for":[5],"rule":[6],"discovery":[7],"in":[8,66],"the":[9,38,49,71],"area":[10],"of":[11,37,48,61],"gene":[12,32,39,67,73],"regulation.":[13],"The":[14],"method":[15],"is":[16,23],"based":[17],"on":[18],"supervised":[19],"machine":[20],"learning":[21],"and":[22,31],"designed":[24],"to":[25],"reveal":[26],"relationships":[27],"between":[28],"transcription":[29,62],"factors":[30],"expression.":[33],"As":[34],"representation":[36],"regulatory":[40,68],"circuit":[41],"we":[42],"have":[43],"chosen":[44],"special":[46],"form":[47],"IF-THEN":[50],"rules":[51],"associating":[52],"predefined":[53],"features,":[54],"taken":[55],"here":[56],"as":[57],"generalized":[59],"idea":[60],"factor":[63],"binding":[64],"sites":[65],"regions,":[69],"with":[70],"corresponding":[72],"expression":[74],"profiles.":[75]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
