{"id":"https://openalex.org/W2115870954","doi":"https://doi.org/10.1093/bioinformatics/btr704","title":"CLARE: Cracking the LAnguage of Regulatory Elements","display_name":"CLARE: Cracking the LAnguage of Regulatory Elements","publication_year":2011,"publication_date":"2011-12-22","ids":{"openalex":"https://openalex.org/W2115870954","doi":"https://doi.org/10.1093/bioinformatics/btr704","mag":"2115870954","pmid":"https://pubmed.ncbi.nlm.nih.gov/22199387"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr704","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/581/48878726/bioinformatics_28_4_581.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/581/48878726/bioinformatics_28_4_581.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053257775","display_name":"Leila Taher","orcid":"https://orcid.org/0000-0002-2013-5426"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["IN","US"],"is_corresponding":true,"raw_author_name":"Leila Taher","raw_affiliation_strings":["1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I3125981224","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078875370","display_name":"Leelavati Narlikar","orcid":"https://orcid.org/0000-0001-6820-1878"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Leelavati Narlikar","raw_affiliation_strings":["1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I3125981224","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071763912","display_name":"Ivan Ovcharenko","orcid":"https://orcid.org/0000-0002-9730-7732"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Ivan Ovcharenko","raw_affiliation_strings":["1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA and 2Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I3125981224","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053257775"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I3125981224","https://openalex.org/I4210109390"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2661,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.59399605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"4","first_page":"581","last_page":"583"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9984999895095825,"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":0.9984999895095825,"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":0.988099992275238,"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":0.9842000007629395,"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/set","display_name":"Set (abstract data type)","score":0.6535759568214417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6380775570869446},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5303274989128113},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5171603560447693},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5075660943984985},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4523022770881653},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4260011613368988},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37749987840652466},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3425951600074768},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.325068861246109},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2502425014972687},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.24642476439476013},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22214674949645996},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17394959926605225}],"concepts":[{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6535759568214417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6380775570869446},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5303274989128113},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5171603560447693},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5075660943984985},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4523022770881653},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4260011613368988},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37749987840652466},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3425951600074768},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.325068861246109},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2502425014972687},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.24642476439476013},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22214674949645996},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17394959926605225}],"mesh":[{"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":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016548","descriptor_name":"Prosencephalon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016548","descriptor_name":"Prosencephalon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016548","descriptor_name":"Prosencephalon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr704","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/581/48878726/bioinformatics_28_4_581.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22199387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22199387","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},{"id":"pmh:oai:europepmc.org:2571846","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3278760","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr704","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/581/48878726/bioinformatics_28_4_581.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115870954.pdf","grobid_xml":"https://content.openalex.org/works/W2115870954.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1976148686","https://openalex.org/W2005244073","https://openalex.org/W2027352426","https://openalex.org/W2035539647","https://openalex.org/W2085315537","https://openalex.org/W2095718954","https://openalex.org/W2098212444","https://openalex.org/W2104698381","https://openalex.org/W2111729969","https://openalex.org/W2123564569","https://openalex.org/W2126060886","https://openalex.org/W2135030836","https://openalex.org/W2135046866","https://openalex.org/W2151754128","https://openalex.org/W2153024250","https://openalex.org/W2156627746"],"related_works":["https://openalex.org/W2112284452","https://openalex.org/W3085798047","https://openalex.org/W2374269412","https://openalex.org/W371123309","https://openalex.org/W2085500676","https://openalex.org/W2186272223","https://openalex.org/W3104152981","https://openalex.org/W2365096715","https://openalex.org/W2152844235","https://openalex.org/W2376454312"],"abstract_inverted_index":{"CLARE":[0],"is":[1],"freely":[2],"accessible":[3],"at":[4],"http://clare.dcode.org/.":[5]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}