{"id":"https://openalex.org/W2151234222","doi":"https://doi.org/10.1109/bibe.2003.1188949","title":"Performance comparison of algorithms for finding transcription factor binding sites","display_name":"Performance comparison of algorithms for finding transcription factor binding sites","publication_year":2003,"publication_date":"2003-11-21","ids":{"openalex":"https://openalex.org/W2151234222","doi":"https://doi.org/10.1109/bibe.2003.1188949","mag":"2151234222"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2003.1188949","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188949","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"},"type":"article","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/A5101657008","display_name":"Saurabh Sinha","orcid":"https://orcid.org/0000-0001-6033-7746"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Sinha","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","Rockefeller University, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Rockefeller University, New York, NY, USA","institution_ids":["https://openalex.org/I83399316"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008676408","display_name":"Martin Tompa","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Tompa","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3748,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.80145381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"15","issue":null,"first_page":"214","last_page":"220"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9847999811172485,"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/T10604","display_name":"RNA Research and Splicing","score":0.9843000173568726,"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/motif","display_name":"Motif (music)","score":0.855050802230835},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5542343854904175},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5329134464263916},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45985251665115356},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4543664753437042},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4530772864818573},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4121624827384949},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35584789514541626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27486371994018555},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24205967783927917},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.16173520684242249},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09656667709350586}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.855050802230835},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5542343854904175},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5329134464263916},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45985251665115356},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4543664753437042},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4530772864818573},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4121624827384949},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35584789514541626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27486371994018555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24205967783927917},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.16173520684242249},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09656667709350586},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2003.1188949","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188949","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1872867777","https://openalex.org/W1956090332","https://openalex.org/W1998300401","https://openalex.org/W2003967338","https://openalex.org/W2028904582","https://openalex.org/W2032231928","https://openalex.org/W2037940015","https://openalex.org/W2039286232","https://openalex.org/W2084908610","https://openalex.org/W2102787800","https://openalex.org/W6634719314","https://openalex.org/W6635200387","https://openalex.org/W6639198454","https://openalex.org/W6641001594","https://openalex.org/W6659963394"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2379997263","https://openalex.org/W2367493320","https://openalex.org/W2112717966","https://openalex.org/W2131580913","https://openalex.org/W3083097828","https://openalex.org/W1576021314","https://openalex.org/W2125854412","https://openalex.org/W2499916532"],"abstract_inverted_index":{"We":[0],"compare":[1],"the":[2,9,22,38,42,79,87,97,101,112,115,130],"accuracy":[3,113],"of":[4,11,21,37,75,114],"three":[5],"motif-finding":[6],"algorithms":[7,23],"for":[8,30],"discovery":[10],"novel":[12],"transcription":[13],"factor":[14],"binding":[15,31],"sites":[16,32],"among":[17],"co-regulated":[18,76],"genes.":[19],"One":[20],"(YMF)":[24],"uses":[25],"a":[26,49,108],"motif":[27,39,52,139],"model":[28,53],"tailored":[29],"and":[33,46,54],"an":[34],"enumerative":[35,88],"search":[36,56],"space,":[40],"while":[41],"other":[43,98],"two":[44,99],"(MEME":[45],"AlignACE)":[47],"use":[48],"more":[50,94],"general":[51],"local":[55],"techniques.":[57],"The":[58,118],"comparison":[59],"is":[60,90,107],"done":[61],"on":[62,71,100,120],"synthetic":[63,121],"data":[64,73,103,122],"with":[65],"planted":[66,135],"motifs,":[67],"as":[68,70],"well":[69],"real":[72],"sets":[74],"genes":[77],"from":[78],"yeast":[80,102],"S.":[81],"cerevisiae.":[82],"More":[83],"often":[84],"than":[85,96],"not,":[86],"algorithm":[89,128],"found":[91],"to":[92,137],"be":[93],"accurate":[95],"sets,":[104],"though":[105],"there":[106],"noticeable":[109],"exclusivity":[110],"in":[111],"different":[116],"algorithms.":[117],"experiments":[119],"reveal,":[123],"not":[124],"surprisingly,":[125],"that":[126],"each":[127],"outperforms":[129],"others":[131],"when":[132],"motifs":[133],"are":[134],"according":[136],"its":[138],"model.":[140]},"counts_by_year":[{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}