{"id":"https://openalex.org/W2912072079","doi":"https://doi.org/10.1109/bibm.2018.8621093","title":"Fast and Accurate Genome-Scale Identification of DNA-Binding Sites","display_name":"Fast and Accurate Genome-Scale Identification of DNA-Binding Sites","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2912072079","doi":"https://doi.org/10.1109/bibm.2018.8621093","mag":"2912072079"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621093","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-01967466","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024964336","display_name":"David I. K. Martin","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4412460525"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"David Martin","raw_affiliation_strings":["Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034438093","display_name":"Vincent Maillol","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4412460525"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Maillol","raw_affiliation_strings":["Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010392318","display_name":"\u00c9ric Rivals","orcid":"https://orcid.org/0000-0003-3791-3973"},"institutions":[{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4412460525"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eric Rivals","raw_affiliation_strings":["Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Methods & Algorithms Bioinformatics LIRMM, UMR 5506 CNRS, Universit\u00e9 de Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024964336"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"],"apc_list":null,"apc_paid":null,"fwci":0.0919,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49221356,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"33","issue":null,"first_page":"201","last_page":"205"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9991999864578247,"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/genome","display_name":"Genome","score":0.6408424377441406},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5543231964111328},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5386857986450195},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4888750910758972},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.48059460520744324},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4220646917819977},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.42115330696105957},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3623947501182556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3623119294643402},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.35932332277297974},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32219040393829346},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1410042941570282},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.08819118142127991}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6408424377441406},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5543231964111328},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5386857986450195},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4888750910758972},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.48059460520744324},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4220646917819977},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.42115330696105957},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3623947501182556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3623119294643402},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.35932332277297974},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32219040393829346},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1410042941570282},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.08819118142127991},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"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":2,"locations":[{"id":"doi:10.1109/bibm.2018.8621093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621093","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:lirmm-01967466v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-01967466","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://orienta.ugr.es/bibm2018/","raw_type":"Conference papers"}],"best_oa_location":{"id":"pmh:oai:HAL:lirmm-01967466v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-01967466","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://orienta.ugr.es/bibm2018/","raw_type":"Conference papers"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1987122345","https://openalex.org/W1988393300","https://openalex.org/W2003967338","https://openalex.org/W2026690931","https://openalex.org/W2029201460","https://openalex.org/W2030165987","https://openalex.org/W2033781392","https://openalex.org/W2068577315","https://openalex.org/W2131581981","https://openalex.org/W2133335149","https://openalex.org/W2137428312","https://openalex.org/W2142570576","https://openalex.org/W2158485480","https://openalex.org/W2158698691","https://openalex.org/W2161361792","https://openalex.org/W2165102934","https://openalex.org/W2509668036","https://openalex.org/W2517241835","https://openalex.org/W2547528004","https://openalex.org/W2561544479","https://openalex.org/W2784936077","https://openalex.org/W4247794781"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2605676258","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2902352756","https://openalex.org/W2377079823","https://openalex.org/W2599962286","https://openalex.org/W2319582300","https://openalex.org/W4400799920"],"abstract_inverted_index":{"Discovering":[0],"DNA":[1],"binding":[2,19,75],"sites":[3,20,76],"in":[4,31,77,81],"genome":[5,46,79,116],"sequences":[6,47,80],"is":[7,134],"crucial":[8],"for":[9,17,52,71,96,101,124],"understanding":[10],"genomic":[11,33],"regulation.":[12],"Currently":[13],"available":[14,135],"computational":[15],"tools":[16],"finding":[18],"with":[21],"Position":[22],"Weight":[23],"Matrices":[24],"of":[25,36,44,55,58,62],"known":[26],"motifs":[27],"are":[28],"often":[29],"used":[30],"restricted":[32],"regions":[34],"because":[35],"their":[37,97],"long":[38],"run":[39],"times.":[40],"The":[41],"ever-increasing":[42],"number":[43],"complete":[45],"points":[48],"to":[49,94],"the":[50,92,108,115,127],"need":[51],"new":[53,69],"generations":[54],"algorithms":[56],"capable":[57],"processing":[59],"large":[60],"amounts":[61],"data.":[63],"Here":[64],"we":[65],"present":[66],"MOTIF,":[67],"a":[68,82,87,137],"algorithm":[70],"seeking":[72],"transcription":[73],"factor":[74],"whole":[78],"few":[83],"seconds.":[84],"We":[85],"propose":[86],"web":[88,138],"service":[89,109],"that":[90],"enables":[91],"users":[93],"search":[95],"own":[98],"matrix":[99],"or":[100],"multiple":[102],"JASPAR":[103],"matrices.":[104],"Beyond":[105],"its":[106,131],"efficacy,":[107],"properly":[110],"handles":[111],"undetermined":[112],"positions":[113],"within":[114],"sequence":[117],"and":[118,130],"provides":[119],"an":[120],"adequate":[121],"output":[122],"listing":[123],"each":[125],"position":[126],"matching":[128],"word":[129],"score.":[132],"MOTIF":[133],"through":[136],"interface":[139],"at":[140],"http://www.atgc-montpellier.fr/motif.":[141]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
