{"id":"https://openalex.org/W2547834322","doi":"https://doi.org/10.1186/s12859-016-1298-9","title":"Evaluating tools for transcription factor binding site prediction","display_name":"Evaluating tools for transcription factor binding site prediction","publication_year":2016,"publication_date":"2016-11-02","ids":{"openalex":"https://openalex.org/W2547834322","doi":"https://doi.org/10.1186/s12859-016-1298-9","mag":"2547834322","pmid":"https://pubmed.ncbi.nlm.nih.gov/27806697"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1298-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1298-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1298-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1298-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072566473","display_name":"Narayan Jayaram","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Narayan Jayaram","raw_affiliation_strings":["Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077685746","display_name":"Daniel Usvyat","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Usvyat","raw_affiliation_strings":["Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065605747","display_name":"Andrew C.R. Martin","orcid":"https://orcid.org/0000-0002-2835-2572"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew C. R. Martin","raw_affiliation_strings":["Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. andrew@bioinf.org.uk","Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":"https://orcid.org/0000-0002-2835-2572","affiliations":[{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. andrew@bioinf.org.uk","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1616,"currency":"EUR","value_usd":1742},"fwci":8.0093,"has_fulltext":true,"cited_by_count":149,"citation_normalized_percentile":{"value":0.9793885,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"547","last_page":"547"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9330000281333923,"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":0.9330000281333923,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.023499999195337296,"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":0.009100000374019146,"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/dna-binding-site","display_name":"DNA binding site","score":0.8183271288871765},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6474989652633667},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5481128096580505},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5458217263221741},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5420381426811218},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5306488275527954},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.46927133202552795},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44010475277900696},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41124409437179565},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3505544662475586},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3475719690322876},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3383616805076599},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.1297668218612671},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11289867758750916}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.8183271288871765},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6474989652633667},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5481128096580505},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5458217263221741},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5420381426811218},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5306488275527954},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.46927133202552795},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44010475277900696},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41124409437179565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3505544662475586},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3475719690322876},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3383616805076599},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.1297668218612671},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11289867758750916}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-016-1298-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1298-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1298-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27806697","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27806697","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1524263","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1524263/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   BMC Bioinformatics , 2016     , Article 1298. (2016)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6889335","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6889335","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1298-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1298-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1298-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320286","display_name":"University College London","ror":"https://ror.org/02jx3x895"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2547834322.pdf","grobid_xml":"https://content.openalex.org/works/W2547834322.grobid-xml"},"referenced_works_count":101,"referenced_works":["https://openalex.org/W1532756869","https://openalex.org/W1536240214","https://openalex.org/W1592870802","https://openalex.org/W1606290805","https://openalex.org/W1627262848","https://openalex.org/W1721232948","https://openalex.org/W1853093403","https://openalex.org/W1963553964","https://openalex.org/W1963778673","https://openalex.org/W1964733653","https://openalex.org/W1965267927","https://openalex.org/W1966448776","https://openalex.org/W1989080074","https://openalex.org/W1996423252","https://openalex.org/W1998300401","https://openalex.org/W2003924427","https://openalex.org/W2014529296","https://openalex.org/W2014677321","https://openalex.org/W2029201460","https://openalex.org/W2033169664","https://openalex.org/W2044164623","https://openalex.org/W2045949302","https://openalex.org/W2050515300","https://openalex.org/W2051640319","https://openalex.org/W2054245896","https://openalex.org/W2056863613","https://openalex.org/W2060445972","https://openalex.org/W2063732674","https://openalex.org/W2065192733","https://openalex.org/W2068140368","https://openalex.org/W2071042066","https://openalex.org/W2072443295","https://openalex.org/W2075585183","https://openalex.org/W2079321730","https://openalex.org/W2088990426","https://openalex.org/W2097220641","https://openalex.org/W2100558818","https://openalex.org/W2101025813","https://openalex.org/W2103447044","https://openalex.org/W2104865962","https://openalex.org/W2107768450","https://openalex.org/W2108234281","https://openalex.org/W2108649763","https://openalex.org/W2109459651","https://openalex.org/W2109487010","https://openalex.org/W2110455321","https://openalex.org/W2111164126","https://openalex.org/W2112717966","https://openalex.org/W2115761267","https://openalex.org/W2115979107","https://openalex.org/W2117491433","https://openalex.org/W2118596665","https://openalex.org/W2118628540","https://openalex.org/W2121286812","https://openalex.org/W2121967239","https://openalex.org/W2122712487","https://openalex.org/W2122893035","https://openalex.org/W2123490534","https://openalex.org/W2123861597","https://openalex.org/W2124080033","https://openalex.org/W2124985265","https://openalex.org/W2125114453","https://openalex.org/W2126468786","https://openalex.org/W2128397771","https://openalex.org/W2129767688","https://openalex.org/W2135030836","https://openalex.org/W2135336207","https://openalex.org/W2135825344","https://openalex.org/W2140952049","https://openalex.org/W2141408320","https://openalex.org/W2142067151","https://openalex.org/W2142570576","https://openalex.org/W2145825942","https://openalex.org/W2146539504","https://openalex.org/W2148056478","https://openalex.org/W2148441137","https://openalex.org/W2149627698","https://openalex.org/W2150612336","https://openalex.org/W2151845703","https://openalex.org/W2153091158","https://openalex.org/W2156661861","https://openalex.org/W2157952888","https://openalex.org/W2158221945","https://openalex.org/W2158962723","https://openalex.org/W2159324718","https://openalex.org/W2160697532","https://openalex.org/W2162530919","https://openalex.org/W2162836426","https://openalex.org/W2164814636","https://openalex.org/W2165102934","https://openalex.org/W2166187656","https://openalex.org/W2166429927","https://openalex.org/W2167077887","https://openalex.org/W2171111703","https://openalex.org/W2171808845","https://openalex.org/W2221226238","https://openalex.org/W2259938310","https://openalex.org/W2502420217","https://openalex.org/W4230909169","https://openalex.org/W4245023496","https://openalex.org/W4248318091"],"related_works":["https://openalex.org/W2763663556","https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2067561164","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2090848290"],"abstract_inverted_index":{"BACKGROUND:":[0],"Binding":[1],"of":[2,16,36,49,71,74,117,177,199,221],"transcription":[3,6,201],"factors":[4],"to":[5,13,82,145,196],"factor":[7,202],"binding":[8,203],"sites":[9,204],"(TFBSs)":[10],"is":[11,25,30],"key":[12],"the":[14,47,84,138,178,194,219],"mediation":[15],"transcriptional":[17],"regulation.":[18],"Information":[19],"on":[20],"experimentally":[21],"validated":[22],"functional":[23],"TFBSs":[24,37,56,159],"limited":[26],"and":[27,41,106,127,133,160,170,187,216],"consequently":[28],"there":[29],"a":[31,62,72,115],"need":[32],"for":[33,38,96,99,107,181,188,211],"accurate":[34],"prediction":[35,142,198],"gene":[39,212],"annotation":[40],"in":[42,53,217,225],"applications":[43],"such":[44],"as":[45],"evaluating":[46,218],"effects":[48,220],"single":[50,222],"nucleotide":[51,223],"variations":[52,224],"causing":[54,226],"disease.":[55,227],"are":[57,93],"generally":[58],"recognized":[59],"by":[60,208],"scanning":[61,108,189],"position":[63],"weight":[64],"matrix":[65],"(PWM)":[66],"against":[67,110,148,191],"DNA":[68,149,192],"using":[69,130],"one":[70],"number":[73],"available":[75],"computer":[76],"programs.":[77],"Thus":[78],"we":[79],"set":[80,116],"out":[81],"evaluate":[83],"best":[85,173],"tools":[86,122,143,180],"that":[87,123,135,156,162,168],"can":[88],"be":[89,125],"used":[90,144],"locally":[91,129],"(and":[92],"therefore":[94],"suitable":[95],"large-scale":[97],"analyses)":[98],"creating":[100],"PWMs":[101,147,183,190],"from":[102,184],"high-throughput":[103],"ChIP-Seq":[104,185,209],"data":[105,132,186],"them":[109],"DNA.":[111],"RESULTS:":[112],"We":[113],"evaluated":[114],"de":[118],"novo":[119],"motif":[120],"discovery":[121],"could":[124],"downloaded":[126],"installed":[128],"ENCODE-ChIP-Seq":[131],"showed":[134,167],"rGADEM":[136],"was":[137],"best-performing":[139,179],"tool.":[140],"TFBS":[141],"scan":[146],"fall":[150],"into":[151],"two":[152],"classes":[153],"-":[154],"those":[155,161],"predict":[157],"individual":[158],"identify":[163],"clusters.":[164],"Our":[165],"evaluation":[166],"FIMO":[169],"MCAST":[171],"performed":[172],"respectively.":[174],"CONCLUSIONS:":[175],"Selection":[176],"generating":[182],"has":[193],"potential":[195],"improve":[197],"precise":[200],"within":[205],"regions":[206],"identified":[207],"experiments":[210],"finding,":[213],"understanding":[214],"regulation":[215]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":31},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
