{"id":"https://openalex.org/W2162836426","doi":"https://doi.org/10.1093/bioinformatics/btn198","title":"Eukaryotic transcription factor binding sites\u2014modeling and integrative search methods","display_name":"Eukaryotic transcription factor binding sites\u2014modeling and integrative search methods","publication_year":2008,"publication_date":"2008-04-21","ids":{"openalex":"https://openalex.org/W2162836426","doi":"https://doi.org/10.1093/bioinformatics/btn198","mag":"2162836426","pmid":"https://pubmed.ncbi.nlm.nih.gov/18426806"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn198","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/11/1325/49046691/bioinformatics_24_11_1325.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":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/11/1325/49046691/bioinformatics_24_11_1325.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011962029","display_name":"Sridhar Hannenhalli","orcid":"https://orcid.org/0000-0001-9603-7569"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]},{"id":"https://openalex.org/I4210127693","display_name":"Penn Center for AIDS Research","ror":"https://ror.org/047939x15","country_code":"US","type":"facility","lineage":["https://openalex.org/I102322052","https://openalex.org/I1335321130","https://openalex.org/I4210127693","https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sridhar Hannenhalli","raw_affiliation_strings":["Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA","institution_ids":["https://openalex.org/I4210127693","https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5011962029"],"corresponding_institution_ids":["https://openalex.org/I4210127693","https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.5988,"has_fulltext":true,"cited_by_count":107,"citation_normalized_percentile":{"value":0.97559754,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"24","issue":"11","first_page":"1325","last_page":"1331"},"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":0.9980999827384949,"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":0.9861000180244446,"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":0.8155282139778137},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.7031857371330261},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6928098201751709},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6345964074134827},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5876336693763733},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5520416498184204},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4142625629901886},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4115554094314575},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3704424500465393},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3471211791038513},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3367360532283783},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.21261873841285706},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10831692814826965}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.8155282139778137},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7031857371330261},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6928098201751709},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6345964074134827},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5876336693763733},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5520416498184204},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4142625629901886},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4115554094314575},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3704424500465393},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3471211791038513},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3367360532283783},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.21261873841285706},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10831692814826965},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn198","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/11/1325/49046691/bioinformatics_24_11_1325.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:18426806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18426806","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn198","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/11/1325/49046691/bioinformatics_24_11_1325.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":[{"score":0.6600000262260437,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162836426.pdf","grobid_xml":"https://content.openalex.org/works/W2162836426.grobid-xml"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W1426173733","https://openalex.org/W1587692361","https://openalex.org/W1792654735","https://openalex.org/W1966448776","https://openalex.org/W1968631710","https://openalex.org/W1987122345","https://openalex.org/W1997144871","https://openalex.org/W2008491350","https://openalex.org/W2012354488","https://openalex.org/W2027662098","https://openalex.org/W2029873987","https://openalex.org/W2030816054","https://openalex.org/W2036183597","https://openalex.org/W2038315854","https://openalex.org/W2041096569","https://openalex.org/W2043653128","https://openalex.org/W2051333589","https://openalex.org/W2062872358","https://openalex.org/W2063732674","https://openalex.org/W2064879068","https://openalex.org/W2068011423","https://openalex.org/W2070340804","https://openalex.org/W2071753700","https://openalex.org/W2073727170","https://openalex.org/W2075879183","https://openalex.org/W2079659879","https://openalex.org/W2082736011","https://openalex.org/W2084620487","https://openalex.org/W2084833542","https://openalex.org/W2085270765","https://openalex.org/W2085442947","https://openalex.org/W2087892194","https://openalex.org/W2095617232","https://openalex.org/W2097090208","https://openalex.org/W2097311877","https://openalex.org/W2097832534","https://openalex.org/W2099665470","https://openalex.org/W2100295605","https://openalex.org/W2101025813","https://openalex.org/W2102304447","https://openalex.org/W2106004801","https://openalex.org/W2108011868","https://openalex.org/W2108420379","https://openalex.org/W2111729969","https://openalex.org/W2112717966","https://openalex.org/W2116672274","https://openalex.org/W2117549173","https://openalex.org/W2120200532","https://openalex.org/W2123378898","https://openalex.org/W2125508747","https://openalex.org/W2128923603","https://openalex.org/W2129422961","https://openalex.org/W2129920058","https://openalex.org/W2134877714","https://openalex.org/W2135030836","https://openalex.org/W2135215848","https://openalex.org/W2136726922","https://openalex.org/W2137502130","https://openalex.org/W2140885056","https://openalex.org/W2141395444","https://openalex.org/W2141408320","https://openalex.org/W2141744841","https://openalex.org/W2144857133","https://openalex.org/W2146393977","https://openalex.org/W2147693153","https://openalex.org/W2149769193","https://openalex.org/W2155717510","https://openalex.org/W2155940790","https://openalex.org/W2158544517","https://openalex.org/W2162165765","https://openalex.org/W2166103265","https://openalex.org/W2166277117","https://openalex.org/W2166894044","https://openalex.org/W2167190345","https://openalex.org/W2168817939","https://openalex.org/W2169056802","https://openalex.org/W2171252918","https://openalex.org/W4241523640","https://openalex.org/W6685199251"],"related_works":["https://openalex.org/W2162836426","https://openalex.org/W3089376739","https://openalex.org/W2104330120","https://openalex.org/W2041476574","https://openalex.org/W3098045879","https://openalex.org/W2145627818","https://openalex.org/W151156231","https://openalex.org/W2127161698","https://openalex.org/W2951273973","https://openalex.org/W2019160435"],"abstract_inverted_index":{"A":[0],"comprehensive":[1],"knowledge":[2],"of":[3,15,65,124,130],"transcription":[4,33],"factor":[5,34],"binding":[6,44,66,81,92,99],"sites":[7,45,67,93],"(TFBS)":[8],"is":[9,35],"important":[10],"for":[11,21,42,61],"a":[12,32],"mechanistic":[13],"understanding":[14],"transcriptional":[16],"regulation":[17],"as":[18,20,109],"well":[19],"inferring":[22],"gene":[23],"regulatory":[24],"networks.":[25],"Because":[26],"the":[27,49],"DNA":[28],"motif":[29,51,82,100],"recognized":[30],"by":[31,84],"typically":[36],"short":[37],"and":[38,94,132],"degenerate,":[39],"computational":[40,63,122],"approaches":[41,76,96,131],"identifying":[43],"based":[46],"only":[47],"on":[48,136],"sequence":[50,87],"inevitably":[52],"suffer":[53],"from":[54,89],"high":[55],"error":[56],"rates.":[57],"Current":[58],"state-of-the-art":[59],"techniques":[60],"improving":[62],"identification":[64,123],"can":[68],"be":[69],"broadly":[70],"categorized":[71],"into":[72],"two":[73,128],"classes:":[74],"(1)":[75],"that":[77,97],"aim":[78],"to":[79,120],"improve":[80,121],"models":[83,101],"extracting":[85],"maximal":[86],"information":[88],"experimentally":[90],"determined":[91],"(2)":[95],"supplement":[98],"with":[102,134],"additional":[103],"genomic":[104],"or":[105],"other":[106],"attributes":[107],"(such":[108],"evolutionary":[110],"conservation).":[111],"In":[112],"this":[113],"review":[114],"we":[115],"will":[116],"discuss":[117],"recent":[118],"attempts":[119],"TFBS":[125],"through":[126],"these":[127],"types":[129],"conclude":[133],"thoughts":[135],"future":[137],"development.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}