{"id":"https://openalex.org/W2160626228","doi":"https://doi.org/10.1093/bioinformatics/bti477","title":"A multiple-feature framework for modelling and predicting transcription factor binding sites","display_name":"A multiple-feature framework for modelling and predicting transcription factor binding sites","publication_year":2005,"publication_date":"2005-05-19","ids":{"openalex":"https://openalex.org/W2160626228","doi":"https://doi.org/10.1093/bioinformatics/bti477","mag":"2160626228","pmid":"https://pubmed.ncbi.nlm.nih.gov/15905283"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3082/48971578/bioinformatics_21_14_3082.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3082/48971578/bioinformatics_21_14_3082.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017469362","display_name":"Rainer Pudimat","orcid":null},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"R. Pudimat","raw_affiliation_strings":["Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t Ernst-Abbe-Platz 3, D-07743 Jena, Germany","Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t Ernst-Abbe-Platz 3, D-07743 Jena, Germany","institution_ids":[]},{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108807922","display_name":"Ernst G\u00fcnter Schukat-Talamazzini","orcid":null},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"E.-G. Schukat-Talamazzini","raw_affiliation_strings":["Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"R. Backofen","raw_affiliation_strings":["Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t  Ernst-Abbe-Platz 3, D-07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5017469362"],"corresponding_institution_ids":["https://openalex.org/I76198965"],"apc_list":null,"apc_paid":null,"fwci":5.7038,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.96006906,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"21","issue":"14","first_page":"3082","last_page":"3088"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9771999716758728,"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":0.961899995803833,"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":0.7026029825210571},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.559192955493927},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5230891704559326},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5080051422119141},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.49375423789024353},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4881339967250824},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48683613538742065},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4850868284702301},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4756207764148712},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29409104585647583},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28787535429000854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22700580954551697},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22540047764778137},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2029370367527008},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09717747569084167}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7026029825210571},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.559192955493927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5230891704559326},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5080051422119141},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.49375423789024353},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4881339967250824},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48683613538742065},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4850868284702301},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4756207764148712},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29409104585647583},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28787535429000854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22700580954551697},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22540047764778137},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2029370367527008},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09717747569084167},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3082/48971578/bioinformatics_21_14_3082.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15905283","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15905283","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/bti477","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti477","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/14/3082/48971578/bioinformatics_21_14_3082.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160626228.pdf","grobid_xml":"https://content.openalex.org/works/W2160626228.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1585743408","https://openalex.org/W1593793857","https://openalex.org/W1817561967","https://openalex.org/W1950892569","https://openalex.org/W1987122345","https://openalex.org/W1997144871","https://openalex.org/W2009570821","https://openalex.org/W2013803515","https://openalex.org/W2014915963","https://openalex.org/W2015502807","https://openalex.org/W2022231632","https://openalex.org/W2032548898","https://openalex.org/W2068011423","https://openalex.org/W2071753700","https://openalex.org/W2094036688","https://openalex.org/W2101025813","https://openalex.org/W2110041134","https://openalex.org/W2110863141","https://openalex.org/W2123243961","https://openalex.org/W2140115103","https://openalex.org/W2142705266","https://openalex.org/W2146393977","https://openalex.org/W2149096772","https://openalex.org/W2149769193","https://openalex.org/W2155237411","https://openalex.org/W2158314946","https://openalex.org/W2160917321","https://openalex.org/W2163166770","https://openalex.org/W2166277117","https://openalex.org/W4248460046"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2067561164","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2131580913"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"a":[3],"probabilistic":[4],"modelling":[5],"approach,":[6],"which":[7,34],"allows":[8],"to":[9,16],"consider":[10],"diverse":[11],"characteristic":[12],"binding":[13,22,42,63],"site":[14,43],"properties":[15,25],"obtain":[17],"more":[18],"accurate":[19],"representations":[20],"of":[21,37,61],"sites.":[23,64],"These":[24],"are":[26,35],"modelled":[27],"as":[28],"random":[29],"variables":[30],"in":[31,51],"Bayesian":[32],"networks,":[33],"capable":[36],"dealing":[38],"with":[39],"dependencies":[40],"among":[41],"properties.":[44],"Cross-validation":[45],"on":[46],"several":[47],"datasets":[48],"shows":[49],"improvements":[50],"the":[52,58],"false":[53],"positive":[54],"error":[55],"rate":[56],"and":[57],"significance":[59],"(P-value)":[60],"true":[62]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}