{"id":"https://openalex.org/W2141462396","doi":"https://doi.org/10.1093/bioinformatics/btm629","title":"A hybrid model for robust detection of transcription factor binding sites","display_name":"A hybrid model for robust detection of transcription factor binding sites","publication_year":2008,"publication_date":"2008-01-09","ids":{"openalex":"https://openalex.org/W2141462396","doi":"https://doi.org/10.1093/bioinformatics/btm629","mag":"2141462396","pmid":"https://pubmed.ncbi.nlm.nih.gov/18184687"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm629","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm629","pdf_url":null,"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":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","doaj","pubmed"],"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/A5029700070","display_name":"Sumedha Gunewardena","orcid":"https://orcid.org/0000-0003-2097-135X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Sumedha Gunewardena","raw_affiliation_strings":["Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009847434","display_name":"Zhaolei Zhang","orcid":"https://orcid.org/0000-0002-7303-6472"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Zhaolei Zhang","raw_affiliation_strings":["Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009847434","https://openalex.org/A5029700070"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.0392,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.75766305,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"4","first_page":"484","last_page":"491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9241999983787537,"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":0.9241999983787537,"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":0.048900000751018524,"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":0.008200000040233135,"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/transcription-factor","display_name":"Transcription factor","score":0.6118574738502502},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5273227095603943},{"id":"https://openalex.org/keywords/factor","display_name":"Factor (programming language)","score":0.5147066712379456},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.47402435541152954},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.46078693866729736},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45057517290115356},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27296701073646545},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26391422748565674},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.17122960090637207},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16624775528907776},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11502444744110107},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08901861310005188}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6118574738502502},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5273227095603943},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.5147066712379456},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.47402435541152954},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.46078693866729736},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45057517290115356},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27296701073646545},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26391422748565674},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.17122960090637207},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16624775528907776},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11502444744110107},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08901861310005188}],"mesh":[{"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm629","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm629","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18184687","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18184687","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7400000095367432}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320319905","display_name":"Ontario Genomics Institute","ror":"https://ror.org/00c68jz96"},{"id":"https://openalex.org/F4320322015","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1515935592","https://openalex.org/W1518002808","https://openalex.org/W1567060155","https://openalex.org/W1986902849","https://openalex.org/W1994122295","https://openalex.org/W2003967338","https://openalex.org/W2031501875","https://openalex.org/W2056572892","https://openalex.org/W2064879068","https://openalex.org/W2071753700","https://openalex.org/W2076464177","https://openalex.org/W2078085951","https://openalex.org/W2093886776","https://openalex.org/W2101025813","https://openalex.org/W2105179267","https://openalex.org/W2105355645","https://openalex.org/W2119033016","https://openalex.org/W2141408320","https://openalex.org/W2141936300","https://openalex.org/W2145295592","https://openalex.org/W2148831368","https://openalex.org/W2166277117","https://openalex.org/W2795933076","https://openalex.org/W2995702573","https://openalex.org/W4297959365","https://openalex.org/W6677585095"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2367493320","https://openalex.org/W2090848290","https://openalex.org/W2131580913"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,196],"short":[2],"and":[3,76,89,131,209],"degenerate":[4],"nature":[5],"of":[6,42,72,83,92,102,140,144,153,163,198,216,243],"transcription":[7],"factor":[8],"(TF)":[9],"binding":[10,52,74,94,125,146,165,194,234],"sites":[11,53,75,95,147,166,235],"contributes":[12],"towards":[13],"a":[14,81,100,112,118,150],"low":[15],"signal":[16],"to":[17,24,32,38,116,134,168,224],"noise":[18],"ratio":[19,162],"making":[20],"it":[21],"very":[22],"difficult":[23],"separate":[25],"them":[26],"from":[27,54,236],"their":[28,55,169],"background.":[29],"In":[30,107],"order":[31],"tackle":[33],"this":[34,108,203],"problem":[35],"one":[36],"needs":[37],"look":[39],"at":[40,250],"ways":[41],"capturing":[43],"the":[44,64,69,137,160,164,174,178,199,214,225,244],"underlying":[45],"biophysical":[46],"properties":[47],"that":[48,158,191],"best":[49],"discriminates":[50],"TF":[51,73,93,124,145,193,233],"background":[56,77,170,237],"DNA.":[57,171,238],"One":[58],"such":[59,85],"discriminatory":[60],"property":[61],"lies":[62],"in":[63,68,210,221,231],"observed":[65],"compositional":[66],"differences":[67],"nucleotide":[70],"levels":[71],"DNA":[78],"which":[79],"are":[80],"result":[82],"processes":[84],"as":[86,117],"purifying":[87],"selection":[88],"selective":[90],"preferences":[91],"for":[96,121,187],"particular":[97],"nucleotides":[98,103],"or":[99],"combination":[101],"over":[104],"others.":[105],"RESULTS:":[106],"article,":[109],"we":[110],"present":[111],"hybrid":[113],"model,":[114],"referred":[115],"MonoDi-nucleotide":[119,175,200,245],"model":[120,176,201,246],"robustly":[122],"detecting":[123],"sites.":[126,195],"It":[127],"incorporates":[128],"both":[129],"mono-":[130],"dinucleotide":[132,156],"statistics":[133],"optimally":[135],"partition":[136],"base":[138],"positions":[139],"an":[141],"aligned":[142],"set":[143,205],"(motif)":[148],"into":[149],"non-redundant":[151],"sequence":[152],"mono":[154],"and/or":[155],"segments":[157],"maximizes":[159],"odds":[161],"relative":[167],"We":[172],"tested":[173],"on":[177,202],"benchmark":[179],"dataset":[180],"compiled":[181],"by":[182,229],"Tompa":[183],"et":[184],"al.":[185],"(2005)":[186],"assessing":[188],"computational":[189],"tools":[190],"predict":[192],"performance":[197,215],"data":[204],"compares":[206],"well":[207],"to,":[208],"many":[211],"cases":[212],"exceeds,":[213],"existing":[217],"tools.":[218],"This":[219],"is":[220],"part":[222],"attributed":[223],"significant":[226],"role":[227],"played":[228],"dinucleotides":[230],"discriminating":[232],"AVAILABILITY:":[239],"A":[240],"Matlab":[241],"implementation":[242],"can":[247],"be":[248],"found":[249],"http://www.utoronto.ca/zhanglab/MonoDi/.":[251]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2013,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}