{"id":"https://openalex.org/W2158032351","doi":"https://doi.org/10.1093/bioinformatics/btm606","title":"TFBS identification based on genetic algorithm with combined representations and adaptive post-processing","display_name":"TFBS identification based on genetic algorithm with combined representations and adaptive post-processing","publication_year":2007,"publication_date":"2007-12-06","ids":{"openalex":"https://openalex.org/W2158032351","doi":"https://doi.org/10.1093/bioinformatics/btm606","mag":"2158032351","pmid":"https://pubmed.ncbi.nlm.nih.gov/18065426"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm606","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm606","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/341/705483/btm606.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/341/705483/btm606.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113708498","display_name":"Tak-Ming Chan","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Tak-Ming Chan","raw_affiliation_strings":["Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113582655","display_name":"Kwong\u2010Sak Leung","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Kwong-Sak Leung","raw_affiliation_strings":["Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109898714","display_name":"Kin-Hong Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Kin-Hong Lee","raw_affiliation_strings":["Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5113708498"],"corresponding_institution_ids":["https://openalex.org/I177725633"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.669,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.9047016,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"3","first_page":"341","last_page":"349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.6664999723434448,"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":0.6664999723434448,"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":0.2273000031709671,"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":0.0731000006198883,"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/computer-science","display_name":"Computer science","score":0.6352065205574036},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6342597603797913},{"id":"https://openalex.org/keywords/local-optimum","display_name":"Local optimum","score":0.5792555809020996},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.49988436698913574},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4794979691505432},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.47512537240982056},{"id":"https://openalex.org/keywords/operator","display_name":"Operator (biology)","score":0.4232284724712372},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3428800404071808},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.309331476688385},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09664046764373779}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6352065205574036},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6342597603797913},{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.5792555809020996},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.49988436698913574},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4794979691505432},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.47512537240982056},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.4232284724712372},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3428800404071808},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.309331476688385},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09664046764373779},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm606","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm606","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/341/705483/btm606.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18065426","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18065426","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"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.561.4028","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.561.4028","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2007/12/06/bioinformatics.btm606.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm606","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm606","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/341/705483/btm606.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":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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158032351.pdf","grobid_xml":"https://content.openalex.org/works/W2158032351.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W49093931","https://openalex.org/W1592870802","https://openalex.org/W1965267927","https://openalex.org/W1989080074","https://openalex.org/W1992748956","https://openalex.org/W1998300401","https://openalex.org/W2021809202","https://openalex.org/W2053743126","https://openalex.org/W2065715761","https://openalex.org/W2077013196","https://openalex.org/W2099180682","https://openalex.org/W2111359483","https://openalex.org/W2115603438","https://openalex.org/W2135729552","https://openalex.org/W2149312834","https://openalex.org/W2151638714","https://openalex.org/W2154165587","https://openalex.org/W2158561153","https://openalex.org/W2158962723","https://openalex.org/W2159831212","https://openalex.org/W2504494713","https://openalex.org/W3102715269","https://openalex.org/W6602023597","https://openalex.org/W6635200387","https://openalex.org/W6674742480","https://openalex.org/W6677399227","https://openalex.org/W6682672913","https://openalex.org/W6683187033"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2183246718","https://openalex.org/W2099261052","https://openalex.org/W3209204065","https://openalex.org/W2992415251","https://openalex.org/W2105707930","https://openalex.org/W1755711892","https://openalex.org/W2164205946","https://openalex.org/W2160907113","https://openalex.org/W2382431814"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identification":[1],"of":[2,16,80,116,159,198],"transcription":[3],"factor":[4],"binding":[5],"sites":[6],"(TFBSs)":[7],"plays":[8],"an":[9,105,163],"important":[10],"role":[11],"in":[12,33,40,50,53,62,95,104,146,170],"deciphering":[13],"the":[14,37,63,66,72,81,96,102,139,167,171,234],"mechanisms":[15],"gene":[17],"regulation.":[18],"Recently,":[19],"GAME,":[20,207,233],"a":[21,111,151],"Genetic":[22,117],"Algorithm":[23,118],"(GA)-based":[24],"approach":[25],"with":[26,119,184,195,215,232],"iterative":[27],"post-processing,":[28,64],"has":[29],"shown":[30],"superior":[31,204],"performance":[32,68,205],"TFBS":[34,135],"identification.":[35,136],"However,":[36],"basic":[38],"GA":[39,73],"GAME":[41],"is":[42,174,189,223],"not":[43],"elaborately":[44],"designed,":[45],"and":[46,78,92,123,132,141,149,179,187,210,218,227],"may":[47],"be":[48,85],"trapped":[49],"local":[51,153,181],"optima":[52],"real":[54,219],"problems.":[55],"The":[56],"feature":[57],"operators":[58,94],"are":[59],"only":[60],"applied":[61],"but":[65],"final":[67],"heavily":[69],"depends":[70],"on":[71,212],"output.":[74],"Hence,":[75],"both":[76,130],"effectiveness":[77,131],"efficiency":[79,133],"overall":[82],"algorithm":[83],"can":[84],"improved":[86],"by":[87],"introducing":[88],"more":[89,225],"advanced":[90],"representations":[91,143],"novel":[93,112,152],"GA,":[97],"as":[98,100],"well":[99],"designing":[101],"post-processing":[103,125],"adaptive":[106,124,185],"way.":[107],"RESULTS:":[108],"We":[109],"propose":[110],"framework":[113],"GALF-P,":[114],"consisting":[115],"Local":[120],"Filtering":[121],"(GALF)":[122],"techniques":[126],"(-P),":[127],"to":[128,156,176,191,206],"achieve":[129],"for":[134],"GALF":[137],"combines":[138],"position-led":[140],"consensus-led":[142],"used":[144,175],"separately":[145],"current":[147,235],"GAs":[148],"employs":[150],"filtering":[154],"operator":[155],"get":[157],"rid":[158],"false":[160],"positives":[161],"within":[162],"individual":[164],"efficiently":[165],"during":[166],"evolutionary":[168],"process":[169],"GA.":[172],"Pre-selection":[173],"maintain":[177],"diversity":[178],"avoid":[180],"optima.":[182],"Post-processing":[183],"adding":[186],"removing":[188],"developed":[190],"handle":[192],"general":[193],"cases":[194],"arbitrary":[196],"numbers":[197],"instances":[199],"per":[200],"sequence.":[201],"GALF-P":[202,222],"shows":[203],"MEME,":[208],"BioProspector":[209],"BioOptimizer":[211],"synthetic":[213],"datasets":[214],"difficult":[216],"scenarios":[217],"test":[220],"datasets.":[221],"also":[224],"robust":[226],"reliable":[228],"when":[229],"further":[230],"compared":[231],"state-of-the-art":[236],"approach.":[237],"AVAILABILITY:":[238],"http://www.cse.cuhk.edu.hk/~tmchan/GALFP/.":[239]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
