{"id":"https://openalex.org/W3012405335","doi":"https://doi.org/10.1109/tcbb.2020.2980234","title":"Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps","display_name":"Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps","publication_year":2020,"publication_date":"2020-03-13","ids":{"openalex":"https://openalex.org/W3012405335","doi":"https://doi.org/10.1109/tcbb.2020.2980234","mag":"3012405335","pmid":"https://pubmed.ncbi.nlm.nih.gov/32175870"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.2980234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2980234","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5113898208","display_name":"Yu-Hao Ke","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148468","display_name":"Industrial Technology Research Institute","ror":"https://ror.org/05szzwt63","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I4210148468"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Yu-Hao Ke","raw_affiliation_strings":["Industrial Technology Research Institute, Hsinchu, Taiwan"],"affiliations":[{"raw_affiliation_string":"Industrial Technology Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210148468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016756842","display_name":"Jen-Wei Huang","orcid":"https://orcid.org/0000-0001-5482-8311"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jen-Wei Huang","raw_affiliation_strings":["Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038719850","display_name":"Wei-Chen Lin","orcid":"https://orcid.org/0000-0001-7223-5931"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wei-Chen Lin","raw_affiliation_strings":["Department of Parasitology, Institute of Microbiology and Immunology, National Cheng Kung University, Tainan, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Parasitology, Institute of Microbiology and Immunology, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085834871","display_name":"Bijay Prasad Jaysawal","orcid":"https://orcid.org/0000-0001-6958-0347"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Bijay Prasad Jaysawal","raw_affiliation_strings":["Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5113898208"],"corresponding_institution_ids":["https://openalex.org/I4210148468"],"apc_list":null,"apc_paid":null,"fwci":1.6015,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.87391782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"18","issue":"6","first_page":"2459","last_page":"2470"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T10538","display_name":"Data Mining Algorithms and Applications","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9815000295639038,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9769999980926514,"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/promoter","display_name":"Promoter","score":0.7318097949028015},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6539457440376282},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5780215859413147},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5259671211242676},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5126304030418396},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5034331679344177},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4993596076965332},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46809104084968567},{"id":"https://openalex.org/keywords/promoter-activity","display_name":"Promoter activity","score":0.4670124650001526},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.45564350485801697},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4524773359298706},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44996777176856995},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"Consensus sequence","score":0.44971996545791626},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4342659115791321},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.42016226053237915},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27871572971343994},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.21407368779182434},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11060765385627747},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07535472512245178}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.7318097949028015},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6539457440376282},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5780215859413147},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5259671211242676},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5126304030418396},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5034331679344177},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4993596076965332},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46809104084968567},{"id":"https://openalex.org/C2775871807","wikidata":"https://www.wikidata.org/wiki/Q24963883","display_name":"Promoter activity","level":5,"score":0.4670124650001526},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.45564350485801697},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4524773359298706},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44996777176856995},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.44971996545791626},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4342659115791321},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.42016226053237915},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27871572971343994},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.21407368779182434},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11060765385627747},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07535472512245178},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":"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":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.2980234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2980234","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32175870","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32175870","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7599999904632568,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W176960307","https://openalex.org/W259338706","https://openalex.org/W1214546200","https://openalex.org/W1480489870","https://openalex.org/W1608194207","https://openalex.org/W1641039719","https://openalex.org/W2022148737","https://openalex.org/W2068383400","https://openalex.org/W2076898137","https://openalex.org/W2089064575","https://openalex.org/W2096210973","https://openalex.org/W2133224197","https://openalex.org/W2136197452","https://openalex.org/W2143314089","https://openalex.org/W2147694185","https://openalex.org/W2158454296","https://openalex.org/W2164296513","https://openalex.org/W2189465200","https://openalex.org/W2558947257","https://openalex.org/W2995564009","https://openalex.org/W4239504300","https://openalex.org/W4317639370","https://openalex.org/W6607220651","https://openalex.org/W6628147189","https://openalex.org/W6682094280","https://openalex.org/W6687322159"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2117168988","https://openalex.org/W2103777723","https://openalex.org/W2610941444","https://openalex.org/W1981356107","https://openalex.org/W2156159819","https://openalex.org/W2143172590"],"abstract_inverted_index":{"Identifying":[0],"motifs":[1,118,134,141,161],"in":[2,19,41,91,119,132],"promoter":[3,17,26,42,57,107,122,144,160],"regions":[4,108,145],"is":[5],"crucial":[6],"to":[7,24,53,65,70,113,135,152],"our":[8],"understanding":[9],"of":[10,22,74,81,88,130,165],"transcription":[11,100],"regulation.":[12],"Researchers":[13],"commonly":[14],"use":[15],"known":[16,159],"features":[18,40],"a":[20,92],"variety":[21],"species":[23,36],"predict":[25],"motifs.":[27],"However":[28],"the":[29,55,67,72,86,99,117,120,128,133,147,163,166],"results":[30],"are":[31],"not":[32],"particularly":[33],"useful.":[34],"Different":[35],"rarely":[37],"have":[38],"similar":[39],"binding":[43,58],"sites.":[44],"In":[45],"this":[46],"study,":[47],"we":[48,84],"adopt":[49],"sequence":[50],"analysis":[51],"techniques":[52],"find":[54],"possible":[56,106,121],"sites":[59,102],"among":[60],"different":[61],"species.":[62],"We":[63,115],"sought":[64],"improve":[66],"existing":[68],"algorithm":[69],"suit":[71],"task":[73],"mining":[75],"sequential":[76],"patterns":[77],"with":[78,137,158],"specific":[79],"number":[80,129],"gaps.":[82],"Moreover,":[83],"discuss":[85],"implementation":[87],"proposed":[89,96,148,167],"method":[90,97],"distributed":[93],"environment.":[94],"The":[95,140],"finds":[98],"start":[101],"(TSS)":[103],"and":[104],"extracts":[105],"from":[109,143],"DNA":[110],"sequences":[111],"according":[112],"TSS.":[114],"derived":[116],"regions,":[123],"while":[124],"taking":[125],"into":[126],"account":[127],"gaps":[131],"deal":[136],"unimportant":[138,154],"nucleotides.":[139,155],"generated":[142],"using":[146],"methodology":[149],"were":[150],"shown":[151],"tolerate":[153],"A":[156],"comparison":[157],"verified":[162],"efficacy":[164],"method.":[168]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
