{"id":"https://openalex.org/W2008991558","doi":"https://doi.org/10.1089/106652702760277354","title":"The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions","display_name":"The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions","publication_year":2002,"publication_date":"2002-08-01","ids":{"openalex":"https://openalex.org/W2008991558","doi":"https://doi.org/10.1089/106652702760277354","mag":"2008991558","pmid":"https://pubmed.ncbi.nlm.nih.gov/12323097"},"language":"en","primary_location":{"id":"doi:10.1089/106652702760277354","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652702760277354","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","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/A5016211165","display_name":"Jorng\u2010Tzong Horng","orcid":"https://orcid.org/0000-0002-7671-0573"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jorng-Tzong Horng","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Taiwan and Department of Life Science, National Central University,          Taiwan","Department of Computer Science and Information Engineering, National Central University, Taiwan and Department of Life Science, National Central University, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taiwan and Department of Life Science, National Central University,          Taiwan","institution_ids":["https://openalex.org/I22265921"]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taiwan and Department of Life Science, National Central University, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040277769","display_name":"Hsien\u2010Da Huang","orcid":"https://orcid.org/0000-0003-2857-7023"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Hsien-Da Huang","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109101045","display_name":"Ming-Hui Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Ming-Hui Jin","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103574389","display_name":"Li-Cheng Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Li-Cheng Wu","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016053063","display_name":"Shir\u2010Ly Huang","orcid":"https://orcid.org/0000-0002-9252-1289"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Shir-Ly Huang","raw_affiliation_strings":["Department of Life Science, National Central University, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Science, National Central University, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I22265921"],"apc_list":null,"apc_paid":null,"fwci":1.1452,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.76467999,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"9","issue":"4","first_page":"621","last_page":"640"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9962999820709229,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9962999820709229,"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":0.9930999875068665,"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":0.9898999929428101,"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/orfs","display_name":"ORFS","score":0.7630179524421692},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7096840739250183},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5959227085113525},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5802451968193054},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.5660859942436218},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5500006079673767},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5375250577926636},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49825215339660645},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.4792618751525879},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3941900432109833},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.17672470211982727},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.12324076890945435},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08418259024620056}],"concepts":[{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.7630179524421692},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7096840739250183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5959227085113525},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5802451968193054},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5660859942436218},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5500006079673767},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5375250577926636},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49825215339660645},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.4792618751525879},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3941900432109833},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.17672470211982727},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.12324076890945435},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08418259024620056},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/106652702760277354","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652702760277354","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:12323097","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12323097","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1484413656","https://openalex.org/W1509844421","https://openalex.org/W1514609165","https://openalex.org/W1586233861","https://openalex.org/W1965941177","https://openalex.org/W2032019900","https://openalex.org/W2032231928","https://openalex.org/W2055043387","https://openalex.org/W2071398217","https://openalex.org/W2115772919","https://openalex.org/W2140611547","https://openalex.org/W2151625863","https://openalex.org/W2165011536","https://openalex.org/W2166559705","https://openalex.org/W2998574808","https://openalex.org/W3208191137","https://openalex.org/W3208576060","https://openalex.org/W4245051455","https://openalex.org/W4246925013"],"related_works":["https://openalex.org/W2100847587","https://openalex.org/W2039410154","https://openalex.org/W2051856433","https://openalex.org/W2140948740","https://openalex.org/W2552089663","https://openalex.org/W1976390578","https://openalex.org/W2360726289","https://openalex.org/W2037527629","https://openalex.org/W2781755676","https://openalex.org/W2146517458"],"abstract_inverted_index":{"At":[0],"least":[1],"43%":[2],"of":[3,15,26,48,56,100,114,130,147,149,179,185],"the":[4,16,42,71,85,92,121,131,144,159,176,195],"human":[5],"genome":[6,18,35],"is":[7,19,51,170],"occupied":[8,20],"by":[9,21],"repetitive":[10,22,27,31,57,65,95,101,137,155],"elements.":[11,23],"Moreover,":[12],"around":[13],"51%":[14],"rice":[17],"The":[24,45,61,78,111,153,182,199],"analysis":[25],"elements":[28,32,58,96,102,138,156],"reveals":[29],"that":[30],"in":[33,41,139,143,158],"our":[34],"may":[36,201],"have":[37],"been":[38],"very":[39],"important":[40],"evolutionary":[43],"genomics.":[44],"first":[46],"part":[47,113],"this":[49,115],"study":[50,116],"to":[52,81,119,172,194],"describe":[53],"a":[54],"database":[55,63],"-":[59],"RSDB.":[60],"RSDB":[62,140,186],"contains":[64],"elements,":[66],"which":[67],"are":[68,109,141,161,192],"classified":[69],"into":[70],"following":[72],"categories:":[73],"exact,":[74],"tandem,":[75],"and":[76,83,87,97,106,135,175,187],"similar.":[77],"interfaces":[79],"needed":[80],"query":[82,204],"show":[84],"results":[86],"statistical":[88],"data,":[89],"such":[90],"as":[91],"relationship":[93],"between":[94],"genes,":[98],"cross-references":[99],"among":[103],"different":[104],"organisms,":[105],"so":[107],"on,":[108],"provided.":[110],"second":[112],"then":[117],"attempts":[118],"mine":[120],"putative":[122,189],"binding":[123,165,190],"site":[124],"for":[125],"information":[126],"on":[127],"how":[128],"combinations":[129],"known":[132],"regulatory":[133],"sites":[134,191],"overrepresented":[136,154],"distributed":[142],"promoter":[145,177],"regions":[146,178],"groups":[148],"functionally":[150],"related":[151],"genes.":[152],"appearing":[157],"associations":[160],"possible":[162],"transcription":[163],"factor":[164],"sites.":[166],"Our":[167],"proposed":[168],"approach":[169],"applied":[171],"Saccharomyces":[173],"cerevisiae":[174],"Yeast":[180],"ORFs.":[181],"complete":[183],"contents":[184],"partial":[188,203],"available":[193],"public":[196],"at":[197],"www.rsdb.csie.ncu.edu.tw.":[198],"readers":[200],"download":[202],"results.":[205]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}
