{"id":"https://openalex.org/W2100725064","doi":"https://doi.org/10.1093/bioinformatics/btn243","title":"Retroviral promoters in the human genome","display_name":"Retroviral promoters in the human genome","publication_year":2008,"publication_date":"2008-06-05","ids":{"openalex":"https://openalex.org/W2100725064","doi":"https://doi.org/10.1093/bioinformatics/btn243","mag":"2100725064","pmid":"https://pubmed.ncbi.nlm.nih.gov/18535086"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/14/1563/49046914/bioinformatics_24_14_1563.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/24/14/1563/49046914/bioinformatics_24_14_1563.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077724315","display_name":"Andrew B. Conley","orcid":"https://orcid.org/0000-0001-7966-611X"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew B. Conley","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025385359","display_name":"Jittima Piriyapongsa","orcid":"https://orcid.org/0000-0003-3313-4286"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jittima Piriyapongsa","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062048502","display_name":"I. King Jordan","orcid":"https://orcid.org/0000-0003-4996-2203"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. King Jordan","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077724315"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":14.3474,"has_fulltext":false,"cited_by_count":129,"citation_normalized_percentile":{"value":0.98870383,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"24","issue":"14","first_page":"1563","last_page":"1567"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9994000196456909,"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":0.9962999820709229,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.8135778307914734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7766146659851074},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6768087148666382},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.6671328544616699},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6287133097648621},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6173794865608215},{"id":"https://openalex.org/keywords/endogenous-retrovirus","display_name":"Endogenous retrovirus","score":0.6114485859870911},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.6010942459106445},{"id":"https://openalex.org/keywords/retrovirus","display_name":"Retrovirus","score":0.5364606380462646},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4133136570453644},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38286903500556946},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.34137749671936035}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.8135778307914734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7766146659851074},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6768087148666382},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.6671328544616699},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6287133097648621},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6173794865608215},{"id":"https://openalex.org/C121346293","wikidata":"https://www.wikidata.org/wiki/Q1340715","display_name":"Endogenous retrovirus","level":4,"score":0.6114485859870911},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6010942459106445},{"id":"https://openalex.org/C2778431562","wikidata":"https://www.wikidata.org/wiki/Q189308","display_name":"Retrovirus","level":3,"score":0.5364606380462646},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4133136570453644},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38286903500556946},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.34137749671936035},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"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":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"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":"D020079","descriptor_name":"Terminal Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020079","descriptor_name":"Terminal Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020079","descriptor_name":"Terminal Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/14/1563/49046914/bioinformatics_24_14_1563.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:18535086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18535086","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/btn243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/14/1563/49046914/bioinformatics_24_14_1563.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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100725064.pdf","grobid_xml":"https://content.openalex.org/works/W2100725064.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1817110620","https://openalex.org/W1964941174","https://openalex.org/W1965100590","https://openalex.org/W1980848179","https://openalex.org/W2006117179","https://openalex.org/W2010310827","https://openalex.org/W2011549524","https://openalex.org/W2017936139","https://openalex.org/W2044096520","https://openalex.org/W2044175686","https://openalex.org/W2056898550","https://openalex.org/W2057692691","https://openalex.org/W2102304447","https://openalex.org/W2104905992","https://openalex.org/W2105010972","https://openalex.org/W2107903949","https://openalex.org/W2108871359","https://openalex.org/W2112132489","https://openalex.org/W2114703458","https://openalex.org/W2128969076","https://openalex.org/W2130925862","https://openalex.org/W2131937786","https://openalex.org/W2138247507","https://openalex.org/W2138974722","https://openalex.org/W2145191876","https://openalex.org/W2151587693","https://openalex.org/W2155530972","https://openalex.org/W2156853664","https://openalex.org/W2158714788","https://openalex.org/W2159049360","https://openalex.org/W2161645441","https://openalex.org/W2164242630","https://openalex.org/W2164683872","https://openalex.org/W2168783124","https://openalex.org/W2168909179","https://openalex.org/W2170984819","https://openalex.org/W6638264975","https://openalex.org/W6790425969"],"related_works":["https://openalex.org/W2143045093","https://openalex.org/W2272952900","https://openalex.org/W2410181327","https://openalex.org/W2316628929","https://openalex.org/W2512267281","https://openalex.org/W1911875678","https://openalex.org/W1847671176","https://openalex.org/W2275798086","https://openalex.org/W2123323046","https://openalex.org/W2019505003"],"abstract_inverted_index":{"MOTIVATION:":[0],"Endogenous":[1],"retrovirus":[2],"(ERV)":[3],"elements":[4],"have":[5],"been":[6],"shown":[7],"to":[8,23,44,108,146,159],"contribute":[9,145],"promoter":[10,64,89],"sequences":[11,26,65,82,127,158],"that":[12,66,83,118],"can":[13,105],"initiate":[14,27,67],"transcription":[15,28,68,77,102,110,162],"of":[16,49,61,97,99,111,141,156,172,179],"adjacent":[17],"human":[18,31,54,71,113,161,181],"genes.":[19],"However,":[20],"the":[21,30,47,53,59,70,100,154,175,180],"extent":[22],"which":[24],"retroviral":[25,50,157],"within":[29,69,121],"genome":[32,38],"is":[33,78],"currently":[34],"unknown.":[35],"We":[36,57],"analyzed":[37],"sequence":[39],"and":[40,128,138,144,177],"high-throughput":[41],"expression":[42,143,147],"data":[43,152],"systematically":[45],"evaluate":[46],"presence":[48],"promoters":[51,135],"in":[52,86],"genome.":[55,182],"RESULTS:":[56],"report":[58],"existence":[60],"51,197":[62],"ERV-derived":[63,101],"genome,":[72],"including":[73],"1743":[74],"cases":[75],"where":[76],"initiated":[79,120],"from":[80],"ERV":[81,122,134],"are":[84,119],"located":[85],"gene":[87,132,142],"proximal":[88],"or":[90],"5'":[91],"untranslated":[92],"regions":[93],"(UTRs).":[94],"A":[95],"total":[96],"114":[98],"start":[103],"sites":[104],"be":[106],"demonstrated":[107],"drive":[109,136],"97":[112],"genes,":[114],"producing":[115],"chimeric":[116],"transcripts":[117],"long":[123],"terminal":[124],"repeat":[125],"(LTR)":[126],"read-through":[129],"into":[130],"known":[131],"sequences.":[133],"tissue-specific":[137],"lineage-specific":[139],"patterns":[140],"divergence":[148],"between":[149],"paralogs.":[150],"These":[151],"illustrate":[153],"potential":[155],"regulate":[160],"on":[163,174],"a":[164,169],"large":[165],"scale":[166],"consistent":[167],"with":[168],"substantial":[170],"effect":[171],"ERVs":[173],"function":[176],"evolution":[178]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":9}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}