{"id":"https://openalex.org/W3004616039","doi":"https://doi.org/10.1109/bibm47256.2019.8983023","title":"Computational identification of extra coding RNAs related to HIV-1 infection","display_name":"Computational identification of extra coding RNAs related to HIV-1 infection","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004616039","doi":"https://doi.org/10.1109/bibm47256.2019.8983023","mag":"3004616039"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983023","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983023","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5007555631","display_name":"Ian Huntress","orcid":null},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ian Huntress","raw_affiliation_strings":["Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082687362","display_name":"Erin Harrell","orcid":null},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erin Harrell","raw_affiliation_strings":["Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074479204","display_name":"Hayden Brochu","orcid":"https://orcid.org/0000-0002-7234-3235"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hayden Brochu","raw_affiliation_strings":["Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University,Raleigh,USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Molecular Biomedical Sciences, North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060247652","display_name":"Xinxia Peng","orcid":"https://orcid.org/0000-0002-0117-3582"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinxia Peng","raw_affiliation_strings":["Molecular Biomedical Sciences, Bioinformatics Research Center, North Carolina State University,Raleigh,USA","Molecular Biomedical Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biomedical Sciences, Bioinformatics Research Center, North Carolina State University,Raleigh,USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Molecular Biomedical Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007555631"],"corresponding_institution_ids":["https://openalex.org/I137902535"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1671058,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"2810","last_page":"2815"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9991999864578247,"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/T10604","display_name":"RNA Research and Splicing","score":0.9984999895095825,"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/polyadenylation","display_name":"Polyadenylation","score":0.7909969091415405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7371786832809448},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5837932229042053},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5350609421730042},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5254434943199158},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.48446011543273926},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.48338618874549866},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.47257912158966064},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.45388373732566833}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7909969091415405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7371786832809448},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5837932229042053},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5350609421730042},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5254434943199158},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.48446011543273926},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.48338618874549866},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.47257912158966064},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.45388373732566833}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983023","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983023","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2123973342","https://openalex.org/W2134526812","https://openalex.org/W2169456326","https://openalex.org/W2170741891","https://openalex.org/W2473795341","https://openalex.org/W2951912016"],"related_works":["https://openalex.org/W2083833254","https://openalex.org/W1978448871","https://openalex.org/W2082856106","https://openalex.org/W1973164572","https://openalex.org/W1988731563","https://openalex.org/W2068962637","https://openalex.org/W1995725827","https://openalex.org/W2608025469","https://openalex.org/W2070709105","https://openalex.org/W2289108004"],"abstract_inverted_index":{"A":[0],"few":[1],"studies":[2],"suggest":[3],"that":[4],"many":[5],"protein":[6],"coding":[7,172],"loci":[8,55,109],"also":[9],"transcribe":[10],"extra-coding":[11],"RNAs":[12,88],"(ecRNAs),":[13],"a":[14,102,118,182],"distinct":[15],"class":[16],"of":[17,50,60,67,94,120,125,135,144,154,164,169,185,188],"long":[18],"non-coding":[19],"RNAs.":[20,98],"These":[21],"ecRNAs":[22,43,61,165,189],"span":[23],"over":[24],"and":[25,39,71,89,138,141,197],"beyond":[26],"mRNAs":[27,51],"originating":[28],"from":[29,52,86,110,166],"the":[30,48,53,65,95,123,131,142,186],"same":[31,54],"loci,":[32],"are":[33],"much":[34],"less":[35],"abundant":[36],"than":[37],"mRNAs,":[38,85],"lack":[40,66],"polyadenylation.":[41],"Previously,":[42],"were":[44],"found":[45],"to":[46,74,105,127,146,194],"regulate":[47],"transcription":[49],"epigenetically.":[56],"However,":[57],"further":[58],"investigation":[59],"is":[62],"impeded":[63],"by":[64],"accurate":[68],"ecRNA":[69,107],"annotation":[70],"quantification.":[72],"Here,":[73],"uncover":[75],"these":[76,176],"mRNA-overlapping":[77],"ecRNAs,":[78],"we":[79,100,160],"first":[80],"depleted":[81],"polyadenylated":[82],"RNAs,":[83],"i.e.":[84],"total":[87,97],"performed":[90],"deep":[91],"sequencing":[92,113],"analysis":[93],"remaining":[96],"Next,":[99],"devised":[101],"computational":[103,178],"strategy":[104],"identify":[106],"transcribing":[108],"this":[111,151],"unique":[112],"data.":[114],"Our":[115],"approach":[116],"uses":[117],"combination":[119],"features":[121],"including":[122],"ratio":[124,143],"intronic":[126,147],"exonic":[128],"read":[129,133,148],"counts,":[130],"percent":[132],"coverage":[134],"introns,":[136],"exons,":[137],"flanking":[139,145],"regions,":[140],"counts.":[149],"In":[150],"pilot":[152],"study":[153],"HIV-1":[155],"infected":[156],"CD4+":[157],"T":[158],"cells,":[159],"observed":[161],"transcriptional":[162],"signatures":[163],"880":[167],"(~11%)":[168],"7,690":[170],"expressed":[171],"genes.":[173],"We":[174],"expect":[175],"custom":[177],"developments":[179],"will":[180],"enable":[181],"better":[183],"understanding":[184],"involvement":[187],"in":[190,198],"regulating":[191],"host":[192],"response":[193],"HIV":[195],"infection":[196],"other":[199],"conditions.":[200]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
