{"id":"https://openalex.org/W3118308909","doi":"https://doi.org/10.1145/3431943.3432289","title":"A Pipeline to Identify Novel 3\u2019 UTRs and Widespread Intergenic Transcription by Combination of Polyadenylation Sites and RNA-seq Data","display_name":"A Pipeline to Identify Novel 3\u2019 UTRs and Widespread Intergenic Transcription by Combination of Polyadenylation Sites and RNA-seq Data","publication_year":2020,"publication_date":"2020-10-16","ids":{"openalex":"https://openalex.org/W3118308909","doi":"https://doi.org/10.1145/3431943.3432289","mag":"3118308909"},"language":"en","primary_location":{"id":"doi:10.1145/3431943.3432289","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3431943.3432289","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 9th International Conference on Bioinformatics and Biomedical Science","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/A5113864080","display_name":"Hongjuan Fu","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongjuan Fu","raw_affiliation_strings":["Xiamen University"],"affiliations":[{"raw_affiliation_string":"Xiamen University","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042421637","display_name":"Yibo Zhuang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yibo Zhuang","raw_affiliation_strings":["Xiamen YLZ Yihui Technology Co. Ltd"],"affiliations":[{"raw_affiliation_string":"Xiamen YLZ Yihui Technology Co. Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091165765","display_name":"Xiaohui Wu","orcid":"https://orcid.org/0000-0003-0356-7785"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Wu","raw_affiliation_strings":["Xiamen University"],"affiliations":[{"raw_affiliation_string":"Xiamen University","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101822620","display_name":"Guoli Ji","orcid":"https://orcid.org/0000-0002-0474-5523"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoli Ji","raw_affiliation_strings":["Xiamen University, China"],"affiliations":[{"raw_affiliation_string":"Xiamen University, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5113864080"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12885815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"126","last_page":"132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9998000264167786,"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":0.9987999796867371,"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":0.7650049328804016},{"id":"https://openalex.org/keywords/intergenic-region","display_name":"Intergenic region","score":0.6892232894897461},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5737733244895935},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5244413018226624},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4863736927509308},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4285668730735779},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40753373503685},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3861759901046753},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34915274381637573},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34063640236854553},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1572445034980774}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7650049328804016},{"id":"https://openalex.org/C195139083","wikidata":"https://www.wikidata.org/wiki/Q3463539","display_name":"Intergenic region","level":4,"score":0.6892232894897461},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5737733244895935},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5244413018226624},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4863736927509308},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4285668730735779},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40753373503685},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3861759901046753},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34915274381637573},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34063640236854553},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1572445034980774},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3431943.3432289","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3431943.3432289","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 9th International Conference on Bioinformatics and Biomedical Science","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":1,"referenced_works":["https://openalex.org/W2102619694"],"related_works":["https://openalex.org/W1976007281","https://openalex.org/W195216885","https://openalex.org/W1968152888","https://openalex.org/W2081082232","https://openalex.org/W4205787488","https://openalex.org/W2065213545","https://openalex.org/W2414745490","https://openalex.org/W2134976499","https://openalex.org/W2025859988","https://openalex.org/W1490227039"],"abstract_inverted_index":{"Recent":[0],"genomic":[1,145],"studies":[2],"continue":[3],"to":[4,19,35,99],"uncover":[5],"widespread":[6],"occurrences":[7],"of":[8,23,129],"polyadenylation":[9],"poly(A)":[10,51],"sites":[11],"in":[12,85,108],"presumed":[13],"intergenic":[14,28,43,105,111,122],"regions,":[15],"providing":[16],"new":[17,116],"opportunities":[18],"investigate":[20],"the":[21,127],"complex":[22],"3\u2019":[24,38,73,80,90,117],"untranslated":[25],"regions":[26,112],"and":[27,42,49,55,87,103,121,132],"transcription.":[29],"Here":[30],"we":[31],"developed":[32],"a":[33,63],"pipeline":[34],"detect":[36],"novel":[37,40,72,101,119],"UTRs,":[39,118],"genes,":[41,120],"transcribed":[44,106,123],"units":[45,107,124],"by":[46],"combining":[47],"real":[48],"predicted":[50],"sites,":[52],"archival":[53],"ESTs,":[54],"RNA-seq":[56],"data.":[57],"Using":[58],"data":[59],"from":[60],"Medicago":[61],"truncatula,":[62],"model":[64],"organism":[65],"for":[66,142],"legume":[67],"biology,":[68],"more":[69,143],"than":[70],"3100":[71],"UTRs":[74,81,91],"were":[75,113],"identified,":[76],"including":[77],"1932":[78],"normal":[79],"averaging":[82],"1482":[83],"nt":[84],"length":[86],"1261":[88],"distal":[89],"each":[92],"with":[93],"elongation":[94],"\u2265":[95],"5000":[96],"nt.":[97],"Up":[98],"632":[100],"genes":[102],"12,765":[104],"previously":[109],"uncharacterized":[110],"discovered.":[114],"These":[115],"substantially":[125],"extend":[126],"scope":[128],"plant":[130],"transcriptome":[131],"should":[133],"be":[134],"incorporated":[135],"into":[136],"current":[137],"M.":[138],"truncatula":[139],"genome":[140],"annotation":[141],"comprehensive":[144],"study,":[146],"e.g.,":[147],"searching":[148],"microRNA":[149],"targets":[150],"or":[151],"other":[152],"regulatory":[153],"elements.":[154]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}