{"id":"https://openalex.org/W2955517832","doi":"https://doi.org/10.1093/bib/bbz068","title":"A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data","display_name":"A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data","publication_year":2019,"publication_date":"2019-05-15","ids":{"openalex":"https://openalex.org/W2955517832","doi":"https://doi.org/10.1093/bib/bbz068","mag":"2955517832","pmid":"https://pubmed.ncbi.nlm.nih.gov/31267126"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz068","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz068","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5037885284","display_name":"Moliang Chen","orcid":"https://orcid.org/0009-0008-4408-9912"},"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":"Moliang Chen","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen 361005, China","Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111373172","display_name":"Guoli Ji","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":false,"raw_author_name":"Guoli Ji","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen 361005, China","Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China","institution_ids":[]}]},{"author_position":"middle","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":false,"raw_author_name":"Hongjuan Fu","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen 361005, China","Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102391116","display_name":"Qianmin Lin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qianmin Lin","raw_affiliation_strings":["Xiang' an hospital of Xiamen university, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiang' an hospital of Xiamen university, Xiamen 361005, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032396845","display_name":"Congting Ye","orcid":"https://orcid.org/0000-0003-4803-2098"},"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":"Congting Ye","raw_affiliation_strings":["Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062005196","display_name":"Wenbin Ye","orcid":"https://orcid.org/0000-0002-7811-2710"},"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":"Wenbin Ye","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen 361005, China","Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041339417","display_name":"Yaru Su","orcid":"https://orcid.org/0000-0002-9539-8511"},"institutions":[{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaru Su","raw_affiliation_strings":["College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China","institution_ids":["https://openalex.org/I80947539"]}]},{"author_position":"last","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":true,"raw_author_name":"Xiaohui Wu","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen 361005, China","Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091165765"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.7446,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.85204859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"4","first_page":"1261","last_page":"1276"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9957000017166138,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/polyadenylation","display_name":"Polyadenylation","score":0.7415802478790283},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7200210094451904},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5663235187530518},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.561834454536438},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.544435977935791},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5266777276992798},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.48929354548454285},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.452882319688797},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41433846950531006},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3532717525959015},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32950064539909363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3064561188220978},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24472296237945557},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22538381814956665},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19670593738555908}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7415802478790283},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7200210094451904},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5663235187530518},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.561834454536438},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.544435977935791},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5266777276992798},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.48929354548454285},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.452882319688797},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41433846950531006},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3532717525959015},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32950064539909363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3064561188220978},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24472296237945557},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22538381814956665},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19670593738555908},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbz068","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz068","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31267126","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31267126","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1188635553","display_name":null,"funder_award_id":"61802323","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3773187572","display_name":"\u96c6\u6210\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u7684\u9009\u62e9\u6027\u591a\u805a\u817a\u82f7\u5316\u7f51\u7edc\u5efa\u6a21\u7814\u7a76","funder_award_id":"61871463","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4705860316","display_name":null,"funder_award_id":"2017J01068","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"},{"id":"https://openalex.org/G7435240018","display_name":null,"funder_award_id":"61573296","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7522156796","display_name":null,"funder_award_id":"2016J01295","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321878","display_name":"Natural Science Foundation of Fujian Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":96,"referenced_works":["https://openalex.org/W1542927170","https://openalex.org/W1606725617","https://openalex.org/W1924421407","https://openalex.org/W1964727443","https://openalex.org/W1967637890","https://openalex.org/W1969412365","https://openalex.org/W1974379434","https://openalex.org/W1979529569","https://openalex.org/W1979764753","https://openalex.org/W1982675984","https://openalex.org/W1985267020","https://openalex.org/W1997703164","https://openalex.org/W2000875411","https://openalex.org/W2013228575","https://openalex.org/W2018300670","https://openalex.org/W2026663202","https://openalex.org/W2027455260","https://openalex.org/W2036065307","https://openalex.org/W2037434756","https://openalex.org/W2063151549","https://openalex.org/W2065213545","https://openalex.org/W2072770570","https://openalex.org/W2073461718","https://openalex.org/W2078223785","https://openalex.org/W2083196263","https://openalex.org/W2087789109","https://openalex.org/W2096465161","https://openalex.org/W2098980484","https://openalex.org/W2099578065","https://openalex.org/W2099915768","https://openalex.org/W2100305481","https://openalex.org/W2101815618","https://openalex.org/W2105545925","https://openalex.org/W2106352274","https://openalex.org/W2108264419","https://openalex.org/W2110768394","https://openalex.org/W2117688129","https://openalex.org/W2118834857","https://openalex.org/W2119204091","https://openalex.org/W2121690903","https://openalex.org/W2122364231","https://openalex.org/W2124433979","https://openalex.org/W2126456089","https://openalex.org/W2133019267","https://openalex.org/W2133237718","https://openalex.org/W2135592053","https://openalex.org/W2137307000","https://openalex.org/W2144137440","https://openalex.org/W2148223953","https://openalex.org/W2151562469","https://openalex.org/W2152239989","https://openalex.org/W2155804510","https://openalex.org/W2159730169","https://openalex.org/W2160391145","https://openalex.org/W2161030070","https://openalex.org/W2163741321","https://openalex.org/W2170669858","https://openalex.org/W2171791048","https://openalex.org/W2172208515","https://openalex.org/W2187341930","https://openalex.org/W2227231914","https://openalex.org/W2272187370","https://openalex.org/W2347006509","https://openalex.org/W2461965332","https://openalex.org/W2466240270","https://openalex.org/W2525507785","https://openalex.org/W2530884444","https://openalex.org/W2533379596","https://openalex.org/W2534208693","https://openalex.org/W2582462755","https://openalex.org/W2609219502","https://openalex.org/W2612122212","https://openalex.org/W2615053258","https://openalex.org/W2616950861","https://openalex.org/W2617657422","https://openalex.org/W2626386567","https://openalex.org/W2733002388","https://openalex.org/W2740888839","https://openalex.org/W2751247278","https://openalex.org/W2763864472","https://openalex.org/W2765871673","https://openalex.org/W2766614445","https://openalex.org/W2767898033","https://openalex.org/W2769224587","https://openalex.org/W2788174495","https://openalex.org/W2790178665","https://openalex.org/W2790970997","https://openalex.org/W2794907827","https://openalex.org/W2795614118","https://openalex.org/W2887117829","https://openalex.org/W2898881712","https://openalex.org/W2905621830","https://openalex.org/W2916580767","https://openalex.org/W2920773417","https://openalex.org/W2949671734","https://openalex.org/W6649807386"],"related_works":["https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4362592482","https://openalex.org/W4362511560"],"abstract_inverted_index":{"Alternative":[0],"polyadenylation":[1],"(APA)":[2],"has":[3,33],"been":[4],"implicated":[5],"to":[6,25,48,86,131,162,203,209,227,237],"play":[7],"an":[8],"important":[9],"role":[10],"in":[11,73],"post-transcriptional":[12],"regulation":[13],"by":[14],"regulating":[15],"mRNA":[16],"abundance,":[17],"stability,":[18],"localization":[19],"and":[20,28,50,125,127,184,230,233],"translation,":[21],"which":[22,76],"contributes":[23],"considerably":[24],"transcriptome":[26,39],"diversity":[27],"gene":[29],"expression":[30],"regulation.":[31],"RNA-seq":[32,69,117,174,241],"become":[34],"a":[35,99,133,186],"routine":[36],"approach":[37],"for":[38,60,90],"profiling,":[40],"generating":[41],"unprecedented":[42],"data":[43,70,118,129],"that":[44,82,144,155],"could":[45],"be":[46,84],"used":[47],"identify":[49],"quantify":[51],"APA":[52,62,66,167,171,191,239],"site":[53,168],"usage.":[54],"A":[55],"number":[56,188],"of":[57,102,105,136,148,160,166,189,213],"computational":[58,108],"approaches":[59],"identifying":[61],"sites":[63,192],"and/or":[64],"dynamic":[65,170],"events":[67,172],"from":[68,120,173,179,240],"have":[71],"emerged":[72],"the":[74,91,103,145,164,211,214,223],"literature,":[75],"provide":[77],"valuable":[78],"yet":[79],"preliminary":[80],"results":[81,178],"should":[83],"refined":[85],"yield":[87],"credible":[88],"guidelines":[89],"scientific":[92],"community.":[93],"In":[94],"this":[95],"review,":[96],"we":[97,201],"provided":[98],"comprehensive":[100],"overview":[101],"status":[104],"currently":[106],"available":[107],"approaches.":[109],"We":[110,217],"also":[111,218],"conducted":[112],"objective":[113],"benchmarking":[114,141],"analysis":[115],"using":[116],"sets":[119,130],"different":[121,198],"species":[122],"(human,":[123],"mouse":[124],"Arabidopsis)":[126],"simulated":[128],"present":[132],"systematic":[134],"evaluation":[135],"11":[137],"representative":[138],"methods.":[139],"Our":[140],"study":[142],"showed":[143],"overall":[146],"performance":[147],"all":[149],"tools":[150,181],"investigated":[151],"is":[152,157],"moderate,":[153],"reflecting":[154],"there":[156],"still":[158],"lot":[159],"scope":[161],"improve":[163],"prediction":[165,177],"or":[169,193],"data.":[175,242],"Particularly,":[176],"individual":[180],"differ":[182],"considerably,":[183],"only":[185],"limited":[187],"predicted":[190],"genes":[194],"are":[195],"common":[196],"among":[197],"tools.":[199],"Accordingly,":[200],"attempted":[202],"give":[204],"some":[205],"advice":[206],"on":[207,222],"how":[208],"assess":[210],"reliability":[212],"obtained":[215],"results.":[216],"proposed":[219],"practical":[220],"recommendations":[221],"appropriate":[224],"method":[225],"applicable":[226],"diverse":[228],"scenarios":[229],"discussed":[231],"implications":[232],"future":[234],"directions":[235],"relevant":[236],"profiling":[238]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
