{"id":"https://openalex.org/W2790970997","doi":"https://doi.org/10.1093/bioinformatics/bty029","title":"APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data","display_name":"APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data","publication_year":2018,"publication_date":"2018-01-17","ids":{"openalex":"https://openalex.org/W2790970997","doi":"https://doi.org/10.1093/bioinformatics/bty029","mag":"2790970997","pmid":"https://pubmed.ncbi.nlm.nih.gov/29360928"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1841/25121690/bty029.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/34/11/1841/25121690/bty029.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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, China"],"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, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072324207","display_name":"Yuqi Long","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":"Yuqi Long","raw_affiliation_strings":["Department of Automation, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]},{"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, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011758500","display_name":"Qingshun Quinn Li","orcid":"https://orcid.org/0000-0003-4105-1480"},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Qingshun Quinn Li","raw_affiliation_strings":["Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA","Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA","institution_ids":["https://openalex.org/I93393672"]},{"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, China","institution_ids":["https://openalex.org/I191208505"]}]},{"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, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011758500","https://openalex.org/A5091165765"],"corresponding_institution_ids":["https://openalex.org/I191208505","https://openalex.org/I93393672"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.8467,"has_fulltext":false,"cited_by_count":126,"citation_normalized_percentile":{"value":0.97118985,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"34","issue":"11","first_page":"1841","last_page":"1849"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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":0.9991000294685364,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9819999933242798,"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/rna-seq","display_name":"RNA-Seq","score":0.7475082874298096},{"id":"https://openalex.org/keywords/polyadenylation","display_name":"Polyadenylation","score":0.7322521805763245},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7277491092681885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6408134698867798},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43580445647239685},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37618640065193176},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3683777451515198},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.24956777691841125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2355022132396698},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1236279308795929},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08845293521881104}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7475082874298096},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7322521805763245},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7277491092681885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6408134698867798},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43580445647239685},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37618640065193176},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3683777451515198},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.24956777691841125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2355022132396698},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1236279308795929},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08845293521881104},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1841/25121690/bty029.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:29360928","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29360928","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/bty029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1841/25121690/bty029.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":[{"id":"https://openalex.org/G1429155505","display_name":null,"funder_award_id":"201606315010","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G300104265","display_name":null,"funder_award_id":"2016YFE0108800","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G4931056859","display_name":null,"funder_award_id":"61673323","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5955914378","display_name":null,"funder_award_id":"IOS-154173","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2790970997.pdf","grobid_xml":"https://content.openalex.org/works/W2790970997.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1606725617","https://openalex.org/W1967637890","https://openalex.org/W1969412365","https://openalex.org/W1970699617","https://openalex.org/W1971560447","https://openalex.org/W1979529569","https://openalex.org/W1982675984","https://openalex.org/W1997703164","https://openalex.org/W2002555696","https://openalex.org/W2018300670","https://openalex.org/W2018658742","https://openalex.org/W2022954469","https://openalex.org/W2027455260","https://openalex.org/W2036065307","https://openalex.org/W2037434756","https://openalex.org/W2053057991","https://openalex.org/W2072770570","https://openalex.org/W2073461718","https://openalex.org/W2075220000","https://openalex.org/W2078223785","https://openalex.org/W2083196263","https://openalex.org/W2087789109","https://openalex.org/W2091310902","https://openalex.org/W2095930993","https://openalex.org/W2098980484","https://openalex.org/W2099578065","https://openalex.org/W2100305481","https://openalex.org/W2101815618","https://openalex.org/W2105060337","https://openalex.org/W2108264419","https://openalex.org/W2110065044","https://openalex.org/W2114672936","https://openalex.org/W2118834857","https://openalex.org/W2133019267","https://openalex.org/W2137307000","https://openalex.org/W2144137440","https://openalex.org/W2148223953","https://openalex.org/W2156631105","https://openalex.org/W2159730169","https://openalex.org/W2160673349","https://openalex.org/W2161030070","https://openalex.org/W2163741321","https://openalex.org/W2178279848","https://openalex.org/W2302658801","https://openalex.org/W2347006509","https://openalex.org/W2461965332","https://openalex.org/W2466240270","https://openalex.org/W2487617124","https://openalex.org/W2525507785","https://openalex.org/W2530884444","https://openalex.org/W2582462755","https://openalex.org/W2615053258","https://openalex.org/W6649807386"],"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/W2082559221","https://openalex.org/W2414745490","https://openalex.org/W2124120782","https://openalex.org/W2074164095"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":3}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}
