{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T01:38:25Z","timestamp":1780364305771,"version":"3.54.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871463"],"award-info":[{"award-number":["61871463"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61573296"],"award-info":[{"award-number":["61573296"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61802323"],"award-info":[{"award-number":["61802323"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically. Studies based on 3\u2032 end sequencing and\/or RNA-seq have profiled poly(A) sites in various species with diverse pipelines, yet no unified and easy-to-use toolkit is available for comprehensive APA analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed an R package called movAPA for modeling and visualization of dynamics of alternative polyadenylation across biological samples. movAPA incorporates rich functions for preprocessing, annotation and statistical analyses of poly(A) sites, identification of poly(A) signals, profiling of APA dynamics and visualization. Particularly, seven metrics are provided for measuring the tissue-specificity or usages of APA sites across samples. Three methods are used for identifying 3\u2032 UTR shortening\/lengthening events between conditions. APA site switching involving non-3\u2032 UTR polyadenylation can also be explored. Using poly(A) site data from rice and mouse sperm cells, we demonstrated the high scalability and flexibility of movAPA in profiling APA dynamics across tissues and single cells.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/BMILAB\/movAPA.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa997","type":"journal-article","created":{"date-parts":[[2020,11,17]],"date-time":"2020-11-17T20:12:39Z","timestamp":1605643959000},"page":"2470-2472","source":"Crossref","is-referenced-by-count":21,"title":["movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples"],"prefix":"10.1093","volume":"37","author":[{"given":"Wenbin","family":"Ye","sequence":"first","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongjuan","family":"Fu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4803-2098","authenticated-orcid":false,"given":"Congting","family":"Ye","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoli","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiamen 361005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,1]]},"reference":[{"key":"2023051609060011800_btaa997-B1","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1093\/bib\/bbz068","article-title":"A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data","volume":"21","author":"Chen","year":"2020","journal-title":"Brief. Bioinf"},{"key":"2023051609060011800_btaa997-B2","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1101\/gr.210757.116","article-title":"Genome-wide dynamics of alternative polyadenylation in rice","volume":"26","author":"Fu","year":"2016","journal-title":"Genome Res"},{"key":"2023051609060011800_btaa997-B3","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/s41576-019-0145-z","article-title":"Alternative cleavage and polyadenylation in health and disease","volume":"20","author":"Gruber","year":"2019","journal-title":"Nat. Rev. Genet"},{"key":"2023051609060011800_btaa997-B4","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/bib\/bbu011","article-title":"Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes","volume":"16","author":"Ji","year":"2015","journal-title":"Brief. 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