{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:46:47Z","timestamp":1765547207029,"version":"3.41.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T00:00:00Z","timestamp":1710460800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2222007"],"award-info":[{"award-number":["T2222007"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations. vizAPA also enables identification of genes with differential APA usage across biological samples and\/or cell types. vizAPA provides four unique modules for extensively visualizing APA dynamics across biological samples and at the single-cell level. vizAPA could serve as a plugin in many routine APA analysis pipelines to augment studies for APA dynamics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/BMILAB\/vizAPA.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae099","type":"journal-article","created":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T03:49:45Z","timestamp":1710474585000},"source":"Crossref","is-referenced-by-count":2,"title":["vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data"],"prefix":"10.1093","volume":"40","author":[{"given":"Xingyu","family":"Bi","sequence":"first","affiliation":[{"name":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7811-2710","authenticated-orcid":false,"given":"Wenbin","family":"Ye","sequence":"additional","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California , Irvine, CA 92697, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Industrial Design, Pukyong National University , Busan 48513, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0356-7785","authenticated-orcid":false,"given":"Xiaohui","family":"Wu","sequence":"additional","affiliation":[{"name":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,3,14]]},"reference":[{"key":"2024032000532769800_btae099-B1","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1186\/s12859-022-04939-w","article-title":"APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data","volume":"23","author":"Fahmi","year":"2022","journal-title":"BMC Bioinf"},{"key":"2024032000532769800_btae099-B2","doi-asserted-by":"crossref","DOI":"10.1016\/j.crmeth.2024.100707","article-title":"PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data","author":"Jonnakuti","year":"2024","journal-title":"Cell Rep Methods"},{"key":"2024032000532769800_btae099-B3","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/s41580-022-00507-5","article-title":"Context-specific regulation and function of mRNA alternative polyadenylation","volume":"23","author":"Mitschka","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024032000532769800_btae099-B4","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1186\/s12864-020-6542-z","article-title":"Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets","volume":"21","author":"Ozaki","year":"2020","journal-title":"BMC Genomics"},{"key":"2024032000532769800_btae099-B5","doi-asserted-by":"crossref","first-page":"10027","DOI":"10.1093\/nar\/gkz781","article-title":"Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data","volume":"47","author":"Shulman","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024032000532769800_btae099-B6","article-title":"RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes","volume":"3","author":"Stephenson","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2024032000532769800_btae099-B7","doi-asserted-by":"crossref","first-page":"e1008195","DOI":"10.1371\/journal.pcbi.1008195","article-title":"VALERIE: visual-based inspection of alternative splicing events at single-cell resolution","volume":"16","author":"Wen","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2024032000532769800_btae099-B8","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaa273","article-title":"scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data","volume":"22","author":"Wu","year":"2021","journal-title":"Briefings Bioinf"},{"key":"2024032000532769800_btae099-B9","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1093\/bioinformatics\/btz701","article-title":"scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data","volume":"36","author":"Ye","year":"2019","journal-title":"Bioinformatics"},{"key":"2024032000532769800_btae099-B10","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.gpb.2022.09.005","article-title":"A survey on methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq, and single-cell RNA-seq","volume":"21","author":"Ye","year":"2023","journal-title":"Genom. Proteom. Bioinf"},{"key":"2024032000532769800_btae099-B11","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1093\/bioinformatics\/btaa997","article-title":"movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples","volume":"37","author":"Ye","year":"2021","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae099\/56975843\/btae099.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae099\/57021768\/btae099.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae099\/57021768\/btae099.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T00:53:52Z","timestamp":1710896032000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae099\/7629129"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,3,1]]},"references-count":11,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae099","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,3,1]]},"article-number":"btae099"}}