{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T10:43:55Z","timestamp":1774521835199,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"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\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["U01HG009417"],"award-info":[{"award-number":["U01HG009417"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["U01CA204695"],"award-info":[{"award-number":["U01CA204695"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA-sequencing (RNA-seq) enables global identification of RNA-editing sites in biological systems and disease. A salient step in many studies is to identify editing sites that statistically associate with treatment (e.g. case versus control) or covary with biological factors, such as age. However, RNA-seq has technical features that incumbent tests (e.g. t-test and linear regression) do not consider, which can lead to false positives and false negatives.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we demonstrate the limitations of currently used tests and introduce the method, RNA-editing tests (REDITs), a suite of tests that employ beta-binomial models to identify differential RNA editing. The tests in REDITs have higher sensitivity than other tests, while also maintaining the type I error (false positive) rate at the nominal level. Applied to the GTEx dataset, we unveil RNA-editing changes associated with age and gender, and differential recoding profiles between brain regions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>REDITs are implemented as functions in R and freely available for download at https:\/\/github.com\/gxiaolab\/REDITs. The repository also provides a code example for leveraging parallelization using multiple cores.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa066","type":"journal-article","created":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T20:11:36Z","timestamp":1579896696000},"page":"2796-2804","source":"Crossref","is-referenced-by-count":30,"title":["Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling"],"prefix":"10.1093","volume":"36","author":[{"given":"Stephen S","family":"Tran","sequence":"first","affiliation":[{"name":"Bioinformatics Interdepartmental Program"}]},{"given":"Qing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Bioinformatics Interdepartmental Program"},{"name":"Department of Statistics"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9362-8029","authenticated-orcid":false,"given":"Xinshu","family":"Xiao","sequence":"additional","affiliation":[{"name":"Bioinformatics Interdepartmental Program"},{"name":"Department of Integrative Biology and Physiology"},{"name":"Molecular Biology Institute"},{"name":"Institute for Quantitative and Computational Biology, UCLA , Los Angeles, CA 90095, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"key":"2023013111484737500_btaa066-B1","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1101\/gr.124107.111","article-title":"Accurate identification of A-to-I RNA editing in human by transcriptome sequencing","volume":"22","author":"Bahn","year":"2012","journal-title":"Genome Res"},{"key":"2023013111484737500_btaa066-B2","doi-asserted-by":"crossref","first-page":"6355","DOI":"10.1038\/ncomms7355","article-title":"Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways","volume":"6","author":"Bahn","year":"2015","journal-title":"Nat. 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