{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T15:36:15Z","timestamp":1783697775404,"version":"3.55.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2017,7,24]],"date-time":"2017-07-24T00:00:00Z","timestamp":1500854400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671367"],"award-info":[{"award-number":["31671367"]}],"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":["31471245"],"award-info":[{"award-number":["31471245"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003395","name":"Shanghai Municipal Education Commission","doi-asserted-by":"publisher","award":["13ZZ006"],"award-info":[{"award-number":["13ZZ006"]}],"id":[{"id":"10.13039\/501100003395","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA editing generates post-transcriptional sequence alterations. Detection of RNA editing sites (RESs) typically requires the filtering of SNVs called from RNA-seq data using an SNP database, an obstacle that is difficult to overcome for most organisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a novel method named SPRINT that identifies RESs without the need to filter out SNPs. SPRINT also integrates the detection of hyper RESs from remapped reads, and has been fully automated to any RNA-seq data with reference genome sequence available. We have rigorously validated SPRINT\u2019s effectiveness in detecting RESs using RNA-seq data of samples in which genes encoding RNA editing enzymes are knock down or over-expressed, and have also demonstrated its superiority over current methods. We have applied SPRINT to investigate RNA editing across tissues and species, and also in the development of mouse embryonic central nervous system. A web resource (http:\/\/sprint.tianlab.cn) of RESs identified by SPRINT has been constructed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software and related data are available at http:\/\/sprint.tianlab.cn.<\/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\/btx473","type":"journal-article","created":{"date-parts":[[2017,7,21]],"date-time":"2017-07-21T11:08:42Z","timestamp":1500635322000},"page":"3538-3548","source":"Crossref","is-referenced-by-count":104,"title":["SPRINT: an SNP-free toolkit for identifying RNA editing sites"],"prefix":"10.1093","volume":"33","author":[{"given":"Feng","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China"},{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulan","family":"Lu","sequence":"additional","affiliation":[{"name":"The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute, Children\u2019s Hospital of Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sijia","family":"Yan","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Fudan University, Shanghai, China"},{"name":"Institute of Biomedical Sciences, Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghe","family":"Xing","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Fudan University, Shanghai, China"},{"name":"Institute of Biomedical Sciences, Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weidong","family":"Tian","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China"},{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,7,24]]},"reference":[{"key":"2023051308273456400_btx473-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":"2023051308273456400_btx473-B2","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/380391a0","article-title":"RNA editing. 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