{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T14:13:57Z","timestamp":1772892837139,"version":"3.50.1"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100004189","name":"Max-Planck-Gesellschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-016-1432-8","type":"journal-article","created":{"date-parts":[[2017,1,3]],"date-time":"2017-01-03T08:41:29Z","timestamp":1483432889000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":101,"title":["JACUSA: site-specific identification of RNA editing events from replicate sequencing data"],"prefix":"10.1186","volume":"18","author":[{"given":"Michael","family":"Piechotta","sequence":"first","affiliation":[]},{"given":"Emanuel","family":"Wyler","sequence":"additional","affiliation":[]},{"given":"Uwe","family":"Ohler","sequence":"additional","affiliation":[]},{"given":"Markus","family":"Landthaler","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9468-6311","authenticated-orcid":false,"given":"Christoph","family":"Dieterich","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,1,3]]},"reference":[{"key":"1432_CR1","doi-asserted-by":"crossref","unstructured":"Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Ann Rev Biochem. 2010; 79:321\u201349. doi: http:\/\/dx.doi.org\/10.1146\/annurev-biochem-060208-105251 .","DOI":"10.1146\/annurev-biochem-060208-105251"},{"key":"1432_CR2","doi-asserted-by":"crossref","unstructured":"Alseth I, Dalhus BR, Bj\u00f8r\u00e5s M. Inosine in DNA and RNA. Curr Opin Genet Dev. 2014; 26:116\u201323. doi: http:\/\/dx.doi.org\/10.1016\/j.gde.2014.07.008 .","DOI":"10.1016\/j.gde.2014.07.008"},{"key":"1432_CR3","doi-asserted-by":"crossref","unstructured":"Slotkin W, Nishikura K. Adenosine-to-inosine RNA editing and human disease. Genome Med. 2013; 5(11):105. doi: http:\/\/dx.doi.org\/10.1186\/gm508 .","DOI":"10.1186\/gm508"},{"key":"1432_CR4","doi-asserted-by":"crossref","unstructured":"Kawahara Y, Ito K, Sun H, Aizawa H, Kanazawa I, Kwak S. Glutamate receptors: RNA editing and death of motor neurons. Nature. 2004; 427(6977):801. doi: http:\/\/dx.doi.org\/10.1038\/427801a .","DOI":"10.1038\/427801a"},{"key":"1432_CR5","doi-asserted-by":"crossref","unstructured":"Daniel C, Lagergren J, \u00d6hman M. Rna editing of non-coding rna and its role in gene regulation. Biochimie. 2015. doi: http:\/\/dx.doi.org\/10.1016\/j.biochi.2015.05.020 .","DOI":"10.1016\/j.biochi.2015.05.020"},{"key":"1432_CR6","doi-asserted-by":"crossref","unstructured":"Deininger P. Alu elements: know the sines. Genome Biol. 2011; 12(12):236. doi: http:\/\/dx.doi.org\/10.1186\/gb-2011-12-12-236 .","DOI":"10.1186\/gb-2011-12-12-236"},{"key":"1432_CR7","doi-asserted-by":"crossref","unstructured":"Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science (New York, N.Y.) 2011; 333(6038):53\u20138. doi: http:\/\/dx.doi.org\/10.1126\/science.1210624 .","DOI":"10.1126\/science.1210624"},{"issue":"9","key":"1432_CR8","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1261\/rna.033233.112","volume":"18","author":"CL Kleinman","year":"2012","unstructured":"Kleinman CL, Adoue V, Majewski J. Rna editing of protein sequences: a rare event in human transcriptomes. RNA. 2012; 18(9):1586\u201396.","journal-title":"RNA"},{"key":"1432_CR9","doi-asserted-by":"crossref","unstructured":"Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (Oxford, England). 2011; 27(21):2987\u201393. doi: http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr509 .","DOI":"10.1093\/bioinformatics\/btr509"},{"key":"1432_CR10","doi-asserted-by":"crossref","unstructured":"Picardi E, Pesole G. REDItools: High-throughput RNA editing detection made easy. Bioinformatics. 2013; 29(14):1813\u20131814. doi: http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btt287 .","DOI":"10.1093\/bioinformatics\/btt287"},{"key":"1432_CR11","doi-asserted-by":"crossref","unstructured":"Porath HT, Carmi S, Levanon EY. A genome-wide map of hyper-edited RNA reveals numerous new sites. Nat Commun. 2014; 5:4726. doi: http:\/\/dx.doi.org\/10.1038\/ncomms5726 .","DOI":"10.1038\/ncomms5726"},{"issue":"2","key":"1432_CR12","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nmeth.2330","volume":"10","author":"G Ramaswami","year":"2013","unstructured":"Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, O\u2019Connell MA, Li JB. Identifying rna editing sites using rna sequencing data alone. Nat Methods. 2013; 10(2):128\u201332.","journal-title":"Nat Methods"},{"key":"1432_CR13","doi-asserted-by":"crossref","unstructured":"Wang IX, So E, Devlin JL, Zhao Y, Wu M, Cheung VG. ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression. Cell Rep. 2013; 5(3):849\u201360. doi: http:\/\/dx.doi.org\/10.1016\/j.celrep.2013.10.002 .","DOI":"10.1016\/j.celrep.2013.10.002"},{"key":"1432_CR14","doi-asserted-by":"crossref","unstructured":"Piechotta M, Dieterich C. ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores. Bioinformatics. 2013; 29(14):1809\u201310. doi: http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btt268 .","DOI":"10.1093\/bioinformatics\/btt268"},{"key":"1432_CR15","doi-asserted-by":"crossref","unstructured":"Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013; 31(3):213\u20139. doi: http:\/\/dx.doi.org\/10.1038\/nbt.2514 . NIHMS150003 .","DOI":"10.1038\/nbt.2514"},{"key":"1432_CR16","doi-asserted-by":"crossref","unstructured":"Li JB, Church GM. Deciphering the functions and regulation of brain-enriched a-to-i rna editing. Nat Neurosci. 2013; 16(11):1518\u201322. doi: http:\/\/dx.doi.org\/10.1038\/nn.3539 .","DOI":"10.1038\/nn.3539"},{"issue":"6","key":"1432_CR17","doi-asserted-by":"crossref","first-page":"2426","DOI":"10.1093\/nar\/gkr1073","volume":"40","author":"V Heinrich","year":"2012","unstructured":"Heinrich V, Stange J, Dickhaus T, Imkeller P, Kr\u00fcger U, Bauer S, Mundlos S, Robinson PN, Hecht J, Krawitz PM. The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process. Nucleic Acids Res. 2012; 40(6):2426\u201331.","journal-title":"Nucleic Acids Res"},{"key":"1432_CR18","doi-asserted-by":"crossref","unstructured":"Poortema K. On modelling overdispersion of counts. Statistica Neerlandica. 1999; 53(1):5\u201320. doi: http:\/\/dx.doi.org\/10.1111\/1467-9574.00094 .","DOI":"10.1111\/1467-9574.00094"},{"key":"1432_CR19","unstructured":"Minka T. Estimating a Dirichlet distribution. Technical report, MIT. 2000."},{"issue":"3","key":"1432_CR20","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Green P. Base-calling of automated sequencer traces using phred. ii. error probabilities. Genome Res. 1998; 8(3):186\u201394.","journal-title":"Genome Res"},{"key":"1432_CR21","doi-asserted-by":"crossref","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data. Genome Res. 2010; 20(9):1297\u2013303. doi: http:\/\/dx.doi.org\/10.1101\/gr.107524.110 .","DOI":"10.1101\/gr.107524.110"},{"issue":"2","key":"1432_CR22","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.celrep.2014.12.019","volume":"10","author":"A Ivanov","year":"2015","unstructured":"Ivanov A, Memczak S, Wyler E, Torti F, Porath HT, Orejuela MR, Piechotta M, Levanon EY, Landthaler M, Dieterich C, et al.Analysis of intron sequences reveals hallmarks of circular rna biogenesis in animals. Cell Rep. 2015; 10(2):170\u20137.","journal-title":"Cell Rep"},{"key":"1432_CR23","doi-asserted-by":"crossref","unstructured":"Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):36. doi: http:\/\/dx.doi.org\/10.1186\/gb-2013-14-4-r36 .","DOI":"10.1186\/gb-2013-14-4-r36"},{"key":"1432_CR24","unstructured":"Smit A, Hubley R, Green P. Repeatmasker open-4.0. 2013-2015. http:\/\/www.repeatmasker.org ."},{"issue":"1","key":"1432_CR25","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.molcel.2012.05.002","volume":"47","author":"J Rodriguez","year":"2012","unstructured":"Rodriguez J, Menet JS, Rosbash M. Nascent-seq indicates widespread cotranscriptional rna editing in drosophila. Mol Cell. 2012; 47(1):27\u201337.","journal-title":"Mol Cell"},{"key":"1432_CR26","doi-asserted-by":"crossref","unstructured":"Baltz AG, Munschauer M, Schwanh\u00e4usser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mrna-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell. 2012; 46(5):674\u201390. doi: http:\/\/dx.doi.org\/10.1016\/j.molcel.2012.05.021 .","DOI":"10.1016\/j.molcel.2012.05.021"},{"issue":"2","key":"1432_CR27","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/nsmb.1975","volume":"18","author":"BR Rosenberg","year":"2011","unstructured":"Rosenberg BR, Hamilton CE, Mwangi MM, Dewell S, Papavasiliou FN. Transcriptome-wide sequencing reveals numerous apobec1 mrna-editing targets in transcript 3 utrs. Nat Struct Mol Biol. 2011; 18(2):230\u20136.","journal-title":"Nat Struct Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1432-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,25]],"date-time":"2017-06-25T03:09:54Z","timestamp":1498360194000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1432-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,3]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1432"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1432-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,3]]},"article-number":"7"}}