{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T02:17:29Z","timestamp":1722737849585},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived.<\/jats:p>\n               <jats:p>Results: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets.<\/jats:p>\n               <jats:p>Availability: Our methods are available as the Bioconductor (www.bioconductor.org) package segmentSeq (version 1.5.6 and above).<\/jats:p>\n               <jats:p>Contact: \u00a0tjh48@cam.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr687","type":"journal-article","created":{"date-parts":[[2011,12,11]],"date-time":"2011-12-11T01:23:20Z","timestamp":1323566600000},"page":"457-463","source":"Crossref","is-referenced-by-count":29,"title":["Identifying small interfering RNA loci from high-throughput sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Thomas J.","family":"Hardcastle","sequence":"first","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}]},{"given":"Krystyna A.","family":"Kelly","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}]},{"given":"David C.","family":"Baulcombe","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,12,9]]},"reference":[{"key":"2023012512183221700_B1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023012512183221700_B2","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","article-title":"Whole-genome re-sequencing","volume":"16","author":"Bentley","year":"2006","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2023012512183221700_B3","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512183221700_B4","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1016\/j.cell.2009.01.035","article-title":"Origins and mechanisms of miRNAs and siRNAs","volume":"136","author":"Carthew","year":"2009","journal-title":"Cell"},{"key":"2023012512183221700_B5","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nbt1394","article-title":"Discovering microRNAs from deep sequencing data using miRDeep","volume":"26","author":"Friedl\u00e4nder","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2023012512183221700_B6","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nmeth.1613","article-title":"Computational methods for transcriptome annotation and quantification using RNA-seq","volume":"8","author":"Garber","year":"2011","journal-title":"Nat. Methods"},{"key":"2023012512183221700_B7","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/35005107","article-title":"An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells","volume":"404","author":"Hammond","year":"2000","journal-title":"Nature"},{"key":"2023012512183221700_B8","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1186\/1471-2105-11-422","article-title":"baySeq: empirical Bayesian methods for identifying differential expression in sequence count data","volume":"11","author":"Hardcastle","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512183221700_B9","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2023012512183221700_B10","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1371\/journal.pbio.0050057","article-title":"Genome-wide profiling and analysis of Arabidopsis siRNAs","volume":"5","author":"Kasschau","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012512183221700_B11","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/1471-2105-11-93","article-title":"Finding sRNA generative locales from high-throughput sequencing data with NiBLS","volume":"11","author":"MacLean","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512183221700_B12","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"2023012512183221700_B13","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nature02873","article-title":"Mechanisms of gene silencing by double-stranded RNA","volume":"431","author":"Meister","year":"2004","journal-title":"Nature"},{"key":"2023012512183221700_B14","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012512183221700_B15","doi-asserted-by":"crossref","first-page":"2252","DOI":"10.1093\/bioinformatics\/btn428","article-title":"A toolkit for analysing large-scale plant small RNA datasets","volume":"24","author":"Moxon","year":"2008","journal-title":"Bioinformatics"},{"issue":"11 Suppl.","key":"2023012512183221700_B16","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012512183221700_B17","doi-asserted-by":"crossref","first-page":"D1009","DOI":"10.1093\/nar\/gkm965","article-title":"The Arabidopsis Information Resource (TAIR): gene structure and function annotation","volume":"36","author":"Swarbreck","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512183221700_B18","doi-asserted-by":"crossref","first-page":"pe43","DOI":"10.1126\/stke.3002005pe43","article-title":"MicroRNA-dependent trans-acting siRNA production","volume":"2005","author":"Vaucheret","year":"2005","journal-title":"Science STKE"},{"key":"2023012512183221700_B19","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nature Rev. Genet."},{"key":"2023012512183221700_B20","doi-asserted-by":"crossref","first-page":"2614","DOI":"10.1093\/bioinformatics\/btr430","article-title":"miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants","volume":"27","author":"Yang","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/4\/457\/48880873\/bioinformatics_28_4_457.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/4\/457\/48880873\/bioinformatics_28_4_457.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:01:37Z","timestamp":1674658897000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/4\/457\/211764"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,9]]},"references-count":20,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2012,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr687","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,2,15]]},"published":{"date-parts":[[2011,12,9]]}}}