{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,14]],"date-time":"2025-10-14T11:24:47Z","timestamp":1760441087579},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1502,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output.<\/jats:p>\n               <jats:p>Availability: \u00a0shortran is freely available and can be downloaded from http:\/\/users-mb.au.dk\/pmgrp\/shortran\/<\/jats:p>\n               <jats:p>Contact: \u00a0vgupta@cs.au.dk or sua@mb.au.dk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts496","type":"journal-article","created":{"date-parts":[[2012,8,23]],"date-time":"2012-08-23T00:15:38Z","timestamp":1345680938000},"page":"2698-2700","source":"Crossref","is-referenced-by-count":22,"title":["<i>shortran<\/i>: a pipeline for small RNA-seq data analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Vikas","family":"Gupta","sequence":"first","affiliation":[{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"},{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katharina","family":"Markmann","sequence":"additional","affiliation":[{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian N. S.","family":"Pedersen","sequence":"additional","affiliation":[{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Stougaard","sequence":"additional","affiliation":[{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stig U.","family":"Andersen","sequence":"additional","affiliation":[{"name":"1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10 and 2Bioinformatics Research Centre, Aarhus University, C. F. M\u00f8llers All\u00e9 8, 8000 Aarhus C, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,8,22]]},"reference":[{"key":"2023012513162523500_bts496-B1","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1101\/gr.123547.111","article-title":"High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis","volume":"22","author":"Breakfield","year":"2012","journal-title":"Genome Res."},{"key":"2023012513162523500_bts496-B2","doi-asserted-by":"crossref","first-page":"3318","DOI":"10.1073\/pnas.0611119104","article-title":"Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis","volume":"104","author":"Chen","year":"2007","journal-title":"Proc. Natl. Acad. Sci. 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