{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T12:35:37Z","timestamp":1773146137142,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2017,2,14]],"date-time":"2017-02-14T00:00:00Z","timestamp":1487030400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present \u2018Threshold-seq,\u2019 a new approach for determining thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset before it can be considered different from \u2018background.\u2019 The proposed scheme is easy to implement and incorporate into existing pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Source code of Threshold-seq is freely available as an R package at: http:\/\/cm.jefferson.edu\/threshold-seq\/<\/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\/btx073","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T08:58:08Z","timestamp":1487149088000},"page":"2034-2036","source":"Crossref","is-referenced-by-count":13,"title":["Threshold-seq: a tool for determining the threshold in short RNA-seq datasets"],"prefix":"10.1093","volume":"33","author":[{"given":"Rogan","family":"Magee","sequence":"first","affiliation":[{"name":"Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phillipe","family":"Loher","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Londin","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isidore","family":"Rigoutsos","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,14]]},"reference":[{"key":"2023020206010348600_btx073-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":"2023020206010348600_btx073-B2","doi-asserted-by":"crossref","first-page":"R126.","DOI":"10.1186\/gb-2011-12-12-r126","article-title":"MicroRNAs and their isomiRs function cooperatively to target common biological pathways","volume":"12","author":"Cloonan","year":"2011","journal-title":"Genome Biol"},{"key":"2023020206010348600_btx073-B3","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1093\/bib\/bbs046","article-title":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","volume":"14","author":"Dillies","year":"2013","journal-title":"Brief. 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