{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T21:42:42Z","timestamp":1780695762762,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T00:00:00Z","timestamp":1665878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005690","name":"Saarland University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005690","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A significant fraction of mature miRNA transcripts carries sequence and\/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients\u2019 samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 \u00d7 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (&amp;gt;1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence\/absence of a particular miRNA\/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https:\/\/www.ccb.uni-saarland.de\/isomirdb.<\/jats:p>","DOI":"10.1093\/nar\/gkac884","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T09:59:00Z","timestamp":1665914340000},"page":"D179-D185","source":"Crossref","is-referenced-by-count":27,"title":["isomiRdb: microRNA expression at isoform resolution"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3470-1425","authenticated-orcid":false,"given":"Ernesto","family":"Aparicio-Puerta","sequence":"first","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9627-9223","authenticated-orcid":false,"given":"Georges P","family":"Schmartz","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1967-2918","authenticated-orcid":false,"given":"Tobias","family":"Fehlmann","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Rejuvenome, Astera Institute , Berkeley, CA 94705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Keller","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Department for Internal Medicine II, Saarland University Hospital , 66421 Homburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annika","family":"Engel","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8223-3750","authenticated-orcid":false,"given":"Fabian","family":"Kern","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)\u2013Helmholtz Centre for Infection Research (HZI), Saarland University Campus , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hackenberg","sequence":"additional","affiliation":[{"name":"Genetics Department, Faculty of Science, Universidad de Granada , 18071 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)\u2013Helmholtz Centre for Infection Research (HZI), Saarland University Campus , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804200425800_B1","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41580-018-0045-7","article-title":"Regulation of microRNA function in animals","volume":"20","author":"Gebert","year":"2018","journal-title":"Nat. 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