{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T23:15:47Z","timestamp":1782861347736,"version":"3.54.5"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T00:00:00Z","timestamp":1534982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01-GM099962"],"award-info":[{"award-number":["R01-GM099962"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U54-AG052427"],"award-info":[{"award-number":["U54-AG052427"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U01-AG032984"],"award-info":[{"award-number":["U01-AG032984"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U24-AG041689"],"award-info":[{"award-number":["U24-AG041689"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["UF1-AG047133"],"award-info":[{"award-number":["UF1-AG047133"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["T32-AG00255"],"award-info":[{"award-number":["T32-AG00255"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U24-AG041689"],"award-info":[{"award-number":["U24-AG041689"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Small non-coding RNAs (sncRNAs, &amp;lt;100 nts) are highly abundant RNAs that regulate diverse and often tissue-specific cellular processes by associating with transcription factor complexes or binding to mRNAs. While thousands of sncRNA genes exist in the human genome, no single resource provides searchable, unified annotation, expression and processing information for full sncRNA transcripts and mature RNA products derived from these larger RNAs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our goal is to establish a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human sncRNA genes and mature products derived from all major RNA classes. DASHR (Database of small human non-coding RNAs) v2.0 database is the first that integrates human sncRNA gene and mature products profiles obtained from multiple RNA-seq protocols. Altogether, 185 tissues\/cell types and sncRNA annotations and &amp;gt;800 curated experiments from ENCODE and GEO\/SRA across multiple RNA-seq protocols for both GRCh38\/hg38 and GRCh37\/hg19 assemblies are integrated in DASHR. Moreover, DASHR is the first to contain both known and novel, previously un-annotated sncRNA loci identified by unsupervised segmentation (13 times more loci with 1 678 800 total). Additionally, DASHR v2.0 adds &amp;gt;3 200 000 annotations for non-small RNA genes and other genomic features (long-noncoding RNAs, mRNAs, promoters, repeats). Furthermore, DASHR v2.0 introduces an enhanced user interface, interactive experiment-by-locus table view, sncRNA locus sorting and filtering by biological features. All annotation and expression information directly downloadable and accessible as UCSC genome browser tracks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DASHR v2.0 is freely available at https:\/\/lisanwanglab.org\/DASHRv2.<\/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\/bty709","type":"journal-article","created":{"date-parts":[[2018,8,22]],"date-time":"2018-08-22T19:19:20Z","timestamp":1534965560000},"page":"1033-1039","source":"Crossref","is-referenced-by-count":53,"title":["DASHR 2.0: integrated database of human small non-coding RNA genes and mature products"],"prefix":"10.1093","volume":"35","author":[{"given":"Pavel P","family":"Kuksa","sequence":"first","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Amlie-Wolf","sequence":"additional","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"},{"name":"Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u017divadin","family":"Katani\u0107","sequence":"additional","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Otto","family":"Valladares","sequence":"additional","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-San","family":"Wang","sequence":"additional","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"},{"name":"Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuk Yee","family":"Leung","sequence":"additional","affiliation":[{"name":"Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,23]]},"reference":[{"key":"2023013107265436500_bty709-B3","doi-asserted-by":"crossref","first-page":"D925","DOI":"10.1093\/nar\/gkw1084","article-title":"YM500v3: a Database for small RNA sequencing in human cancer research","volume":"45","author":"Chung","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013107265436500_bty709-B4","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature11233","article-title":"Landscape of transcription in human cells","volume":"489","author":"Djebali","year":"2012","journal-title":"Nature"},{"key":"2023013107265436500_bty709-B6","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1038\/nbt.3701","article-title":"Single-cell sequencing of the small-RNA transcriptome","volume":"34","author":"Faridani","year":"2016","journal-title":"Nat. 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