{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T03:34:26Z","timestamp":1781667266159,"version":"3.54.5"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T00:00:00Z","timestamp":1652313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["765492"],"award-info":[{"award-number":["765492"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Government","award":["AGL2017-88702-C2-2-R"],"award-info":[{"award-number":["AGL2017-88702-C2-2-R"]}]},{"name":"Troms\u00f8forskningsstiftelse","award":["20_SG_BF"],"award-info":[{"award-number":["20_SG_BF"]}]},{"name":"Stichting Cancer Center Amsterdam","award":["CCA2021-9-77"],"award-info":[{"award-number":["CCA2021-9-77"]}]},{"name":"TKI-Health Holland"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https:\/\/arn.ugr.es\/srnatoolbox\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac363","type":"journal-article","created":{"date-parts":[[2022,4,28]],"date-time":"2022-04-28T19:31:17Z","timestamp":1651174277000},"page":"W710-W717","source":"Crossref","is-referenced-by-count":92,"title":["sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms"],"prefix":"10.1093","volume":"50","author":[{"given":"Ernesto","family":"Aparicio-Puerta","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 \u00a0Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0866-4103","authenticated-orcid":false,"given":"Cristina","family":"G\u00f3mez-Mart\u00edn","sequence":"additional","affiliation":[{"name":"Department of Pathology, Cancer Center Amsterdam , Amsterdam UMC, VU University, Amsterdam \u00a01081HV, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stavros","family":"Giannoukakos","sequence":"additional","affiliation":[{"name":"Genetics Department, Faculty of Science, Universidad de Granada , Campus de Fuentenueva s\/n,\u00a018071\u00a0 Granada , Spain"},{"name":"Bioinformatics Laboratory, Biomedical Research Centre (CIBM) , PTS, Avda. del Conocimiento s\/n,\u00a018100\u00a0 Granada , Spain"},{"name":"Excellence Research Unit \u201cModeling Nature\u201d (MNat), University of Granada , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9\u00a0Mar\u00eda","family":"Medina","sequence":"additional","affiliation":[{"name":"Genetics Department, Faculty of Science, Universidad de Granada , Campus de Fuentenueva s\/n,\u00a018071\u00a0 Granada , Spain"},{"name":"Bioinformatics Laboratory, Biomedical Research Centre (CIBM) , PTS, Avda. del Conocimiento s\/n,\u00a018100\u00a0 Granada , Spain"},{"name":"Excellence Research Unit \u201cModeling Nature\u201d (MNat), University of Granada , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4243-0095","authenticated-orcid":false,"given":"Chantal","family":"Scheepbouwer","sequence":"additional","affiliation":[{"name":"Department of Pathology, Cancer Center Amsterdam , Amsterdam UMC, VU University, Amsterdam \u00a01081HV, Netherlands"},{"name":"Department of Neurosurgery, Cancer Center Amsterdam , Amsterdam UMC, VU University, Amsterdam \u00a01081HV, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5715-4962","authenticated-orcid":false,"given":"Adri\u00e1n","family":"Garc\u00eda-Moreno","sequence":"additional","affiliation":[{"name":"Centre for Genomics and Oncological Research. 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