{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:09:14Z","timestamp":1767175754458,"version":"build-2238731810"},"update-to":[{"DOI":"10.12688\/f1000research.18142.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T00:00:00Z","timestamp":1561593600000}}],"reference-count":29,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T00:00:00Z","timestamp":1561593600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson\u2019s disease.<\/ns4:p>","DOI":"10.12688\/f1000research.18142.2","type":"journal-article","created":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T04:30:50Z","timestamp":1561609850000},"page":"232","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Visualization of the small RNA transcriptome using 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Feng","year":"2012","journal-title":"RNA."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/8-232\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/8-232\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/8-232\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T04:30:57Z","timestamp":1561609857000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/8-232\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,27]]},"references-count":29,"URL":"https:\/\/doi.org\/10.12688\/f1000research.18142.2","relation":{},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,27]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/8-232\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.19842.r45803, Xavier Bofill-De Ros, RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA, 18 Mar 2019, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/8-232\/v1#referee-response-45803","order":0,"name":"referee-response-45803","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Lorena Pantano Rubino<\/b>; \n<i>Posted: 10 Apr 2019<\/i>; Dear Xavier Bofill-De Ros,Thanks a lot to find time to review this article. I will take actions on all the points I can address in the next month and report an update as soon as possible.Cheers","URL":"https:\/\/f1000research.com\/articles\/8-232\/v2#referee-comment-4562","order":1,"name":"referee-comment-4562","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.19842.r45091, Stefan Scholten, Crop Plant Genetics, Georg-August-University G\u00f6ttingen, G\u00f6ttingen, Germany, 01 Apr 2019, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/8-232\/v1#referee-response-45091","order":2,"name":"referee-response-45091","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Lorena Pantano Rubino<\/b>; \n<i>Posted: 10 Apr 2019<\/i>; Dear Stefan Scholten,Thanks for finding time to review this article. I will work on your recommendation to add that information to the tool, it is a very good idea we missed.I'll post back the update version here.Cheers","URL":"https:\/\/f1000research.com\/articles\/8-232\/v2#referee-comment-4561","order":3,"name":"referee-comment-4561","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The author(s) declared that no grants were involved in supporting this work","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}