{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T23:20:29Z","timestamp":1773616829515,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":216,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data.<\/jats:p>\n               <jats:p>Availability and Implementation : Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org.<\/jats:p>\n               <jats:p>Contact : piotr@ibb.waw.pl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw189","type":"journal-article","created":{"date-parts":[[2016,4,10]],"date-time":"2016-04-10T00:08:01Z","timestamp":1460246881000},"page":"2722-2724","source":"Crossref","is-referenced-by-count":81,"title":["Tools4miRs \u2013 one place to gather all the tools for miRNA analysis"],"prefix":"10.1093","volume":"32","author":[{"given":"Anna","family":"Lukasik","sequence":"first","affiliation":[{"name":"1 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland"}]},{"given":"Maciej","family":"W\u00f3jcikowski","sequence":"additional","affiliation":[{"name":"1 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland"}]},{"given":"Piotr","family":"Zielenkiewicz","sequence":"additional","affiliation":[{"name":"1 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland"},{"name":"2 Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, 02-096 Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2016,4,8]]},"reference":[{"key":"2023020112590462700_btw189-B1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1093\/nar\/gkv1221","article-title":"Bioinformatic tools for microRNA dissection","volume":"44","author":"Akhtar","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020112590462700_btw189-B2","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1126\/science.1215691","article-title":"miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay","volume":"336","author":"Djuranovic","year":"2012","journal-title":"Science"},{"key":"2023020112590462700_btw189-B3","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1038\/cr.2012.80","article-title":"What comes first: translational repression or mRNA degradation? The deepening mystery of microRNA function","volume":"22","author":"Hu","year":"2012","journal-title":"Cell Res"},{"key":"2023020112590462700_btw189-B4","doi-asserted-by":"crossref","first-page":"7.","DOI":"10.3389\/fbioe.2015.00007","article-title":"R. Computational prediction of miRNA genes from small RNA sequencing data","volume":"3","author":"Kang","year":"2015","journal-title":"Front. Bioeng. Biotechnol"},{"key":"2023020112590462700_btw189-B5","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/j.jbi.2013.02.002","article-title":"Where we stand, where we are moving: surveying computational techniques for identifying miRNA genes and uncovering their regulatory role","volume":"46","author":"Kleftogiannis","year":"2013","journal-title":"J. Biomed. Inf"},{"key":"2023020112590462700_btw189-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bib\/bbs075","article-title":"Identifying miRNAs, targets and functions","volume":"15","author":"Liu","year":"2014","journal-title":"Brief. Bioinf"},{"key":"2023020112590462700_btw189-B7","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1161\/CIRCRESAHA.110.227496","article-title":"The art of microRNA research","volume":"108","author":"van Rooij","year":"2011","journal-title":"Circ. Res"},{"key":"2023020112590462700_btw189-B8","doi-asserted-by":"crossref","first-page":"5911","DOI":"10.1016\/j.febslet.2005.07.070","article-title":"MicroRNA function in animal development","volume":"579","author":"Wienholds","year":"2005","journal-title":"FEBS Lett"},{"key":"2023020112590462700_btw189-B9","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-62703-083-0","volume-title":"MicroRNA Protocols","author":"Ying","year":"2013"},{"key":"2023020112590462700_btw189-B10","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/jcp.20869","article-title":"MicroRNAs and their regulatory roles in animals and plants","volume":"210","author":"Zhang","year":"2007","journal-title":"J. Cell Physiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2722\/49022460\/bioinformatics_32_17_2722.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2722\/49022460\/bioinformatics_32_17_2722.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:59:02Z","timestamp":1675292342000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/17\/2722\/2450725"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,8]]},"references-count":10,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2016,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw189","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,1]]},"published":{"date-parts":[[2016,4,8]]}}}