{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:23:30Z","timestamp":1760171010803},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,11,18]],"date-time":"2016-11-18T00:00:00Z","timestamp":1479427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT (integrative Small RNA Tool-kit), an automated pipeline to analyze smallRNA-Seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington\u2019s Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp:\/\/labmedmolge-1.unisa.it (User: iSmart - Password: password)<\/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\/btw734","type":"journal-article","created":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T20:05:49Z","timestamp":1479326749000},"page":"938-940","source":"Crossref","is-referenced-by-count":18,"title":["iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data"],"prefix":"10.1093","volume":"33","author":[{"given":"Riccardo","family":"Panero","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"},{"name":"Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy"}]},{"given":"Antonio","family":"Rinaldi","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Domenico","family":"Memoli","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Giovanni","family":"Nassa","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"},{"name":"Genomix4Life, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Maria","family":"Ravo","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Francesca","family":"Rizzo","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Roberta","family":"Tarallo","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Luciano","family":"Milanesi","sequence":"additional","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy"}]},{"given":"Alessandro","family":"Weisz","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"}]},{"given":"Giorgio","family":"Giurato","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u2032Scuola Medica Salernitana\u2032, University of Salerno, Baronissi, SA, Italy"},{"name":"Genomix4Life, University of Salerno, Baronissi, SA, Italy"}]}],"member":"286","published-online":{"date-parts":[[2016,11,18]]},"reference":[{"key":"2023020204512056400_btw734-B1","author":"Alexa","year":"2010"},{"key":"2023020204512056400_btw734-B2","doi-asserted-by":"crossref","first-page":"3147","DOI":"10.1093\/bioinformatics\/bts587","article-title":"ncPRO-Seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data","volume":"28","author":"Chen","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020204512056400_btw734-B3","doi-asserted-by":"crossref","first-page":"8289","DOI":"10.1074\/jbc.M112.433185","article-title":"HECT domain-containing E3 ubiquitin ligase NEDD4L negatively regulates Wnt signaling by targeting dishevelled for proteasomal degradation","volume":"288","author":"Ding","year":"2013","journal-title":"J. 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