{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T17:51:43Z","timestamp":1777571503629,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":347,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0catRAPID signature can be accessed at http:\/\/s.tartaglialab.com\/new_submission\/signature.<\/jats:p>\n               <jats:p>Contact: \u00a0gian.tartaglia@crg.es or gian@tartaglialab.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv629","type":"journal-article","created":{"date-parts":[[2015,11,1]],"date-time":"2015-11-01T00:38:37Z","timestamp":1446338317000},"page":"773-775","source":"Crossref","is-referenced-by-count":115,"title":["<i>cat<\/i>RAPID <i>signature<\/i>: identification of ribonucleoproteins and RNA-binding regions"],"prefix":"10.1093","volume":"32","author":[{"given":"Carmen Maria","family":"Livi","sequence":"first","affiliation":[{"name":"1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,"},{"name":"2 Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petr","family":"Klus","sequence":"additional","affiliation":[{"name":"1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,"},{"name":"2 Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Delli Ponti","sequence":"additional","affiliation":[{"name":"1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,"},{"name":"2 Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gian Gaetano","family":"Tartaglia","sequence":"additional","affiliation":[{"name":"1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,"},{"name":"2 Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and"},{"name":"3 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,31]]},"reference":[{"key":"2023020110450440300_btv629-B1","doi-asserted-by":"crossref","first-page":"2928","DOI":"10.1093\/bioinformatics\/btt495","article-title":"catRAPID omics: a web server for large-scale prediction of protein-RNA interactions","volume":"29","author":"Agostini","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020110450440300_btv629-B2","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/nature11737","article-title":"FMRP targets distinct mRNA sequence elements to regulate protein expression","volume":"492","author":"Ascano","year":"2012","journal-title":"Nature"},{"key":"2023020110450440300_btv629-B3","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1016\/j.molcel.2012.05.021","article-title":"The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts","volume":"46","author":"Baltz","year":"2012","journal-title":"Mol. 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