{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T23:05:25Z","timestamp":1784588725688,"version":"3.55.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T00:00:00Z","timestamp":1566950400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["RIBOMYLOME_309545"],"award-info":[{"award-number":["RIBOMYLOME_309545"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BFU2017-86970-P"],"award-info":[{"award-number":["BFU2017-86970-P"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and double-stranded regions of RNAs in vivo using predictions of protein interactions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Trained on icSHAPE data in presence (m6a+) and absence of N6 methyladenosine modification (m6a-), CROSSalive achieves cross-validation accuracies between 0.70 and 0.88 in identifying high-confidence single- and double-stranded regions. The algorithm was applied to the long non-coding RNA Xist (17 900\u2009nt, not present in the training) and shows an Area under the ROC curve of 0.83 in predicting structured regions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CROSSalive webserver is freely accessible at http:\/\/service.tartaglialab.com\/new_submission\/crossalive<\/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\/btz666","type":"journal-article","created":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T07:37:44Z","timestamp":1566891464000},"page":"940-941","source":"Crossref","is-referenced-by-count":20,"title":["<i>CROSSalive<\/i>\n                    : a web server for predicting the\n                    <i>in vivo<\/i>\n                    structure of RNA molecules"],"prefix":"10.1093","volume":"36","author":[{"given":"Riccardo Delli","family":"Ponti","sequence":"first","affiliation":[{"name":"Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandros","family":"Armaos","sequence":"additional","affiliation":[{"name":"Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Vandelli","sequence":"additional","affiliation":[{"name":"Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gian Gaetano","family":"Tartaglia","sequence":"additional","affiliation":[{"name":"Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08003, Spain"},{"name":"Institucio Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) , Barcelona 08010, Spain"},{"name":"Department of Biology \u2018Charles Darwin\u2019, Sapienza University of Rome , Rome 00185, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,28]]},"reference":[{"key":"2023013110090078000_btz666-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\u2013RNA interactions","volume":"29","author":"Agostini","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013110090078000_btz666-B2","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nmeth.1611","article-title":"Predicting protein associations with long noncoding RNAs","volume":"8","author":"Bellucci","year":"2011","journal-title":"Nat. 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