{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T20:22:07Z","timestamp":1774988527254,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T00:00:00Z","timestamp":1735603200000},"content-version":"vor","delay-in-days":39,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2014NextGenerationEU"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>microRNAs (miRNAs) are central post-transcriptional gene expression regulators in healthy and diseased states. Despite decades of effort, deciphering miRNA targets remains challenging, leading to an incomplete miRNA interactome and partially elucidated miRNA functions. Here, we introduce microT-CNN, an avant-garde deep convolutional neural network model that moves the needle by integrating hundreds of tissue-matched (in-)direct experiments from 26 distinct cell types, corresponding to a unique training and evaluation set of &amp;gt;60\u00a0000 miRNA binding events and\u2009~30\u00a0000 unique miRNA\u2013gene target pairs. The multilayer sequence-based design enables the prediction of both host and virus-encoded miRNA interactions, providing for the first time up to 67% of direct genuine Epstein\u2013Barr virus\u2013 and Kaposi\u2019s sarcoma\u2013associated herpesvirus\u2013derived miRNA\u2013target pairs corresponding to one out of four binding events of virus-encoded miRNAs. microT-CNN fills the existing gap of the miRNA\u2013target prediction by providing functional targets beyond the canonical sites, including 3\u2032 compensatory miRNA pairings, prompting 1.4-fold more validated miRNA binding events compared to other implementations and shedding light on previously unexplored facets of the miRNA interactome.<\/jats:p>","DOI":"10.1093\/bib\/bbae678","type":"journal-article","created":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T05:44:01Z","timestamp":1735623841000},"source":"Crossref","is-referenced-by-count":1,"title":["microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3566-7135","authenticated-orcid":false,"given":"Elissavet","family":"Zacharopoulou","sequence":"first","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]},{"name":"Hellenic Pasteur Institute , 127 Vasilissis Sofias Avenue, Athens 11521 ,","place":["Greece"]},{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Maria D","family":"Paraskevopoulou","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Spyros","family":"Tastsoglou","sequence":"additional","affiliation":[{"name":"Hellenic Pasteur Institute , 127 Vasilissis Sofias Avenue, Athens 11521 ,","place":["Greece"]},{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Athanasios","family":"Alexiou","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]},{"name":"Hellenic Pasteur Institute , 127 Vasilissis Sofias Avenue, Athens 11521 ,","place":["Greece"]},{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Anna","family":"Karavangeli","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Vasilis","family":"Pierros","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Stefanos","family":"Digenis","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Galatea","family":"Mavromati","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Artemis G","family":"Hatzigeorgiou","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]},{"name":"Hellenic Pasteur Institute , 127 Vasilissis Sofias Avenue, Athens 11521 ,","place":["Greece"]},{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly , Papasiopoulou 2-4, Lamia 35131 ,","place":["Greece"]}]},{"given":"Dimitra","family":"Karagkouni","sequence":"additional","affiliation":[{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , 330 Brookline Ave, Boston, MA 02215 ,","place":["United States"]},{"name":"Harvard Medical School , 229 Longwood Ave, Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,12,31]]},"reference":[{"key":"2024123105434230300_ref1","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/nature02871","article-title":"The functions of animal 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