{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T14:02:12Z","timestamp":1774274532614,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T00:00:00Z","timestamp":1707091200000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Fonden","doi-asserted-by":"publisher","award":["NNF20OC0062606"],"award-info":[{"award-number":["NNF20OC0062606"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this article, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localization of RNA molecules via fine-tuning. We constructed DeepLocRNA using a comprehensive dataset with variant RNA types and evaluated it on the held-out dataset. Our model achieved state-of-the-art performance in predicting RNA subcellular localization in mRNA and miRNA. It has also demonstrated great generalization capabilities, performing well on both human and mouse RNA. Additionally, a motif analysis was performed to enhance the interpretability of the model, highlighting signal factors that contributed to the predictions. The proposed model provides general and powerful prediction abilities for different RNA types and species, offering valuable insights into the localization patterns of RNA molecules and contributing to our understanding of cellular processes at the molecular level. A user-friendly web server is available at: https:\/\/biolib.com\/KU\/DeepLocRNA\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae065","type":"journal-article","created":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T16:05:43Z","timestamp":1706803543000},"source":"Crossref","is-referenced-by-count":15,"title":["DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9532-0917","authenticated-orcid":false,"given":"Jun","family":"Wang","sequence":"first","affiliation":[{"name":"Bioinformatics Centre, Department of Biology, University of Copenhagen , K\u00f8benhavn \u00d8 2100, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7884-7135","authenticated-orcid":false,"given":"Marc","family":"Horlacher","sequence":"additional","affiliation":[{"name":"Computational Health Center, Helmholtz Center Munich , Neuherberg 85764, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9427-383X","authenticated-orcid":false,"given":"Lixin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Shenzhen People\u2019s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University , Shenzhen 518020, China"}]},{"given":"Ole","family":"Winther","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Department of Biology, University of Copenhagen , K\u00f8benhavn \u00d8 2100, Denmark"},{"name":"Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital) , Copenhagen 2100, Denmark"},{"name":"Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark , Kongens Lyngby 2800, 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