{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T02:03:41Z","timestamp":1774922621969,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,11]],"date-time":"2026-01-11T00:00:00Z","timestamp":1768089600000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Research, Technology and Space","award":["031L0287B"],"award-info":[{"award-number":["031L0287B"]}]},{"name":"German Federal Ministry of Research, Technology and Space (BMFTR) within the framework of the *e:Med* research and funding concept","award":["01ZX1908A"],"award-info":[{"award-number":["01ZX1908A"]}]},{"name":"German Federal Ministry of Research, Technology and Space (BMFTR) within the framework of the *e:Med* research and funding concept","award":["01ZX2208A"],"award-info":[{"award-number":["01ZX2208A"]}]},{"name":"German Federal Ministry of Research, Technology and Space (BMFTR) within the framework of the *e:Med* research and funding concept","award":["01ZX2208B"],"award-info":[{"award-number":["01ZX2208B"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Alternative splicing is a crucial mechanism of gene regulation that enables condition- and tissue-specific expression of gene isoforms. Its dysregulation plays a role in various diseases such as cancer, neurological disorders, and metabolic conditions. Despite its importance, accurate detection of alternative splicing events remains challenging. Comprehensive alternative splicing event detection typically requires deep sequencing with over 100 million reads; however, much of the publicly accessible RNA sequencing data is of lower sequencing depth. Recent advances, particularly deep learning models working with genomic sequences, offer new avenues for predicting alternative splicing without reliance on high sequencing depth data. Our study addresses the question: Can we utilize the vast repository of publicly available RNA sequencing data for comprehensive alternative splicing detection, despite the low sequencing depth? Our results demonstrate the potential of sequence-based deep learning tools such as AlphaGenome, SpliceAI and DeepSplice for initial hypothesis development and as additional filters in standard RNA sequencing pipelines, especially when sequencing depth is limited. Nonetheless, validation with higher sequencing depths remains essential for confirmation of splice events. Overall, our findings underscore the need for integrative methods combining genomic sequence data and RNA sequencing data for the prediction of tissue- and condition-specific alternative splicing in resource-limited settings.<\/jats:p>","DOI":"10.1093\/bib\/bbaf705","type":"journal-article","created":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T13:02:36Z","timestamp":1765976556000},"source":"Crossref","is-referenced-by-count":1,"title":["Detection of alternative splicing: deep sequencing or deep learning?"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7472-6224","authenticated-orcid":false,"given":"Lena Maria","family":"Hackl","sequence":"first","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg , Albert-Einstein-Ring 8-10, Hamburg 22761 , Hamburg,","place":["Germany"]}]},{"given":"Fabian","family":"Neuhaus","sequence":"additional","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg , Albert-Einstein-Ring 8-10, Hamburg 22761 , Hamburg,","place":["Germany"]}]},{"given":"Sabine","family":"Ameling","sequence":"additional","affiliation":[{"name":"Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Felix-Hausdorff-Stra\u00dfe 8, Greifswald 17475, Mecklenburg-Vorpommern ,","place":["Germany"]}]},{"given":"Uwe","family":"V\u00f6lker","sequence":"additional","affiliation":[{"name":"Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Felix-Hausdorff-Stra\u00dfe 8, Greifswald 17475, Mecklenburg-Vorpommern ,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0282-0462","authenticated-orcid":false,"given":"Jan","family":"Baumbach","sequence":"additional","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg , Albert-Einstein-Ring 8-10, Hamburg 22761 , Hamburg,","place":["Germany"]},{"name":"Institute of Mathematics and Computer Science, University of Southern Denmark , Campusvej 55, Odense 5230 , Syddanmark,","place":["Denmark"]}]},{"given":"Olga","family":"Tsoy","sequence":"additional","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg , Albert-Einstein-Ring 8-10, Hamburg 22761 , Hamburg,","place":["Germany"]},{"name":"Department of Computer Science, Bioinformatics, Vrije Universiteit Amsterdam , De Boelelaan 1105, Amsterdam 1081 HV , Noord-Holland,","place":["The Netherlands"]}]}],"member":"286","published-online":{"date-parts":[[2026,1,11]]},"reference":[{"key":"2026011104410683700_ref1","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41568-022-00541-7","article-title":"RNA splicing dysregulation and the hallmarks of cancer","volume":"23","author":"Bradley","year":"2023","journal-title":"Nat Rev 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