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Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the difficulty in selecting an optimal sequence for exon skipping. The efficacy of ASOs is often unpredictable, because of the numerous factors involved in exon skipping. To address this gap, we have developed a computational method using machine-learning algorithms that factors in many parameters as well as experimental data to design highly effective ASOs for exon skipping. eSkip-Finder (https:\/\/eskip-finder.org) is the first web-based resource for helping researchers identify effective exon skipping ASOs. eSkip-Finder features two sections: (i) a predictor of the exon skipping efficacy of novel ASOs and (ii) a database of exon skipping ASOs. The predictor facilitates rapid analysis of a given set of exon\/intron sequences and ASO lengths to identify effective ASOs for exon skipping based on a machine learning model trained by experimental data. We confirmed that predictions correlated well with in vitro skipping efficacy of sequences that were not included in the training data. The database enables users to search for ASOs using queries such as gene name, species, and exon number.<\/jats:p>","DOI":"10.1093\/nar\/gkab442","type":"journal-article","created":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T11:22:41Z","timestamp":1620904961000},"page":"W193-W198","source":"Crossref","is-referenced-by-count":42,"title":["eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping"],"prefix":"10.1093","volume":"49","author":[{"given":"Shuntaro","family":"Chiba","sequence":"first","affiliation":[{"name":"HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama\u00a0230-0045, Japan"}]},{"given":"Kenji\u00a0Rowel\u00a0Q","family":"Lim","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Narin","family":"Sheri","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Saeed","family":"Anwar","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Esra","family":"Erkut","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Md\u00a0Nur\u00a0Ahad","family":"Shah","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Tejal","family":"Aslesh","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Stanley","family":"Woo","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Omar","family":"Sheikh","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Rika","family":"Maruyama","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]},{"given":"Hiroaki","family":"Takano","sequence":"additional","affiliation":[{"name":"HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama\u00a0230-0045, Japan"}]},{"given":"Katsuhiko","family":"Kunitake","sequence":"additional","affiliation":[{"name":"Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan"}]},{"given":"William","family":"Duddy","sequence":"additional","affiliation":[{"name":"Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK"}]},{"given":"Yasushi","family":"Okuno","sequence":"additional","affiliation":[{"name":"HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama\u00a0230-0045, Japan"},{"name":"Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto\u00a0606-8507, Japan"}]},{"given":"Yoshitsugu","family":"Aoki","sequence":"additional","affiliation":[{"name":"Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7316-3546","authenticated-orcid":false,"given":"Toshifumi","family":"Yokota","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada"}]}],"member":"286","published-online":{"date-parts":[[2021,6,9]]},"reference":[{"key":"2021070812154903800_B1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-4939-8651-4_1","article-title":"Invention and early history of exon skipping and splice modulation","volume":"1828","author":"Lim","year":"2018","journal-title":"Methods Mol. 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