{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T10:20:54Z","timestamp":1783938054026,"version":"3.55.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T00:00:00Z","timestamp":1746748800000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272094"],"award-info":[{"award-number":["62272094"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62472120"],"award-info":[{"award-number":["62472120"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation for Distinguished Young Scholars of China","award":["62225109"],"award-info":[{"award-number":["62225109"]}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2022YFF1202101"],"award-info":[{"award-number":["2022YFF1202101"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Structural variations (SVs) are genomic rearrangements larger than 50\u00a0bp, that are widely present in the human genome and are associated with various complex diseases. Existing long-read-based SV detection tools often rely on fixed rules or heuristic algorithms, which can oversimplify the complexity of SV signatures. Therefore, these methods usually lack flexibility and cannot fully capture SV signals, leading to reduced accuracy and robustness. To address these issues, we propose SVHunter, a transformer-based method for long-read SV detection. SVHunter combines convolutional neural networks and transformers to capture both local and global SV signatures, enabling accurate identification of SVs. Additionally, SVHunter employs the mean shift clustering algorithm, which dynamically adjusts bandwidth parameters to accommodate different types of SVs without requiring a preset number of clusters, thus allowing precise breakpoint clustering. Validation across multiple sequencing platforms and datasets demonstrates that SVHunter excels at detecting various types of SVs, with a notable reduction in the false discovery rate. This highlights considerable strong potential for both research and clinical applications.<\/jats:p>","DOI":"10.1093\/bib\/bbaf203","type":"journal-article","created":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T05:35:35Z","timestamp":1744868135000},"source":"Crossref","is-referenced-by-count":11,"title":["SVHunter: long-read-based structural variation detection through the transformer model"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-0870-6693","authenticated-orcid":false,"given":"Runtian","family":"Gao","sequence":"first","affiliation":[{"name":"College of Life Science, Northeast Forestry University , Harbin 150000 ,","place":["China"]},{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9505-4049","authenticated-orcid":false,"given":"Heng","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Life Science, Northeast Forestry University , Harbin 150000 ,","place":["China"]},{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongjun","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Life Science, Northeast Forestry University , Harbin 150000 ,","place":["China"]},{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuqi","family":"Cao","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology , Harbin 150001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-2374","authenticated-orcid":false,"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150000 ,","place":["China"]},{"name":"School of Computer Science and Technology, Harbin Institute of Technology , Harbin 150001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7219-0999","authenticated-orcid":false,"given":"Yuming","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, 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