{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T07:58:10Z","timestamp":1773734290520,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,14]],"date-time":"2024-11-14T00:00:00Z","timestamp":1731542400000},"content-version":"vor","delay-in-days":52,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62172369"],"award-info":[{"award-number":["62172369"]}],"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":["42107148"],"award-info":[{"award-number":["42107148"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Support Plan for High level Talents in Zhejiang Province","award":["2021R52019"],"award-info":[{"award-number":["2021R52019"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical treatments. During nanopore sequencing, methylation modifications on DNA bases cause changes in electrical current intensity. Therefore, constructing deep neural network models to decode the electrical signals of nanopore sequencing has become a crucial step in methylation site identification. In this study, we utilized nanopore sequencing data containing diverse DNA methylation types and motif sequence diversity. We proposed a feature encoding method based on current signal clustering and leveraged the powerful attention mechanism in the Transformer framework to construct the PoreFormer model for identifying DNA methylation sites in nanopore sequencing. The model demonstrated excellent performance under conditions of multi-class methylation and motif sequence diversity, offering new insights into related research fields.<\/jats:p>","DOI":"10.1093\/bib\/bbae596","type":"journal-article","created":{"date-parts":[[2024,11,14]],"date-time":"2024-11-14T16:09:58Z","timestamp":1731600598000},"source":"Crossref","is-referenced-by-count":28,"title":["Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network"],"prefix":"10.1093","volume":"25","author":[{"given":"Qi","family":"Dai","sequence":"first","affiliation":[{"name":"College of Life Science and medicine, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0540-7036","authenticated-orcid":false,"given":"Hu","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Life Science and medicine, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]},{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science , No. 7 Jinsui Road, Tianhe District, Guangzhou 510060 ,","place":["China"]}]},{"given":"Wen-Jing","family":"Yi","sequence":"additional","affiliation":[{"name":"College of Life Science and medicine, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]},{"name":"Bioinformatics Laboratory, The First Hospital of Jilin University , No. 461 Xinjiang Street, Chaoyang District, Changchun 130000 ,","place":["China"]}]},{"given":"Jia-Ning","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Computer Science and technology, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and technology, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3749-1483","authenticated-orcid":false,"given":"Ping-An","family":"He","sequence":"additional","affiliation":[{"name":"College of Sciences, Zhejiang Sci-Tech University , Second Street 928, Qiantang District, Hangzhou 310018 ,","place":["China"]}]},{"given":"Xiao-Qing","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Sciences, Hangzhou Dianzi University , Second Street 1158, Qiantang District, Hangzhou 310018 ,","place":["China"]}]},{"given":"Ying-Feng","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and 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