{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T17:46:41Z","timestamp":1782409601958,"version":"3.54.5"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFF1205600"],"award-info":[{"award-number":["2023YFF1205600"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFF1206200"],"award-info":[{"award-number":["2024YFF1206200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62472171"],"award-info":[{"award-number":["62472171"]}],"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":["T2525003"],"award-info":[{"award-number":["T2525003"]}],"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":["62273008"],"award-info":[{"award-number":["62273008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>5-Methylcytosine (5mC) plays an important role in gene regulation and development. Although nanopore sequencing has enabled direct detection of 5mC, existing methods still face several limitations, including poor generalization across species and sequence contexts (CpG\/CHG\/CHH), as well as suboptimal integration of sequence and current signals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present MethyNano, a deep learning framework incorporating a contrastive learning strategy to detect 5mC from nanopore reads. By encouraging more discriminative and stable representations, the contrastive objective improves the model\u2019s sensitivity to rare sequence contexts and reduces its prediction uncertainty in challenging regions. Across datasets from Arabidopsis thaliana, Oryza sativa, and Homo sapiens, our model achieves superior performance on key metrics compared with other existing methods. Extensive cross-species and cross-motif experiments demonstrate the robust generalization performance of MethyNano, while dimensionality-reduction visualizations of learned features provide an intuitive view of the model\u2019s efficient representation capability. Moreover, our ablation studies show that MethyNano\u2019s architecture enables more effective integration of critical features, leading to higher predictive accuracy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The project code is available at https:\/\/github.com\/baigeHUI\/MethyNano and https:\/\/doi.org\/10.5281\/zenodo.19858400.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag348","type":"journal-article","created":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T11:41:27Z","timestamp":1779882087000},"source":"Crossref","is-referenced-by-count":0,"title":["MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-4246-4977","authenticated-orcid":false,"given":"Jiahui","family":"Yan","sequence":"first","affiliation":[{"name":"School of Control and Computer Engineering, North China Electric Power University , Beijing 102206,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Control and Computer Engineering, North China Electric Power University , Beijing 102206,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yucong","family":"Gong","sequence":"additional","affiliation":[{"name":"School of Computer Science, Key Laboratory of High Confidence Software Technologies, Peking University , Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Key Laboratory of High Confidence Software Technologies, Peking University , Beijing 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Control and Computer Engineering, North China Electric Power University , Beijing 102206,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"2026062512560005200_btag348-B1","doi-asserted-by":"crossref","first-page":"gkaf673","DOI":"10.1093\/nar\/gkaf673","article-title":"ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing","volume":"53","author":"Alagna","year":"2025","journal-title":"Nucleic Acids 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