{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T06:32:27Z","timestamp":1782455547508,"version":"3.54.5"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T00:00:00Z","timestamp":1635379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ITN-CONTRA EU","award":["H2020 MSCA-ITN-2017-766030"],"award-info":[{"award-number":["H2020 MSCA-ITN-2017-766030"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>DNA methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods use either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present DeepMP, a convolutional neural network-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on Escherichia coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>DeepMP is implemented and freely available under MIT license at https:\/\/github.com\/pepebonet\/DeepMP.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab745","type":"journal-article","created":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T15:13:43Z","timestamp":1635174823000},"page":"1235-1243","source":"Crossref","is-referenced-by-count":28,"title":["DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2625-3503","authenticated-orcid":false,"given":"Jose","family":"Bonet","sequence":"first","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , 08028 Barcelona, Spain"},{"name":"Research Program on Biomedical Informatics, Universitat Pompeu Fabra , 08002 Barcelona, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1880-1730","authenticated-orcid":false,"given":"Mandi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , 114 28 Stockholm, Sweden"},{"name":"Science for Life Laboratory, 171 65 Solna Stockholm , Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Dabad","sequence":"additional","affiliation":[{"name":"CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , 08002 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Heath","sequence":"additional","affiliation":[{"name":"CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , 08002 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8582-4660","authenticated-orcid":false,"given":"Abel","family":"Gonzalez-Perez","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , 08028 Barcelona, Spain"},{"name":"Research Program on Biomedical Informatics, Universitat Pompeu Fabra , 08002 Barcelona, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuria","family":"Lopez-Bigas","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , 08028 Barcelona, Spain"},{"name":"Research Program on Biomedical Informatics, Universitat Pompeu Fabra , 08002 Barcelona, Catalonia, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) , 08010 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Lagergren","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , 114 28 Stockholm, Sweden"},{"name":"Science for Life Laboratory, 171 65 Solna Stockholm , Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,28]]},"reference":[{"key":"2023020108544247300_btab745-B1","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/nsmb.2518","article-title":"DNA methylation dynamics in health and disease","volume":"20","author":"Bergman","year":"2013","journal-title":"Nat. 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