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Novel computational methods are required to improve the accuracy and robustness of DNA methylation state prediction using Nanopore reads.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we develop DeepSignal, a deep learning method to detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads of Homo sapiens (H. sapiens), Escherichia coli (E. coli) and pUC19 shows that DeepSignal can achieve higher performance at both read level and genome level on detecting 6\u2009mA and 5mC methylation states comparing to previous hidden Markov model (HMM) based methods. DeepSignal achieves similar performance cross different DNA methylation bases, different DNA methylation motifs and both singleton and mixed DNA CpG. Moreover, DeepSignal requires much lower coverage than those required by HMM and statistics based methods. DeepSignal can achieve 90% above accuracy for detecting 5mC and 6\u2009mA using only 2\u00d7 coverage of reads. Furthermore, for DNA CpG methylation state prediction, DeepSignal achieves 90% correlation with bisulfite sequencing using just 20\u00d7 coverage of reads, which is much better than HMM based methods. Especially, DeepSignal can predict methylation states of 5% more DNA CpGs that previously cannot be predicted by bisulfite sequencing. DeepSignal can be a robust and accurate method for detecting methylation states of DNA bases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>DeepSignal is publicly available at https:\/\/github.com\/bioinfomaticsCSU\/deepsignal.<\/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\/btz276","type":"journal-article","created":{"date-parts":[[2019,4,11]],"date-time":"2019-04-11T15:55:07Z","timestamp":1554998107000},"page":"4586-4595","source":"Crossref","is-referenced-by-count":231,"title":["DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning"],"prefix":"10.1093","volume":"35","author":[{"given":"Peng","family":"Ni","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, Central South University , Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neng","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University , Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University , Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"De-Peng","family":"Wang","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Liang","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Miao","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences , Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuan-Le","family":"Xiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , Guangzhou 510060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Computing, Clemson University , Clemson, SC 29634, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University , Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,4,17]]},"reference":[{"key":"2023020108351217000_btz276-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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