{"id":"https://openalex.org/W2951434717","doi":"https://doi.org/10.1093/bioinformatics/btz276","title":"DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning","display_name":"DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning","publication_year":2019,"publication_date":"2019-04-11","ids":{"openalex":"https://openalex.org/W2951434717","doi":"https://doi.org/10.1093/bioinformatics/btz276","mag":"2951434717","pmid":"https://pubmed.ncbi.nlm.nih.gov/30994904"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz276","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4586/30706897/btz276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4586/30706897/btz276.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090322041","display_name":"Peng Ni","orcid":"https://orcid.org/0000-0002-0801-7574"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Ni","raw_affiliation_strings":["School of Information Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054096088","display_name":"Neng Huang","orcid":"https://orcid.org/0000-0001-7187-0749"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Neng Huang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100410691","display_name":"Zhi Zhang","orcid":"https://orcid.org/0000-0002-4237-1948"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi Zhang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101952062","display_name":"Depeng Wang","orcid":"https://orcid.org/0000-0001-9014-710X"},"institutions":[{"id":"https://openalex.org/I4210089756","display_name":"Bioscience (China)","ror":"https://ror.org/0072d4h61","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210089756"]},{"id":"https://openalex.org/I4210156771","display_name":"Grandomics (China)","ror":"https://ror.org/044snnt75","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210156771"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"De-Peng Wang","raw_affiliation_strings":["GrandOmics Biosciences , Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GrandOmics Biosciences , Beijing 102206, China","institution_ids":["https://openalex.org/I4210089756","https://openalex.org/I4210156771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080032910","display_name":"Fan Liang","orcid":"https://orcid.org/0000-0003-1556-1436"},"institutions":[{"id":"https://openalex.org/I4210089756","display_name":"Bioscience (China)","ror":"https://ror.org/0072d4h61","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210089756"]},{"id":"https://openalex.org/I4210156771","display_name":"Grandomics (China)","ror":"https://ror.org/044snnt75","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210156771"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Liang","raw_affiliation_strings":["GrandOmics Biosciences , Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GrandOmics Biosciences , Beijing 102206, China","institution_ids":["https://openalex.org/I4210089756","https://openalex.org/I4210156771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018554791","display_name":"Miao Yu","orcid":"https://orcid.org/0000-0003-2963-8254"},"institutions":[{"id":"https://openalex.org/I4210089756","display_name":"Bioscience (China)","ror":"https://ror.org/0072d4h61","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210089756"]},{"id":"https://openalex.org/I4210156771","display_name":"Grandomics (China)","ror":"https://ror.org/044snnt75","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210156771"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Miao","raw_affiliation_strings":["GrandOmics Biosciences , Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GrandOmics Biosciences , Beijing 102206, China","institution_ids":["https://openalex.org/I4210089756","https://openalex.org/I4210156771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029540163","display_name":"Chuan\u2010Le Xiao","orcid":"https://orcid.org/0000-0002-4680-0682"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuan-Le Xiao","raw_affiliation_strings":["State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , Guangzhou 510060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University , Guangzhou 510060, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100683466","display_name":"Feng Luo","orcid":"https://orcid.org/0000-0002-4813-2403"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Feng Luo","raw_affiliation_strings":["School of Computing, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100438360","https://openalex.org/A5100683466"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I8078737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.8638,"has_fulltext":false,"cited_by_count":275,"citation_normalized_percentile":{"value":0.99219533,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"35","issue":"22","first_page":"4586","last_page":"4595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4864000082015991,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4864000082015991,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.3862000107765198,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.03799999877810478,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7186177372932434},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.6985548138618469},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.6129657626152039},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5647964477539062},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5268722176551819},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5030736327171326},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.49474379420280457},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.46693697571754456},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.45820948481559753},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.41530752182006836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3993023633956909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3538696765899658},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23996469378471375},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19641268253326416}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7186177372932434},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.6985548138618469},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.6129657626152039},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5647964477539062},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5268722176551819},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5030736327171326},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.49474379420280457},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.46693697571754456},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.45820948481559753},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.41530752182006836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3993023633956909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3538696765899658},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23996469378471375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19641268253326416},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz276","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4586/30706897/btz276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30994904","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30994904","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz276","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4586/30706897/btz276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1187543282","display_name":null,"funder_award_id":"61772557","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3432038435","display_name":null,"funder_award_id":"61828205","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G358564744","display_name":null,"funder_award_id":"61420106009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4686191493","display_name":"ABI Innovation: Fast Algorithms and Tools for Single-Molecule Sequencing Reads","funder_award_id":"1759856","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8379494251","display_name":null,"funder_award_id":"2017-70016-26051","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951434717.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W757829720","https://openalex.org/W1984783889","https://openalex.org/W1987557775","https://openalex.org/W1997866877","https://openalex.org/W2004336032","https://openalex.org/W2031191277","https://openalex.org/W2073105380","https://openalex.org/W2080324830","https://openalex.org/W2085492504","https://openalex.org/W2095705004","https://openalex.org/W2097117768","https://openalex.org/W2129729311","https://openalex.org/W2131374955","https://openalex.org/W2131774270","https://openalex.org/W2132083557","https://openalex.org/W2201760124","https://openalex.org/W2259938310","https://openalex.org/W2590641123","https://openalex.org/W2591367881","https://openalex.org/W2598333982","https://openalex.org/W2607669908","https://openalex.org/W2770144912","https://openalex.org/W2787788280","https://openalex.org/W2789843538","https://openalex.org/W2790527784","https://openalex.org/W2807709032","https://openalex.org/W2808531159","https://openalex.org/W2949348780","https://openalex.org/W4254751698","https://openalex.org/W6674330103","https://openalex.org/W6674914833","https://openalex.org/W6748810007"],"related_works":["https://openalex.org/W3200718802","https://openalex.org/W4387876522","https://openalex.org/W4386105821","https://openalex.org/W3088570659","https://openalex.org/W2494580947","https://openalex.org/W4401897769","https://openalex.org/W2088375436","https://openalex.org/W4399475300","https://openalex.org/W3129972012","https://openalex.org/W2584039926"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"Oxford":[2],"Nanopore":[3,38,57,62],"sequencing":[4,58,172],"enables":[5],"to":[6,26,51,98],"directly":[7],"detect":[8,52],"methylation":[9,34,54,95,113,117,163,191,216],"states":[10,55,96,192,217],"of":[11,32,64,157,177,193,218],"bases":[12],"in":[13],"DNA":[14,33,53,112,116,124,161,196,219],"from":[15,56],"reads":[16,63],"without":[17],"extra":[18],"laboratory":[19],"techniques.":[20],"Novel":[21],"computational":[22],"methods":[23],"are":[24,234],"required":[25,134],"improve":[27],"the":[28],"accuracy":[29,146],"and":[30,73,86,93,119,122,137,150,211],"robustness":[31],"state":[35,164],"prediction":[36],"using":[37,153,173],"reads.":[39,59,158],"RESULTS:":[40],"In":[41],"this":[42],"study,":[43],"we":[44],"develop":[45],"DeepSignal,":[46],"a":[47,209],"deep":[48],"learning":[49],"method":[50,213],"Testing":[60],"on":[61,89],"Homo":[65],"sapiens":[66],"(H.":[67],"sapiens),":[68],"Escherichia":[69],"coli":[70],"(E.":[71],"coli)":[72],"pUC19":[74],"shows":[75],"that":[76,198],"DeepSignal":[77,106,127,141,166,188,206,224],"can":[78,142,189,207],"achieve":[79,143],"higher":[80],"performance":[81,109],"at":[82,228,236],"both":[83,120],"read":[84],"level":[85,88],"genome":[87],"detecting":[90,148,215],"6":[91,151],"mA":[92,152],"5mC":[94,149],"comparing":[97],"previous":[99],"hidden":[100],"Markov":[101],"model":[102],"(HMM)":[103],"based":[104,139,185],"methods.":[105,140,186],"achieves":[107,167],"similar":[108],"cross":[110],"different":[111,115],"bases,":[114],"motifs":[118],"singleton":[121],"mixed":[123],"CpG.":[125],"Moreover,":[126],"requires":[128],"much":[129,181],"lower":[130],"coverage":[131,156,176],"than":[132,183],"those":[133],"by":[135,203],"HMM":[136,184],"statistics":[138],"90%":[144,168],"above":[145],"for":[147,160,214],"only":[154],"2\u00d7":[155],"Furthermore,":[159],"CpG":[162],"prediction,":[165],"correlation":[169],"with":[170],"bisulfite":[171,204],"just":[174],"20\u00d7":[175],"reads,":[178],"which":[179],"is":[180,225],"better":[182],"Especially,":[187],"predict":[190],"5%":[194],"more":[195],"CpGs":[197],"previously":[199],"cannot":[200],"be":[201,208],"predicted":[202],"sequencing.":[205],"robust":[210],"accurate":[212],"bases.":[220],"AVAILABILITY":[221],"AND":[222],"IMPLEMENTATION:":[223],"publicly":[226],"available":[227,235],"https://github.com/bioinfomaticsCSU/deepsignal.":[229],"SUPPLEMENTARY":[230],"INFORMATION:":[231],"Supplementary":[232],"data":[233],"bioinformatics":[237],"online.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":23},{"year":2025,"cited_by_count":31},{"year":2024,"cited_by_count":34},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":45},{"year":2021,"cited_by_count":62},{"year":2020,"cited_by_count":36},{"year":2019,"cited_by_count":10}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}