{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T07:32:45Z","timestamp":1784359965665,"version":"3.55.0"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T00:00:00Z","timestamp":1668556800000},"content-version":"vor","delay-in-days":0,"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":["32100519"],"award-info":[{"award-number":["32100519"]}],"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":["31671373"],"award-info":[{"award-number":["31671373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-E-51"],"award-info":[{"award-number":["KSF-E-51"]}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-P-02"],"award-info":[{"award-number":["KSF-P-02"]}]},{"name":"Scientific Research Foundation for Advanced Talents of Fujian Medical University","award":["XRCZX202109"],"award-info":[{"award-number":["XRCZX202109"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http:\/\/www.rnamd.org\/directRMDB\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac1061","type":"journal-article","created":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T08:20:54Z","timestamp":1668586854000},"page":"D106-D116","source":"Crossref","is-referenced-by-count":86,"title":["DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology"],"prefix":"10.1093","volume":"51","author":[{"given":"Yuxin","family":"Zhang","sequence":"first","affiliation":[{"name":"Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University , Fuzhou, Fujian 350004, China"},{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiongming","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University , Fuzhou, Fujian 350004, China"},{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Life Course and Medical Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6271-6547","authenticated-orcid":false,"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Department of Computer Science, University of Liverpool , L69 7ZB , Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8586-0573","authenticated-orcid":false,"given":"Bowen","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-205X","authenticated-orcid":false,"given":"Jia","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"AI University Research Centre, Xi\u2019an Jiaotong-Liverpool University , Suzhou , Jiangsu \u00a0215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4186-6922","authenticated-orcid":false,"given":"Guifang","family":"Jia","sequence":"additional","affiliation":[{"name":"Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6363-2465","authenticated-orcid":false,"given":"Jo\u00e3o Pedro","family":"de\u00a0Magalh\u00e3es","sequence":"additional","affiliation":[{"name":"Institute of Life Course and Medical Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel\u00a0J","family":"Rigden","sequence":"additional","affiliation":[{"name":"Institute of Systems, Molecular and Integrative Biology, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daiyun","family":"Hang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019anJiaotong-Liverpool University , Suzhou, Jiangsu 215123, China"},{"name":"Department of Computer Science, University of Liverpool , L69 7ZB , Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6025-8957","authenticated-orcid":false,"given":"Kunqi","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University , Fuzhou, Fujian 350004, 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