{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T21:31:22Z","timestamp":1781731882781,"version":"3.54.5"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,4,15]],"date-time":"2022-04-15T00:00:00Z","timestamp":1649980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01-AI073898"],"award-info":[{"award-number":["R01-AI073898"]}]},{"name":"National Institute of Health","award":["R01-GM056927"],"award-info":[{"award-number":["R01-GM056927"]}]},{"name":"National Institute of Health","award":["AI130618"],"award-info":[{"award-number":["AI130618"]}]},{"name":"National Institute of Health","award":["AI147163"],"award-info":[{"award-number":["AI147163"]}]},{"name":"National Institute of Health","award":["AI145266"],"award-info":[{"award-number":["AI145266"]}]},{"name":"National Institute of Health","award":["AI121321"],"award-info":[{"award-number":["AI121321"]}]},{"name":"National Institute of Health","award":["AI118891"],"award-info":[{"award-number":["AI118891"]}]},{"name":"National Cancer Institute T32 Training Grant in Tumor Virology","award":["CA115299"],"award-info":[{"award-number":["CA115299"]}]},{"name":"Individual National Research Service Award","award":["AI138432"],"award-info":[{"award-number":["AI138432"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,26]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https:\/\/github.com\/DepledgeLab\/DRUMMER.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac274","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T11:10:15Z","timestamp":1649934615000},"page":"3113-3115","source":"Crossref","is-referenced-by-count":70,"title":["DRUMMER\u2014rapid detection of RNA modifications through comparative nanopore sequencing"],"prefix":"10.1093","volume":"38","author":[{"given":"Jonathan S","family":"Abebe","sequence":"first","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine , New York, NY 10016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4654-4604","authenticated-orcid":false,"given":"Alexander M","family":"Price","sequence":"additional","affiliation":[{"name":"Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia , Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1463-3111","authenticated-orcid":false,"given":"Katharina E","family":"Hayer","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia , Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Mohr","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine , New York, NY 10016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9713-167X","authenticated-orcid":false,"given":"Matthew D","family":"Weitzman","sequence":"additional","affiliation":[{"name":"Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia , Philadelphia, PA 19104, USA"},{"name":"Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine , Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-4164","authenticated-orcid":false,"given":"Angus C","family":"Wilson","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine , New York, NY 10016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4292-0599","authenticated-orcid":false,"given":"Daniel P","family":"Depledge","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine , New York, NY 10016, USA"},{"name":"Institute of Virology, Hannover Medical School , Hannover 30625, Germany"},{"name":"German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,15]]},"reference":[{"key":"2023041403080159900_","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA modifications in cancer","volume":"20","author":"Barbieri","year":"2020","journal-title":"Nat. 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