{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T02:49:04Z","timestamp":1790390944175,"version":"4.1.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T00:00:00Z","timestamp":1713398400000},"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":["31671373"],"award-info":[{"award-number":["31671373"]}],"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":["61971422"],"award-info":[{"award-number":["61971422"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-T-01"],"award-info":[{"award-number":["KSF-T-01"]}]},{"name":"AI University Research Centre","award":["KSF-P-02"],"award-info":[{"award-number":["KSF-P-02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.<\/jats:p>","DOI":"10.1093\/nar\/gkae280","type":"journal-article","created":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T14:23:25Z","timestamp":1713450205000},"page":"4830-4842","source":"Crossref","is-referenced-by-count":14,"title":["m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq"],"prefix":"10.1093","volume":"52","author":[{"given":"Haokai","family":"Ye","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou , Jiangsu\u00a0 215123 , China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , L7 8TX\u00a0 Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tenglong","family":"Li","sequence":"additional","affiliation":[{"name":"Wisdom Lake Academy of Pharmacy, Xi\u2019an Jiaotong-Liverpool University , Suzhou\u00a0 215123 , China"},{"name":"Department of Biostatistics, School of Public Health, Boston University , Boston , MA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J","family":"Rigden","sequence":"additional","affiliation":[{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , L7 8TX\u00a0 Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1614-9614","authenticated-orcid":false,"given":"Zhen","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University , Suzhou , Jiangsu\u00a0 215123 , China"},{"name":"Institute of Life Course and Medical Sciences, University of Liverpool , L7 8TX\u00a0 Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,4,18]]},"reference":[{"key":"2024052209481589500_B1","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1038\/nchembio.482","article-title":"Grand challenge commentary: RNA epigenetics?","volume":"6","author":"He","year":"2010","journal-title":"Nat. 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