{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T01:15:44Z","timestamp":1783214144530,"version":"3.54.6"},"reference-count":48,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000027","name":"National Institute on Alcohol Abuse and Alcoholism","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000027","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["P30 AG010133"],"award-info":[{"award-number":["P30 AG010133"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R25HG012325,5U10AA008401"],"award-info":[{"award-number":["R25HG012325,5U10AA008401"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.compbiolchem.2026.109204","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T16:30:49Z","timestamp":1782318649000},"page":"109204","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"P2","title":["Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection"],"prefix":"10.1016","volume":"124","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2712-0526","authenticated-orcid":false,"given":"Steven","family":"Brooks","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa","family":"Robins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyu","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuhong","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwangsik","family":"Nho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Saykin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunlong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0307-9351","authenticated-orcid":false,"given":"Gang","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2026.109204_bib1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/s13072-025-00616-3","article-title":"Comparison of current methods for genome-wide DNA methylation profiling","volume":"18","author":"de Abreu","year":"2025","journal-title":"Epigenetics Chromatin"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.expneurol.2014.05.008","article-title":"5-Hydroxymethylcytosine: a new player in brain disorders?","volume":"268","author":"Cheng","year":"2015","journal-title":"Exp. Neurol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib3","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1080\/15592294.2022.2051861","article-title":"Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts","volume":"17","author":"Christiansen","year":"2022","journal-title":"Epigenetics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib4","article-title":"The long and short of it: benchmarking viromics using Illumina, nanopore and PacBio sequencing technologies","volume":"10","author":"Cook","year":"2024","journal-title":"Microb. Genom."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib5","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/s13237-021-00367-y","article-title":"DNA methylation and regulation of gene expression: Guardian of our health","volume":"64","author":"Dhar","year":"2021","journal-title":"Nucleus"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib6","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.tig.2023.04.006","article-title":"Genomics in the long-read sequencing era","volume":"39","author":"Dijk","year":"2023","journal-title":"Trends Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib7","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","volume":"36","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib8","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1186\/1471-2105-11-587","article-title":"Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis","volume":"11","author":"Du","year":"2010","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.gene.2020.144577","article-title":"Epigenetic modifications in gastric cancer: focus on DNA methylation","volume":"742","author":"Ebrahimi","year":"2020","journal-title":"Gene"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib10","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib11","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s10815-017-0895-5","article-title":"Role of DNA methylation in imprinting disorders: an updated review","volume":"34","author":"Elhamamsy","year":"2017","journal-title":"J. Assist. Reprod. Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib12","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1093\/hmg\/ddac112","article-title":"Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays","volume":"31","author":"Flynn","year":"2022","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib13","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1186\/s13059-021-02529-2","article-title":"The SEQC2 epigenomics quality control (EpiQC) study","volume":"22","author":"Foox","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib14","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s40478-022-01371-2","article-title":"DNA methylation as a diagnostic tool","volume":"10","author":"Galbraith","year":"2022","journal-title":"Acta Neuropathol. Commun."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib15","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib16","doi-asserted-by":"crossref","unstructured":"Guanzon, D., Ross, J.P., Ma, C., Berry, O. & Liew, Y.J. Comparing methylation levels assayed in GC-rich regions with current and emerging methods. 2023.09.06.556603 Preprint at \u3008https:\/\/doi.org\/10.1101\/2023.09.06.556603\u3009 (2024).","DOI":"10.1101\/2023.09.06.556603"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib17","doi-asserted-by":"crossref","first-page":"74","DOI":"10.3389\/fgene.2011.00074","article-title":"DNA methylation: a timeline of methods and applications","volume":"2","author":"Harrison","year":"2011","journal-title":"Front. Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib18","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/s41597-020-00743-4","article-title":"Highly accurate long-read HiFi sequencing data for five complex genomes","volume":"7","author":"Hon","year":"2020","journal-title":"Sci. Data"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib19","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","article-title":"The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community","volume":"17","author":"Jain","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib20","doi-asserted-by":"crossref","DOI":"10.1155\/2020\/1047896","article-title":"Epigenetic clock: DNA methylation in aging","volume":"2020","author":"Jiang","year":"2020","journal-title":"Stem Cells Int."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib21","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1111\/acel.12349","article-title":"DNA methylation and healthy human aging","volume":"14","author":"Jones","year":"2015","journal-title":"Aging Cell."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib22","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s43682-023-00021-5","article-title":"Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip","volume":"3","author":"Kaur","year":"2023","journal-title":"Epigenetics Commun."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib23","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1038\/s41592-023-01993-x","article-title":"Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation","volume":"20","author":"Kolmogorov","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib24","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41576-022-00559-5","article-title":"Navigating the pitfalls of mapping DNA and RNA modifications","volume":"24","author":"Kong","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib25","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","article-title":"Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications","volume":"27","author":"Krueger","year":"2011","journal-title":"Bioinforma. Oxf. Engl."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib26","first-page":"143","article-title":"A Clinician\u2019s Guide to Bioinformatics for Next-Generation Sequencing","volume":"18","author":"Larson","year":"2023","journal-title":"J. Thorac. Oncol. Off. Publ. Int. Assoc. Study Lung Cancer"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for Computing and Annotating Genomic Ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib28","doi-asserted-by":"crossref","DOI":"10.4061\/2011\/870726","article-title":"Distribution of 5-hydroxymethylcytosine in different human tissues","volume":"2011","author":"Li","year":"2011","journal-title":"J. Nucleic Acids"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib29","first-page":"1","article-title":"Chapter One - DNA methylation and histone variants in aging and cancer","volume":"364","author":"Mangelinck","year":"2021"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib30","doi-asserted-by":"crossref","unstructured":"Martin, M., , 2016. WhatsHap fast accurate Read. Based phasing10.1101\/085050.","DOI":"10.1101\/085050"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib31","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1016\/j.tig.2022.03.010","article-title":"DNA methylation: a historical perspective","volume":"38","author":"Mattei","year":"2022","journal-title":"Trends Genet."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib32","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/npp.2012.112","article-title":"DNA methylation and its basic function","volume":"38","author":"Moore","year":"2013","journal-title":"Neuropsychopharmacology"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib33","doi-asserted-by":"crossref","DOI":"10.1080\/15592294.2023.2185742","article-title":"Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome","volume":"18","author":"Noguera-Castells","year":"2023","journal-title":"Epigenetics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib34","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1093\/bioinformatics\/btw026","article-title":"Differential methylation analysis for BS-seq data under general experimental design","volume":"32","author":"Park","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib35","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1186\/s13059-016-1066-1","article-title":"Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling","volume":"17","author":"Pidsley","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib36","unstructured":"R: The R Project for Statistical Computing. \u3008https:\/\/www.r-project.org\/\u3009."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib37","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s12915-020-00910-4","article-title":"Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites","volume":"18","author":"Schmidt","year":"2020","journal-title":"BMC Biol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib38","doi-asserted-by":"crossref","DOI":"10.1002\/ange.202215704","article-title":"Third-generation sequencing of epigenetic DNA","volume":"135","author":"Searle","year":"2023","journal-title":"Angew. Chem."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib39","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1080\/15592294.2022.2097473","article-title":"Whole human genome 5\u2019-mC methylation analysis using long read nanopore sequencing","volume":"17","author":"Silva","year":"2022","journal-title":"Epigenetics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib40","first-page":"443","article-title":"DNA methylation dynamics in cellular commitment and differentiation","volume":"15","author":"Suelves","year":"2016","journal-title":"Brief. Funct. Genom."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib41","unstructured":"Tiedemann, F. gghalves: Compose Half-Half Plots Using Your Favourite Geoms. (2022)."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib42","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1101\/gr.266551.120","article-title":"Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA","volume":"31","author":"Vaisvila","year":"2021","journal-title":"Genome Res."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib43","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib44","series-title":"Ggplot2","author":"Wickham","year":"2016"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib45","doi-asserted-by":"crossref","DOI":"10.3389\/fpsyt.2023.1198502","article-title":"5hmC modification regulates R-loop accumulation in response to stress","volume":"14","author":"Xu","year":"2023","journal-title":"Front. Psychiatry"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib46","first-page":"1123","article-title":"TET enzymes and 5hmC epigenetic mark: new key players in carcinogenesis and progression in gynecological cancers","volume":"28","author":"Zacapala-G\u00f3mez","year":"2024","journal-title":"Eur. Rev. Med. Pharmacol. Sci."},{"key":"10.1016\/j.compbiolchem.2026.109204_bib47","doi-asserted-by":"crossref","DOI":"10.1080\/15592294.2024.2333660","article-title":"Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays","volume":"19","author":"Zhang","year":"2024","journal-title":"Epigenetics"},{"key":"10.1016\/j.compbiolchem.2026.109204_bib48","article-title":"Comparison of Infinium MethylationEPIC v2.0 to v1.0 for human population epigenetics: considerations for addressing EPIC version differences in DNA methylation-based tools","author":"Zhuang","year":"2024","journal-title":"bioRxiv"}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126003312?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126003312?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T00:26:17Z","timestamp":1783211177000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927126003312"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":48,"alternative-id":["S1476927126003312"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109204","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109204","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"109204"}}