{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T15:56:17Z","timestamp":1775836577974,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"23","funder":[{"name":"Center for Environmental Genetics","award":["NIEHS"],"award-info":[{"award-number":["NIEHS"]}]},{"name":"Center for Environmental Genetics","award":["P30ES00606"],"award-info":[{"award-number":["P30ES00606"]}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"crossref","award":["ES022071"],"award-info":[{"award-number":["ES022071"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Intramural Research Program of the NIH","award":["NIEHS Z01 ES049033"],"award-info":[{"award-number":["NIEHS Z01 ES049033"]}]},{"name":"Intramural Research Program of the NIH","award":["Z01 ES049032"],"award-info":[{"award-number":["Z01 ES049032"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,1]]},"abstract":"<jats:p>Motivation: 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic regulators of gene expression. 5mC and 5hmC levels can be computationally inferred at single base resolution using sequencing or array data from paired DNA samples that have undergone bisulfite and oxidative bisulfite conversion. Current estimation methods have been shown to produce irregular estimates of 5hmC level or are extremely computation intensive.<\/jats:p>\n               <jats:p>Results: We developed an efficient method oxBS-MLE based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that it outperformed alternative methods in estimate accuracy and computation speed.<\/jats:p>\n               <jats:p>Availability and Implementation: oxBS-MLE is implemented in Bioconductor package ENmix.<\/jats:p>\n               <jats:p>Contact: \u00a0niulg@ucmail.uc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw527","type":"journal-article","created":{"date-parts":[[2016,8,14]],"date-time":"2016-08-14T00:17:57Z","timestamp":1471133877000},"page":"3667-3669","source":"Crossref","is-referenced-by-count":33,"title":["oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA"],"prefix":"10.1093","volume":"32","author":[{"given":"Zongli","family":"Xu","sequence":"first","affiliation":[{"name":"1Epidemiology Branch"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack A.","family":"Taylor","sequence":"additional","affiliation":[{"name":"1Epidemiology Branch"},{"name":"2Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuet-Kin","family":"Leung","sequence":"additional","affiliation":[{"name":"3Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuk-Mei","family":"Ho","sequence":"additional","affiliation":[{"name":"3Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Niu","sequence":"additional","affiliation":[{"name":"3Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,8,13]]},"reference":[{"key":"2023020114065363400_btw527-B1","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1126\/science.1220671","article-title":"Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution","volume":"336","author":"Booth","year":"2012","journal-title":"Science"},{"key":"2023020114065363400_btw527-B2","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1038\/nprot.2013.115","article-title":"Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine","volume":"8","author":"Booth","year":"2013","journal-title":"Nat. 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