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Oxford University Press (OUP), Bioinformatics, 20(29), p. 2645-2646

DOI: 10.1093/bioinformatics/btt459

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MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation

Journal article published in 2013 by Jianghan Qu, Meng Zhou ORCID, Qiang Song ORCID, Elizabeth E. Hong, Andrew D. Smith
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Motivation: The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels.