title: oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.
abstract: 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.
  
  
  
  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.
  
  
  
  oxBS-MLE is implemented in Bioconductor package ENmix.
  
  
  
  niulg@ucmail.uc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
authors: Epidemiology Branch.
authors: Zongli
authors: Z
authors: Xu
authors: Epidemiology Branch.|Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
authors: Jack A
authors: JA
authors: Taylor
authors: Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
authors: Yuet-Kin
authors: YK
authors: Leung
authors: Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
authors: Shuk-Mei
authors: SM
authors: Ho
authors: Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
authors: Liang
authors: L
authors: Niu
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D018899:CpG Islands; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D008962:Models, Theoretical; D017422:Sequence Analysis, DNA
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D004247:DNA