ArticleBioinformatics (Oxford, England)2016
oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Profiling of 5-hydroxymethylcytosine in blood reveals preferential enrichment at exon-intron junctions and predictive value for Parkinson's disease.NPJ Parkinson's disease · 2026Article
- Epigenetic age and cardiometabolic disease in Guatemalan adults: a cross-sectional analysis.Journal of health, population, and nutrition · 2026Article
- Parkinson's disease-associated alterations in DNA methylation and hydroxymethylation in human brain.NPJ Parkinson's disease · 2025Article
- Early-life nutrition supplementation and epigenetic age in middle-adulthood among Guatemalan adults.bioRxiv : the preprint server for biology · 2025Article
- Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain in PD-related genes, including PARK19 (DNAJC6) and PTPRN2 (IA-2β).Research square · 2024Article
- Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors.Nature communications · 2024Article
- Hydroxymethylation alterations in progenitor-like cell types of pediatric central nervous system tumors are associated with cell type-specific transcriptional changes.Research square · 2023Article
- DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome.Frontiers in genetics · 2022Review
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Epigenetic Deregulation of the Histone MethyltransferaseFrontiers in cell and developmental biology · 2021Article
- Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- HPG-DHunter: an ultrafast, friendly tool for DMR detection and visualization.BMC bioinformatics · 2020Article
- The Impact of Environmental Factors on 5-Hydroxymethylcytosine in the Brain.Current environmental health reports · 2020Review
- Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor.Scientific reports · 2020Article
- New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation.Genome research · 2019Article
- A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-Methylcytosine and 5-Hydroxymethylcytosine Data in Neuroepigenetics.Frontiers in genetics · 2019Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
motivation5-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.
resultsWe 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. AVAILABILITY AND IMPLEMENTATION: oxBS-MLE is implemented in Bioconductor package ENmix. CONTACT: niulg@ucmail.uc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.