ArticleNucleic acids research2021
Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Methylation profile of individuals with sickle cell trait.Epigenetics · 2025Pooled it
- Vitamin C supplementation to pregnant smokers alters asthma- and allergy-associated CpGs in child buccal DNA at 5 years of age.Clinical epigenetics · 2025Trial
- Improvements in lung function following vitamin C supplementation to pregnant smokers are associated with buccal DNA methylation at 5 years of age.Clinical epigenetics · 2024Trial
- Article
- Multi-omics integration uncovers epigenetic control of metabolic reprogramming in triple-negative breast cancer.Journal of the Egyptian National Cancer Institute · 2026Article
- MultiDMPcaller: a one-stop software for detection and visualization of differentially methylated positions and regions.Bioinformatics (Oxford, England) · 2026Article
- Sex-specific trajectories of nonlinear immune aging at single-cell level.Nature communications · 2026Article
- Skeletal muscle reprogramming of metabolic, ribosomal and developmental pathways contributes to Roux-en-Y gastric bypass-induced adaptation in women.EBioMedicine · 2026Article
- RegRegSEA: a web server for regulatory region set enrichment analysis of epigenomic data.Nucleic acids research · 2026Article
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- metileneNature communications · 2026Article
- DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage.Nature communications · 2026Article
- DNA methylation signatures of inflammation in youth living with perinatally-acquired HIV.Clinical epigenetics · 2026Article
- APOL1 risk genotypes influence DNA methylation across multiple genomic elements in APOL1-APOL4- MYH9 region in African Americans.Clinical epigenetics · 2026Article
- Cell-type specific allelic dampening of sex-linked genes in sex chromosome aneuploidy.bioRxiv : the preprint server for biology · 2026Article
- DNA methylation signatures associated with early-onset schizophrenia in Chinese patients.Translational psychiatry · 2026Article
- Genome-Wide DNA Methylation Study Reveals Specific Signatures in the Affected Arterial Tissue of Patients With Giant Cell Arteritis.Arthritis & rheumatology (Hoboken, N.J.) · 2026Article
- 5-methylcytosine and 5-hydroxymethylcytosine are synergistic biomarkers for early detection of colorectal cancer.Communications medicine · 2026Article
- diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application.Bioinformatics (Oxford, England) · 2026Article
- From tissue to blood: an integrated multi-omics signature identifies fibrogenesis and neutrophil activation as key drivers of ulcerative colitis severity.Frontiers in immunology · 2026Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome bisulphite sequencing (WGBS) permits the genome-wide study of single molecule methylation patterns. One of the key goals of mammalian cell-type identity studies, in both normal differentiation and disease, is to locate differential methylation patterns across the genome. We discuss the most desirable characteristics for DML (differentially methylated locus) and DMR (differentially methylated region) detection tools in a genome-wide context and choose a set of statistical methods that fully or partially satisfy these considerations to compare for benchmarking. Our data simulation strategy is both biologically informed-employing distribution parameters derived from large-scale consortium datasets-and thorough. We report DML detection ability with respect to coverage, group methylation difference, sample size, variability and covariate size, both marginally and jointly, and exhaustively with respect to parameter combination. We also benchmark these methods on FDR control and computational time. We use this result to backend and introduce an expanded version of DMRcate: an existing DMR detection tool for microarray data that we have extended to now call DMRs from WGBS data. We compare DMRcate to a set of alternative DMR callers using a similarly realistic simulation strategy. We find DMRcate and RADmeth are the best predictors of DMRs, and conclusively find DMRcate the fastest.
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