ArticleBioinformatics (Oxford, England)2016
Differential methylation analysis for BS-seq data under general experimental design.
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 289 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
289 citing papers in PubMed, 2 syntheses or guidelines pooled it, 554 citations in OpenAlex.
- Graph neural networks for single-cell omics data: a review of approaches and applications.Briefings in bioinformatics · 2025Pooled it
- Conservation and divergence of canonical and non-canonical imprinting in murids.Genome biology · 2023Pooled it
- Conserved sex-biased DNA methylation patterns target key developmental genes and reproductive function in two Poeciliidae species.G3 (Bethesda, Md.) · 2026Article
- DNA methylation dynamics associated with seasonal wing plasticity of Bicyclus anynana butterflies.Molecular biology and evolution · 2026Article
- Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection.Computational biology and chemistry · 2026Article
- Development of an investigational epigenetic silencer therapy to transcriptionally inactivate viral DNA in chronic hepatitis B.Nature biomedical engineering · 2026Article
- Posttraumatic Stress Disorder Epigenome-Wide Association Studies in the Million Veteran Program.medRxiv : the preprint server for health sciences · 2026Article
- The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development.The Plant journal : for cell and molecular biology · 2026Article
- DiffMethylTools: a toolbox for the detection, annotation, and visualization of differential methylation.Life science alliance · 2026Article
- Differentially Methylated Regions in Human Rhombic Lip Compartments Are Enriched in Putative Active Enhancers, Human Accelerated Regions, and Medulloblastoma Copy Number Aberrations.Cerebellum (London, England) · 2026Article
- Long-read, whole-genome sequencing and chemotherapy response of two patient-derived organoids from a TP53- and KRAS-mutant ovarian carcinoma.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.BMC genomics · 2026Article
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- Integration of DNA methylation and gene expression analysis in Gephyrocapsa huxleyi provides insight into genes related to calcification.G3 (Bethesda, Md.) · 2026Article
- A progeria syndrome links DNA hypermethylation to age-related pathology.Nature genetics · 2026Article
- Mapping DNA Methylation Signatures to Identify Epigenetic Variation Across Subcortical Regions of the Human Posttraumatic Stress Disorder Brain.Biological psychiatry · 2026Article
- Non-ablative fractional laser 1940-nm treatment modulates epigenetic signatures associated with skin aging in a split-face investigation.Scientific reports · 2026Article
- Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica.Nature communications · 2026Article
- Initial leukemic epigenomic state determines hypomethylating agent response.Nature communications · 2026Article
- FUSE: data-driven functional segmentation of DNA methylation data.Bioinformatics (Oxford, England) · 2026Article
229 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
motivationDNA methylation is an epigenetic modification with important roles in many biological processes and diseases. Bisulfite sequencing (BS-seq) has emerged recently as the technology of choice to profile DNA methylation because of its accuracy, genome coverage and higher resolution. Current statistical methods to identify differential methylation mainly focus on comparing two treatment groups. With an increasing number of experiments performed under a general and multiple-factor design, particularly in reduced representation bisulfite sequencing, there is a need to develop more flexible, powerful and computationally efficient methods.
resultsWe present a novel statistical model to detect differentially methylated loci from BS-seq data under general experimental design, based on a beta-binomial regression model with 'arcsine' link function. Parameter estimation is based on transformed data with generalized least square approach without relying on iterative algorithm. Simulation and real data analyses demonstrate that our method is accurate, powerful, robust and computationally efficient. AVAILABILITY AND IMPLEMENTATION: It is available as Bioconductor package DSS. CONTACT: yongpark@pitt.edu or hao.wu@emory.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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.