ArticleGenome biology2014
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
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- Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.Nature methods · 2023Article
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA.Nature protocols · 2019Article
- A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction.BMC bioinformatics · 2019Article
- RnBeads 2.0: comprehensive analysis of DNA methylation data.Genome biology · 2019Article
- MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data.BMC bioinformatics · 2018Article
- MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.Bioinformatics (Oxford, England) · 2017Article
- QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments.Nucleic acids research · 2017Article
- Methyl-binding DNA capture Sequencing for Patient Tissues.Journal of visualized experiments : JoVE · 2016Article
- A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.Genome biology · 2016Article
- Techniques and Approaches to Genetic Analyses in Nephrological Disorders.Journal of pediatric genetics · 2016Review
- Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies.American journal of epidemiology · 2016Article
- MethylAction: detecting differentially methylated regions that distinguish biological subtypes.Nucleic acids research · 2016Article
- methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.BMC bioinformatics · 2015Article
- MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution.Journal of molecular cell biology · 2015Article
- PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.Bioinformatics (Oxford, England) · 2014Article
- Comprehensive analysis of DNA methylation data with RnBeads.Nature methods · 2014Article
- BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach.Genome biology · 2014Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Affinity capture of DNA methylation combined with high-throughput sequencing strikes a good balance between the high cost of whole genome bisulfite sequencing and the low coverage of methylation arrays. We present BayMeth, an empirical Bayes approach that uses a fully methylated control sample to transform observed read counts into regional methylation levels. In our model, inefficient capture can readily be distinguished from low methylation levels. BayMeth improves on existing methods, allows explicit modeling of copy number variation, and offers computationally efficient analytical mean and variance estimators. BayMeth is available in the Repitools Bioconductor package.
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