A hidden Markov model for identifying differentially methylated sites in bisulfite sequencing data

DOI10.1111/BIOM.12965MaRDI QIDQ5214465zbMATH OpenOpenAlexWikidataFDO

Authors Farhad Shokoohi, David A. Stephens, Guillaume Bourque, Tomi Pastinen, Celia M. T. Greenwood, Aurelie Labbe

Publication date 7 February 2020

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1111/biom.12965

zbMATH Keywords

blood cell-separated datadifferentially methylated regionnext-generation sequencingread-depth

Mathematics Subject Classification ID

Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

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• A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type
• Assessing genome-wide significance for the detection of differentially methylated regions
• \texttt{MLML2R}: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions
• MethCP: differentially methylated region detection with change point models
• Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression
• HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test
• HMM-DM: identifying differentially methylated regions using a hidden Markov model
• Comparing five statistical methods of differential methylation identification using bisulfite sequencing data
• Error correction in methylation profiling from NGS bisulfite protocols
• Incorporating genomic annotation into a hidden Markov model for DNA methylation tiling array data
• A Bayesian hidden Markov model for detecting differentially methylated regions
• A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation

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