Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons

Genome-wide DNA methylation profiling in human breast tissue by illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray

(2020) Nan Lin et al.   Epigenetics

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

(2019) Yibin Liu et al.   NATURE BIOTECHNOLOGY

DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)

(2019) Giancarlo Bonora et al.   PLoS One

Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

(2018) Ovidiu Paun et al.   NEW PHYTOLOGIST

Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites

(2018) Millissia Ben Maamar et al.   Scientific Reports

Characterization of Genetic and Epigenetic Variation in Sperm and Red Blood Cells from Adult Hatchery and Natural-Origin Steelhead, Oncorhynchus mykiss

(2018) Mackenzie R. Gavery et al.   G3-Genes Genomes Genetics

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

(2017) Ksenia Skvortsova et al.   Epigenetics & Chromatin

Profiling genome-wide DNA methylation

(2016) Wai-Shin Yong et al.   Epigenetics & Chromatin

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(2015) Fiona Allum et al.   Nature Communications

Role of CpG deserts in the epigenetic transgenerational inheritance of differential DNA methylation regions

(2014) Michael K Skinner et al.   BMC GENOMICS

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Parallel mechanisms of epigenetic reprogramming in the germline

(2012) Jamie A. Hackett et al.   TRENDS IN GENETICS

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

(2011) Shalima S. Nair et al.   Epigenetics

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Epigenetic transgenerational actions of environmental factors in disease etiology

(2010) Michael K. Skinner et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY