Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain

(2017) Christopher L. Keown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease

(2015) Ender Karaca et al.   NEURON

The interplay between DNA methylation and sequence divergence in recent human evolution

(2015) Irene Hernando-Herraez et al.   NUCLEIC ACIDS RESEARCH

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

(2015) Jörg Hagmann et al.   PLoS Genetics

Genome-Wide Methylation Profiling of Schizophrenia

(2015) B. Rukova et al.   Balkan Journal of Medical Genetics

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

(2014) Daniela Pignatta et al.   eLife

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization

(2013) K. D. Hansen et al.   GENOME RESEARCH

Comprehensive Characterization of Human Genome Variation by High Coverage Whole-Genome Sequencing of Forty Four Caucasians

(2013) Hui Shen et al.   PLoS One

Human-specific CpG “beacons” identify loci associated with human-specific traits and disease

(2012) Christopher G. Bell et al.   Epigenetics

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

(2010) Michael James Clark et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE