Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers

(2015) Sarah K Harten et al.   BMC BIOLOGY

Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment

(2015) Matt J Silver et al.   GENOME BIOLOGY

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS): Genome-Wide DNA Methylation Analysis of IAP LTR Retrotransposon

(2014) Muhammad B. Ekram et al.   PLoS One

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

(2014) N. Ari Wijetunga et al.   Nature Communications

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Inactive or moderately active human promoters are enriched for inter-individual epialleles

(2013) Carolina Gemma et al.   GENOME BIOLOGY

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Retrotransposons as a major source of epigenetic variations in the mammalian genome

(2012) Muhammad B. Ekram et al.   Epigenetics

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance

(2012) J. Li et al.   GENOME RESEARCH

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Reduced dosage of the modifiers of epigenetic reprogramming Dnmt1, Dnmt3L, SmcHD1 and Foxo3a has no detectable effect on mouse telomere length in vivo

(2011) Amity R. Roberts et al.   CHROMOSOMA

An expression microarray approach for the identification of metastable epialleles in the mouse genome

(2011) Caren Weinhouse et al.   Epigenetics

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

(2011) Rita Rebollo et al.   PLoS Genetics

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model

(2010) Nina Kaminen-Ahola 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

DNA methylation profiles in monozygotic and dizygotic twins

(2009) Zachary A Kaminsky et al.   NATURE GENETICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH