LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

(2018) Julien Richard Albert et al.   BMC GENOMICS

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes

(2017) Vedran Franke et al.   GENOME RESEARCH

Lineage-specific functions of TET1 in the postimplantation mouse embryo

(2017) Rita Khoueiry et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

ChAsE: chromatin analysis and exploration tool

(2016) Hamid Younesy et al.   BIOINFORMATICS

Maternal DNA Methylation Regulates Early Trophoblast Development

(2016) Miguel R. Branco et al.   DEVELOPMENTAL CELL

Pervasive polymorphic imprinted methylation in the human placenta

(2016) Courtney W. Hanna et al.   GENOME RESEARCH

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

Endogenous retroviral promoter exaptation in human cancer

(2016) Artem Babaian et al.   Mobile DNA

VisRseq: R-based visual framework for analysis of sequencing data

(2015) Hamid Younesy et al.   BMC BIOINFORMATICS

Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape

(2015) Takao Yokoyama et al.   BMC GENOMICS

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Dynamic changes in histone modifications precede de novo DNA methylation in oocytes

(2015) Kathleen R. Stewart et al.   GENES & DEVELOPMENT

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes

(2015) David J. Adams et al.   MAMMALIAN GENOME

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting

(2015) Marta Sanchez-Delgado et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

(2014) Alexander Hayward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

(2014) Hiroaki Okae et al.   PLoS Genetics

A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

(2013) Matyas Flemr et al.   CELL

An Interactive Analysis and Exploration Tool for Epigenomic Data

(2013) H. Younesy et al.   COMPUTER GRAPHICS FORUM

Rates and patterns of great ape retrotransposition

(2013) F. Hormozdiari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

(2012) Charlotte Proudhon et al.   MOLECULAR CELL

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

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

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Silencing of endogenous retroviruses: when and why do histone marks predominate?

(2011) Danny C. Leung et al.   TRENDS IN BIOCHEMICAL SCIENCES

Characterization and potential functional significance of human-chimpanzee large INDEL variation

(2011) Nalini Polavarapu et al.   Mobile DNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS