Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

(2014) Daniel C. Factor et al.   Cell Stem Cell

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

The Histone H3 Lysine 9 Methyltransferases G9a and GLP Regulate Polycomb Repressive Complex 2-Mediated Gene Silencing

(2014) Chiara Mozzetta et al.   MOLECULAR CELL

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

(2014) Thorsten Boroviak et al.   NATURE CELL BIOLOGY

Aberrant DNA Methylation in ES Cells

(2014) Guy Ludwig et al.   PLoS One

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

(2013) Jia-Hui Ng et al.   DEVELOPMENTAL CELL

Naive pluripotency is associated with global DNA hypomethylation

(2013) Harry G Leitch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells

(2013) Irina A Maksakova et al.   Epigenetics & Chromatin

Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture

(2013) Carola Ingrid Weidner et al.   Scientific Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency

(2013) Jamie A. Hackett et al.   Stem Cell Reports

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

Protein Kinase A Determines Timing of Early Differentiation through Epigenetic Regulation with G9a

(2012) Kohei Yamamizu et al.   Cell Stem Cell

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

(2012) Mangmang Li et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells

(2011) Katsuhiko Hayashi et al.   CELL

Switching stem cell state through programmed germ cell reprogramming

(2011) Astrid Gillich et al.   DIFFERENTIATION

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

The Rhox Homeobox Gene Cluster Is Imprinted and Selectively Targeted for Regulation by Histone H1 and DNA Methylation

(2011) J. A. MacLean et al.   MOLECULAR AND CELLULAR BIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

(2011) Florian Lienert et al.   PLoS Genetics

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo

(2009) J. Nichols et al.   DEVELOPMENT

Self-renewing epiblast stem cells exhibit continual delineation of germ cells with epigenetic reprogramming in vitro

(2009) K. Hayashi et al.   DEVELOPMENT

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells

(2009) Siqin Bao et al.   NATURE

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

DNA Oxidation as Triggered by H3K9me2 Demethylation Drives Estrogen-Induced Gene Expression

(2008) B. Perillo et al.   SCIENCE