Embryonic transcription is controlled by maternally defined chromatin state

Establishing pluripotency in early development

(2015) Sarita S. Paranjpe et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Recruiting polycomb to chromatin

(2015) Ila van Kruijsbergen et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Genome-wide view of TGF /Foxh1 regulation of the early mesendoderm program

(2014) W. T. Chiu et al.   DEVELOPMENT

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma

(2014) Gang Wu et al.   NATURE GENETICS

Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification

(2014) Yuuri Yasuoka et al.   Nature Communications

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

(2014) Robert Huether et al.   Nature Communications

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

(2013) Sarita S Paranjpe et al.   BMC GENOMICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos

(2013) Lan Jiang et al.   CELL

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Principles of nucleation of H3K27 methylation during embryonic development

(2013) S. J. van Heeringen et al.   GENOME RESEARCH

The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos

(2013) Ozren Bogdanović et al.   METHODS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

(2013) George E. Gentsch et al.   Cell Reports

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

(2012) Femke Simmer et al.   Epigenetics

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

An essential role for transcription before the MBT in Xenopus laevis

(2011) Jennifer Skirkanich et al.   DEVELOPMENTAL BIOLOGY

Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation

(2011) Leif C. Lindeman et al.   DEVELOPMENTAL CELL

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

(2011) Ozren Bogdanović et al.   GENOME RESEARCH

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

β-Catenin Primes Organizer Gene Expression by Recruiting a Histone H3 Arginine 8 Methyltransferase, Prmt2

(2010) Shelby A. Blythe et al.   DEVELOPMENTAL CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

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

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY