Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Paternal H3K4 methylation is required for minor zygotic gene activation and early mouse embryonic development

(2015) K. Aoshima et al.   EMBO REPORTS

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

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

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

H3K4me3 epigenomic landscape derived from ChIP-Seq of 1 000 mouse early embryonic cells

(2014) Jie Shen et al.   CELL RESEARCH

Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes

(2014) Li Shen et al.   Cell Stem Cell

Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote

(2014) Fan Guo et al.   Cell Stem Cell

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

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

(2013) Alex S. Nord et al.   CELL

Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis

(2013) S.-J. Park et al.   GENES & DEVELOPMENT

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

(2013) Serap Erkek et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen 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

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing

(2010) Claudia V. Andreu-Vieyra et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain

(2009) Junji Otani et al.   EMBO REPORTS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

A rapid micro chromatin immunoprecipitation assay (ChIP)

(2008) John Arne Dahl et al.   Nature Protocols

Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo

(2008) W. A. Kues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA