Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

Maternal H3K27me3 controls DNA methylation-independent imprinting

(2017) Azusa Inoue et al.   NATURE

Deficiency of microRNAmiR-34aexpands cell fate potential in pluripotent stem cells

(2017) Yong Jin Choi et al.   SCIENCE

Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals

(2016) Hui Zheng et al.   MOLECULAR CELL

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

(2015) Bin Xia Yang et al.   CELL

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

(2015) Yuki Hatanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogramming the genome to totipotency in mouse embryos

(2015) Li-quan Zhou et al.   TRENDS IN CELL BIOLOGY

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

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

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis

(2014) Adam Burton et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Beyond DNA: Programming and Inheritance of Parental Methylomes

(2013) Jamie A. Hackett et al.   CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos

(2012) Toshinobu Nakamura et al.   NATURE

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

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

(2012) Zachary D. Smith et al.   NATURE

Trim28 Is Required for Epigenetic Stability During Mouse Oocyte to Embryo Transition

(2012) D. M. Messerschmidt et al.   SCIENCE

Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo

(2011) A. Burton et al.   Briefings in Functional Genomics

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

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Polycomb Group Proteins Set the Stage for Early Lineage Commitment

(2010) Lauren E. Surface et al.   Cell Stem Cell

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

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genetic and epigenetic control of early mouse development

(2009) Mareike Albert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells

(2009) P. Yuan et al.   GENES & DEVELOPMENT

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

(2009) Da Wei Huang et al.   Nature Protocols

PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos

(2008) Mareike Puschendorf et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY