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

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing

(2016) Wenqiang Liu et al.   Cell Discovery

Establishing pluripotency in early development

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

Impairment of Preimplantation Porcine Embryo Development by Histone Demethylase KDM5B Knockdown Through Disturbance of Bivalent H3K4me3-H3K27me3 Modifications1

(2015) Jiaojiao Huang et al.   BIOLOGY OF REPRODUCTION

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

Absence of canonical marks of active chromatin in developmentally regulated genes

(2015) Sílvia Pérez-Lluch et al.   NATURE GENETICS

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

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

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

(2013) Gang Chang et al.   CELL RESEARCH

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo

(2013) Michael Sachs et al.   Cell Reports

Mechanisms of histone H3 lysine 27 trimethylation remodeling during early mammalian development

(2012) Yanina S. Bogliotti et al.   Epigenetics

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

(2012) Yin Shen et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Histone methylation: a dynamic mark in health, disease and inheritance

(2012) Eric L. Greer et al.   NATURE REVIEWS GENETICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Defective Chromatin Structure in Somatic Cell Cloned Mouse Embryos

(2009) Miao Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2009) Da Wei Huang et al.   Nature Protocols

Epigenetic Temporal Control of Mouse Hox Genes in Vivo

(2009) N. Soshnikova et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY