Pluripotency-related, Valproic Acid (VPA)-induced Genome-wide Histone H3 Lysine 9 (H3K9) Acetylation Patterns in Embryonic Stem Cells

Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains

(2011) Hao Jiang et al.   CELL

Stem cells do play with dice: A statistical physics view of transcription

(2011) Sol Efroni et al.   CELL CYCLE

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling

(2011) Richard P. Koche et al.   Cell Stem Cell

H3K9 histone acetylation predicts pluripotency and reprogramming capacity of ES cells

(2011) Hadas Hezroni et al.   Nucleus

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

Chromatin plasticity and genome organization in pluripotent embryonic stem cells

(2010) Anna Mattout et al.   CURRENT OPINION IN CELL BIOLOGY

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation

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

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

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

(2010) Michael P. Schnetz et al.   PLoS Genetics

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

Role of the Murine Reprogramming Factors in the Induction of Pluripotency

(2009) Rupa Sridharan et al.   CELL

Histone Deacetylase Inhibition Elicits an Evolutionarily Conserved Self-Renewal Program in Embryonic Stem Cells

(2009) Carol B. Ware et al.   Cell Stem Cell

Genome-wide reduction in H3K9 acetylation during human embryonic stem cell differentiation

(2009) Jana Krejčí et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

Epigenome and chromatin structure in human embryonic stem cells undergoing differentiation

(2008) Eva Bártová et al.   DEVELOPMENTAL DYNAMICS

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis

(2008) Efthimia Karantzal et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY