Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype

The Histone H3 Lysine 9 Methyltransferases G9a and GLP Regulate Polycomb Repressive Complex 2-Mediated Gene Silencing

(2014) Chiara Mozzetta et al.   MOLECULAR CELL

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells

(2013) Deqing Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition

(2013) Jose P. Lopez-Atalaya et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Reprogramming of human fibroblasts toward a cardiac fate

(2013) Y.-J. Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb

(2013) A. R. Pengelly et al.   SCIENCE

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

REST regulates the pool size of the different neural lineages by restricting the generation of neurons and oligodendrocytes from neural stem/progenitor cells

(2012) M. V. Covey et al.   DEVELOPMENT

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

(2012) P. Arnold et al.   GENOME RESEARCH

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

(2012) Nikolaj Dietrich et al.   PLoS Genetics

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

Maintaining a memory by transcriptional autoregulation

(2011) Oliver Hobert   CURRENT BIOLOGY

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells

(2011) Hong-Bing Yu et al.   GENOME RESEARCH

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Repressor element 1 silencing transcription factor (REST) controls radial migration and temporal neuronal specification during neocortical development

(2011) G. Mandel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells

(2009) H. F. Jorgensen et al.   DEVELOPMENT

Is REST required for ESC pluripotency?

(2009) Helle F. Jørgensen et al.   NATURE

Is REST a regulator of pluripotency?

(2009) Noel J. Buckley et al.   NATURE

Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells

(2009) Jonghwan Kim et al.   Nature Protocols

Profiling RE1/REST-mediated histone modifications in the human genome

(2009) Deyou Zheng et al.   GENOME BIOLOGY

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

CDYL Bridges REST and Histone Methyltransferases for Gene Repression and Suppression of Cellular Transformation

(2008) Peter Mulligan et al.   MOLECULAR CELL

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

REST Regulates Distinct Transcriptional Networks in Embryonic and Neural Stem Cells

(2008) Rory Johnson et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY