Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

Cell Fate and Developmental Regulation Dynamics by Polycomb Proteins and 3D Genome Architecture

(2019) Vincent Loubiere et al.   BIOESSAYS

PRC1 Fine-tunes Gene Repression and Activation to Safeguard Skin Development and Stem Cell Specification

(2018) Idan Cohen et al.   Cell Stem Cell

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

(2018) Jelle Jacobs et al.   NATURE GENETICS

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

(2017) Jelena Erceg et al.   GENES & DEVELOPMENT

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycomb repressive complex 1 modifies transcription of active genes

(2017) Michelle Pherson et al.   Science Advances

The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation

(2016) Susan L Kloet et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation

(2016) Susan L Kloet et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms

(2015) Lluis Morey et al.   Cell Stem Cell

Genome-wide activities of Polycomb complexes control pervasive transcription

(2015) Hun-Goo Lee et al.   GENOME RESEARCH

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Polycomb Potentiates Meis2 Activation in Midbrain by Mediating Interaction of the Promoter with a Tissue-Specific Enhancer

(2014) Takashi Kondo et al.   DEVELOPMENTAL CELL

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

(2014) J. O. Yanez-Cuna et al.   GENOME RESEARCH

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

(2013) Daniel J. McKay et al.   DEVELOPMENTAL CELL

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

(2013) A. Mortazavi et al.   GENOME RESEARCH

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Da Wei Huang et al.   Nature Protocols

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY