Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Models of chromosome structure

(2014) Mario Nicodemi et al.   CURRENT OPINION IN CELL BIOLOGY

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Transcriptional Silencing by Polycomb-Group Proteins

(2014) U. Grossniklaus et al.   Cold Spring Harbor Perspectives in Biology

A model of the large-scale organization of chromatin

(2013) Mariano Barbieri et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Chromosomal Contact Permits Transcription between Coregulated Genes

(2013) Stephanie Fanucchi et al.   CELL

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Polycomb complexes in stem cells and embryonic development

(2013) L. Aloia et al.   DEVELOPMENT

In vivo live imaging of RNA polymerase II transcription factories in primary cells

(2013) A. Ghamari et al.   GENES & DEVELOPMENT

Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus

(2013) M. Barbieri et al.   Soft Matter

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Colocalization of Multiple DNA Loci: A Physical Mechanism

(2012) Valentino Bianco et al.   BIOPHYSICAL JOURNAL

Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs

(2012) Emily Brookes et al.   Cell Stem Cell

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

PRC1 and PRC2 Are Not Required for Targeting of H2A.Z to Developmental Genes in Embryonic Stem Cells

(2012) Robert S. Illingworth et al.   PLoS One

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A view of nuclear Polycomb bodies

(2011) Vincenzo Pirrotta et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Conformation Regulation of the X Chromosome Inactivation Center: A Model

(2011) Antonio Scialdone et al.   PLoS Computational Biology

Passive DNA shuttling

(2010) A. Scialdone et al.   EPL

Poised Transcription Factories Prime Silent uPA Gene Prior to Activation

(2010) Carmelo Ferrai et al.   PLOS BIOLOGY

Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus

(2009) Mario Nicodemi et al.   BIOPHYSICAL JOURNAL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Modifications of RNA polymerase II are pivotal in regulating gene expression states

(2009) Emily Brookes et al.   EMBO REPORTS

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology

(2009) Marieke Simonis et al.   NATURE METHODS

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

(2008) Xi Chen et al.   CELL

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics