Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

(2018) Jill M. Brown et al.   Nature Communications

Between form and function: the complexity of genome folding

(2017) A. Marieke Oudelaar et al.   HUMAN MOLECULAR GENETICS

Bladder Cancer: 4 Big questions

(2017) Chris Berdik   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

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

(2017) Mariano Barbieri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

(2017) A. Marieke Oudelaar et al.   NUCLEIC ACIDS RESEARCH

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

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

(2017) Mariano Barbieri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Scc2/Nipbl hops between chromosomal cohesin rings after loading

(2017) James Rhodes et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

TADtool: visual parameter identification for TAD-calling algorithms

(2016) Kai Kruse et al.   BIOINFORMATICS

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

(2016) Pedro Olivares-Chauvet et al.   NATURE

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

UMI-4C for quantitative and targeted chromosomal contact profiling

(2016) Omer Schwartzman et al.   NATURE METHODS

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

(2016) Tingting Jiang et al.   NUCLEIC ACIDS RESEARCH

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Polymer physics of chromosome large-scale 3D organisation

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

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

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

Quantitative analysis of genomic element interactions by molecular colony technique

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

The hypersensitive sites of the murine  -globin locus control region act independently to affect nuclear localization and transcriptional elongation

(2012) M. A. Bender et al.   BLOOD

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

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