Three-dimensional folding dynamics of the Xenopus tropicalis genome

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Alteration of genome folding via contact domain boundary insertion

(2020) Di Zhang et al.   NATURE GENETICS

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

(2019) Claudia Cattoglio et al.   eLife

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

(2019) Judhajeet Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Key role for CTCF in establishing chromatin structure in human embryos

(2019) Xuepeng Chen et al.   NATURE

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

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

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries

(2016) Tung BK Le et al.   EMBO JOURNAL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

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

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

A genetic map of Xenopus tropicalis

(2011) Dan E. Wells et al.   DEVELOPMENTAL BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

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

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