Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

(2016) Johannes Stigler et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

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

(2015) Ya Guo et al.   CELL

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

(2015) Stephan R. Starick et al.   GENOME 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

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

(2014) Suhas S.P. Rao et al.   CELL

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

(2014) B. Daniel et al.   GENES & DEVELOPMENT

MACE: model based analysis of ChIP-exo

(2014) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Closing the cohesin ring: Structure and function of its Smc3-kleisin interface

(2014) T. G. Gligoris et al.   SCIENCE

ATPase-dependent auto-phosphorylation of the open condensin hinge diminishes DNA binding

(2014) Y. Akai et al.   Open Biology

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Chromatin Insulators: Linking Genome Organization to Cellular Function

(2013) Jennifer E. Phillips-Cremins et al.   MOLECULAR CELL

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Cohesin-mediated chromatin interactions--into the third dimension of gene regulation

(2012) S. Sofueva et al.   Briefings in Functional Genomics

Cohesin, a chromatin engagement ring

(2012) Silvia Remeseiro et al.   CURRENT OPINION IN CELL BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity

(2011) T. Xiao et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cohesin: a regulator of genome integrity and gene expression

(2010) Katherine M. Feeney et al.   BIOCHEMICAL JOURNAL

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

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

A handcuff model for the cohesin complex

(2008) Nenggang Zhang et al.   JOURNAL OF CELL BIOLOGY

The cohesin ring concatenates sister DNA molecules

(2008) Christian H. Haering et al.   NATURE

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY