7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

The interferon-stimulated gene TRIM22 : A double-edged sword in HIV-1 infection

(2018) Elisa Vicenzi et al.   CYTOKINE & GROWTH FACTOR REVIEWS

ZNF143 is a regulator of chromatin loop

(2018) Zi Wen et al.   CELL BIOLOGY AND TOXICOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach

(2017) Raphaël Mourad et al.   PLoS Computational Biology

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

(2017) Tomasz Dzida et al.   PeerJ

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

(2016) Peter Hansen et al.   BMC GENOMICS

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

(2016) Gergely Nagy et al.   BMC GENOMICS

Chromosome conformation capture technologies and their impact in understanding genome function

(2016) Satish Sati et al.   CHROMOSOMA

ZNF143 is involved in CTCF-mediated chromatin interactions by cooperation with cohesin and other partners

(2016) B.-Y. Ye et al.   MOLECULAR BIOLOGY

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles

(2016) Yong Chen et al.   NUCLEIC ACIDS RESEARCH

CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data

(2016) Timothy O'Connor et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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

PETModule: a motif module based approach for enhancer target gene prediction

(2016) Changyong Zhao et al.   Scientific Reports

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

(2015) Nathan Harmston et al.   BMC GENOMICS

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

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks

(2015) Peter Hansen et al.   GENOME RESEARCH

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

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

(2015) Elizabeth A. Hoffman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination

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

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome

(2015) Magali Naville et al.   Nature Communications

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

(2014) Timothy R. O'Connor et al.   NUCLEIC ACIDS RESEARCH

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

(2014) Galip Gürkan Yardımcı et al.   NUCLEIC ACIDS RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

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

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations

(2008) V. K. Tiwari et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY