Quantitative prediction of enhancer–promoter interactions

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

(2019) Wenran Li et al.   NUCLEIC ACIDS RESEARCH

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

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

(2019) Jonas Ibn-Salem et al.   BMC GENOMICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

In silico prediction of high-resolution Hi-C interaction matrices

(2019) Shilu Zhang et al.   Nature Communications

Interpreting Chromosomal Rearrangements in the Context of 3-Dimentional Genome Organization: A Practical Guide for Medical Genetics

(2018) V. S. Fishman et al.   BIOCHEMISTRY-MOSCOW

Predicting CTCF-mediated chromatin loops using CTCF-MP

(2018) Ruochi Zhang et al.   BIOINFORMATICS

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

Allele-Specific Biased Expression of the CNTN6 Gene in iPS Cell-Derived Neurons from a Patient with Intellectual Disability and 3p26.3 Microduplication Involving the CNTN6 Gene

(2018) Maria M. Gridina et al.   MOLECULAR NEUROBIOLOGY

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Reconstructing spatial organizations of chromosomes through manifold learning

(2018) Guangxiang Zhu et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits

(2018) Yang Wu et al.   Nature Communications

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

(2018) Ziad Al Bkhetan et al.   Scientific Reports

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

(2018) Adam Buckle et al.   MOLECULAR CELL

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

(2018) Fei Sun et al.   MOLECULAR CELL

3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin

(2018) Veniamin Fishman et al.   NUCLEIC ACIDS RESEARCH

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

(2018) Yan Kai et al.   Nature Communications

Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy

(2018) Wang Xi et al.   PLoS Computational Biology

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Potential energy landscapes identify the information-theoretic nature of the epigenome

(2017) Garrett Jenkinson et al.   NATURE GENETICS

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

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

(2017) Qin Cao et al.   NATURE GENETICS

The interplay of epigenetic marks during stem cell differentiation and development

(2017) Yaser Atlasi et al.   NATURE REVIEWS GENETICS

Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution

(2017) Hui Zhang 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

A genome-wide association study yields five novel thyroid cancer risk loci

(2017) Julius Gudmundsson et al.   Nature Communications

Three-dimensional genome architecture and emerging technologies: looping in disease

(2017) Arpit Mishra et al.   Genome Medicine

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

From profiles to function in epigenomics

(2016) Stefan H. Stricker et al.   NATURE REVIEWS GENETICS

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

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

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

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

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

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

Polymer physics of chromosome large-scale 3D organisation

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

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

(2015) Zhonghui Tang et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

(2015) Benjamin L Moore et al.   GENOME BIOLOGY

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

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS