Deciphering Hi-C: from 3D genome to function

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

(2018) Han Chen et al.   CELL

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

(2018) Sofia A. Quinodoz et al.   CELL

Three-dimensional organization and dynamics of the genome

(2018) Przemyslaw Szalaj et al.   CELL BIOLOGY AND TOXICOLOGY

Developing novel methods to image and visualize 3D genomes

(2018) Tszshan Ma et al.   CELL BIOLOGY AND TOXICOLOGY

3D genome and its disorganization in diseases

(2018) Ruifeng Li et al.   CELL BIOLOGY AND TOXICOLOGY

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

(2018) Da Lin et al.   NATURE GENETICS

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Creating a functional single-chromosome yeast

(2018) Yangyang Shao et al.   NATURE

HiCDB: a sensitive and robust method for detecting contact domain boundaries

(2018) Fengling Chen et al.   NUCLEIC ACIDS RESEARCH

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Modeling three-dimensional genomic organization in evolution and pathogenesis

(2018) Alon Diament et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du 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

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

(2017) Yu Zhang et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome

(2017) Yinan Wang et al.   NUCLEIC ACIDS RESEARCH

Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence

(2017) Alon Diament et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Olga Dudchenko et al.   SCIENCE

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

(2017) Zhengyu Liang et al.   Nature Communications

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

(2017) Arpit Mishra et al.   Genome Medicine

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Mapping 3D genome architecture through in situ DNase Hi-C

(2016) Vijay Ramani et al.   Nature Protocols

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Genome-wide mapping and analysis of chromosome architecture

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

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

(2016) Guipeng Li et al.   NUCLEIC ACIDS RESEARCH

Co-regulation of paralog genes in the three-dimensional chromatin architecture

(2016) Jonas Ibn-Salem et al.   NUCLEIC ACIDS RESEARCH

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt 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

3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data

(2016) Ruifeng Li et al.   Scientific Reports

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

Gene regulation during development in the light of topologically associating domains

(2015) Silvia Remeseiro et al.   Wiley Interdisciplinary Reviews-Developmental Biology

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

(2014) Suhas S.P. Rao et al.   CELL

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

(2014) Alon Diament et al.   Nature Communications

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

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

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Chromosomes: now in 3D!

(2013) Giacomo Cavalli   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

(2013) Emily V. Chambers et al.   PLoS Computational Biology

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

The genome in space and time: Does form always follow function?

(2012) Zhijun Duan et al.   BIOESSAYS

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

(2012) Tom Sexton et al.   CELL

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Genome architecture and the role of transcription

(2010) Argyris Papantonis et al.   CURRENT OPINION IN CELL BIOLOGY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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