Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability

Functional annotation of rare structural variation in the human brain

(2020) Lide Han et al.   Nature Communications

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

(2020) Suzanne E. de Bruijn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DeepC: predicting 3D genome folding using megabase-scale transfer learning

(2020) Ron Schwessinger et al.   NATURE METHODS

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

3D genome evolution and reorganization in the Drosophila melanogaster species group

(2020) Nicole S. Torosin et al.   PLoS Genetics

Most chromatin interactions are not in linkage disequilibrium

(2019) Sean Whalen et al.   GENOME RESEARCH

Chromatin features constrain structural variation across evolutionary timescales

(2019) Geoff Fudenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

(2019) William W. Greenwald et al.   Nature Communications

Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species

(2019) Margaux L.A. Hujoel et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

(2019) Jingting Yu et al.   BMC GENETICS

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF

(2019) Yang Yang et al.   Cell Systems

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

Functional disease architectures reveal unique biological role of transposable elements

(2019) Farhad Hormozdiari et al.   Nature Communications

Quantifying the similarity of topological domains across normal and cancer human cell types

(2018) Natalie Sauerwald et al.   BIOINFORMATICS

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

(2018) Yakir A. Reshef et al.   NATURE GENETICS

Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations

(2018) Steven Gazal et al.   NATURE GENETICS

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

(2017) Steven Gazal et al.   NATURE GENETICS

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

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

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

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

Genetic variants associated with subjective well-being, depressive symptoms and neuroticism identified through genome-wide analyses

(2016) Aysu Okbay et al.   NATURE GENETICS

Genome-wide analysis identifies 12 loci influencing human reproductive behavior

(2016) Nicola Barban et al.   NATURE GENETICS

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

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

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

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

(2016) Anthony D. Schmitt et al.   Cell Reports

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

(2015) Darío G. Lupiáñez et al.   CELL

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

A genome-wide association study of anorexia nervosa

(2014) V Boraska et al.   MOLECULAR PSYCHIATRY

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture

(2014) Job Dekker   Epigenetics & Chromatin

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis

(2013)   LANCET

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Higher-order chromatin domains link eQTLs with the expression of far-away genes

(2013) Geet Duggal et al.   NUCLEIC ACIDS RESEARCH

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

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

(2012) Tom Sexton et al.   CELL

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

(2011) Geoff Fudenberg et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

Higher-order Genome Organization in Human Disease

(2010) T. Misteli   Cold Spring Harbor Perspectives in Biology

Disease-specific gene repositioning in breast cancer

(2009) Karen J. Meaburn et al.   JOURNAL OF CELL BIOLOGY

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

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