High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

(2021) Aneta Mikulasova et al.   GENOME RESEARCH

Complex small-world regulatory networks emerge from the 3D organisation of the human genome

(2021) C. A. Brackley et al.   Nature Communications

Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease

(2020) Shinae Park et al.   FEBS Journal

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

Polymer compaction and bridging-induced clustering of protein-inspired patchy particles

(2020) C A Brackley   JOURNAL OF PHYSICS-CONDENSED MATTER

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

(2020) Leina Lu et al.   MOLECULAR CELL

Mechanistic modeling of chromatin folding to understand function

(2020) Chris A. Brackey et al.   NATURE METHODS

Super-enhancers in cancer

(2019) Palaniraja Thandapani   PHARMACOLOGY & THERAPEUTICS

Microhomology-mediated end joining drives complex rearrangements and over expression of MYC and PVT1 in multiple myeloma

(2019) Aneta Mikulasova et al.   HAEMATOLOGICA

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

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

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes

(2018) Shilpa S. Dhar et al.   MOLECULAR CELL

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

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

(2018) Yixiao Gong et al.   Nature Communications

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

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

(2018) Adam Buckle et al.   MOLECULAR CELL

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

(2018) Noelia Díaz et al.   Nature Communications

Crossed wires: 3D genome misfolding in human disease

(2017) Heidi K. Norton et al.   JOURNAL OF CELL BIOLOGY

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

(2017) Pengze Wu et al.   Nature Communications

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin

(2017) Asa Thibodeau et al.   Scientific Reports

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

TAD disruption as oncogenic driver

(2016) Anne-Laure Valton et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Restraint-based three-dimensional modeling of genomes and genomic domains

(2015) François Serra et al.   FEBS LETTERS

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 biogenesis of chromosome translocations

(2014) Vassilis Roukos et al.   NATURE CELL BIOLOGY

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The immunoglobulin heavy chain locus: genetic variation, missing data and implications for human disease

(2012) C T Watson et al.   GENES AND IMMUNITY

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

Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease

(2012) Jesse M. Engreitz et al.   PLoS One

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Advances in the understanding of mantle cell lymphoma

(2008) Pedro Jares et al.   BRITISH JOURNAL OF HAEMATOLOGY