Jim R. Hughes

Generation of bivalent chromatin domains during cell fate decisions.

An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment.

Intragenic enhancers act as alternative promoters.

Nprl3 is required for normal development of the cardiovascular system.

Causes and consequences of chromatin variation between inbred mice.

MIG: Multi-Image Genome viewer.

ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes.

Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters.

MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation.

Functional characterisation of -regulatory elements governing dynamic expression in the early mouse embryo.

Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo.

Hepcidin is regulated by promoter-associated histone acetylation and HDAC3.

Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia.

Between form and function: the complexity of genome folding.

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.

Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist.

High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates.

DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation.

Nrf2 controls iron homeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin.

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus.

A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells.

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis.

Dynamics of the 4D genome during in vivo lineage specification and differentiation.

Genetic and functional insights into CDA-I prevalence and pathogenesis.

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder.

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

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale.

Enhancers predominantly regulate gene expression during differentiation via transcription initiation.

Multi Locus View: an extensible web-based tool for the analysis of genomic data.

Defining genome architecture at base-pair resolution.

A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker.

Reactivation of a developmentally silenced embryonic globin gene.

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus.

Making connections: enhancers in cellular differentiation.

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.

Natural and Experimental Rewiring of Gene Regulatory Regions.

Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells.

The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin.

LanceOtron: a deep learning peak caller for genome sequencing experiments.

Assessment of Multiway Interactions with Tri-C.

GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.

Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.

Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells.