Jim R. Hughes

MRC Molecular Haematology Unit, University of Oxford

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 10	2023

Other Publications

Article	Year
Generation of bivalent chromatin domains during cell fate decisions. Epigenetics & chromatin\| PubMed ID: 21645363	2011
An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. The EMBO journal\| PubMed ID: 22056776	2011
Intragenic enhancers act as alternative promoters. Molecular cell\| PubMed ID: 22264824	2012
Nprl3 is required for normal development of the cardiovascular system. Mammalian genome : official journal of the International Mammalian Genome Society\| PubMed ID: 22538705	2012
Causes and consequences of chromatin variation between inbred mice. PLoS genetics\| PubMed ID: 23785304	2013
MIG: Multi-Image Genome viewer. Bioinformatics (Oxford, England)\| PubMed ID: 23842811	2013
ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes. Cell reports\| PubMed ID: 25865896	2015
Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. EMBO reports\| PubMed ID: 27506891	2016
MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation. Experimental hematology\| PubMed ID: 27856324	2017
Functional characterisation of -regulatory elements governing dynamic expression in the early mouse embryo. Development (Cambridge, England)\| PubMed ID: 28174238	2017
Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nature cell biology\| PubMed ID: 28737770	2017
Hepcidin is regulated by promoter-associated histone acetylation and HDAC3. Nature communications\| PubMed ID: 28864822	2017
Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia. Nature communications\| PubMed ID: 28871148	2017
Between form and function: the complexity of genome folding. Human molecular genetics\| PubMed ID: 28977451	2017
Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nucleic acids research\| PubMed ID: 29186505	2017
Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells. Bio-protocol\| PubMed ID: 29270442	2017
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature genetics\| PubMed ID: 30374068	2018
The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nature genetics\| PubMed ID: 31133748	2019
High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates. Methods and protocols\| PubMed ID: 31164571	2018
DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nature communications\| PubMed ID: 31243293	2019
Nrf2 controls iron homeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin. Nature metabolism\| PubMed ID: 31276102	2019
A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nature communications\| PubMed ID: 31776347	2019
A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells. Cell reports\| PubMed ID: 32075757	2020
Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Molecular cell\| PubMed ID: 32330456	2020
Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nature communications\| PubMed ID: 32483172	2020
Genetic and functional insights into CDA-I prevalence and pathogenesis. Journal of medical genetics\| PubMed ID: 32518175	2021
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell stem cell\| PubMed ID: 32991838	2020
DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nature methods\| PubMed ID: 33046896	2020
High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature communications\| PubMed ID: 33483495	2021
Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Molecular cell\| PubMed ID: 33539786	2021
Multi Locus View: an extensible web-based tool for the analysis of genomic data. Communications biology\| PubMed ID: 34035422	2021
Defining genome architecture at base-pair resolution. Nature\| PubMed ID: 34108683	2021
A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nature communications\| PubMed ID: 34155213	2021
Reactivation of a developmentally silenced embryonic globin gene. Nature communications\| PubMed ID: 34290235	2021
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nature genetics\| PubMed ID: 34737427	2021
Making connections: enhancers in cellular differentiation. Trends in genetics : TIG\| PubMed ID: 34753603	2022
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature protocols\| PubMed ID: 35121852	2022
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nature communications\| PubMed ID: 35140205	2022
Natural and Experimental Rewiring of Gene Regulatory Regions. Annual review of genomics and human genetics\| PubMed ID: 35472292	2022
Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. PLoS genetics\| PubMed ID: 35709096	2022
The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin. Nature communications\| PubMed ID: 35710802	2022
LanceOtron: a deep learning peak caller for genome sequencing experiments. Bioinformatics (Oxford, England)\| PubMed ID: 35866989	2022
Assessment of Multiway Interactions with Tri-C. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 35867247	2022
GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell stem cell\| PubMed ID: 37146586	2023
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature protocols\| PubMed ID: 37369851	2023
Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells. Wellcome open research\| PubMed ID: 37736013	2023