J. Hughes

发表

Heterogeneity of the 7q36 breakpoints in the t(7;12) involving ETV6 in infant leukemia

S. Scherer, L. Kearney, J. Harbott, 2003, Genes, chromosomes & cancer.

Enhancers predominantly regulate gene expression during differentiation via transcription initiation.

R. Schwessinger, D. Downes, J. Hughes, 2021, Molecular cell.

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

J. Hughes, D. Higgs, J. Sharpe, 2012, The EMBO journal.

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

D. Downes, M. Suciu, Stephanie J. Hill, 2018, Methods and protocols.

Reactivation of a developmentally silenced embryonic globin gene

S. Orkin, L. Pennacchio, D. Downes, 2021, Nature Communications.

Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

Matthew E. Gosden, D. Downes, J. Hughes, 2017, Nature Cell Biology.

Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis

William J. R. Longabaugh, P. Shannon, W. Longabaugh, 2019, bioRxiv.

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

M. Gobbi, E. Giannoulatou, J. Hughes, 2014, Nature Genetics.

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

D. Dickel, A. Visel, T. Swigut, 2020, Cell stem cell.

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

J. Todd, J. Knight, I. Melero, 2021, Nature Genetics.

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Calliope A. Dendrou, I. Pavord, J. Todd, 2021, Cell.

Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo

J. Hughes, S. Taylor, T. Sauka-Spengler, 2019, Developmental cell.

Reconstruction of the global neural crest gene regulatory network in vivo

J. Telenius, J. Hughes, S. Taylor, 2018, bioRxiv.

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

Monika S. Kowalczyk, C. Ponting, A. C. Marques, 2013, Genome Biology.

ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner

Steven J. M. Jones, J. Ragoussis, I. Dunham, 2010, Cell.

Genome-wide identification of TAL1's functional targets: insights into its mechanisms of action in primary erythroid cells.

Shamit Soneji, Stephen Taylor, Jim R Hughes, 2010, Genome research.

Hepcidin is regulated by promoter-associated histone acetylation and HDAC3

S. Rivella, P. Olinga, M. Muckenthaler, 2017, Nature Communications.

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

D. Downes, J. Hughes, A. M. Oudelaar, 2022, Nature Protocols.

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

D. Downes, J. Hughes, D. Higgs, 2021, Nature Communications.

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

Vip Viprakasit, Chris Fisher, Douglas R Higgs, 2009, Proceedings of the National Academy of Sciences.

A functional overlap between actively transcribed genes and chromatin boundary elements

Matthew E. Gosden, D. Downes, J. Hughes, 2020, bioRxiv.

Genetic dissection of the α-globin super-enhancer in vivo

L. Pennacchio, J. Telenius, J. Hughes, 2016, Nature Genetics.

Making connections: enhancers in cellular differentiation.

J. Hughes, Robert A. Beagrie, J. C. Herrmann, 2021, Trends in genetics : TIG.

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

J. Telenius, R. Schwessinger, J. Hughes, 2017, Genome research.

Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity

K. Soo, H. Ong, P. Chow, 2016, Nature Communications.

CSynth: an interactive modelling and visualization tool for 3D chromatin structure

Stephen Taylor, Stephen Todd, Peter Todd, 2020, Bioinform..

DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease

E. Li, J. Hughes, D. Higgs, 2017, Proceedings of the National Academy of Sciences.

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

Claire S. Simon, D. Downes, D. Higgs, 2017, Development.

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

R. Schwessinger, Matthew E. Gosden, D. Downes, 2021, Nature Communications.

Targeted high-resolution chromosome conformation capture at genome-wide scale

J. Telenius, R. Schwessinger, Matthew E. Gosden, 2020, bioRxiv.

An integrated platform to systematically identify causal variants and genes for polygenic human traits

Calliope A. Dendrou, J. Todd, G. Lunter, 2019, bioRxiv.

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

Jelena Telenius, Jim R. Hughes, J. Hughes, 2018, bioRxiv.

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

J. Telenius, J. Hughes, S. McGowan, 2015, Nature Methods.

MIG: Multi-Image Genome viewer

Stephen Taylor, Jim R. Hughes, Simon J. McGowan, 2013, Bioinform..

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

Simona Bianco, Mario Nicodemi, Damien J Downes, 2018, Nature Genetics.

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Davide Marenduzzo, Jim R. Hughes, Dominic Waithe, 2016, Genome Biology.

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

P. Vyas, D. Downes, J. Hughes, 2019, Nature Communications.

Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA‐1 and GATA‐2

G. Blobel, J. Hughes, D. Higgs, 2004, The EMBO journal.

Nrf2 controls iron homoeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin

P. Klenerman, C. Willberg, J. Hughes, 2019, Nature Metabolism.

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

R. Schwessinger, Matthew E. Gosden, D. Downes, 2022, Nature Communications.

Loop extrusion by cohesin plays a key role in enhancer-activated gene expression during differentiation

D. Downes, J. Hughes, Robert A. Beagrie, 2023, bioRxiv.

LanceOtron: a deep learning peak caller for genome sequencing experiments

D. Downes, J. Hughes, S. Taylor, 2022, Bioinform..

Defining genome architecture at base-pair resolution

R. Schwessinger, D. Downes, J. Hughes, 2021, Nature.

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

Lucas V. Greder, R. Schwessinger, D. Downes, 2021, bioRxiv.

Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

D. Downes, J. Hughes, Sophie Lèbre, 2021, Nucleic acids research.

LanceOtron: a deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq

D. Downes, J. Hughes, S. Taylor, 2021, bioRxiv.

Recapitulation of erythropoiesis in congenital dyserythropoietic anemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities

M. Brand, D. Ferguson, R. Schwessinger, 2020, Haematologica.

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

Yee Whye Teh, Gerton Lunter, Jim R Hughes, 2020, Nature Methods.

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

Daniel Hidalgo, M. Socolovsky, Matthew E. Gosden, 2019 .

Modelling erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I)

M. Brand, D. Ferguson, R. Schwessinger, 2019, bioRxiv.

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Jens Lichtenberg, Berthold Göttgens, Feng Yue, 2019, bioRxiv.

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

I. Dunham, Christoph M. Koch, J. Hughes, 2007, Blood.

Generation of bivalent chromatin domains during cell fate decisions

P. Vyas, T. Enver, S. Jacobsen, 2011, Epigenetics & Chromatin.

Manipulating the Mouse Genome to Engineer Precise Functional Syntenic Replacements with Human Sequence

J. Hughes, D. Higgs, J. Sharpe, 2007, Cell.

The worm has turned

J. Hughes, D. Higgs, Deborah Hay, 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

Simone G. Riva, P. Sopp, P. Vyas, 2023, Cell stem cell.

The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains

J. Hughes, P. Harris, C. Ward, 1995, Nature Genetics.

Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features

M. Caulfield, D. Bentley, M. Ross, 2022, Nature Genetics.

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

J. Telenius, J. Hughes, D. Higgs, 2017, Nature Communications.

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

J. Telenius, J. Hughes, M. Nicodemi, 2020, Cell reports.

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

Daniel Hidalgo, M. Socolovsky, D. Higgs, 2020, Nature Communications.

DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning

Yee Whye Teh, Jelena Telenius, Gerton Lunter, 2019, bioRxiv.

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

P. Sopp, P. Vyas, Matthew E. Gosden, 2017, Nature Communications.

A Regulatory SNP Causes a Human Genetic Disease by Creating a New Transcriptional Promoter

Vip Viprakasit, Jan-Fang Cheng, Edward M. Rubin, 2006, Science.

Intragenic enhancers act as alternative promoters.

Monika S. Kowalczyk, Thomas A Milne, Douglas R Higgs, 2012, Molecular cell.

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

Keith W. Vance, J. Hughes, Robert J. Williams, 2021, bioRxiv.

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

T. Jenuwein, J. Hughes, D. Higgs, 2015, Cell reports.

A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition

R. Hardison, G. Blobel, M. Weiss, 2016, Nature Medicine.