Publications — Radcliffe Department of Medicine

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Single-cell technologies meet Hi-C.

Hughes JR. and Davies JOJ., (2024), Nat Genet

Deciphering cis-regulatory elements using REgulamentary

Riva SG. et al, (2024)

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.

Xiang G. et al, (2023), bioRxiv

Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases.

Pagnamenta AT. et al, (2023), Genome Med, 15

Ancient genomic linkage couples metabolism with erythroid development.

Preston AE. et al, (2023), bioRxiv

CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.

Riva SG. et al, (2023), J Vis Exp

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

Stolper RJ. et al, (2023)

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

Downes DJ. et al, (2023), Nat Protoc

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

Turkalj S. et al, (2023), Cell Stem Cell, 30, 722 - 740.e11

Direct correction of haemoglobin E β-thalassaemia using base editors.

Badat M. et al, (2023), Nat Commun, 14

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

Torres JM. et al, (2023), Wellcome Open Res, 8

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors

Williams R. et al, (2022)

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

Robbe P. et al, (2022), Nat Genet, 54, 1675 - 1689

Natural and Experimental Rewiring of Gene Regulatory Regions.

Downes DJ. and Hughes JR., (2022), Annu Rev Genomics Hum Genet, 23, 73 - 97

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

Hentges LD. et al, (2022), Bioinformatics

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

Truch J. et al, (2022), Nat Commun, 13

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

Pavlaki I. et al, (2022), PLoS genetics, 18

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.

Owens DDG. et al, (2022), Nat Commun, 13

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

Downes DJ. et al, (2022), Nat Protoc

Assessment of Multiway Interactions with Tri-C.

Oudelaar AM. et al, (2022), Methods Mol Biol, 2532, 95 - 112

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