Damien J. Downes

This study identifies the transcriptional regulatory mechanisms governing ERFE expression in human erythroblasts using genomic approaches.

The paper shows that active enhancers recruit cohesin to form cell-specific chromatin domains, using the alpha globin cluster as a model.

The paper identifies a de novo enhancer mutation in KCNB1 causing ST Depression Syndrome, a cardiac arrhythmia, and shows it can be predicted by a deep neural network.

The paper investigates the role of cohesin-mediated loop extrusion in enhancer-promoter proximity and gene expression during mouse erythropoiesis, finding that it is important but not exclusive for gene activation.

The paper uses targeted chromatin interaction profiling to identify causal genes at type 2 diabetes GWAS loci with higher sensitivity and resolution than genome-wide methods.

The paper shows that super-enhancers function directionally and orientation-dependently, unlike regular enhancers, by analyzing the β-globin super-enhancer.

The paper examines how dynamic chromatin boundaries around the Runx1 gene influence its expression during hematopoietic development in mice.

MLV is a web-based tool for visualizing, analyzing, and annotating genomic datasets, enabling multi-scale interaction and integration of multiple data tracks.

LanceOtron improves peak calling in ATAC-seq, ChIP-seq, and DNase-seq by using deep learning to better capture peak shapes and outperforms MACS2 in selectivity and sensitivity.

DeepC predicts chromatin interactions from DNA sequence using deep learning and transfer learning, generalizing across cell types and resolutions.

The paper shows that actively transcribed genes can function as chromatin boundary elements, similar to CTCF-bound sites, by stalling chromatin loop extrusion.

The paper quantifies transcription factor abundances during human erythropoiesis and reveals gene regulatory principles and imbalances in coactivator-corepressor ratios.

The paper introduces a new method, NuTi Capture-C, that improves high-resolution chromosome conformation capture by reducing noise and increasing sequencing content, enabling reproducible genome-wide interaction profiles.

CaptureCompendium provides software tools to simplify the design, analysis, and visualization of 3C experiments, addressing the need for specialized bioinformatics skills in genome folding studies.

The paper develops a platform combining ATAC-seq, DNaseI footprints, NG Capture-C, and machine learning to identify causal variants and genes for polygenic human traits.

This study shows that enhancers primarily regulate gene expression by promoting transcription initiation rather than by affecting RNA polymerase II pausing.

This study models erythropoiesis in CDA-I by analyzing patient-derived erythroblasts, identifying abnormalities in DNA accessibility, proliferation, and enucleation, with genotype-phenotype correlations.

The paper identifies a distinct class of enhancers in leukemia cells that depend on H3K79 methylation and shows that DOT1L inhibition disrupts their function.

The paper develops Tri-C, a single-cell 3C method, to reveal dynamic chromatin interactions and regulatory hubs in mammalian cells.