Jim R. Hughes

Zone Equalisation Normalisation For Improved Alignment of Epigenetic Signal

This paper introduces ZEN, a normalization method for genomic data that reduces technical noise while preserving biological signals, improving alignment across different experimental platforms.

Regulation of Human Erythroferrone Expression

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

CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer

CREP predicts cis-regulatory element identity from DNA sequence using a fine-tuned Enformer model trained on cell-type-specific annotations.

Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning

The paper develops a machine learning framework to assess quality of chromatin accessibility bigWig tracks using biologically relevant features and internal controls.

Expert-Guided Supervised Annotation of Erythroid Differentiation in Single-Cell RNA-seq

This paper develops a supervised framework for annotating erythroid differentiation stages in scRNA-seq using expert-curated data, achieving high accuracy across cell states and transferability to bulk RNA-seq and external datasets.

Enformer-Based Phylogenetic Tree Reconstruction

The paper uses Enformer to reconstruct phylogenetic trees across multiple species by analyzing regulatory signals from orthologous genes, showing strong correlation with known evolutionary relationships.

Deciphering cis-regulatory elements using REgulamentary

REgulamentary is a tool for cell-type specific annotation of cis-regulatory elements, outperforming existing methods and applied to GWAS data to prioritize causal variants.

TRANCERs: Engineering enhancers into autonomous tissue-specific expression cassettes

TRANCERs convert enhancers into autonomous tissue-specific promoters, enabling precise and programmable gene expression for research and therapy.

ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

ChatMDV provides a natural language interface for generating interactive visualizations of biological data using large language models and the MDV platform.

REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites

REnformer predicts chromatin accessibility from single-cell ATAC-seq data, outperforming Enformer in accuracy and error rates, and validates its utility with a known thalassemia variant.

CREST-GV: Cell types Ranking and Enrichment Score for selecTive Genetic Variants

CREST-GV prioritizes disease-relevant cell types by analyzing genetic variants intersecting open chromatin regions across hundreds of cell types.

Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions

This study shows that MYB activity sustains enhancer-promoter interactions and transcription by maintaining enhancer function in leukemia.

Active regulatory elements recruit cohesin to establish cell-specific chromatin domains.

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

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

The paper identifies enhancers regulating Chd7 expression in neural crest cells and validates their function in chick embryos, revealing tissue-specific regulation of a chromatin remodeller.

An autosomal dominant cardiac arrhythmia syndrome, ST Depression Syndrome, is caused by the de novo creation of a cardiomyocyte enhancer.

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.

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

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

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

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.

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

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.

Multipartite super-enhancers function in an orientation-dependent manner

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

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

The paper identifies Wnt-responsive cis-regulatory elements that coordinate Paupar-Pax6 expression in neuronal cells through chromatin interactions.

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

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

Multi Locus View: An Extensible Web Based Tool for the Analysis of Genomic Data

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

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

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

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

A functional overlap between actively transcribed genes and chromatin boundary elements

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

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

The paper studies chromatin architecture changes during mouse erythroid differentiation using Tiled-C and shows enhancer-promoter interactions form during differentiation, not before gene expression.

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

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

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

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.

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

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

CaptureCompendium: a comprehensive toolkit for 3C analysis.

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.