John Ray

This study identifies IRF5 as a critical driver of iHPC differentiation and MAS pathogenesis, showing it can be targeted pharmacologically.

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

The paper identifies 545 expression-modulating variants in CD4+ T cells linked to autoimmune diseases and shows they regulate genes in a lymphocyte activation network.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.

The paper identifies causal genetic variants in autoimmune diseases by combining allele-specific reporter assays with chromatin accessibility data, showing their impact on gene expression and T cell function.

The paper identifies 482 SLE risk variants with enhancer activity and characterizes allelic regulatory mechanisms at 27 risk loci using MPRA.

The paper uses the ABC Model to map enhancer-gene regulation across 131 cell types and tissues, linking GWAS variants to disease genes, particularly in IBD.

MAUDE improves analysis of sorting-based CRISPR screens by quantifying guide RNA effects on gene expression and estimating statistical significance.