Joseph Mears

Deep profiling of lupus nephritis kidneys reveals dynamic changes in myeloid cells associated with disease progression

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze myeloid cell dynamics in lupus nephritis, showing shifts in immune responses linked to disease progression.

Early and late RNA eQTL are driven by different genetic mechanisms

The paper identifies distinct genetic mechanisms for early (nuclear) and late (cellular) RNA eQTL by comparing their genomic localization and functional effects across tissues.

Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries

This study demonstrates nanopore sequencing of 10x Genomics multiome libraries to capture full-length transcripts and identify TSS, showing concordance with short-read methods despite higher error rates.

A population-scale atlas of blood and tissue in lupus nephritis

A single-cell atlas of blood and tissue samples from lupus nephritis patients and healthy controls identifies stromal and immune populations, including scar-associated macrophages, which correlate with disease activity.

Granzyme K drives a newly-intentified pathway of complement activation

This study identifies granzyme K as a driver of a novel complement activation pathway independent of classical, lectin, or alternative pathways.

Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles

The paper develops SCENT, a method to create cell-type-specific enhancer-gene maps from single-cell multimodal data, identifying causal variants and genes for diseases.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

The paper performs population-scale single-nucleus multi-omic profiling of skeletal muscle to identify genetic regulation across cell types and traits.

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

The paper maps cell-type-specific eQTLs for HLA genes across multiple tissues and identifies dynamic regulation of HLA-DQ genes in immune cells.

Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

This study identifies eQTLs in psoriatic skin that are modulated by local inflammation, showing that gene regulation is primarily influenced by skin-specific factors rather than systemic variables.

Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis

The paper deconstructs RA synovium using single-cell data to identify six cell type abundance phenotypes associated with distinct inflammatory states.

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation

The paper identifies a common inflammatory macrophage phenotype across severe COVID-19 and other inflammatory diseases, driven by IFN-γ and TNF-α, and suggests potential therapeutic targets.