Deepak A. Rao

The paper identifies domain-specific phenotypic effects of MACF1 variants outside the GAR domain, revealing broader neurodevelopmental and craniofacial anomalies.

This study defines the single-cell landscape of Class II lupus nephritis and identifies fibroblast transcriptional programs and chronicity index as potential predictors of kidney outcomes.

This study identifies MAIT cells as regulators of Treg responses in skin inflammation, showing their ability to resolve inflammation through IL-15-dependent mechanisms.

This study identifies two distinct Treg states in RA synovial tissues using scRNA-seq, showing one is dysfunctional and reversible through TNFR2 engagement.

This paper demonstrates that ensilication preserves DNA integrity at ambient temperature, enabling diagnostic-quality long-read sequencing without cold-chain infrastructure.

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.

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

This study identifies pre-treatment naive CD4+ T cell abundance as a predictor of severe irAEs in patients receiving anti-PD-1/CTLA4 checkpoint inhibitor therapy for melanoma.

This study uses single-cell RNA sequencing to identify CD4+ T cell phenotypes in psoriasis patients associated with response to IL-23 blockade.

This study uses spatial transcriptomics to identify CD8+ T cell-driven mechanisms of kidney damage in ICI-AIN, showing increased IFN-γ signaling and proinflammatory myeloid cell activation.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The paper introduces TCAT, a pipeline to annotate T-cell GEPs, identifying 46 reproducible programs across diverse tissues and diseases.

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.

The paper identifies three immunologically distinct groups in lupus nephritis patients based on blood immunophenotyping, correlating with histopathology, treatment response, and renal outcomes.

The paper identifies activated lymphocyte phenotypes in individuals at risk for rheumatoid arthritis using mass cytometry and develops an immunophenotype score to distinguish these individuals from controls.

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

The paper identifies a CD57+ cytotoxic CD8 T cell subset expanded in SSc-ILD patients and links it to lung injury through CD155-CD226 interactions.

This study shows clonal overlap between Tph and Tfh cells in SLE patients and mice, suggesting shared developmental pathways and potential implications for immunosuppressive treatment.

This study identifies a GPVI-platelet-neutrophil-NET axis that drives systemic sclerosis fibrosis and presents it as a therapeutic target.

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.

The paper identifies a non-coding variant that increases ICOS expression, leading to more T peripheral helper cells and contributing to autoimmune diseases.

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

The paper identifies dynamic allele-specific expression changes in T cell activation, particularly in HLA genes, showing regulatory effects linked to autoimmune risk.

A newly identified human macrophage phenotype in RA promotes joint tissue invasiveness and shows variable responses to anti-inflammatory medications.

The paper identifies in vivo eQTL interactions with cytokine levels in a lupus trial, finding novel regulatory mechanisms and potential therapeutic targets.

The paper introduces MASC, a method to identify disease-associated cell subsets in single-cell data, and finds an expanded Th1-skewed cytotoxic CD4+ T cell subset in rheumatoid arthritis.

This paper establishes a protocol for preserving and analyzing single-cell transcriptomes from cryopreserved renal tissue and urine samples in lupus nephritis studies.