Soumya Raychaudhuri

Powerful and accurate case-control analysis of spatial molecular data

This paper introduces VIMA, a method for analyzing spatial molecular data to identify disease-associated spatial features, showing improved performance over existing methods in simulations and real datasets.

Efficient genome-wide mapping of reproducible, context-dependent eQTLs at single-cell resolution

The paper introduces Dynema, a method for genome-wide mapping of context-dependent and independent eQTLs at single-cell resolution, showing improved detection compared to pseudobulking approaches.

Rethinking the Benign Nature of Class II Lupus Nephritis

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.

Identifying the causal allele in the CD40 autoimmune locus enables discovery of context-specific trans-effects in B cells

The paper identifies a causal allele in the CD40 locus and demonstrates context-specific trans-effects in B cells using CITE-seq and CRAFT-seq.

TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes

The paper maps common TCR alleles in 2,668 donors, finds natural selection on TRAJ and TRAV genes, and shows allelic polymorphism affects T cell function.

cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution

cellGeometry deconvolutes bulk RNA-Seq using geometric methods, offering faster and more accurate results than existing approaches.

SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

Functional and dysfunctional T regulatory cell states in human tissues in RA and other autoimmune arthritic diseases

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

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.

Multi-ancestral GWAS with the VA Million Veteran Program enables functional interpretation of rheumatoid arthritis alleles

This study conducts a multi-ancestry GWAS of rheumatoid arthritis using the VA Million Veteran Program, identifying 152 genome-wide significant loci and improving fine-mapping resolution.

Integration of large, complex single-cell datasets with Harmony2

Harmony2 integrates large single-cell RNA-seq datasets efficiently and accurately, preventing overintegration in biologically diverse data.

An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans

The paper identifies an age-related expansion of an inflammatory and quiescent HSC subpopulation using integrated single-cell data.

Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions

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

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.

Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach

The paper benchmarks snATAC-seq integration pipelines using multimodal datasets and recommends SnapATAC2 + Harmony with ENCODE cCRE features for effective integration.

Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis

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.

Estimating the cis-heritability of gene expression using single cell expression profiles controls false positive rate of eGene detection

The paper introduces scGeneHE, a method to estimate cis-heritability from scRNA-seq data, reducing false positives in eGene detection.

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.

Wnt signaling drives stromal inflammation in inflammatory arthritis

This study shows Wnt signaling drives inflammation in fibroblasts of inflammatory arthritis, suggesting it as a therapeutic target.

Identifying genetic variants that influence the abundance of cell states in single-cell data

The paper introduces GeNA, a tool to identify genetic variants influencing cell state abundance in single-cell data, finding five loci associated with immune cell state shifts.

The influence of HLA genetic variation on plasma protein expression

This study identifies 504 plasma proteins influenced by HLA genetic variation in 45,330 Europeans, revealing their roles in immune function and disease.

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.

Defining the function of disease variants with CRISPR editing and multimodal single cell sequencing

The paper uses CRISPR editing and multimodal single-cell sequencing to identify the functional effects of disease variants in primary human cells.

Integrating spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns

The effect of altitude on the expression of immune-related genes in Peruvian rural indigenous

This study identifies altitude-associated immune gene expression differences in Peruvian Andean populations, revealing distinct transcriptomic profiles linked to high-altitude adaptation.

Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs

The paper demonstrates that modeling single-cell perturbation states improves detection of reQTLs by accounting for cell-level heterogeneity in perturbation responses.

Leveraging single-cell ATAC-seq to identify disease-critical fetal and adult brain cell types

The paper integrates GWAS with scATAC-seq and scRNA-seq data to identify disease-critical fetal and adult brain cell types for multiple traits.

High-dimensional phenotyping to define the genetic basis of cellular morphology

This study identifies genetic variants associated with cellular morphology using high-content imaging and genomic data from iPSCs.

Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant

The paper identifies a regulatory pathway involving rs7034653, FRA2, and TRAF1 that explains how a non-coding variant increases risk of inflammatory arthritis.