Soumya Raychaudhuri

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

Harmony alternates diversity-penalized soft clustering with cluster-specific linear correction of PCA embeddings, integrating single-cell datasets over multiple covariates and handling 500,000 cells in 7.2GB of memory.

This paper develops G-Prob, a method converting genetic data into disease probabilities for inflammatory arthritis, improving diagnostic accuracy in rheumatology.

The paper constructs cell-type-specific TF binding annotations by combining sequence-based predictions with chromatin data, showing increased heritability enrichment for 49 diseases.

The paper identifies a genetic variant on 3q23 associated with early progression from Mycobacterium tuberculosis exposure to active tuberculosis in Peruvians, showing higher heritability than general TB susceptibility.

One-versus-all rank-sum across 10 groups and 1,000 features on a sparse 1-million-observation simulation finished in 17 seconds instead of 6.4 hours, with the same pass yielding auROC.

Benchmarker evaluates gene prioritization algorithms using GWAS data through cross-validation, showing that combining strategies improves gene prioritization quality.

The paper assesses gene network connectivity's role in disease heritability using LD score regression and finds that network annotations are enriched but largely explained by regulatory annotations.

IMPACT improves regulatory element annotation by integrating TF binding profiles with epigenomic data, showing better performance in predicting eQTLs and capturing RA heritability.

A common missense variant in FBN1 reduces height by 2.2 cm in Peruvians, showing strong positive selection and higher frequency in coastal Native American populations.

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

This paper identifies shared genetic risk factors between schizophrenia and 19 immune diseases, including three variants with pleiotropic effects and significant genetic correlations for several immune diseases.

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 study fine-maps RA and T1D loci outside the MHC, identifying causal variants and confirming their functional impact through allele-specific binding and enhancer activity.

The paper identifies two distinct fibroblast subsets in arthritis that drive inflammation or tissue damage, showing their unique roles in disease progression.

The paper uses gene expression data and GWAS summary statistics to identify disease-relevant tissues and cell types by detecting heritability enrichments in gene-specific expression regions.

This study investigates whether immune gene variation contributes to schizophrenia by analyzing genome-wide association data, finding limited immune gene enrichment beyond the MHC region compared to five autoimmune diseases.

The paper introduces BUHMBOX, a statistical method to distinguish pleiotropy from heterogeneity in genetic data, finding shared genetic bases in autoimmune diseases and between MDD and schizophrenia.

The paper identifies lymphoma risk SNPs enriched in regulatory elements using a multiscale approach and develops an algorithm to analyze GWAS results.

This paper partitions heritability across functional genomic elements using GWAS summary statistics to identify trait-specific enrichments.

The paper develops a statistical method to distinguish causal non-coding variants from colocalizing annotations in complex trait loci, identifying independent effects in disease-associated regions.

The paper shows regulatory variants explain significantly more heritability than coding variants for 11 diseases, using imputed data across 218 cell types.