Kamil Slowikowski

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

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

The paper analyzes 6 million T cells from 91 studies to identify TCR sequence convergence patterns and their association with functional and cellular T cell phenotypes.

The paper generates a multi-modal atlas of thyroid and blood cells from HT, GD, and controls, revealing shared immune niches despite distinct disease mechanisms.

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

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

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

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

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.

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.

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.

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.

UBiT2 is a client-side web application for analyzing RNA-seq and qPCR data, offering offline analysis and visualization with interactive tools and exportable figures.

The paper shows that many de novo protein truncating variants in neurodevelopmental disorders are common in population cohorts and do not contribute to risk, using data from 9246 families and 60,706 adults.

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