Kathryn Weinand

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

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

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.

This paper introduces scDRS, a method to identify disease-associated cells in scRNA-seq data using polygenic risk scores, finding novel subpopulations linked to diseases like IBD and schizophrenia.

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

Symphony maps query cells to large reference atlases efficiently, enabling rapid identification of cell states and phenotypes across diverse datasets.

The paper identifies BDNF-specific chromatin accessibility changes in neurons and links them to gene regulation and neurodevelopmental traits.

The paper introduces scPOST, a tool for estimating statistical power in single-cell studies, and shows that larger sample sizes, reduced batch effects, and lower cell state variability increase power to detect clinically associated cell state shifts.

The paper shows GA-repeats on mammalian X chromosomes support Ohno's hypothesis of dosage compensation by transcriptional upregulation through convergent evolution.