Catherine Snopkowski

Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing

GIFT enables high-accuracy genotyping in single cells, revealing mutation-dependent hematopoietic responses in MPN patients.

Ecological determinants of disease and immunity in myelodysplastic syndromes

This study uses spatial transcriptomics and single-cell analysis to reveal how MDS bone marrow microenvironments are altered, showing TGFβ dysregulation in malignant cells and immune escape mechanisms.

Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition

In mouse pancreatic cancer models, p53, CDKN2A and SMAD4 programs converge on a rare Kras-mutant progenitor-like state whose niche KRAS inhibition collapses and p53 loss expands.

The covariance environment defines cellular niches for spatial inference

This paper introduces COVET and ENVI to model spatial niches and improve gene expression imputation and spatial context inference from single-cell data.

Transcript-specific enrichment enables profiling rare cell states via scRNA-seq

This paper introduces PERFF-seq, a method to profile rare cell states via scRNA-seq by enriching for specific RNA transcripts, demonstrating its application in immune and brain tissues.

Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts

This study uses scRNA-seq to analyze kidney allograft biopsies and identifies recipient-derived fibroblasts and other cell states associated with fibrosis and rejection.