Alexandra Trinks

Tumor-versus-non-tumor T cell enrichment supported by single-cell and spatial phenotyping enables antigen-agnostic prioritization of candidate tumor-reactive TCRs

The paper identifies tumor-reactive TCRs using T/N ratios and validates them with single-cell and spatial data, showing their tumor association and effector phenotype.

The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo

This study creates a single-cell atlas of gene expression, transcription, and chromatin accessibility in sea urchin embryos, revealing dynamic regulatory elements and lineage-specific gene activation patterns.

Reporter-based screening identifies RAS-RAF stabilizing mutations as drivers of resistance to broad-spectrum RAS inhibition in colorectal cancer

High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment

The paper develops CCISM to distinguish cancer cells from normal epithelial cells in single-cell data, identifying a novel stem-like cell state in the colorectal cancer microenvironment.

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos

The paper uses sci-ATAC-seq and a new tool, ScregSeg, to analyze chromatin dynamics in zebrafish embryos, revealing roles of npas4l/cloche in cell and regulatory states.