Emily H. Stoops

This paper introduces Shorkie, a DNA language model pretrained on fungal genomes that improves gene expression prediction in budding yeast by capturing regulatory motif dynamics and variant effects.

The paper aggregates and analyzes phenotypic data from yeast knock-out screens to identify gene functions and relationships, revealing new biological insights.

The paper develops YETI, a yeast library with inducible gene expression, and shows low native expression can bias promoter-perturbing screens.