William Connell

This study benchmarks zero-shot single-cell foundation model embeddings for perturbation effect prediction and finds they do not consistently improve over baseline models under distribution shift.

The paper develops ChemProbe, a model that predicts cellular sensitivity to compounds using transcriptomes and chemical structures, and identifies genes driving ferroptosis.

This paper predicts cellular drug sensitivity by conditioning gene expression on small molecule structures, achieving an R2 of 0.7190.