Patrick Emmet Duffy

A low-rank covariance probe on Evo 2 embeddings predicts ClinVar pathogenicity across SNVs and indels, while annotation probes plus an LLM produce mechanistic hypotheses; scores released for 4.2 million variants.

This study identifies antibody gene features linked to binding and functional activity in vaccine-derived human mAbs against malaria parasites, showing adjuvant effects on clonotype diversity.

This study finds that genetic variants affecting IFN-λ4 production are linked to increased risk and earlier occurrence of gastrointestinal, respiratory, and malaria infections in Malian children.