Rose Orenbuch

evedesign provides a unified framework for conditional biosequence design, enabling multiobjective workflows and experimental integration across various applications.

This paper introduces popEVE, a deep generative model for proteome-wide disease variant prediction, identifying 442 genes in a developmental disorder cohort, including 123 novel candidates.

LOL-EVE predicts promoter variant effects using a transformer model trained on mammalian promoter sequences, showing improved performance in indel prediction and haplotype analysis.

ProteinGym unifies over 250 deep mutational scans and ~65k clinical variants to benchmark over 70 models in zero-shot and supervised settings; TranceptEVE ranks best overall.

arcasHLA is a tool for high-resolution HLA typing from RNA sequencing data, achieving high accuracy and speed compared to existing methods.