Venkatesh P. Mysore

Measuring peptide-MHC generalization to unseen alleles across both HLA classes

The paper evaluates peptide-MHC generalization to unseen alleles and introduces a benchmark and model that improves prediction accuracy for rare HLA alleles.

Protein solubility depends on centrifugation: Aiki-Sol, a per-regime predictor for E. coli

The paper introduces Aiki-Sol, a predictor for E. coli protein solubility that accounts for centrifugation regimes, improving performance by treating regime as a feature rather than noise.

Aiki-GeNano: Multi-Stage Preference Optimization for Generative Design of Developable Nanobodies

Aiki-GeNano improves nanobody design by integrating developability signals into training, enhancing thermal stability and reducing liabilities while preserving humanness.

Aiki-XP: leakage-controlled multimodal prediction of within-species relative protein expression at pan-bacterial scale

Aiki-XP predicts within-species relative protein expression across bacteria using multimodal data, outperforming single-omics models in leakage-controlled settings.

A structural model of a Ras-Raf signalosome

The paper proposes an atomistic structural model of a Ras-Raf signalosome based on molecular dynamics simulations, mutagenesis, electron microscopy, and cell-based experiments.