Papers

2026

1. Mechanistic Modelling of Recessive Disease through Allelic Integration of Variant Effects

   Hasan Çubuk, Marcin Plech, Vahid Aslanzadeh, Marie Zikanova, Vaclava Skopova, Stanislav Kmoch, Yuxin Shen, Joseph A Marsh, and Grzegorz Kudla

   Cell Systems, 2026

2025

1. Improving the generalization of protein expression models with mechanistic sequence information

   Yuxin Shen, Grzegorz Kudla, and Diego A Oyarzún

   Nucleic Acids Research, 2025
2. Optimization of regulatory DNA with active learning

   Yuxin Shen, Grzegorz Kudla, and Diego A Oyarzún

   Computational and Structural Biotechnology Journal, 2025
3. Effective sequence-to-expression prediction for membrane proteins using machine learning and computational protein design

   Yuxin Shen, Juno Underhill, Adrian J Mulholland, Diego A Oyarzun, and Paul Curnow

   bioRxiv, 2025