Papers

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

   bioRxiv, 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
4. 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

   bioRxiv, 2025