References

  1. Hino, T. et al. (2023). An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell, 186(22), 4920–4935.e23. https://doi.org/10.1016/j.cell.2023.08.031

  2. Kaiyi Jiang et al. (2025). Rapid in silico directed evolution by a protein language model with EVOLVEpro. Science. DOI:10.1126/science.adr6006

  3. Roshan Rao et al. (2021). MSA Transformer. bioRxiv. doi: https://doi.org/10.1101/2021.02.12.430858

  4. Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4

  5. Pedregosa et al. (2011) Scikit-learn: Machine Learning in Python, JMLR 12, pp. 2825-2830, 2011.

  6. Wilke C (2024). cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'. R package version 1.1.3, https://wilkelab.org/cowplot/.

Special thanks to:

  • Dr. Marcotte and Zoya Ansari
  • Authors of EvolvePro for making their code open source
  • Creators of ESM for making the model weights open
  • Members of the Wilke Lab and BioML Society at UT Austin for introducing me to PLMs