References
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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
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Kaiyi Jiang et al. (2025). Rapid in silico directed evolution by a protein language model with EVOLVEpro. Science. DOI:10.1126/science.adr6006
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Roshan Rao et al. (2021). MSA Transformer. bioRxiv. doi: https://doi.org/10.1101/2021.02.12.430858
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Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4
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Pedregosa et al. (2011) Scikit-learn: Machine Learning in Python, JMLR 12, pp. 2825-2830, 2011.
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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