publications
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Computational design of cysteine proteases
H. Choi, B. Coventry, M. Bauer, P. Venkatesh, A. Chen, D. Kim, A. K. Bera, A. Kang, H. Nguyen, E. Joyce, B. Shankaran, T. R. Thompson, J. M. Gershon, A. F. Shida, G. R. Lee, D. Hilvert, S. J. Pellock, D. Baker
bioRxiv, 2025 paper
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Multistate and functional protein design using RoseTTAFold sequence space diffusion
S. L. Lisanza, J. M. Gershon, S. W. K. Tipps, J. N. Sims, L. Arnoldt, S. J. Hendel, M. K. Simma, G. Liu, M. Yase, H. Wu, C. D. Tharp, X. Li, A. Kang, E. Brackenbrough, A. K. Bera, S. Gerben, B. J. Wittmann, A. C. McShan, D. Baker
Nature Biotechnology 43(8):1288–1298, 2025 paper code
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Hierarchical protein backbone generation with latent and structure diffusion
J. Yim, M. Jaakik, G. Liu, J. Gershon, K. Kreis, D. Baker, R. Barzilay, T. Jaakkola
arXiv:2504.09374, 2025 paper
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Protein Design at Library Scale
J. M. Gershon
PhD thesis, University of Washington, 2025
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Integrating Generative and Experimental Platforms for Biomolecular Design
C.-H. Liu, J. Rector-Brooks, S. Yang, S. L. Lisanza, F.-Z. Li, H. Stark, J. Gershon, L. Hong, P. Chatterjee, Y. Bengio
ICLR 2025 Workshop Proposals, 2024 openreview
Talks
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Towards Guiding Generative Models with Experimental Data
ML Protein Engineering Seminar, 2024 video