Jacob Merle Gershon

I am a protein designer working on deep generative models for de novo protein and enzyme design. I completed my PhD in the Baker lab at the University of Washington Institute for Protein Design, through the Molecular Engineering and Sciences Institute, and I hold a B.S. and M.S. in Biomedical Engineering from SUNY Binghamton.

My research sits at the point where generative machine learning meets wet-lab protein engineering. I co-developed ProteinGenerator, a RoseTTAFold-based sequence space diffusion model that generates protein sequence and structure together, which makes it possible to design directly against sequence-level constraints such as amino acid composition, internal repeats, and multistate behavior. More recently my work has focused on designing proteins at library scale, and on generative methods for de novo enzymes.

I am interested in using synthetic biology and protein engineering to address environmental rehabilitation, clean water, and the sustainable manufacturing of textiles, goods, and chemicals. Traditional textile manufacturing generates toxic byproducts, and I think de novo enzymes are a credible route to alleviating that.

I also help organize the GEM workshop on generative and experimental platforms for biomolecular design at ICLR.

In my free time I love to eat tomatoes, make riddles, and watch F1.