Old Friends & New Partners: AI-driven Models and Agents for Genome and Cell Engineering

Our research focuses on two areas for precision gene and cell engineering: new tool development and AI-enabled engineering. First, we are moving beyond the current limitations of CRISPR-Cas9 by focusing on new enzymes for large, no-DNA-damage gene insertions. We have engineered single-strand annealing proteins (SSAPs) for cleavage-free knock-in and are excited to collaboratively apply these tools in ex vivo and animal models. Second, to accelerate the pace of gene and cell engineering, our lab is developing AI agents for biomedical research to automate gene editing, cell engineering, and genomic discovery, from hypothesis generation to data interpretation. This AI-native approach has shown significant potential in areas such as CRISPR-GPT for gene-editing, RNAGenesis for therapeutic RNA design, and in stem cell engineering and functional screening (AutoScreen, Stella), showcased at genomics.stanford.edu. Our work demonstrates the broad utility of new tools, AI models and agents in accelerating genome and cell engineering.