Aadyot Bhatnagar

Jan 6, 2025 | biorxiv.org | Stephen Nayfach |Aadyot Bhatnagar |Gabriella O. Estevam |Andrey Novichkov

AbstractCRISPR-Cas enzymes must recognize a protospacer-adjacent motif (PAM) to edit a genomic site, significantly limiting the range of targetable sequences in a genome.

Aug 3, 2024 | biorxiv.org | Jeffrey A. Ruffolo |Aadyot Bhatnagar |Stephen Nayfach |Joel Beazer

AbstractGenerative models for protein design trained on experimentally determined structures have proven useful for a variety of design tasks. However, such methods are limited by the quantity and diversity of structures used for training, which represent a small, biased fraction of protein space. Here, we describe proseLM, a method for protein sequence design based on adaptation of protein language models to incorporate structural and functional context.

Apr 22, 2024 | biorxiv.org | Jeffrey A. Ruffolo |Stephen Nayfach |Joseph Gallagher |Aadyot Bhatnagar

AbstractGene editing has the potential to solve fundamental challenges in agriculture, biotechnology, and human health. CRISPR-based gene editors derived from microbes, while powerful, often show significant functional tradeoffs when ported into non-native environments, such as human cells. Artificial intelligence (AI) enabled design provides a powerful alternative with potential to bypass evolutionary constraints and generate editors with optimal properties.