Evolutionary Design of Genetic Circuits and Cell-Cell Communications. - Yohei Yokobayashi; Cynthia H. Collins; Jared R. Leadbetter; Frances H. Arnold; Ron Weiss (Adv. Complex Syst., 2003)

A Dual Selection Module for Directed Evolution of Genetic Circuits. - Yohei Yokobayashi; Frances H. Arnold (Nat. Comput., 2005)

Random Field Model Reveals Structure of the Protein Recombinational Landscape. - Philip A. Romero; Frances H. Arnold (PLoS Comput. Biol., 2012)

Navigating the protein fitness landscape with Gaussian processes. - Philip A. Romero; Andreas Krause 001; Frances H. Arnold (Proc. Natl. Acad. Sci. USA, 2013)

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization. - Claire N. Bedbrook; Kevin K. Yang; Austin J. Rice; Viviana Gradinaru; Frances H. Arnold (PLoS Comput. Biol., 2017)

Learned protein embeddings for machine learning. - Kevin K. Yang; Zachary Wu; Claire N. Bedbrook; Frances H. Arnold (Bioinform., 2018)

Machine learning-assisted directed protein evolution with combinatorial libraries. - Zachary Wu; S. B. Jennifer Kan; Russell D. Lewis; Bruce J. Wittmann; Frances H. Arnold (Proc. Natl. Acad. Sci. USA, 2019)

Protein sequence design with deep generative models. - Zachary Wu; Kadina E. Johnston; Frances H. Arnold; Kevin K. Yang (CoRR, 2021)

CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes. - Jason Yang; Ariane Mora; Shengchao Liu; Bruce J. Wittmann; Animashree Anandkumar; Frances H. Arnold; Yisong Yue (NeurIPS, 2024)

Steering Generative Models with Experimental Data for Protein Fitness Optimization. - Jason Yang; Wenda Chu; Daniel Khalil; Raul Astudillo; Bruce J. Wittmann; Frances H. Arnold; Yisong Yue (CoRR, 2025)