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)

Batched Stochastic Bayesian Optimization via Combinatorial Constraints Design. - Kevin K. Yang; Yuxin Chen 001; Alycia Lee; Yisong Yue (AISTATS, 2019)

FLIP: Benchmark tasks in fitness landscape inference for proteins. - Christian Dallago; Jody Mou; Kadina E. Johnston; Bruce J. Wittmann; Nicholas Bhattacharya; Samuel Goldman; Ali Madani; Kevin K. Yang (NeurIPS Datasets and Benchmarks, 2021)

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

Adaptive machine learning for protein engineering. - Brian L. Hie; Kevin K. Yang (CoRR, 2021)

Exploring evolution-based & -free protein language models as protein function predictors. - Mingyang Hu; Fajie Yuan; Kevin K. Yang; Fusong Ju; Jin Su; Hui Wang; Fei Yang; Qiuyang Ding (CoRR, 2022)

Protein structure generation via folding diffusion. - Kevin E. Wu; Kevin K. Yang; Rianne van den Berg; James Y. Zou; Alex X. Lu; Ava P. Amini (CoRR, 2022)

Machine learning modeling of family wide enzyme-substrate specificity screens. - Samuel Goldman; Ria Das; Kevin K. Yang; Connor W. Coley (PLoS Comput. Biol., 2022)

A topological data analytic approach for discovering biophysical signatures in protein dynamics. - Wai-Shing Tang; Gabriel Monteiro da Silva; Henry Kirveslahti; Erin Skeens; Bibo Feng; Timothy Sudijono; Kevin K. Yang; Sayan Mukherjee 001; Brenda M. Rubenstein; Lorin Crawford (PLoS Comput. Biol., 2022)

From noise to protein with image models. - Ava P. Amini; Kevin K. Yang (Nat. Comput. Sci., 2023)

Deep self-supervised learning for biosynthetic gene cluster detection and product classification. - Carolina Rios-Martinez; Nicholas Bhattacharya; Ava P. Amini; Lorin Crawford; Kevin K. Yang (PLoS Comput. Biol., 2023)

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models. - Francesca-Zhoufan Li; Ava P. Amini; Yisong Yue; Kevin K. Yang; Alex Xijie Lu (ICML, 2024)

EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics. - Chenqing Hua; Yong Liu; Dinghuai Zhang; Odin Zhang; Sitao Luan; Kevin K. Yang; Guy Wolf; Doina Precup; Shuangjia Zheng (CoRR, 2024)

Tokenized and continuous embedding compressions of protein sequence and structure. - Amy X. Lu; Wilson Yan; Kevin K. Yang; Vladimir Gligorijevic; Kyunghyun Cho; Pieter Abbeel; Richard Bonneau; Nathan C. Frey (Patterns, 2025)

Benchmarking uncertainty quantification for protein engineering. - Kevin P. Greenman; Ava P. Amini; Kevin K. Yang (PLoS Comput. Biol., 2025)

MotifBench: A standardized protein design benchmark for motif-scaffolding problems. - Zhuoqi Zheng; Bo Zhang; Kieran Didi; Kevin K. Yang; Jason Yim; Joseph L. Watson; Hai-Feng Chen; Brian L. Trippe (CoRR, 2025)