Neural Bandits for Protein Sequence Optimization. - Chenyu Wang; Joseph C. Kim; Le Cong; Mengdi Wang (CISS, 2022)

Bandit Theory and Thompson Sampling-Guided Directed Evolution for Sequence Optimization. - Hui Yuan 002; Chengzhuo Ni; Huazheng Wang; Xuezhou Zhang; Le Cong; Csaba Szepesvári; Mengdi Wang (NeurIPS, 2022)

Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. - Henry Cousins; Taryn Hall; Yinglong Guo; Luke Tso; Kathy T. H. Tzeng; Le Cong; Russ B. Altman (Bioinform., 2023)

CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments. - Kaixuan Huang; Yuanhao Qu; Henry Cousins; William A. Johnson; Di Yin; Mihir Shah; Denny Zhou; Russ B. Altman; Mengdi Wang; Le Cong (CoRR, 2024)

Latent Diffusion Models for Controllable RNA Sequence Generation. - Kaixuan Huang; Yukang Yang; Kaidi Fu; Yanyi Chu; Le Cong; Mengdi Wang (CoRR, 2024)

FoldMark: Protecting Protein Generative Models with Watermarking. - Zaixi Zhang; Ruofan Jin; Kaidi Fu; Le Cong; Marinka Zitnik; Mengdi Wang (CoRR, 2024)

A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions. - Yanyi Chu; Dan Yu; Yupeng Li; Kaixuan Huang; Yue Shen; Le Cong; Jason Zhang; Mengdi Wang (Nat. Mac. Intell., 2024)

Author Correction: A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions. - Yanyi Chu; Dan Yu; Yupeng Li; Kaixuan Huang; Yue Shen; Le Cong; Jason Zhang; Mengdi Wang (Nat. Mac. Intell., 2024)

Genome-Bench: A Scientific Reasoning Benchmark from Real-World Expert Discussions. - Ming Yin; Yuanhao Qu; Dyllan Liu; Ling Yang; Le Cong; Mengdi Wang (CoRR, 2025)

GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance. - Zaixi Zhang; Zhenghong Zhou; Ruofan Jin; Le Cong; Mengdi Wang (CoRR, 2025)

STELLA: Self-Evolving LLM Agent for Biomedical Research. - Ruofan Jin; Zaixi Zhang; Mengdi Wang; Le Cong (CoRR, 2025)