Masayuki Nagai
Computational Biologist | Ph.D. candidate | Cold Spring Harbor Laboratory, New York
About Me
I’m a third-year Ph.D. student in Dr. Peter Koo’s Lab, developing AI methods for regulatory genomics to achieve generalization across diverse genetic variation and cellular contexts.
My research focuses on designing and integrating causally informative perturbations to bridge wet-lab experimentation and computational modeling, extracting mechanistic biological insights, and characterizing model failure modes, with a key application in programmable regulatory sequence design. I am also committed to the responsible advancement of biological AI models, with particular attention to biosecurity and AI alignment to mitigate dual-use risks and support safe deployment.
Outside of research, I’m passionate about tennis and climbing mountains!
Interests
- Continual Learning: Refining causal understanding through perturbation data integration
- Active Learning: Identifying the most informative experiments to guide research
- Sequence Design: Engineering sequences with desired functional properties
- Biosecurity: Preventing misuse and mitigating dual-use risks of biological AI models
- Mechanistic Interpretability: Understanding the inner workings of deep learning models
News
- Apr 2026 Research highlight on AlphaGenome in Cell Research (co-first author). Overview on X.
- Mar 2026 Talk on Improving Genomic Deep Learning Models using Continual Learning at the CSHL Systems Biology meeting.
- Feb 2026 Review/perspective Toward Interpretable and Generalizable AI in Regulatory Genomics, posted on arXiv (co-first author). Overview on X.
- Aug 2025 Talk on Causal Refinement for Genomic Deep Learning Models at MLCB 2025 (YouTube).
- Aug 2024 Joined Dr. Peter Koo's group.
- Aug 2023 Started Ph.D. at Cold Spring Harbor Laboratory.