About Me

I am Wenduo Cheng, a 3rd-year Ph.D. student in the Ray and Stephanie Lane Computational Biology Department at Carnegie Mellon University. I am fortunate to be advised by Jian Ma. Before my Ph.D., I completed an M.S. in Computational Biology at CMU and a B.S. in Genetics and Genomics at Duke Kunshan University.

My background spans bioinformatic sequence analysis, evolutionary biology, environmental science, genome-wide association studies, and deep learning for computational biology. My current research interests lie in applying AI to accelerate biological discovery, particularly through biological foundation models and autonomous agents. My work centers on these directions:

• Biological Foundation Models: I build biologically meaningful “virtual cell” models that capture evolutionary and regulatory constraints, aiming for representations that generalize across cell types, modalities, and biological contexts.
• Autonomous Agents for Science: I develop LLM agents that accelerate experimental design, computational analysis, and lab automation, turning open-ended scientific questions into reproducible, executable workflows.
• Gene Regulation & Multimodal Modeling: I study the principles of gene regulation through multimodal modeling, integrating sequence, structure, and functional signals to reveal how regulatory information is encoded and read out.

🔥 News

📝 Selected Publications

A full list of publications is available here. († indicates equal contribution.)

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🎓 Education

Carnegie Mellon University

Ray and Stephanie Lane Computational Biology Department

Ph.D. in Computational Biology (2024 – present)

M.S. in Computational Biology (2022 – 2024)

Duke Kunshan University / Duke University

B.S. in Genetics and Genomics (2018 – 2022)