About Me
I am Wenduo Cheng, a 2nd-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. I am especially interested in:
- Building biologically meaningful “virtual cell” models that capture evolutionary and regulatory constraints.
- Using large language models and autonomous agents to accelerate both experimental design and computational analysis.
- Revealing the principles of gene regulation through multimodal modeling.
🔥 News
April 2026: 🎉 Our SKILLFOUNDRY preprint is now available on arXiv!
November 2025: 🎉 DNALongBench has been featured for the Nature Communications Editors’ Highlights collection – Computational and Theoretical Biology!
September 2025: 🎉 Our DNALongBench work is accepted by Nature Communications!
August 2025: 🎉 Our L2G paper is accepted by TMLR 2025!
📝 Publications
- SKILLFOUNDRY: Building Self-Evolving Agent Skill Libraries from Heterogeneous Scientific Resources (paper • code • project page) — arXiv preprint arXiv:2604.03964, 2026. Shuaike Shen†, Wenduo Cheng†, Mingqian Ma, Alistair Turcan, Martin Jinye Zhang, Jian Ma.
- DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks (paper • code) — Nature Communications 16, p.10108, 2025. Editors’ Highlights. Wenduo Cheng†, Zhenqiao Song†, Yang Zhang†, Shike Wang, Danqing Wang, Muyu Yang, Lei Li, Jian Ma.
- L2G: Repurposing Language Models for Genomics Tasks (paper • code) — Transactions on Machine Learning Research, 2025. Wenduo Cheng, Junhong Shen, Mikhail Khodak, Jian Ma, Ameet Talwalkar.
- Specialized Foundation Models Struggle to Beat Supervised Baselines (paper • code) — International Conference on Learning Representations (ICLR) 2025. Zongzhe Xu, Ritvik Gupta, Wenduo Cheng, Alexander Shen, Junhong Shen, Ameet Talwalkar, Mikhail Khodak.
- The Special and General Mechanism of Cyanobacterial Harmful Algal Blooms (paper) — Microorganisms 11(4), p.987, 2023. Wenduo Cheng†, Somin Hwang†, Qisen Guo, Leyuan Qian, Weile Liu, Yang Yu, Li Liu, Yi Tao, Huansheng Cao.
- Draft Genome Sequence of an Epibiotic Bacterium, Bacillus cereus, Isolated from Cyanobacterial Blooms in Lake Taihu, China (paper) — Microbiology Resource Announcements 12(3), e00936–22, 2023. Xiaoyuan Chen, Yinuo Yang, Yang Yu, Qisen Guo, Somin Hwang, Wenduo Cheng, Huansheng Cao.
- Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication (paper) — Microbiology Spectrum 12(3), e03194–22, 2022. Yang Yu†, Wenduo Cheng†, Xiaoyuan Chen, Qisen Guo, Huansheng Cao.
- RNA-sequencing and Mathematical Modeling Identify Suite of Light-Sensitive Circadian Genes in an Orb-Web Weaving Spider (paper) — Preprint, Research Square, 2021. Natalia Toporikova, Wenduo Cheng, Leyuan Qian, Andrew Mah, Thomas Clarke, Thomas C. Jones, Darrell Moore, Nadia A. Ayoub.
🎓 Education
- 2024–present, Ph.D. in Computational Biology, Carnegie Mellon University
- 2022-2024, M.S. in Computational Biology, Carnegie Mellon University
- 2018-2022, B.S. in Genetics and Genomics, Duke Kunshan University
🎲 Miscellaneous
I’m obsessed with anything involving a racket (pickleball, tennis, squash, badminton, you name it), plus ultimate frisbee and climbing whenever I can sneak it in. I’m also competitive at board games (e.g., 狼人杀, 三国杀, 剧本杀). And I spend a lot of time in the kitchen, happily experimenting with Chinese cuisine.