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📝 Selected Publications

A full list of publications is available here. († indicates equal contribution.)
· genomic foundation model agent
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  1. AgentCo-op teaser
    AgentCo-op: Retrieval-Based Synthesis of Interoperable Multi-Agent Workflows
    Shuaike Shen†, Wenduo Cheng†, Shike Wang, Mingqian Ma, Jian Ma
    arXiv preprint arXiv:2605.20425, 2026.
    Paper Code Project Page
  2. SkillFoundry teaser
    SKILLFOUNDRY: Building Self-Evolving Agent Skill Libraries from Heterogeneous Scientific Resources
    Shuaike Shen†, Wenduo Cheng†, Mingqian Ma, Alistair Turcan, Martin Jinye Zhang, Jian Ma
    Conference on Language Modeling (COLM), 2026.
    Paper Code Project Page
  3. DNALongBench teaser
    DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks
    Wenduo Cheng†, Zhenqiao Song†, Yang Zhang†, Shike Wang, Danqing Wang, Muyu Yang, Lei Li, Jian Ma
    Nature Communications 16, p.10108, 2025. Editors' Highlights.
    Paper Code
  4. L2G teaser
    L2G: Repurposing Language Models for Genomics Tasks
    Wenduo Cheng, Junhong Shen, Mikhail Khodak, Jian Ma, Ameet Talwalkar
    Transactions on Machine Learning Research (TMLR), 2025.
    Paper Code
  5. Specialized Foundation Models teaser
    Specialized Foundation Models Struggle to Beat Supervised Baselines
    Zongzhe Xu, Ritvik Gupta, Wenduo Cheng, Alexander Shen, Junhong Shen, Ameet Talwalkar, Mikhail Khodak
    International Conference on Learning Representations (ICLR), 2025.
    Paper Code
  6. Cyanobacterial blooms selection teaser
    Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication
    Yang Yu†, Wenduo Cheng†, Xiaoyuan Chen, Qisen Guo, Huansheng Cao
    Microbiology Spectrum 12(3), e03194–22, 2022.
    Paper
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