Biography

• Welcome to my homepage! I am a Ph.D. student at the Department of Quantitative and Computational Biology, University of Southern California, advised by Prof. Fengzhu Sun. I got my M.S. degree in Applied Mathematics from ISTBI, Fudan University, advised by Prof. Shanfeng Zhu. I am advised by Prof. Le Song during my internship at Genbio AI. I also had a great time interning at ByteDance and Biomap.
• My research interests lie in Biology Foundation Model and its applications in areas like Homologous Protein Search.
• See my CV for more of what we can do with protein language models.

Publications

• PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
  Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang*, and Shanfeng Zhu*
  Nature Communications, 2024, Invited to present on WAIC 2023 (World Artificial Intelligence Conference), RECOMB 2024, ISMB 2024. [DOI], [WebServer], [GitHub] Included in Large Language Models (LLMs) in Protein Bioinformatics Book, Part of the book series: Methods in Molecular Biology, Springer Nature 2025. [DOI]

• Effective binning of metagenomic contigs using contrastive multi-view representation learning
  Ziye Wang, Ronghui You, Haitao Han, Wei Liu, Fengzhu Sun*, and Shanfeng Zhu*
  Nature Communications, 2024. [DOI], [GitHub]

Competition awards

• 2024, CASP 16, Rank 1 in ”Per-atom/per-residue accuracy estimates” Track (Group Name: PLMFold). [LINK]
• 2023, Kaggle — CAFA 5 Protein Function Prediction, Rank 1 in the Leaderboard (Group Name: GOCurator). [LINK]
• 2021, China Computer Federation Bioinformatics Conference Challenge 2, Rank 3.
• 2018, ACM-ICPC Asian Regional Competition Nanjing Station, Bronze Medal.