Publications

* equal contribution, # corresponding author. Please also see Google Scholar for more recent works.

2026

  1. RECOMB
    Integrative Multi-Scale Sequence–Structure Modeling for Antimicrobial Peptide Prediction and Design
    J. Li, Y. Shao, Y. Li#, Q. Yu#
    RECOMB, 2026
    Full text
  2. Nature BME
    Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models
    Q. Yu*, H. Liu*, H. Shi*, Y. Abdrakhmanov, J. Shen, C. Zhang, Z. Dong, L. Zong, L. Si, L. Dai#, Y. Li#
    Nature Biomedical Engineering, 2026
    Full text

2025

  1. Cell Host Microbe
    Exploring Functional Insights into the Human Gut Microbiome via the Structural Proteome
    H. Liu*, J. Shen*, Z. Zhang*, J. Wang*, C. Zhang*, L. Zheng, H. Ni, L. Hong, J. Zhang, D. Xue, J. Chen, Q. Yu, Z. Qu, Y. Ma, T. Si, L. Zheng, S. Wang, C. Jiang, Y. Li#, K. Wang#, L. Dai#
    Cell Host & Microbe, 2025
    Full text
  2. Bioinf.
    GS-DTI: A Graph-Structure-Aware Framework Leveraging Large Language Models for Drug–Target Interaction Prediction
    Q. Yu, C. Zhou, J. Jiang, X. Shi, Y. Li#
    Bioinformatics, 2025
    Full text
  3. OFID
    The MEFIER Score—A Risk Score to Stratify Infective Endocarditis in Patients With Enterococcus faecalis Bacteremia Based on an 11-Year Territory-Wide Cohort
    C.K.C. Lai#, E. Leung, A.L.H. Lee, Q. Yu, Y. He, Y. Li, R.K.K. Leung, G.C.Y. Lui, T.C.F. Yip, G.L.H. Wong, A.P.W. Lee, R.H.L. Wong, M. Ip
    Open Forum Infectious Diseases, 2025
    Full text

2024

  1. Nature CS
    Deep generative design of RNA aptamers using structural predictions
    F. Wong, D. He, A. Krishnan, L. Hong, A.Z. Wang, J. Wang, Z. Hu, S. Omori, A. Li, J. Rao, Q. Yu, W. Jin, T. Zhang, K. Ilia, J.X. Chen, S. Zheng, I. King, Y. Li#, J.J. Collins#
    Nature Computational Science, 2024
    Full text
  2. Adv. Mater.
    Revisiting the Epitaxial Growth Mechanism of 2D TMDC Single Crystals
    C. Li, F. Zheng, J. Min, N. Yang, Y. Chang, H. Liu, Y. Zhang, P. Yang, Q. Yu, Y. Li, Z. Luo, A. Alijarb, K. Shih, J. Huang, L. Li#, Y. Wan#
    Advanced Materials, 2024
    Full text
  3. JID
    A machine learning-based risk score for prediction of infective endocarditis among patients with Staphylococcus aureus bacteraemia - The SABIER score
    C. Lai#, E. Leung, Y. He, C-C. Cheung, O. Mui, Q. Yu, T. Li, A. Lee, Y. Li, C-Y. Lui
    The Journal of Infectious Diseases, 2024
    Full text

2023

  1. Nature CS
    Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model
    J. Shen*, Q. Yu*, S. Chen*, Q. Tan, J. Li, Y. Li#
    Nature Computational Science, 2023
    Full text
  2. RECOMB
    Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning
    Z. Hu*, Q. Yu*, Y. Guo, T. Wang, I. King, X. Gao#, L. Song#, Y. Li#
    RECOMB, 2023
    Full text

2021

  1. BigData
    Session-based Recommendation Via Contrastive Learning On Heterogeneous Graph
    H. Li, X. Luo#, Q. Yu, H. Wang
    IEEE BigData, 2021
    Full text