publications

A selection of peer-reviewed research in protein machine learning and bioinformatics.

RESEARCH OUTPUT

For a complete and up-to-date record, visit Google Scholar or ORCID.

2026

  1. Preview for RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates
    RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates
    Lei Wang, and Zilu Zeng
    Bioinformatics 2026
    Code
  2. Interdiscip. Sci.
    ProtFormer-Site: Ultra-fast and Accurate Prediction of Protein-Protein Interaction Sites with Protein Language Model
    Lei Wang, Shali Dong, Han Zhang, and 4 more authors
    Interdisciplinary Sciences: Computational Life Sciences 2026
    Code
  3. J. Mol. Biol.
    LocPred-Prok: Prokaryotic protein subcellular localization prediction with a dual-branch architecture and protein language model
    Zilu Zeng, and Lei Wang
    Journal of Molecular Biology 2026
    Code
  4. Comput. Biol. Chem.
    SPLiNet: Lightweight prediction of protein-RNA interaction sites by integrating a structure-aware protein language model with a dual-branch network
    H. Ye, C. Zheng, Lei Wang, and 2 more authors
    Computational Biology and Chemistry 2026

2025

  1. arXiv
    A Comprehensive Review of Protein Language Models
    Lei Wang, Xudong Li, Han Zhang, and 4 more authors
    arXiv preprint arXiv:2502.06881 2025
    Website
  2. Comput. Biomed.
    A comprehensive review on neuropeptides: databases and computational tools
    Wei Xu, Lei Wang, Mingxia Wang, and 3 more authors
    Computational Biomedicine 2025
  3. BIBM
    ProtSSSD: A Novel Approach for Intrinsically Disordered Protein Region Prediction Using Protein Language Model
    Lei Wang, Zilu Zeng, Yan Wang, and 1 more author
    In IEEE International Conference on Bioinformatics and Biomedicine 2025
    Code
  4. bioRxiv
    MetaFold-RNA: Accurate prediction of RNA secondary structure using a meta-learning-guided deep network
    Lei Wang, Han Zhang, Xudong Li, and 2 more authors
    bioRxiv 2025
    Code
  5. bioRxiv
    SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale
    Lei Wang, Xuchao Zhang, Yan Wang, and 1 more author
    bioRxiv 2025
    Code
  6. iScience
    Sensory plasticity caused by up-down regulation encodes the information of short-term learning and memory
    P. Z. Wang, M. H. Ge, P. Su, and 7 more authors
    iScience 2025
  7. Methods Mol. Biol.
    Exploring ProtFlash: An Efficient Approach to Protein Data Analysis
    Lei Wang, Zhidong Xue, and Yan Wang
    2025
    Code
  8. CCIS
    Protein-Protein Contact Prediction Using Structure-Informed Sequences and Protein Language Models
    Qiyuan Huang, Lei Wang, Zhihong Zhang, and 2 more authors
    2025

2024

  1. arXiv
    Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
    Shujian Jiao, Bingxuan Li, Lei Wang, and 4 more authors
    arXiv preprint arXiv:2404.15805 2024
  2. CSBJ
    DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model
    Lei Wang, Zilu Zeng, Zhidong Xue, and 1 more author
    Computational and Structural Biotechnology Journal 2024
    Code

2023

  1. J. Mol. Biol.
    NeuroPep 2.0: An Updated Database Dedicated to Neuropeptide and Its Receptor Annotations
    Mingxia Wang, Lei Wang, Wei Xu, and 5 more authors
    Journal of Molecular Biology 2023
    Code
  2. Cell Rep. Phys. Sci.
    Deciphering the protein landscape with ProtFlash, a lightweight language model
    Lei Wang, Hui Zhang, Wei Xu, and 2 more authors
    Cell Reports Physical Science 2023
    Code
  3. Preview for NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model
    NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model
    Lei Wang, Chen Huang, Mingxia Wang, and 2 more authors
    Briefings in Bioinformatics 2023
    Code

2022

  1. CSBJ
    Improving the topology prediction of α-helical transmembrane proteins with deep transfer learning
    Lei Wang, Haolin Zhong, Zhidong Xue, and 1 more author
    Computational and Structural Biotechnology Journal 2022
    Code
  2. Bioinform. Adv.
    Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM
    Lei Wang, Haolin Zhong, Zhidong Xue, and 2 more authors
    Bioinformatics Advances 2022
    Code
  3. ISBRA
    GNN-Dom: An Unsupervised Method for Protein Domain Partition via Protein Contact Map
    Lei Wang, and Yan Wang
    In International Symposium on Bioinformatics Research and Applications 2022