Portrait of Shida He

Shida He

Email: heshida@tju.edu.cn

Education

  • University of Tsukuba, 2021–2024, Japan
    Ph.D. in Computer Science
  • Tianjin University, 2018–2021, China
    M.Eng. in Computer Technology
  • Hebei University of Science and Technology, 2013–2017, China
    B.Eng. in Software Engineering

Research Interests

Bioinformatics; AI for drug discovery; Dimensionality Reduction

Publications

  1. Shida He, Lesong Wei, Weidong Ye, et al. MEGPNM as a multiscale edge-aware GAT network with hybrid pooling predicting permeability of non-peptidic macrocycles. Communications Chemistry. 2026, 9:301.
  2. Lesong Wei, Shida He, Quan Zou, et al. Harnessing Terminal Signal-Aware Deep Learning for Accurate Multi-Class Secreted Effector Identification. IEEE Journal of Biomedical and Health Informatics. 2026.
  3. Lesong Wei, Shida He, Zhengyang Fan. Machine Learning for the Prediction of Gram-Negative Bacterial Secreted Effectors: Advances and Challenges. Frontiers in Chemistry. 2026, 14:1810136.
  4. Shida He, Zhongyu He, Yuting Zhang, et al. DualBAN: Unifying Intra- and Inter-Molecular Features for Compound-Protein Interaction Prediction. IEEE Journal of Biomedical and Health Informatics. 2026.
  5. Shida He, Zixu Wang, Jing Li, et al. BiGvCL: Bipartite Graph-Based Cross-Domain Contrastive Learning Model for Predicting Drug-Gene Interactions. Briefings in Bioinformatics. 2026, 27(1).
  6. Jing Li, Shida He, Jian Zhang, et al. T4Seeker: A Hybrid Model for Type IV Secretion Effectors Identification. BMC Biology. 2024, 22:259.
  7. Shida He, Lijun Dou, Xiucai Ye, et al. FIAMol-AB: Feature Fusion and Attention-Based Deep Learning Method for Enhanced Antibiotic Discovery. Computers in Biology and Medicine. 2024, 168:107762.
  8. Shida He, Xiucai Ye, Tetsuya Sakurai. CLOP-hERG: The Contrastive Learning Optimized Pre-Trained Model for Representation Learning in Predicting Drug-Induced hERG Channel Blockers. Medinformatics. 2024.
  9. Shida He, Xiucai Ye, Tetsuya Sakurai, et al. MRMD3.0: A Python Tool and Webserver for Dimensionality Reduction and Data Visualization via an Ensemble Strategy. Journal of Molecular Biology. 2023, 435(14):168116.
  10. Shida He, Lijun Dou, Xuchong Li, et al. Review of Bioinformatics in Alzheimer’s Disease Research. Computers in Biology and Medicine. 2022, 143:105269.
  11. Shida He, Xin Liu, Xiucai Ye, et al. Analysis of Drug Repositioning and Prediction Techniques: A Concise Review. Current Topics in Medicinal Chemistry. 2022, 22(23):1897–1906.
  12. Jing Li, Shida He, Fei Guo, et al. HSM6AP: A High-Precision Predictor for the Homo sapiens N6-Methyladenosine (m6A) Based on Multiple Weights and Feature Stitching. RNA Biology. 2021, 18(11):1882–1892.
  13. Jing Li, Lichao Zhang, Shida He, et al. SubLocEP: A Novel Ensemble Predictor of Subcellular Localization of Eukaryotic mRNA Based on Machine Learning. Briefings in Bioinformatics. 2021, 22(5).
  14. Shida He, Fei Guo, Quan Zou, et al. MRMD2.0: A Python Tool for Machine Learning with Feature Ranking and Reduction. Current Bioinformatics. 2020, 15(10):1213–1222.