CV
Education
- Ph.D. candidate in the Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri-Columbia, USA, December 2025 (expected)
- Ph.D. in the Department of Bioinformatics, College of Computer Science and Technology, Jilin University, China, June 2015
- M.S. in the Department of Bioinformatics, College of Computer Science and Technology, Jilin University, China, June 2010
- B.S. in the College of Computer Science and Technology, Jilin University, China, June 2007
Work experience
- January 2023 – December 2025: Graduate Research
- Department of Electrical Engineering and Computer Science, College of Engineering
- University of Missouri-Columbia
- Advisor: Dong Xu
- July 2022 – November 2022: Associate Professor
- Department of Computer Science, School of Information Science and Technology
- Northeast Normal University
- Master’s advisor
- August 2015 – June 2022: Lecturer
- Department of Computer Science, School of Information Science and Technology
- Northeast Normal University
- Master’s advisor
Grants
- 2021-2024: Protein Docking Conformation Ranking Based on Capsule Networks
- Principal Investigator
- General fund
- Jilin Provincial Natural Science Foundation, China
- ¥ 100,000
- 2019-2021: Target Protein–Ligand Complex Activity Prediction Integrating Multi-view 3D Depth Descriptors
- Principal Investigator
- Young Scientists Fund
- National Natural Science Foundation of China
- ¥ 260,000
- 2019-2020: Hybrid Deep Learning Model for Dynamic Protein Interaction Networks
- Principal Investigator
- Scientific Research Project
- Jilin Provincial Department of Education, China
- ¥ 25,000
- 2017-2018: Deep Learning Network with Adaptive and Self-Learning Characteristics for Texture Analysis
- Principal Investigator
- Outstanding Youth Fund
- Jilin Provincial Natural Science Foundation, China
- ¥ 80,000
- 2016-2017: Protein Docking Conformation Ranking Based on Capsule Networks
- Principal Investigator
- Youth Exploration and Development Fund
- Scientific Research Funding for Central Universities, China
- ¥ 80,000
Selected Publications
You can find all full publication list on my Google Schole profile h-index:20, i10-index: 32, citation > 1400
Predicting the location of coordinated metal ion-ligand binding sites using geometry-aware graph neural networks
Essien, Clement, Ning Wang, Yang Yu, Salhuldin Alqarghuli, Yongfang Qin, Negin Manshour, Fei He, and Dong Xu. "Predicting the location of coordinated metal ion-ligand binding sites using geometry-aware graph neural networks." Computational and Structural Biotechnology Journal 27 (2025): 137-148.
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs
F. He et al., "Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs." 2024 IEEE International Conference on Medical Artificial Intelligence (MedAI), 2024, 9-20
pathclip: Detection of genes and gene relations from biological pathway figures through image-text contrastive learning
F. He et al., "pathCLIP: Detection of Genes and Gene Relations From Biological Pathway Figures Through Image-Text Contrastive Learning,". IEEE Journal of Biomedical and Health Informatics, vol. 28, no. 8, pp. 5007-5019
Meta-learning for T cell receptor binding specificity and beyond
Wang, D., He, F., Yu, Y. et al. "Meta-learning for T cell receptor binding specificity and beyond". Nature Machine Intelligence 5, 337–339 (2023).
Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning
Chang, Yuzhou, Fei He, Juexin Wang, Shuo Chen, Jingyi Li, Jixin Liu, Yang Yu et al. "Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning." Computational and structural biotechnology journal 20 (2022): 4600-4617.
Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles
F. He et al., "Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles." 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021. 398-405
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization
Duolin Wang, Dongpeng Liu, Jiakang Yuchi, Fei He, Yuexu Jiang, Siteng Cai, Jingyi Li, Dong Xu. "MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization". Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W140–W146
Talks
Deep Learning Methods for Single-Cell Data Analyses
invited talk at Shanghai Institute for Mathematics and Interdisciplinary Sciences, Online
Enhancing adaptation of single cell large language models in single cell analyses through parameter efficient fine-tuning
Workshop talk at The International Conference on Intelligent Biology and Medicine (ICIBM), Houston, TX
Discover the Binding Domain of Transmembrane Proteins Based on Structural Universality
Conference proceedings talk at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Online
Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles
Conference proceedings talk at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Online
Quality Assessment of Protein Docking Models Based on Graph Neural Network
Conference proceedings talk at 28th Conference on Intelligent Systems for Molecular Biology (ISMB), Online
Protein ubiquitylation and sumoylation site prediction based on ensemble and transfer learning
Conference proceedings talk at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA
Extracting molecular entities and their interactions from pathway figures based on deep learning
Conference proceedings talk at 10th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), Niagara Falls, NY
A multimodal deep architecture for large-scale protein ubiquitylation site prediction
Conference proceedings talk at IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO
Teaching
Service
- Journal Reviewer
- Nature Communications, Pattern Recognition, Briefings in Bioinformatics, Neurocomputing, International Journal of Biological Macromolecules, Life Sciences, Computers in Biology and Medicine, BMC Medical Informatics and Decision Making, Scientific Reports, Journal of Imaging Informatics in Medicine, Engineering Applications of Artificial Intelligence, Digital Chinese Medicine, etc.
- Conference Reviewer
- IEEE International Conference on Bioinformatics and Biomedicine (2019, 2023-2024, co-reviewed with Prof.Trupti Joshi)
- Grant Reviewer
- National Natural Science Foundation of China (2024-2025).
Skills
- Programming
- Python, R, C#/C++/C
- Data Analysis
- numPy, Pandas, SciPy, scikit-learn, Matplotlib, Scanpy, Seurat, BioPython, rdkit, AlphaFold, LIME, SHAP
- Model Construction
- PyTorch, HuggingFace Transformer, FlashAttention, TensorFlow, Keras
- Languages
- English (fluent), Mandarin (native), Cantonese (native)