Publications

36 peer-reviewed papers | 700+ citations | H-index: 15

Please refer to my Google Scholar for a complete publication list.

* denotes equal contribution, † denotes corresponding author

Drug-Target Affinity

Drug-Target Affinity Prediction

Advanced deep learning models for predicting drug-target interactions and binding affinities, enabling efficient drug discovery and repurposing.

1 Interaction-Based Inductive Bias in Graph Neural Networks: Enhancing Protein-Ligand Binding Affinity Predictions From 3D Structures IF: 20.8
Z. Yang, W. Zhong, Q. Lv, T. Dong, G. Chen, C.Y.-C. Chen†
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2024
[Paper]
2 MMFA-DTA: Multi-Modal Feature Attention Fusion Network for Drug-Target Affinity Prediction for Drug Repurposing Against SARS-CoV-2 IF: 5.7
G. Chen*, H. He*, Q. Lv*, L. Zhao, C.Y.-C. Chen†
Journal of Chemical Theory and Computation, 2024, 20(18): 8071-8087
[Paper]
3 GINCM-DTA: A graph isomorphic network with protein contact map representation for transferable drug repurposing against COVID-19 IF: 8.665
G. Chen*, H. He*, L. Zhao, Q. Lv, C.Y.-C. Chen†
Expert Systems with Applications, 2024, 236: 121274
[Paper]
4 MFAE: Multilevel Feature Aggregation Enhanced Drug-Target Affinity Prediction for Drug Repurposing Against Colorectal Cancer IF: 6.8
G. Chen*, H. He*, C.Y.-C. Chen†
Advanced Intelligent Systems, 2024, 6(3): 2300546
[Paper]
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5 Integrating Sequence and Graph Information for Enhanced Drug-Target Affinity Prediction IF: 7.3
H. He*, G. Chen*, C.Y.-C. Chen†
Science China Information Sciences, 2024, 67(2): 129101
[Paper]
6 NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug-target binding affinity prediction IF: 6.931
H. He*, G. Chen*, C.Y.-C. Chen†
Bioinformatics, 2023, 39(6): btad355
[Paper]
7 FusionDTA: attention-based feature polymerizer and knowledge distillation for drug-target binding affinity prediction IF: 13.99
W. Yuan*, G. Chen*, C.Y.-C. Chen†
Briefings in Bioinformatics, 2022, 23(1): bbab506
[Paper]
8 Predicting drug-target interactions with deep-embedding learning of graphs and sequences IF: 2.94
W. Chen*, G. Chen*, L. Zhao, C.Y.-C. Chen†
The Journal of Physical Chemistry A, 2021, 125(25): 5633-5642
[Paper]
Graph Neural Networks

Graph Neural Networks for Drug Discovery

Advancing GNN architectures for molecular property prediction, drug-drug interactions, and low-data drug discovery scenarios.

1 Meta-MolNet: A Cross-Domain Benchmark for Few Examples Drug Discovery IF: 10.2
Q. Lv, G. Chen, Z. Yang, W. Zhong, C.Y.-C. Chen†
IEEE Transactions on Neural Networks and Learning Systems, 2024
[Paper]
2 Meta learning with graph attention networks for low-data drug discovery IF: 14.26
Q. Lv, G. Chen, Z. Yang, W. Zhong, C.Y.-C. Chen†
IEEE Transactions on Neural Networks and Learning Systems, 2023
[Paper]
3 DSIL-DDI: a domain-invariant substructure interaction learning for generalizable drug-drug interaction prediction IF: 14.26
Z. Tang, G. Chen, H. Yang, W. Zhong, C.Y.-C. Chen†
IEEE Transactions on Neural Networks and Learning Systems, 2023
[Paper]
4 3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction IF: 13.99
H. He*, G. Chen*, C.Y.-C. Chen†
Briefings in Bioinformatics, 2022, 23(3): bbac134
[Paper]
5 Machine learning and graph neural network for finding potential drugs related to multiple myeloma IF: 3.93
H. He*, G. Chen*, C.Y.-C. Chen†
New Journal of Chemistry, 2022, 46(11): 5188-5200
[Paper]
6 Mol2Context-vec: learning molecular representation from context awareness for drug discovery IF: 13.99
Q. Lv*, G. Chen*, L. Zhao, W. Zhong, C.Y.-C. Chen†
Briefings in Bioinformatics, 2021, 22(6): bbab317
[Paper]
Multi-modal AI

Multi-modal AI & Cellular Data Integration

Developing advanced multi-modal fusion methods for integrating heterogeneous biological data including single-cell, drug-target, and molecular representations.

1 Modal-NexT: Toward unified heterogeneous cellular data integration IF: 15.5
Z. Tang, G. Chen, S. Chen, H. He, J. Huang, T. Dong, J. Zhou, L. Zhao, L. You†, C.Y.-C. Chen†
Information Fusion, 2025, 125: 103479
[Paper]
2 Dual modality feature fused neural network integrating binding site information for drug target affinity prediction IF: 12.4
H. He*, G. Chen*, Z. Tang, C.Y.-C. Chen†
npj Digital Medicine, 2025, 8(1): 67
[Paper]
3 Modal-nexus auto-encoder for multi-modality cellular data integration and imputation IF: 14.7
Z. Tang, G. Chen, S. Chen, L. You†, C.Y.-C. Chen†
Nature Communications, 2024, 15(1): 9021
[Paper]
4 Comprehensive View Embedding Learning for Single-Cell Multimodal Integration CCF A
Z. Tang, J. Huang, G. Chen, C.Y.-C. Chen†
Proceedings of the AAAI Conference on Artificial Intelligence, 2024, 38(14): 15292-15300
[Paper]
TCM AI

AI for Traditional Chinese Medicine

Building the world's largest TCM database and developing AI methods to modernize traditional medicine for drug discovery.

1 AI Empowering Traditional Chinese Medicine? IF: 8.4
Z. Song*, G. Chen*, C.Y.-C. Chen†
Chemical Science, 2024, 15(41): 16844-16886
[Paper]
2 TCMBank: bridges between the largest herbal medicines, chemical ingredients, target proteins, and associated diseases with intelligence text mining IF: 8.4
Q. Lv*, G. Chen*, H. Hao*, Z. Yang, L. Zhao, C.Y.-C. Chen†
Chemical Science, 2023, 14(39): 10684-10701
[Paper]
3 TCMBank-the largest TCM database provides deep learning-based Chinese-Western medicine exclusion prediction IF: 39.3
Q. Lv*, G. Chen*, H. Hao*, Z. Yang, L. Zhao, K. Zhang, C.Y.-C. Chen†
Signal Transduction and Targeted Therapy, 2023, 8(1)
[Paper]
Protein Design

Protein Structure & Antibody Design

Leveraging transformer networks and language models for protein secondary structure prediction, antibody generation, and molecular design.

1 Pre-trained language models for protein and molecular design IF: 2.9
E. Zhang, Z. Pan, Z. Yao, T. Dong, G. Chen, T. Deng, S. Chen, C.Y.-C. Chen†
Physical Chemistry Chemical Physics, 2025, 27(27): 14189-14216
[Paper]
2 De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model IF: 14.7
H. He, B. He†, L. Guan, Y. Zhao, F. Jiang, G. Chen, Q. Zhu, C.Y.-C. Chen†, T. Li†, J. Yao†
Nature Communications, 2024, 15(1): 6867
[Paper]
3 MFTrans: A multi-feature transformer network for protein secondary structure prediction IF: 7.7
Y. Chen*, G. Chen*, C.Y.-C. Chen†
International Journal of Biological Macromolecules, 2024, 267: 131311
[Paper]
4 PSSP-MFFNet: A Multifeature Fusion Network for Protein Secondary Structure Prediction IF: 3.7
Y. Chen*, G. Chen*, C.Y.-C. Chen†
ACS omega, 2024, 9(5): 5985-5994
[Paper]
Clinical Applications

Clinical Applications & Medical Imaging

Translating AI research into clinical practice through collaborations on cancer diagnosis, biomarker discovery, and personalized treatment.

1 Knowledge-Based Inductive Bias and Domain Adaptation: Enhancing Cell Type Annotation Across Batches IF: 5.2
Z. Tang, G. Chen, S. Chen, H. He, L. You†, C.Y.-C. Chen†
Communications Biology, 2024, 7(1): 1440
[Paper]
2 Dynamic network biomarker C1QTNF1 regulates tumor formation at the tipping point of hepatocellular carcinoma IF: 3.1
H. Yu*, X. Yan*, G. Chen*, R. Li, Z. Yang, Z. Liang, L. Ye†, Y. Chen†, Y. Li†
Biomolecules and Biomedicine, 2024, 24(4): 939
[Paper]
3 Discovery of Kinetin in inhibiting colorectal cancer progression via enhancing PSMB1-mediated RAB34 degradation IF: 9.1
X. Jiang*, L. Yang*, G. Chen, X. Feng, Y. Liu, Q. Gao, M. Mai, C.Y.-C. Chen, S. Ye, Z. Yang†
Cancer Letters, 2024, 584: 216600
[Paper]
4 MRI-based automated machine learning model for preoperative identification of variant histology in muscle-invasive bladder carcinoma IF: 5.9
J. Huang*, G. Chen*, H. Liu, W. Jiang, S. Mai, L. Zhang, H. Zeng, S. Wu, C.Y.-C. Chen†, Z. Wu†
European Radiology, 2024, 34(3): 1804-1815
[Paper]
5 Aquaporin 9 is involved in CRC metastasis through DVL2-dependent Wnt/β-catenin signaling activation IF: 3.8
Y. Liu*, Q. Gao*, X. Feng*, G. Chen, X. Jiang, D. Chen, Z. Yang†
Gastroenterology Report, 2023, 11: goad033
[Paper]
Drug Repurposing

Drug Repurposing for Specific Diseases

AI-driven drug repurposing targeting major diseases including colorectal cancer, breast cancer, Alzheimer's disease, and diabetes.

1 Multi-perspective neural network for dual drug repurposing in Alzheimer's disease IF: 8.8
L. Zhao, Z. Li, G. Chen, Y. Yin, C.Y.-C. Chen†
Knowledge-Based Systems, 2024, 283: 111195
[Paper]
2 Hybrid Neural Network Approaches to Predict Drug-Target Binding Affinity for Drug Repurposing: Screening for Potential Leads for Alzheimer's Disease IF: 5.0
X. Wu, Z. Li, G. Chen, Y. Yin, C.Y.-C. Chen†
Frontiers in Molecular Biosciences, 2023, 10: 1227371
[Paper]
3 VAERHNN: Voting-averaged ensemble regression and hybrid neural network to investigate potent leads against colorectal cancer IF: 8.14
G. Chen, X. Jiang, Q. Lv, X. Tan, Z. Yang, C.Y.-C. Chen†
Knowledge-Based Systems, 2022, 257: 109925
[Paper]
4 Adaptive boost approach for possible leads of triple-negative breast cancer IF: 4.18
G. Chen, H. He, L. Zhao, K.-B. Chen, S. Li, C.Y.-C. Chen†
Chemometrics and Intelligent Laboratory Systems, 2022, 231: 104690
[Paper]
5 Novel and versatile artificial intelligence algorithms for investigating possible GHSR1a and DRD1 agonists for Alzheimer's disease IF: 4.04
Z. Tang*, L. Zhao*, G. Chen, C.Y.-C. Chen†
RSC advances, 2021, 11(12): 6423-6446
[Paper]
6 A novel artificial intelligence protocol to investigate potential leads for diabetes mellitus IF: 3.36
J. Gong*, L. Zhao*, G. Chen*, X. Chen, Z. Chen, C.Y.-C. Chen†
Molecular Diversity, 2021, 25: 1375-1393
[Paper]