PRESM: personalized reference editor for somatic mutation discovery in cancer genomics. - Chen Cao 002; Lauren Mak; Guangxu Jin; Paul Gordon; Kai Ye 001; Quan Long (Bioinform., 2019)

Using discriminative vector machine model with 2DPCA to predict interactions among proteins. - Zhengwei Li 001; Ru Nie; Zhuhong You; Chen Cao 002; Jiashu Li (BMC Bioinform., 2019)

kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes. - Chen Cao 002; Devin Kwok; Shannon Edie; Qing Li 076; Bowei Ding; Pathum Kossinna; Simone Campbell; Jingjing Wu 002; Matthew Greenberg; Quan Long (Briefings Bioinform., 2021)

WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization. - Chen Cao 002; Matthew Greenberg; Quan Long (Bioinform., 2021)

Botanical drugs: a new strategy for structure-based target prediction. - Xuxu Wei; Xiang Wu; Zeyu Cheng; Qingming Wu; Chen Cao 002; Xue Xu; Hongcai Shang (Briefings Bioinform., 2022)

webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. - Zilong Zhang; Feifei Cui; Wei Su; Lijun Dou; Anqi Xu; Chen Cao 002; Quan Zou 001 (Bioinform., 2022)

A novel method for drug-target interaction prediction based on graph transformers model. - Hongmei Wang; Fang Guo; Mengyan Du; Guishen Wang; Chen Cao 002 (BMC Bioinform., 2022)

Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. - Zilong Zhang; Feifei Cui; Chen Cao 002; Qingsuo Wang; Quan Zou 001 (Comput. Biol. Medicine, 2022)

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. - Chen Cao 002; Jianhua Wang; Devin Kwok; Feifei Cui; Zilong Zhang; Da Zhao; Mulin Jun Li; Quan Zou 001 (Nucleic Acids Res., 2022)

Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems. - Yunyun Su; Feifei Cui; Shiyu Yan; Quan Zou 001; Chen Cao 002; Zilong Zhang (BIBM, 2023)

MMDDI-MGPFF: Multi-Modal Drug Representation Learning with Molecular Graph and Pharmacological Feature Fusion for Drug-Drug Interaction Event Prediction. - Guishen Wang; Zhitong Guo; Guilin You; Ming Xu; Chen Cao 002; Xiaowen Hu (BIBM, 2024)

Multiome-wide Association Studies: Novel Approaches for Understanding Diseases. - Mengting Shao; Kaiyang Chen; Shuting Zhang; Min Tian; Yan Shen; Chen Cao 002; Ning Gu (Genom. Proteom. Bioinform., 2024)

Multimodal Representation Learning via Graph Isomorphism Network for Toxicity Multitask Learning. - Guishen Wang; Hui Feng; Mengyan Du; Yuncong Feng; Chen Cao 002 (J. Chem. Inf. Model., 2024)

EHR-HGCN: An Enhanced Hybrid Approach for Text Classification Using Heterogeneous Graph Convolutional Networks in Electronic Health Records. - Guishen Wang; Xiaoxue Lou; Fang Guo; Devin Kwok; Chen Cao 002 (IEEE J. Biomed. Health Informatics, 2024)

DeepTGIN: a novel hybrid multimodal approach using transformers and graph isomorphism networks for protein-ligand binding affinity prediction. - Guishen Wang; Hangchen Zhang; Mengting Shao; Yuncong Feng; Chen Cao 002; Xiaowen Hu (J. Cheminformatics, 2024)

DTI-BGCGCN: A novel bipartite graph-based cluster graph convolutional network for drug-target interaction prediction in modern and traditional chinese medicine. - Hongmei Wang; Ming Xu; Zhitong Guo; Guilin You; Guishen Wang; Chen Cao 002; Xiaowen Hu (Comput. Biol. Chem., 2025)

BiRNN-DDI: A Drug-Drug Interaction Event Type Prediction Model Based on Bidirectional Recurrent Neural Network and Graph2Seq Representation. - Guishen Wang; Hui Feng; Chen Cao 002 (J. Comput. Biol., 2025)

Heterogeneous Graph Contrastive Learning with Graph Diffusion for Drug Repositioning. - Guishen Wang; Honghan Chen; Handan Wang; Yuyouqiang Fu; Caiye Shi; Chen Cao 002; Xiaowen Hu (J. Chem. Inf. Model., 2025)

MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction. - Guishen Wang; Hangchen Zhang; Mengting Shao; Shisen Sun; Chen Cao 002 (J. Chem. Inf. Model., 2025)

MMDDI-SSE: A Novel Multi-Modal Feature Fusion Model With Static Subgraph Embedding for Drug-Drug Interaction Event Prediction. - Guishen Wang; Honghan Chen; Handan Wang; Hairong Gao; Xiaowen Hu; Chen Cao 002 (IEEE J. Biomed. Health Informatics, 2025)