Xu, Dong

The I-TASSER Suite: protein structure and function prediction

Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 5,596

A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

Peña-Castillo, L., Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. K., et al. (2008) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 248

Single-cell biological network inference using a heterogeneous graph transformer

Ma, A., Wang, X., Li, J., Wang, C., Xiao, T., Liu, Y., Cheng, H., Wang, J., Li, Y., Chang, Y., et al. (2023) · Nature Communications

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 184

Deep learning shapes single-cell data analysis

Ma, Q., & Xu, D. (2022) · Nature Reviews Molecular Cell Biology

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 123

S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure

Wang, D., Pourmirzaei, M., Abbas, U. L., Zeng, S., Manshour, N., Esmaili, F., Poudel, B., Jiang, Y., Shao, Q., Chen, J., et al. (2025) · Advanced Science

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 46

Harnessing the deep learning power of foundation models in single-cell omics

Ma, Q., Jiang, Y., Cheng, H., & Xu, D. (2024) · Nature Reviews Molecular Cell Biology

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 34

Assessing ChatGPT’s Competency in Addressing Interdisciplinary Inquiries on Chatbot Uses in Sports Rehabilitation: Simulation Study (Preprint)

McBee, J. C., Han, D. Y., Liu, L., Ma, L., Adjeroh, D. A., Xu, D., & Hu, G. (2023) · JMIR Medical Education

Artificial Intelligence in Healthcare and EducationArtificial Intelligence Applications

Cited by 14

Assessing ChatGPT’s Competency in Addressing Interdisciplinary Inquiries on Chatbot Uses in Sports Rehabilitation: Simulation Study

McBee, J. C., Han, D. Y., Liu, L., Ma, L., Adjeroh, D. A., Xu, D., & Hu, G. (2024) · JMIR Medical Education

Artificial Intelligence in Healthcare and EducationArtificial Intelligence Applications

Cited by 14

Prediction of Protein Ion-Ligand Binding Sites with ELECTRA

Essien, C., Jiang, L., Wang, D., & Xu, D. (2023) · Molecules

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 5

Prediction of Protein Ion–Ligand Binding Sites with ELECTRA

Essien, C., Jiang, L., Wang, D., & Xu, D. (2023) · Molecules

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 5

Harnessing the power of single-cell large language models with parameter-efficient fine-tuning using scPEFT

He, F., Fei, R., Krull, J. E., Yu, Y., Zhang, X., Wang, X., Cheng, H., Gao, M., Su, L., Chen, Y., et al. (2025) · Nature Machine Intelligence

Single-cell and spatial transcriptomicsDomain Adaptation and Few-Shot Learning

Cited by 5