Yang, Yuedong

Specific interactions for ab initio folding of protein terminal regions with secondary structures

Yang, Y., & Zhou, Y. (2008) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 245

Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks

Zeng, Y., Wei, Z., Yu, W., Yin, R., Yuan, Y., Li, B., Tang, Z., Lu, Y., & Yang, Y. (2022) · Briefings in Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 211

Integrating multi-omics data through deep learning for accurate cancer prognosis prediction

Chai, H., Zhou, X., Zhang, Z., Rao, J., Zhao, H., & Yang, Y. (2021) · Computers in Biology and Medicine

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 194

AlphaFold2-aware protein–DNA binding site prediction using graph transformer

Yuan, Q., Chen, S., Rao, J., Zheng, S., Zhao, H., & Yang, Y. (2022) · Briefings in Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 137

AlphaFold2-aware protein-DNA binding site prediction using graph transformer

Yuan, Q., Chen, S., Rao, J., Zheng, S., Zhao, H., & Yang, Y. (2021) · Briefings in Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 137

Quantitative evaluation of explainable graph neural networks for molecular property prediction

Rao, J., Zheng, S., Lu, Y., & Yang, Y. (2022) · Patterns

Explainable Artificial Intelligence (XAI)Computational Drug Discovery Methods

Cited by 90

Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model

Zeng, Y., Wei, Z., Yuan, Q., Chen, S., Yu, W., Lu, Y., Gao, J., & Yang, Y. (2023) · Bioinformatics

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 73

Enhancing anti-tumor effect of ultrasensitive bimetallic RuCu nanoparticles as radiosensitizers with dual enzyme-like activities

Hu, B., Xiao, X., Chen, P., Qian, J., Yuan, G., Ye, Y., Zeng, L., Zhong, S., Wang, X., Qin, X., et al. (2022) · Biomaterials

Nanoplatforms for cancer theranosticsRadiation Therapy and Dosimetry

Cited by 73

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions

Chen, K., Zhao, H., & Yang, Y. (2022) · Briefings in Bioinformatics

Genomics and Chromatin DynamicsCancer-related molecular mechanisms research

Cited by 33

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model

Xie, J., Chen, S., Lei, J., & Yang, Y. (2024) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 31

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model

Xie, J., Chen, S., Lei, J., & Yang, Y. (2023) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 31

Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting

Lv, X., Chen, J., Lu, Y., Chen, Z., Xiao, N., & Yang, Y. (2020) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 26

Genome-scale annotation of protein binding sites via language model and geometric deep learning

Yuan, Q., Tian, C., & Yang, Y. (2024) · eLife

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 9

Accurate Protein-Protein Interactions Modeling through Physics-informed Geometric Invariant Learning

Rao, J., Liu, D., Zhou, X., Yuan, Q., Wei, W., Lu, W., Zhang, J., Rong, Y., Yang, Y., & Zheng, S. (2025) · Communications Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 1

Genome-scale annotation of protein binding sites via language model and geometric deep learning

Yuan, Q., Tian, C., & Yang, Y. (2024) · eLife

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 0