Author

Zunyun Fu

Chinese Academy of Sciences

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 5

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:graph neural network· 2 Approach:statistical model· 2 Approach:contrastive learning· 1 Approach:deep learning· 1

Frequent Co-Authors

Mingyue ZhengiD· 5 shared Runze ZhangiD· 3 shared Xutong LiiD· 3 shared Jiacheng XiongiD· 2 shared Kaixian CheniD· 2 shared Sulin ZhangiD· 2 shared Xiaohong LiuiD· 2 shared Zhaokun WangiD· 2 shared

Activity by Year

2020-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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5 shared papersBioinformatics

Mingyue ZhengORCID

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5 papers

Recent·Most cited

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Duanhua Cao, Mingan Chen, Runze Zhang, Zhaokun Wang, Manlin Huang, Jie Yu, Xinyu Jiang, Zhehuan Fan, Wei Zhang, Hao Zhou, Xutong Li, Zunyun Fu, Sulin Zhang, Mingyue Zheng

SurfDock improves protein-ligand complex prediction by integrating multiple protein representations into a diffusion model, achieving higher accuracy and physical plausibility than existing methods.

Nature Methods · Nov 27, 2024Peer-reviewedBioinformatics

FAPM: Functional Annotation of Proteins using Multi-Modal Models Beyond Structural Modeling

Wenkai Xiang, Zhaoping Xiong, Huan Chen, Jiacheng Xiong, Wei Zhang, Zunyun Fu, Mingyue Zheng, Bing Liu, Qian Shi

FAPM improves protein functional annotation by combining protein sequence and language models, outperforming sequence-only methods on benchmarks and phage proteins with few homologs.

Bioinformatics · Nov 12, 2024Peer-reviewedBioinformatics

Identify compound-protein interaction with knowledge graph embedding of perturbation transcriptomics

Shengkun Ni, Xiangtai Kong, Yingying Zhang, Zhengyang Chen, Zhaokun Wang, Zunyun Fu, Ruifeng Huo, Xiaochu Tong, Ning Qu, Xiaolong Wu, Kun Wang, Wei Dong Zhang, Runze Zhang, Zimei Zhang, Jiangshan Shi, , Mingyue Zheng

PertKGE improves compound-protein interaction prediction using knowledge graph embedding of perturbation transcriptomics, outperforming baselines in cold-start settings and identifying novel therapeutic targets.

bioRxiv · Apr 8, 2024 · PreprintBioinformatics

Transfer Learning Enhanced Graph Neural Network for Aldehyde Oxidase Metabolism Prediction and Its Experimental Application

Jiacheng Xiong, Rongrong Cui, Zhaojun Steven Li, Wei Zhang, Runze Zhang, Zunyun Fu, Xiaohong Liu, Zhenghao Li, Kaixian Chen, Mingyue Zheng

This study develops AOMP, a graph neural network for predicting AOX metabolism, outperforming benchmarks and identifying new scaffolds validated experimentally.

Acta Pharmaceutica Sinica B · Oct 20, 2023Peer-reviewedBioinformatics

Computational target fishing by mining transcriptional data using a novel Siamese spectral-based graph convolutional network

Feisheng Zhong, Xiaolong Wu, Xutong Li, Dingyan Wang, Zunyun Fu, Xiaohong Liu, Xiaozhe Wan, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng

The paper introduces a Siamese spectral-based graph convolutional network to infer protein targets of chemical compounds from gene expression data, achieving better performance than existing methods.

bioRxiv · Apr 1, 2020 · PreprintBioinformatics