Research Output

Publications

4 results found

^* corresponding author · bold = first author

2026

DeepISO: deep learning-powered prediction of protein–protein interaction rewiring generated by alternative splicing

Xiaokun Guo, Linyang Jiang, Jiajun Li, Mengdi Yuan, Dianke Li, Wenyu Shi^*, Ziding Zhang & Stefan Wuchty^*

Genome Biology, 2026.

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Interpretable deep learning framework for mapping E3–substrate binding interfaces

Dianke Li, Yuting Zhang, Yuan Liu, Zihao Zhang, Yingjie Qu, Jiajun Li, Linyang Jiang, Lihong Diao, Ziding Zhang^*, Lingqiang Zhang^*, Chun-Ping Cui & Dong Li^*

Nature Communications, 2026.

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2025

PPEPFinder: A deep learning framework integrating sequence embeddings and structural graph representations for predicting fungal and oomycete effector proteins

Mengdi Yuan, Shaoke Zhang, Jiajun Li, Jingyan Zheng, Chenping Lei, Zhuojun Wang, Miao Zhao, Wenyu Shi^*, Ziding Zhang^*

The plant journal, 2025.

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Graph neural network integrated with pretrained protein language model for predicting human–virus protein–protein interactions

Linyang Jiang, Xiaodi Yang, Xiaokun Guo, Dianke Li, Jiajun Li, Stefan Wuchty, Wenyu Shi^*, Ziding Zhang^*

Briefings in Bioinformatics, 2025.

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