Author

Hao-Rui Si

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· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Organism:virus· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Assay:proteomics· 1 Approach:statistical model· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Jie CheniD· 2 shared Peng ZhouiD· 2 shared Zhiwei NieiD· 2 shared Fan XuiD· 1 shared Fan XuiD· 1 shared Guoli SongiD· 1 shared Tianyi Dong· 1 shared Tianyi DongiD· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersEvolutionary Biology

Jie ChenORCID

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2 papers

Recent·Most cited

Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution

Xudong Liu, Zhiwei Nie, Hao-Rui Si, Xurui Shen, Yutian Liu, Xiansong Huang, Tianyi Dong, Fan Xu, Zhixiang Ren, Peng Zhou, Jie Chen

This paper develops a deep-learning framework to predict real-world prevalent SARS-CoV-2 mutations using in silico virus evolution and protein language models, achieving accurate predictions of future dominant mutations.

Briefings in Bioinformatics · May 1, 2025Peer-reviewedEvolutionary Biology

E2VD: a unified evolution-driven framework for virus variation drivers prediction

Zhiwei Nie, Xudong Liu, Jie Chen, Zhennan Wang, Yutian Liu, Hao-Rui Si, Tianyi Dong, Fan Xu, Guoli Song, Yu Wang, Peng Zhou, Wen Gao, Yonghong Tian

E2VD predicts virus variation drivers using an evolution-driven framework, outperforming existing methods and identifying critical mutations for viral survival and risk.

bioRxiv · Nov 27, 2023 · PreprintBioinformatics