Publications

Zhiwei Nie, Xudong Liu, Jie Chen, Zhennan Wang, Yutian Liu, Haorui Si, Tianyi Dong, Fan Xu, Guoli Song, Yu Wang, Others (2024). E2VD: a unified evolution-driven framework for virus variation drivers prediction. Nature Machine Intelligence (under peer review).

Zhiwei Nie, Yiming Ma, Jie Chen, Yutian Liu, Zhihong Liu, Peng Yang, Fan Xu, Xiansong Huang, Feng Yin, Zigang Li, Others (2024). Towards anchoring evolutionary fitness for protein stability with virtual chemical environment recovery. Cell Systems (under peer review).

Yutian Liu, Zhiwei Nie, Jie Chen, Xinhao Zheng, Jie Fu, Zhihong Liu, Xudong Liu, Fan Xu, Xiansong Huang, Wen-Bin Zhang, Others (2024). Interpretable antibody-antigen interaction prediction by introducing route and priors guidance. bioRxiv.

Zhiwei Nie, Daixi Li, Jie Chen, Fan Xu, Yutian Liu, Jie Fu, Xudong Liu, Zhennan Wang, Yiming Ma, Kai Wang, Others (2024). Hunting for peptide binders of specific targets with data-centric generative language models. Nature Biomedical Engineering (under peer review).

Zhiying Zhang, Shengming Ma, Shisheng Zheng, Zhiwei Nie, Bingxu Wang, Kai Lei, Shunning Li, Feng Pan (2024). Semantic knowledge graph as a companion for catalyst recommendation. National Science Open.

Mingqing Wang, Zhiwei Nie, Yonghong He, Zhixiang Ren (2024). ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception. arXiv preprint arXiv:2405.15158.

Jie Chen, Zhiwei Nie, Yu Wang, Kai Wang, Fan Xu, Zhiheng Hu, Bing Zheng, Zhennan Wang, Guoli Song, Jingyi Zhang, Others (2023). ACM Gordon Bell Special Prize Finalist - Running ahead of evolution—AI-based simulation for predicting future high-risk SARS-CoV-2 variants. The International Journal of High Performance Computing Applications.

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Shunning Li, Yuanji Liu, Dong Chen, Yi Jiang, Zhiwei Nie, Feng Pan (2022). Encoding the atomic structure for machine learning in materials science. Wiley Interdisciplinary Reviews: Computational Molecular Science.

Zhiwei Nie, Shisheng Zheng, Yuanji Liu, Zhefeng Chen, Shunning Li, Kai Lei, Feng Pan (2022). Automating materials exploration with a semantic knowledge graph for Li-ion battery cathodes. Advanced Functional Materials.

Litao Chen, Wentao Zhang, Zhiwei Nie, Shunning Li, Feng Pan (2021). Generative models for inverse design of inorganic solid materials. J. Mater. Inform.