Deep template-based protein structure prediction. - Fandi Wu; Jinbo Xu (PLoS Comput. Biol., 2021)

Improving protein structure prediction using templates and sequence embedding. - Fandi Wu; Xiaoyang Jing; Xiao Luo; Jinbo Xu (Bioinform., 2023)

A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications. - Jiaqi Han; Jiacheng Cen; Liming Wu; Zongzhao Li; Xiangzhe Kong; Rui Jiao; Ziyang Yu 002; Tingyang Xu; Fandi Wu; Zihe Wang; Hongteng Xu; Zhewei Wei; et al. (CoRR, 2024)

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Yufei Huang 002; Haitao Lin; Lirong Wu; Fandi Wu; Mathieu Blanchette; Stan Z. Li (AAAI, 2025)

IgGM: A Generative Model for Functional Antibody and Nanobody Design. - Rubo Wang; Fandi Wu; Xingyu Gao 001; Jiaxiang Wu 001; Peilin Zhao; Jianhua Yao 001 (ICLR, 2025)

A survey of geometric graph neural networks: data structures, models and applications. - Jiaqi Han; Jiacheng Cen; Liming Wu; Zongzhao Li; Xiangzhe Kong; Rui Jiao; Ziyang Yu 002; Tingyang Xu; Fandi Wu; Zihe Wang; Hongteng Xu; Zhewei Wei; et al. (Frontiers Comput. Sci., 2025)