Publications

Shuang Wu, Xiang Liu, Ang Dong, Claudia Gragnoli, Christopher Griffin, Jie Wu, Shing-Tung Yau, Rongling Wu (2023). The metabolomic physics of complex diseases. The Proceedings of the National Academy of Sciences (PNAS), 120(42), e2308496120.

Jialin Bi, JunJie Wee, Xiang Liu, Cunquan Qu, Guanghui Wang, Kelin Xia (2023). Multiscale Topological Indices for the Quantitative Prediction of SARS CoV-2 Binding Affinity Change upon Mutations. Journal of Chemical Information and Modeling, 63(13), 4216-4227.

Xiang Liu, Huitao Feng, Zhi Lü, Kelin Xia (2023). Persistent Tor-algebra for protein–protein interaction analysis. Briefings in Bioinformatics, 24(2) 2023;, bbad046.

Kelin Xia, Xiang Liu, JunJie Wee (2023). Persistent Homology for RNA Data Analysis. Homology Modeling: Methods in Molecular Biology, 2627:211-229.

Ran Liu, Xiang Liu, Jie Wu (2023). Persistent Path-Spectral (PPS) Based Machine Learning for Protein–Ligand Binding Affinity Prediction. Journal of Chemical Information and Modeling 63(3), 1066-1075.

Xiang Liu, Kelin Xia (2022). Persistent Tor-algebra based stacking ensemble learning (PTA-SEL) for protein-protein binding affinity prediction. ICLR 2022 Workshop on Geometrical and Topological Representation Learning, GTRL 2022 Poster.

Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia (2022). Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein–Protein Binding Affinity Changes upon Mutation. Journal of Chemical Information and Modeling 62(17), 3961-3969.

Li Xiao-Shuang, Xiang Liu, Le Lu, Xian-Sheng Hua, Ying Chi, Kelin Xia (2022). Multiphysical graph neural network (MP-GNN) for COVID-19 drug design. Briefings in Bioinformatics, 23(4); bbac231.

Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia (2022). Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction. Plos Computational Biology, 18(4), e1009943.

Peiran Jiang, Ying Chi, Xiao-Shuang Li, Zhenyu Meng, Xiang Liu, Xian-Sheng Hua, Kelin Xia (2022). Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design. Briefings in Bioinformatics, 23(1); bbab527.

Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia (2021). Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction. Briefings in Bioinformatics, 22(5); bbab127.

Xiang Liu, Kelin Xia (2021). Neighborhood Complex Based Machine Learning (NCML) Models for Drug Design. Interpretability of Machine Intelligence in Medical Image Computing, and Topological Data Analysis and Its Applications for Medical Data. Springer, Cham, 87-97. (Spot Light).

Xiang Liu, Xiangjun Wang, Jie Wu, Kelin Xia (2021). Hypergraph based persistent cohomology (HPC) for molecular representations in drug design. Briefings In Bioinformatics, 22(5); bbaa411.