Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites. - Zhen Chen 009; Ningning He; Yu Huang; Wen Tao Qin; Xuhan Liu; Lei Li 013 (Genom. Proteom. Bioinform., 2018)

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. - Zhen Chen 009; Xuhan Liu; Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Geoffrey I. Webb; Dakang Xu; Alexander Ian Smith; Lei Li 013; Kuo-Chen Chou; et al. (Briefings Bioinform., 2019)

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2019)

Computational Approaches for De Novo Drug Design: Past, Present, and Future. - Xuhan Liu; Adriaan P. IJzerman; Gerard J. P. van Westen (Artificial Neural Networks, 3rd Edition, 2021)

DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Michael T. M. Emmerich; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2021)

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. - Martin Sícho; Xuhan Liu; Daniel Svozil; Gerard J. P. van Westen (J. Cheminformatics, 2021)

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. - Zhen Chen 009; Xuhan Liu; Pei Zhao; Chen Li 021; Yanan Wang 003; Fuyi Li; Tatsuya Akutsu; Chris Bain; Robin B. Gasser; Junzhou Li; Zuoren Yang; Xin Gao 001; et al. (Nucleic Acids Res., 2022)

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning. - Xuhan Liu; Kai Ye 001; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen (J. Cheminformatics, 2023)