Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. - Hansaim Lim; Di He 003; Yue Qiu 002; Patrycja Krawczuk; Xiaoru Sun; Lei Xie 006 (PLoS Comput. Biol., 2019)

A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. - Yue Qiu 002; Tianhuan Lu; Hansaim Lim; Lei Xie 006 (Bioinform., 2020)

MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. - Tian Cai; Hansaim Lim; Kyra Alyssa Abbu; Yue Qiu 002; Ruth Nussinov; Lei Xie 006 (J. Chem. Inf. Model., 2021)

A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. - Thai-Hoang Pham; Yue Qiu 002; Jucheng Zeng; Lei Xie 006; Ping Zhang 016 (Nat. Mach. Intell., 2021)

Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. - Thai-Hoang Pham; Yue Qiu 002; Jiahui Liu; Steven Zimmer; Eric E. O'Neill; Lei Xie 006; Ping Zhang 016 (Patterns, 2022)

Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's disease drug repurposing. - You Wu; Qiao Liu; Yue Qiu 002; Lei Xie 006 (PLoS Comput. Biol., 2022)