Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. - Hansaim Lim; Aleksandar Poleksic; Yuan Yao 001; Hanghang Tong; Di He 003; Luke Zhuang; Patrick Meng; Lei Xie 006 (PLoS Comput. Biol., 2016)

JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. - Jiadong Ji; Di He 003; Yang Feng 002; Yong He; Fuzhong Xue; Lei Xie 006 (Bioinform., 2017)

Association rule mining algorithms on high-dimensional datasets. - Dongmei Ai; Hongfei Pan; Xiaoxin Li; Yingxin Gao; Di He 003 (Artif. Life Robotics, 2018)

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)

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature. - Qiao Liu; Di He 003; Lei Xie 006 (PLoS Comput. Biol., 2019)

A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine. - Di He 003; Lei Xie 006 (CoRR, 2020)

A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. - Di He 003; Lei Xie 006 (Bioinform., 2021)

CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics. - Di He 003; Lei Xie 006 (CoRR, 2021)

Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. - Tian Cai; Li Xie 002; Muge Chen; Yang Liu; Di He 003; Shuo Zhang 010; Cameron Mura; Philip E. Bourne; Lei Xie 006 (CoRR, 2021)

Learn Biologically Meaningful Representation with Transfer Learning. - Di He 003 (2021)

A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening. - Di He 003; Qiao Liu; You Wu; Lei Xie 006 (Nat. Mac. Intell., 2022)

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. - Tian Cai; Li Xie 002; Shuo Zhang 010; Muge Chen; Di He 003; Amitesh Badkul; Yang Liu; Hari Krishna Namballa; Michael Dorogan; Wayne W. Harding; Cameron Mura; Philip E. Bourne; et al. (PLoS Comput. Biol., 2023)