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)

Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. - Hansaim Lim; Lei Xie 006 (BCB, 2018)

ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy. - Annie Wang; Hansaim Lim; Shu-Yuan Cheng; Lei Xie 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Biological representation of chemicals using latent target interaction profile. - Mohamed Ayed; Hansaim Lim; Lei Xie 006 (BMC Bioinform., 2019)

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)

Machine Learning Applications for Drug Repurposing. - Hansaim Lim (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 New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. - Hansaim Lim; Lei Xie 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. - Yang Liu; Hansaim Lim; Lei Xie 006 (BMC Bioinform., 2022)

HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. - Hansaim Lim; Chung-Jung Tsai; Ozlem Keskin; Ruth Nussinov; Attila Gürsoy (Bioinform., 2022)