| Large-scale off-target identification using fast and accurate dual regularized one-class collaborative filtering and its application to drug repurposing H Lim, A Poleksic, Y Yao, H Tong, D He, L Zhuang, P Meng, L Xie PLoS computational biology 12 (10), e1005135, 2016 | 82 | 2016 |
| Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem H Lim, P Gray, L Xie, A Poleksic Scientific reports 6 (1), 38860, 2016 | 69 | 2016 |
| Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology H Lim, D He, Y Qiu, P Krawczuk, X Sun, L Xie PLoS computational biology 15 (6), e1006619, 2019 | 42 | 2019 |
| ANTENNA, a multi-rank, multi-layered recommender system for inferring reliable drug-gene-disease associations: repurposing diazoxide as a targeted anti-cancer therapy A Wang, H Lim, SY Cheng, L Xie IEEE/ACM transactions on computational biology and bioinformatics 15 (6 …, 2018 | 36 | 2018 |
| MSA-regularized protein sequence transformer toward predicting genome-wide chemical-protein interactions: application to GPCRome deorphanization T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie Journal of chemical information and modeling 61 (4), 1570-1582, 2021 | 33 | 2021 |
| A Bayesian approach to accurate and robust signature detection on LINCS L1000 data Y Qiu, T Lu, H Lim, L Xie Bioinformatics 36 (9), 2787-2795, 2020 | 28 | 2020 |
| Artificial intelligence approaches to human-microbiome protein–protein interactions H Lim, F Cankara, CJ Tsai, O Keskin, R Nussinov, A Gursoy Current Opinion in Structural Biology 73, 102328, 2022 | 25 | 2022 |
| Biological representation of chemicals using latent target interaction profile M Ayed, H Lim, L Xie BMC bioinformatics 20 (Suppl 24), 674, 2019 | 14 | 2019 |
| A new weighted imputed neighborhood-regularized tri-factorization one-class collaborative filtering algorithm: Application to target gene prediction of transcription factors H Lim, L Xie IEEE/ACM transactions on computational biology and bioinformatics 18 (1 …, 2020 | 13 | 2020 |
| Exploring landscape of drug-target-pathway-side effect associations H Lim, A Poleksic, L Xie AMIA Summits on Translational Science Proceedings 2018, 132, 2018 | 12 | 2018 |
| Omics data integration and analysis for systems pharmacology H Lim, L Xie Bioinformatics and Drug Discovery, 199-214, 2019 | 10 | 2019 |
| Target gene prediction of transcription factor using a new neighborhood-regularized tri-factorization one-class collaborative filtering algorithm H Lim, L Xie Proceedings of the 2018 ACM International Conference on Bioinformatics …, 2018 | 5 | 2018 |
| HMI-PRED 2.0: a biologist-oriented web application for prediction of host–microbe protein–protein interaction by interface mimicry H Lim, CJ Tsai, O Keskin, R Nussinov, A Gursoy Bioinformatics 38 (21), 4962-4965, 2022 | 4 | 2022 |
| A deep learning framework for elucidating whole-genome chemical interaction space T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie bioRxiv, 2020.10. 08.332346, 2020 | 3 | 2020 |
| Machine learning strategies for identifying repurposed drugs for cancer therapy H Lim, L Xie Drug Repurposing in Cancer Therapy, 55-79, 2020 | 2 | 2020 |
| Genome-wide prediction of small molecule binding to remote orphan proteins using distilled sequence alignment embedding T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie bioRxiv, 2020.08. 04.236729, 2020 | 1 | 2020 |
| Semipres: an Integrated Deep Learning Method of Sequence and 3d Object Detection Models for Host-microbe Interactions by Identification of Protein-protein Contact Residues H Lim, O Keskin, R Nussinov, A Gursoy | | 2022 |
| Machine Learning Applications for Drug Repurposing H Lim City University of New York, 2020 | | 2020 |
| Rational Discovery of Dual-Action Multi-Target Kinase Inhibitor for Precision Anti-Cancer Therapy Using Structural Systems Pharmacology H Lim, D He, Y Qiu, P Krawczuk, X Sun, L Xie bioRxiv, 465054, 2018 | | 2018 |
