| 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 | 76 | 2016 |
| Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature Q Liu, D He, L Xie PLoS computational biology 15 (10), e1007480, 2019 | 46 | 2019 |
| 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 | 39 | 2019 |
| JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data J Ji, D He, Y Feng, Y He, F Xue, L Xie Bioinformatics 33 (19), 3080-3087, 2017 | 30 | 2017 |
| A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening D He, Q Liu, Y Wu, L Xie Nature Machine Intelligence 4 (10), 879-892, 2022 | 27 | 2022 |
| A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype D He, L Xie Bioinformatics 38 (1), 204-210, 2022 | 12 | 2022 |
| End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins T Cai, L Xie, S Zhang, M Chen, D He, A Badkul, Y Liu, HK Namballa, ... PLOS Computational Biology 19 (1), e1010851, 2023 | 8 | 2023 |
| Exploration of dark chemical genomics space via portal learning: applied to targeting the undruggable genome and covid-19 anti-infective polypharmacology T Cai, L Xie, M Chen, Y Liu, D He, S Zhang, C Mura, PE Bourne, L Xie Research Square, 2021 | 4 | 2021 |
| Robust prediction of patient-specific clinical response to unseen drugs from in vitro screens using context-aware deconfounding autoencoder D He, Q Liu, L Xie bioRxiv, 2021.05. 20.445055, 2021 | 4 | 2021 |
| CODE-AE: a coherent de-confounding autoencoder for predicting patient-specific drug response from cell line transcriptomics D He, L Xie arXiv preprint arXiv:2102.00538, 2021 | 3 | 2021 |
| A cross-level information transmission network for predicting phenotype from new genotype: Application to cancer precision medicine D He, L Xie arXiv preprint arXiv:2010.04824, 2020 | 2 | 2020 |
