| Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review Y Si, J Du, Z Li, X Jiang, T Miller, F Wang, WJ Zheng, K Roberts Journal of biomedical informatics 115, 103671, 2021 | 185 | 2021 |
| Pre-trained language models in biomedical domain: A systematic survey B Wang, Q Xie, J Pei, Z Chen, P Tiwari, Z Li, J Fu ACM Computing Surveys 56 (3), 1-52, 2023 | 183 | 2023 |
| Anticancer drug synergy prediction in understudied tissues using transfer learning Y Kim, S Zheng, J Tang, W Jim Zheng, Z Li, X Jiang Journal of the American Medical Informatics Association 28 (1), 42-51, 2021 | 84 | 2021 |
| Identification of protein–protein interactions by detecting correlated mutation at the interface F Guo, Y Ding, Z Li, J Tang Journal of chemical information and modeling 55 (9), 2042-2049, 2015 | 39 | 2015 |
| Identification of 14-3-3 proteins phosphopeptide-binding specificity using an affinity-based computational approach Z Li, J Tang, F Guo PloS one 11 (2), e0147467, 2016 | 35 | 2016 |
| Demon: improved neural network training with momentum decay J Chen, C Wolfe, Z Li, A Kyrillidis ICASSP 2022-2022 IEEE International Conference on Acoustics, Speech and …, 2022 | 29 | 2022 |
| PleThora: Pleural effusion and thoracic cavity segmentations in diseased lungs for benchmarking chest CT processing pipelines KJ Kiser, S Ahmed, S Stieb, ASR Mohamed, H Elhalawani, PYS Park, ... Medical physics 47 (11), 5941-5952, 2020 | 28 | 2020 |
| GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata Z Li, J Li, P Yu Database 2018, bay019, 2018 | 17 | 2018 |
| Learning from real imbalanced data of 14-3-3 proteins binding specificity Z Li, J Tang, F Guo Neurocomputing 217, 83-91, 2016 | 14 | 2016 |
| l1kdeconv: an R package for peak calling analysis with LINCS L1000 data Z Li, J Li, P Yu BMC bioinformatics 18, 1-7, 2017 | 13 | 2017 |
| A Novel Peptide Binding Prediction Approach for HLA‐DR Molecule Based on Sequence and Structural Information Z Li, Y Zhao, G Pan, J Tang, F Guo BioMed Research International 2016 (1), 3832176, 2016 | 10 | 2016 |
| Ensemble pretrained language models to extract biomedical knowledge from literature Z Li, Q Wei, LC Huang, J Li, Y Hu, YS Chuang, J He, A Das, VK Keloth, ... Journal of the American Medical Informatics Association 31 (9), 1904-1911, 2024 | 8 | 2024 |
| Demon: Momentum decay for improved neural network training J Chen, C Wolfe, Z Li, A Kyrillidis | 5 | 2022 |
| Prediction of Brain Metastases Development in Patients With Lung Cancer by Explainable Artificial Intelligence From Electronic Health Records Z Li, R Li, Y Zhou, L Rasmy, D Zhi, P Zhu, A Dono, X Jiang, H Xu, ... JCO clinical cancer informatics 7, e2200141, 2023 | 3 | 2023 |
| UTHealth@ BioCreativeVII: domain-specific transformer models for drug-protein relation extraction A Das, L Zhao, Q Wei Proceedings of the BioCreative VII challenge evaluation workshop 17, 2021 | 3 | 2021 |
| ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures Y Yang, H Kumar, Y Xie, Z Li, R Li, W Chen, CS Diala, MA Ali, Y Xu, A Wu, ... Nucleic Acids Research 53 (D1), D331-D339, 2025 | 1 | 2025 |
| Developing deep learning-based strategies to predict the risk of hepatocellular carcinoma among patients with nonalcoholic fatty liver disease from electronic health records Z Li, L Lan, Y Zhou, R Li, KD Chavin, H Xu, L Li, DJH Shih, WJ Zheng Journal of Biomedical Informatics 152, 104626, 2024 | 1 | 2024 |
| Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks Z Li, R Li, KJ Kiser, L Giancardo, WJ Zheng Proceedings of the 12th ACM International Conference on Bioinformatics …, 2021 | 1 | 2021 |
| GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data R Li, W Chen, J Li, H Xing, H Xu, Z Li, WJ Zheng arXiv preprint arXiv:2410.10899, 2024 | | 2024 |
| Develop and validate a computable phenotype for the identification of Alzheimer's disease patients using electronic health record data X He, R Wei, Y Huang, Z Chen, T Lyu, S Bost, J Tong, L Li, Y Zhou, Z Li, ... Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring 16 (3 …, 2024 | | 2024 |
