| DeepCRISPR: optimized CRISPR guide RNA design by deep learning G Chuai, H Ma, J Yan, M Chen, N Hong, D Xue, C Zhou, C Zhu, K Chen, ... Genome biology 19, 1-18, 2018 | 430 | 2018 |
| A ‘new lease of life’: FnCpf1 possesses DNA cleavage activity for genome editing in human cells M Tu, L Lin, Y Cheng, X He, H Sun, H Xie, J Fu, C Liu, J Li, D Chen, H Xi, ... Nucleic acids research 45 (19), 11295-11304, 2017 | 132 | 2017 |
| FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery S Chen, D Xue, G Chuai, Q Yang, Q Liu Bioinformatics 36 (22-23), 5492-5498, 2020 | 101 | 2020 |
| Advances and challenges in deep generative models for de novo molecule generation D Xue, Y Gong, Z Yang, G Chuai, S Qu, A Shen, J Yu, Q Liu Wiley Interdisciplinary Reviews: Computational Molecular Science 9 (3), e1395, 2019 | 92 | 2019 |
| Structure-informed language models are protein designers Z Zheng, Y Deng, D Xue, Y Zhou, F Ye, Q Gu International conference on machine learning, 42317-42338, 2023 | 72 | 2023 |
| X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis D Xue, H Zhang, D Xiao, Y Gong, G Chuai, Y Sun, H Tian, H Wu, Y Li, ... bioRxiv, 2020.12. 23.424259, 2020 | 46 | 2020 |
| DeepReac+: deep active learning for quantitative modeling of organic chemical reactions Y Gong, D Xue, G Chuai, J Yu, Q Liu Chemical Science 12 (43), 14459-14472, 2021 | 35 | 2021 |
| Benchmarking and integrating genome-wide CRISPR off-target detection and prediction J Yan, D Xue, G Chuai, Y Gao, G Zhang, Q Liu Nucleic acids research 48 (20), 11370-11379, 2020 | 23 | 2020 |
| Diffusion Language Models Are Versatile Protein Learners X Wang, Z Zheng, F Ye, D Xue, S Huang, Q Gu arXiv preprint arXiv:2402.18567, 2024 | 20 | 2024 |
| Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization X Zhou, D Xue, R Chen, Z Zheng, L Wang, Q Gu arXiv preprint arXiv:2403.16576, 2024 | 17 | 2024 |
| Structure-informed language models are protein designers. bioRxiv Z Zheng, Y Deng, D Xue, Y Zhou, F Ye, Q Gu | 13 | 2023 |
| X-mol: largescale pre-training for molecular understanding and diverse molecular analysis. bioRxiv D Xue, H Zhang, D Xiao, Y Gong, G Chuai, Y Sun, H Tian, H Wu, Y Li, ... | 11 | 2021 |
| Dplm-2: A multimodal diffusion protein language model X Wang, Z Zheng, F Ye, D Xue, S Huang, Q Gu arXiv preprint arXiv:2410.13782, 2024 | 5 | 2024 |
| Proteinbench: A holistic evaluation of protein foundation models F Ye, Z Zheng, D Xue, Y Shen, L Wang, Y Ma, Y Wang, X Wang, X Zhou, ... arXiv preprint arXiv:2409.06744, 2024 | 2 | 2024 |
| ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design Y Ma, F Ye, Y Zhou, Z Zheng, D Xue, Q Gu arXiv preprint arXiv:2411.16686, 2024 | | 2024 |
| Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer G Zhang, C Zhu, X Chen, J Yan, D Xue, Z Wei, G Chuai, Q Liu Genomics, Proteomics & Bioinformatics 21 (6), 1237-1245, 2023 | | 2023 |
