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| Liu Q, Hua K, Zhang X, et al. (2022) DeepCAGE: Incorporating transcription factors in genome-wide prediction of chromatin accessibility. Genomics, Proteomics & Bioinformatics |
| Ma S, Chen X, Zhu X, et al. (2022) Leveraging cell-type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm. Proceedings of the National Academy of Sciences of the United States of America. 119 |
| Duren Z, Lu WS, Arthur JG, et al. (2021) Sc-compReg enables the comparison of gene regulatory networks between conditions using single-cell data. Nature Communications. 12: 4763 |
| Li S, Noor ZS, Zeng W, et al. (2021) Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nature Communications. 12: 4172 |
| Zou M, Duren Z, Yuan Q, et al. (2021) MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. Briefings in Bioinformatics |
| Liu Q, Chen S, Jiang R, et al. (2021) Simultaneous deep generative modeling and clustering of single cell genomic data. Nature Machine Intelligence. 3: 536-544 |
| Zhu X, Duren Z, Wong WH. (2021) Modeling regulatory network topology improves genome-wide analyses of complex human traits. Nature Communications. 12: 2851 |
| Liu Q, Xu J, Jiang R, et al. (2021) Density estimation using deep generative neural networks. Proceedings of the National Academy of Sciences of the United States of America. 118 |
| Feng Z, Duren Z, Xiong Z, et al. (2021) hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. Communications Biology. 4: 442 |
| Zhang Y, Ouyang Z, Qian WJ, et al. (2020) Meta-analysis of peptides to detect protein significance. Statistics and Its Interface. 13: 465-474 |