| The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method Z Cui, YL Gao, JX Liu, J Wang, J Shang, LY Dai BMC bioinformatics 20, 1-10, 2019 | 38 | 2019 |
| L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions Z Cui, YL Gao, JX Liu, LY Dai, SS Yuan BMC bioinformatics 20, 1-13, 2019 | 30 | 2019 |
| WGRCMF: A weighted graph regularized collaborative matrix factorization method for predicting novel LncRNA-disease associations JX Liu, Z Cui, YL Gao, XZ Kong IEEE Journal of Biomedical and Health Informatics 25 (1), 257-265, 2020 | 28 | 2020 |
| NPCMF: nearest profile-based collaborative matrix factorization method for predicting miRNA-disease associations YL Gao, Z Cui, JX Liu, J Wang, CH Zheng BMC bioinformatics 20, 1-10, 2019 | 28 | 2019 |
| LncRNA-disease associations prediction using bipartite local model with nearest profile-based association inferring Z Cui, JX Liu, YL Gao, R Zhu, SS Yuan IEEE journal of biomedical and health informatics 24 (5), 1519-1527, 2019 | 27 | 2019 |
| Base-resolution prediction of transcription factor binding signals by a deep learning framework Q Zhang, Y He, S Wang, Z Chen, Z Guo, Z Cui, Q Liu, DS Huang PLoS computational biology 18 (3), e1009941, 2022 | 22 | 2022 |
| LWPCMF: logistic weighted profile-based collaborative matrix factorization for predicting MiRNA-disease associations MM Yin, Z Cui, MM Gao, JX Liu, YL Gao IEEE/ACM transactions on computational biology and bioinformatics 18 (3 …, 2019 | 22 | 2019 |
| Dual-network sparse graph regularized matrix factorization for predicting miRNA–disease associations MM Gao, Z Cui, YL Gao, JX Liu, CH Zheng Molecular omics 15 (2), 130-137, 2019 | 21 | 2019 |
| DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization JX Liu, MM Gao, Z Cui, YL Gao, F Li BMC bioinformatics 22 (Suppl 3), 241, 2021 | 20 | 2021 |
| Multi-label fusion collaborative matrix factorization for predicting LncRNA-disease associations MM Gao, Z Cui, YL Gao, J Wang, JX Liu IEEE journal of biomedical and health informatics 25 (3), 881-890, 2020 | 17 | 2020 |
| Computational prediction and characterization of cell-type-specific and shared binding sites Q Zhang, P Teng, S Wang, Y He, Z Cui, Z Guo, Y Liu, C Yuan, Q Liu, ... Bioinformatics 39 (1), btac798, 2023 | 10 | 2023 |
| RMSCNN: a random multi-scale convolutional neural network for marine microbial bacteriocins identification Z Cui, ZH Chen, QH Zhang, V Gribova, VF Filaretov, DS Huang IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (6 …, 2021 | 10 | 2021 |
| RCMF: a robust collaborative matrix factorization method to predict miRNA-disease associations Z Cui, JX Liu, YL Gao, CH Zheng, J Wang BMC bioinformatics 20, 1-10, 2019 | 9 | 2019 |
| Predicting the sequence specificities of DNA-binding proteins by DNA fine-tuned language model with decaying learning rates Y He, Q Zhang, S Wang, Z Chen, Z Cui, ZH Guo, DS Huang IEEE/ACM Transactions on Computational Biology and Bioinformatics 20 (1 …, 2022 | 7 | 2022 |
| DeepTPpred: A deep learning approach with matrix factorization for predicting therapeutic peptides by integrating length information Z Cui, SG Wang, Y He, ZH Chen, QH Zhang IEEE Journal of Biomedical and Health Informatics 27 (9), 4611-4622, 2023 | 5 | 2023 |
| Dual sparse collaborative matrix factorization method based on Gaussian kernel function for predicting lncRNA-disease associations MM Gao, Z Cui, YL Gao, F Li, JX Liu Intelligent Computing Methodologies: 15th International Conference, ICIC …, 2019 | 5 | 2019 |
| DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes S Wang, Q Zhang, Y He, Z Cui, Z Guo, K Han, DS Huang PLoS Computational Biology 18 (10), e1010572, 2022 | 4 | 2022 |
| Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations F Zhou, MM Yin, CN Jiao, Z Cui, JX Zhao, JX Liu BMC bioinformatics 22, 1-16, 2021 | 4 | 2021 |
| MV-CVIB: a microbiome-based multi-view convolutional variational information bottleneck for predicting metastatic colorectal cancer Z Cui, Y Wu, QH Zhang, SG Wang, Y He, DS Huang Frontiers in Microbiology 14, 1238199, 2023 | 1 | 2023 |
| NPENN: A Noise Perturbation Ensemble Neural Network for Microbiome Disease Phenotype Prediction Z Cui, Y Wu, QH Zhang, SG Wang, ZH Guo IEEE Journal of Biomedical and Health Informatics, 2024 | | 2024 |
