| Discovering personalized driver mutation profiles of single samples in cancer by network control strategy WF Guo, SW Zhang, LL Liu, F Liu, QQ Shi, L Zhang, Y Tang, T Zeng, ... Bioinformatics 34 (11), 1893-1903, 2018 | 113 | 2018 |
| Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data Q Shi, C Zhang, M Peng, X Yu, T Zeng, J Liu, L Chen Bioinformatics 33 (17), 2706-2714, 2017 | 93 | 2017 |
| A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification WF Guo, SW Zhang, QQ Shi, CM Zhang, T Zeng, L Chen Bmc Genomics 19 (Suppl 1), 924, 2018 | 42 | 2018 |
| Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis WF Guo, X Yu, QQ Shi, J Liang, SW Zhang, T Zeng PLoS computational biology 17 (5), e1008962, 2021 | 29 | 2021 |
| Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics Y Hu, K Xiao, H Yang, X Liu, C Zhang, Q Shi Briefings in Bioinformatics 25 (2), 2024 | 24 | 2024 |
| Multi-view subspace clustering analysis for aggregating multiple heterogeneous omics data Q Shi, B Hu, T Zeng, C Zhang Frontiers in genetics 10, 744, 2019 | 20 | 2019 |
| Regulation and control roles of the basal ganglia in the development of absence epileptiform activities B Hu, D Wang, Z Xia, A Yang, J Zhang, Q Shi, H Dai Cognitive Neurodynamics 14 (1), 137-154, 2020 | 16 | 2020 |
| Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network X Li, W Huang, X Xu, HY Zhang, Q Shi Frontiers in Genetics 14, 1202409, 2023 | 15 | 2023 |
| Integration of multiple heterogeneous omics data C Zhang, J Liu, Q Shi, X Yu, T Zeng, L Chen 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2016 | 14 | 2016 |
| Local network component analysis for quantifying transcription factor activities Q Shi, C Zhang, W Guo, T Zeng, L Lu, Z Jiang, Z Wang, J Liu, L Chen Methods 124, 25-35, 2017 | 13 | 2017 |
| Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification C Zhang, X Li, W Huang, L Wang, Q Shi Briefings in Bioinformatics 24 (4), bbad197, 2023 | 12 | 2023 |
| Comparative network stratification analysis for identifying functional interpretable network biomarkers C Zhang, J Liu, Q Shi, T Zeng, L Chen BMC bioinformatics 18 (Suppl 3), 48, 2017 | 12 | 2017 |
| Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics L Wang, Y Hu, K Xiao, C Zhang, Q Shi, L Chen Briefings in Bioinformatics 25 (4), 2024 | 10 | 2024 |
| scDA: single cell discriminant analysis for single-cell RNA sequencing data Q Shi, X Li, Q Peng, C Zhang, L Chen Computational and Structural Biotechnology Journal 19, 3234-3244, 2021 | 10 | 2021 |
| Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics C Zhang, L Wang, Q Shi Computational and Structural Biotechnology Journal 23, 2109-2115, 2024 | 9 | 2024 |
| Differential function analysis: identifying structure and activation variations in dysregulated pathways C Zhang, J Liu, Q Shi, T Zeng, L Chen Science China Information Sciences 60 (1), 012108, 2017 | 7 | 2017 |
| Spatially Aware Domain Adaptation Enables Cell Type Deconvolution from Multi‐Modal Spatially Resolved Transcriptomics L Wang, X Bai, C Zhang, Q Shi, L Chen Small Methods 9 (5), 2401163, 2025 | 4 | 2025 |
| Spatially informed graph transformers for spatially resolved transcriptomics X Bao, X Bai, X Liu, Q Shi, C Zhang Communications Biology 8 (1), 574, 2025 | 4 | 2025 |
| Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks J Sun, Q Shi, X Chen, R Liu Briefings in Bioinformatics 21 (6), 2084-2098, 2020 | 4 | 2020 |
| LANTSA: Landmark-based transferable subspace analysis for single-cell and spatial transcriptomics C Zhang, L Wang, X Li, WF Guo, Q Shi, L Chen bioRxiv, 2022.03. 13.484116, 2022 | 3 | 2022 |
