| Quantifying Waddington’s epigenetic landscape: a comparison of single-cell potency measures J Shi, AE Teschendorff, W Chen, L Chen, T Li Briefings in bioinformatics 21 (1), 248-261, 2020 | 73 | 2020 |
| On the Mathematics of RNA Velocity I: Theoretical Analysis T Li, J Shi, Y Wu, P Zhou CSIAM Trans. Appl. Math. 2 (1), 1-55, 2020 | 44 | 2020 |
| Energy landscape decomposition for cell differentiation with proliferation effect J Shi, K Aihara, T Li, L Chen National Science Review 9 (8), nwac116, 2022 | 35 | 2022 |
| Towards a critical transition theory under different temporal scales and noise strengths J Shi, T Li, L Chen Physical Review E 93 (3), 032137, 2016 | 35 | 2016 |
| Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process J Shi, T Li, L Chen, K Aihara PLoS computational biology 15 (11), e1007488, 2019 | 29 | 2019 |
| Criticality in the Healthy Brain J Shi, K Kirihara, M Tada, M Fujioka, K Usui, D Koshiyama, T Araki, ... Frontiers in Network Physiology 1, 755685, 2022 | 25 | 2022 |
| Embedding entropy: a nonlinear measure of dynamical causality J Shi, L Chen, K Aihara Journal of The Royal Society Interface 19 (188), 20210766, 2022 | 24 | 2022 |
| Dynamics-based data science in biology J Shi, K Aihara, L Chen National Science Review 8 (5), nwab029, 2021 | 23 | 2021 |
| Detecting direct associations in a network by information theoretic approaches J Shi, J Zhao, T Li, L Chen Science China Mathematics 62 (5), 823-838, 2019 | 17 | 2019 |
| Quantifying direct dependencies in biological networks by multiscale association analysis J Shi, J Zhao, X Liu, L Chen, T Li IEEE/ACM transactions on computational biology and bioinformatics 17 (2 …, 2018 | 16 | 2018 |
| Detecting dynamical causality via intervened reservoir computing J Zhao, Z Gan, R Huang, C Guan, J Shi, S Leng Communications Physics 7 (1), 232, 2024 | 7 | 2024 |
| Transfer learning of multicellular organization via single-cell and spatial transcriptomics Y Tan, A Wang, Z Wang, W Lin, Y Yan, Q Nie, J Shi PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.101, 2025 | 6 | 2025 |
| Detecting dynamical causality by intersection cardinal concavity P Tao, Q Wang, J Shi, X Hao, X Liu, B Min, Y Zhang, C Li, H Cui, L Chen Fundamental Research, 2023 | 6 | 2023 |
| Mean-field analysis of Stuart–Landau oscillator networks with symmetric coupling and dynamical noise Y Li, J Shi, K Aihara Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (6), 2022 | 4 | 2022 |
| Unveiling the Mechanism of Compound Ku-Shen Injection in Liver Cancer Treatment through an Ingredient–Target Network Analysis W Zou, J Liu, Z Wei, C Peng, Y Zhao, Y Ding, J Shi, J Zhao Genes 15 (10), 1278, 2024 | 2 | 2024 |
| Dynamical causality under invisible confounders J Yan, SW Zhang, C Zhang, W Huang, J Shi, L Chen arXiv preprint arXiv:2408.05584, 2024 | 2 | 2024 |
| Supplementary Information for “Embedding entropy: a nonlinear measure of dynamical causality” J Shi, L Chen, K Aihara Figshare, 2022 | 2 | 2022 |
| Integrative cross-sample alignment and spatially differential gene analysis for spatial transcriptomics Y Tan, Z Wang, A Wang, Y Yan, W Lin, Q Nie, J Shi bioRxiv, 2025.06. 05.653933, 2025 | 1 | 2025 |
| A Time-Series Foundation Model by Universal Delay Embedding Z Wang, P Tao, J Shi, R Bao, R Liu, L Chen arXiv preprint arXiv:2509.12080, 2025 | | 2025 |
| Utilizing Causal Network Markers to Identify Tipping Points ahead of Critical Transition S Bian, Z Wang, S Leng, W Lin, J Shi Advanced Science, 2025 | | 2025 |
Luonan ChenChair Professor, School of Mathematical Sciences and School of AI, Shanghai Jiao Tong UniversityVerified email at sjtu.edu.cn
