| Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond P Zhou, T Li The Journal of chemical physics 144 (9), 2016 | 88 | 2016 |
| Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics P Zhou, S Wang, T Li, Q Nie Nature communications 12 (1), 5609, 2021 | 64 | 2021 |
| Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data Y Sha, S Wang, P Zhou, Q Nie Nucleic acids research 48 (17), 9505-9520, 2020 | 55 | 2020 |
| On the mathematics of RNA velocity I: theoretical analysis T Li, J Shi, Y Wu, P Zhou bioRxiv, 2020.09. 19.304584, 2020 | 29 | 2020 |
| spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data F Bocci, P Zhou, Q Nie Molecular systems biology 18 (11), e11176, 2022 | 22 | 2022 |
| Inference of intercellular communications and multilayer gene-regulations of epithelial–mesenchymal transition from single-cell transcriptomic data Y Sha, S Wang, F Bocci, P Zhou, Q Nie Frontiers in Genetics 11, 604585, 2021 | 22 | 2021 |
| Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis K Nee, D Ma, QH Nguyen, M Pein, N Pervolarakis, J Insua-Rodríguez, ... Nature genetics 55 (4), 595-606, 2023 | 20 | 2023 |
| Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features J Dong, P Zhou, Y Wu, Y Chen, H Xie, Y Gao, J Lu, J Yang, X Zhang, ... Briefings in Bioinformatics 23 (1), bbab366, 2022 | 15* | 2022 |
| Single-cell RNA-seq analysis reveals the acquisition of cancer stem cell traits and increase of cell–cell signaling during EMT progression F Bocci, P Zhou, Q Nie Cancers 13 (22), 5726, 2021 | 13 | 2021 |
| Reconstructing growth and dynamic trajectories from single-cell transcriptomics data Y Sha, Y Qiu, P Zhou, Q Nie Nature Machine Intelligence 6 (1), 25-39, 2024 | 12 | 2024 |
| Stochasticity triggers activation of the S-phase checkpoint pathway in budding yeast P Zhou, X Gao, X Li, L Li, C Niu, Q Ouyang, H Lou, T Li, F Li Physical Review X 11 (1), 011004, 2021 | 11 | 2021 |
| Divergent resistance mechanisms to immunotherapy explain responses in different skin cancers E Dollinger, D Bergman, P Zhou, SX Atwood, Q Nie Cancers 12 (10), 2946, 2020 | 7 | 2020 |
| exFINDER: identify external communication signals using single-cell transcriptomics data C He, P Zhou, Q Nie Nucleic acids research 51 (10), e58-e58, 2023 | 6 | 2023 |
| DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data M Karikomi, P Zhou, Q Nie Briefings in bioinformatics 23 (4), bbac223, 2022 | 4 | 2022 |
| On the mathematics of RNA velocity II: algorithmic aspects T Li, Y Wang, G Yang, P Zhou arXiv preprint arXiv:2306.05707, 2023 | 1 | 2023 |
| Pre-neoplastic stromal cells drive BRCA1-mediated breast tumorigenesis K Nee, D Ma, QH Nguyen, N Pervolarakis, J Insua-Rodríguez, M Pein, ... bioRxiv, 2021.10. 20.465221, 2021 | 1 | 2021 |
| Spatial transition tensor of single cells P Zhou, F Bocci, T Li, Q Nie Nature Methods, 1-10, 2024 | | 2024 |
| Decoding cell identity with multi-scale explainable deep learning J Zhu, Z Zhang, Y Xiang, B Xie, X Dong, L Xie, P Zhou, R Yao, X Wang, ... bioRxiv, 2024.02. 05.578922, 2024 | | 2024 |
| stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport Q Peng, P Zhou, T Li bioRxiv, 2024.06. 02.596937, 2024 | | 2024 |
| Uncovering Minimal Pathways in Melanoma Initiation H Xiao, J Shiu, CF Chen, J Wu, P Zhou, SS Telang, R Ruiz-Vega, Q Nie, ... bioRxiv, 2023.12. 08.570336, 2023 | | 2023 |
