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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
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portfolio
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publications
Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond
Published in The Journal of Chemical Physics, 2016
From applied mathematics perspective, we investigate the theoretical relations between different proposals to construct energy landscape function for bio-chemical system .
Recommended citation: Peijie Zhou and Tiejun Li. "Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond." The Journal of Chemical Physics 144.9 (2016): 094109. https://aip.scitation.org/doi/abs/10.1063/1.4943096
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data
Published in Nucleic Acids Research, 2020
We combine unsupervised machine learning and dynamical systems modeling to study the single-cell transcriptomic datasets from epithelial-mesenchymal transitions (EMT).
Recommended citation: Yutong Sha, Shuxiong Wang, Peijie Zhou, and Qing Nie. "Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data." Nucleic acids research 48, no. 17 (2020): 9505-9520. https://academic.oup.com/nar/article/48/17/9505/5900115?login=true
Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers
Published in Cancers, 2020
Combining single-cell transcriptome data analysis and stochastic dynamics modeling, we understand the mechanism of different response to immunotherapy between two types of skin cancers – melanoma and basal cell carcinoma (BCC).
Recommended citation: Dollinger, Emmanuel; Bergman, Daniel; Zhou, Peijie; Atwood, Scott X.; Nie, Qing. 2020. "Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers" Cancers 12, no. 10: 2946. https://www.mdpi.com/2072-6694/12/10/2946
Stochasticity Triggers Activation of the S-phase Checkpoint Pathway in Budding Yeast
Published in Physical Review X, 2021
Combining single-cell experiment data analysis and stochastic dynamical system modeling, our results provide the direct evidence of in vivo stochastic cell-state transitions in single cells.
Recommended citation: Peijie Zhou, Xin Gao, Xiaoli Li, Linxi Li, Caoyuan Niu, Qi Ouyang, Huiqiang Lou, Tiejun Li and Fangting Li. "Stochasticity Triggers Activation of the S-phase Checkpoint Pathway in Budding Yeast". Physical Review X 11 (2021): 011004. https://journals.aps.org/prx/abstract/10.1103/PhysRevX.11.011004
Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial–Mesenchymal Transition From Single-Cell Transcriptomic Data
Published in Frontiers in Genetics, 2021
Using single-cell transcriptomic datasets, we infer the cell–cell communications and the multilayer gene–gene regulation networks to analyze and visualize the complex cellular crosstalk and the underlying gene regulatory dynamics along epithelial-mesenchymal transitions (EMT)
Recommended citation: Yutong Sha, Shuxiong Wang, Federico Bocci, Peijie Zhou and Qing Nie (2021) Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial–Mesenchymal Transition From Single-Cell Transcriptomic Data. Front. Genet. 11:604585. doi: 10.3389/fgene.2020.604585 https://www.frontiersin.org/articles/10.3389/fgene.2020.604585/full
On the Mathematics of RNA Velocity I: Theoretical Analysis.
Published in CSIAM Trans. Appl. Math., 2021
Deriving the analytical solution of the RNA velocity model from both deterministic and stochastic point of view; presenting the parameter inference framework based on the maximum likelihood estimate; proving the continuum limit of different downstream kernel-based methods
Recommended citation: Tiejun Li, Jifan Shi, Yichong Wu & Peijie Zhou. (2021). On the Mathematics of RNA Velocity I: Theoretical Analysis. CSIAM Transactions on Applied Mathematics. 2 (1).1-55. doi:10.4208/csiam-am.SO-2020-0001 https://global-sci.org/intro/article_detail/csiam-am/18653.html
Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features
Published in Briefings in Bioinformatics, 2021
Using molecular interaction network features to enhance the analysis of single-cell datasets
Recommended citation: Ji Dong, Peijie Zhou, Yichong Wu, Yidong Chen, Haoling Xie, Yuan Gao, Jiansen Lu, Jingwei Yang, Xiannian Zhang, Lu Wen, Tiejun Li, Fuchou Tang, Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features, Briefings in Bioinformatics, 2021;, bbab366, https://doi.org/10.1093/bib/bbab366 https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab366/6373559
Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics
Published in Nature Communications, 2021
Using multiscale dynamical system theory to analyze single-cell datasets, quantifying transition paths and dynamical manifold
Recommended citation: Zhou, Peijie, Shuxiong Wang, Tiejun Li, and Qing Nie. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics. Nat Commun 12, 5609 (2021). https://doi.org/10.1038/s41467-021-25548-w https://doi.org/10.1038/s41467-021-25548-w
Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell–Cell Signaling during EMT Progression
Published in Cancers, 2021
By integrating multiple analytical tools into a single computational framework, we investigated several single-cell RNA-sequencing (scRNA-seq) datasets and identified the emerging relationship between EMT, acquisition of CSC traits, and cell–cell communication.
Recommended citation: Bocci, F., Zhou, P. and Nie, Q., 2021. Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell–Cell Signaling during EMT Progression. Cancers, 13(22), p.5726. https://www.mdpi.com/2072-6694/13/22/5726
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data
Published in Briefings in Bioinformatics, 2022
We introduce DURIAN (Deconvolution and mUltitask-Regression-based ImputAtioN), an integrative method using iterative scheme between bulk deconvolution and single-cell imputation for recovery of gene expression in single-cell RNA-seq data.
Recommended citation: Karikomi, Matthew, Peijie Zhou, and Qing Nie. "DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data." Briefings in Bioinformatics (2022). https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac223
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data
Published in Molecular Systems Biology, 2022
Using attractor Jacobian to infer cell type stability with mRNA splicing dynamics with scRNA-seq data
Recommended citation: Federico Bocci, Peijie Zhou and Qing Nie. spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data. https://www.embopress.org/doi/full/10.15252/msb.202211176 https://doi.org/10.15252/msb.202211176
Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis
Published in Nature Genetics, 2023
Dissecting BRCA1-driven tumorigenesis with multiscale dynamical models.
Recommended citation: Nee, Kevin, et al. "Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis." Nature Genetics 55.4 (2023): 595-606. https://www.nature.com/articles/s41588-023-01298-x
exFINDER: identify external communication signals using single-cell transcriptomics data
Published in Nucleic Acids Research, 2023
Identifying external signals received by the cells in the single-cell transcriptomics datasets by utilizing the prior knowledge of signaling pathways.
Recommended citation: Changhan He, Peijie Zhou, and Qing Nie. "exFINDER: identify external communication signals using single-cell transcriptomics data." Nucleic Acids Research 51.10 (2023): e58-e58. https://www.nature.com/articles/s41588-023-01298-x
talks
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching Assistant
Undergraduate Upper Division/Graduate Course, Peking University,China, 2016
Mathematical Biophysics (2016 Fall)
Instructor
Undergraduate Lower Division Course, University of California, Irvine, 2020
Math 9 Introduction to Programming in Numerical Analysis (2021 Fall,2022 Winter, 2022 Spring)