Curriculum Vitae

Education

• B.S. in Computational Mathematics, Peking University, China, 2014
  • Elite Undergraduate Program in Applied Mathematics
• Ph.D in Computational Mathematics, Peking University, China, 2019
  • Supervisor: Professor Tiejun Li
  • Thesis: Rare Event Studies in Single-Cell Systems Biology (Excellent Dissertation Award)

Research experience

• 2023 - Present: Tenure-Track Assistant Professor
  • Center for Machine Learning Research, Peking University
• 2020 - 2023: Visiting Assistant Professor
  • Department of Mathematics, University of California, Irvine
  • Supervisor: Professor Qing Nie
• 2019 - 2020: Postdoctoral Scholar
  • Department of Mathematics, University of California, Irvine
  • Supervisor: Professor Qing Nie
• 2018: Visiting Graduate Student
  • Department of Mathematics, University of California, Irvine
  • Supervisor: Professor Qing Nie
• 2012 - 2019: Graduate Research Assistant
  • School of Mathematical Sciences and Center for Quantitative Biology, Peking University, China
  • Supervisor: Professor Tiejun Li and Fangting Li

Skills

• Applied Stochastic Analysis and Dynamical System Modeling (with application in Systems Biology)
• Single-cell Data Analysis (combining machine learning and physical modeling)
• Programming
  • Python
  • R
  • Matlab
  • C/MPI
  • Julia

Publications

Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond

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.

Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data

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.

Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers

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.

Stochasticity Triggers Activation of the S-phase Checkpoint Pathway in Budding Yeast

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.

Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial–Mesenchymal Transition From Single-Cell Transcriptomic Data

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

On the Mathematics of RNA Velocity I: Theoretical Analysis.

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

Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features

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

Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

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

Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell–Cell Signaling during EMT Progression

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.

DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data

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).

spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data

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

Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis

Nee, Kevin, et al. "Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis." Nature Genetics 55.4 (2023): 595-606.

exFINDER: identify external communication signals using single-cell transcriptomics data

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.

Teaching

Teaching Assistant

Instructor

Service and leadership

• Vice President of SIAM Student Chapter, Peking University
• President of Graduate Association, School of Mathematical Sciences, Peking University