YANG Laboratory

Biophysics of Living Systems

Preprints

  • Mitotic waves in frog egg extracts: Transition from phase waves to trigger waves.

    O. Puls, D.R. Reynés, F. Tavella, M. Jin, Y. Kim, L. Gelens, Q. Yang

    bioRxiv (2024).
    DOI: 10.1101/2024.01.18.576267 | Link 

  • A human pluripotent stem cell-based somitogenesis model using microfluidics.

    Y. Liu, Y.S. Kim, X. Xue, N. Kobayashi, S. Sun, Q. Yang, O. Pourquié, J. Fu

    Cell Stem Cell (in press).
    DOI: 10.1101/2023.10.29.564399 | Link 

  • Publications

  • Comprehensive parameter space mapping of cell cycle dynamics under network perturbations.

    Z Li, S Wang, M Sun, M Jin, D Khain, Q Yang

    ACS Synthetic Biology (2024).
    DOI: 10.1021/acssynbio.3c00631 | Link 

  • Nuclear-cytoplasmic compartmentalization promotes robust timing of mitotic events by cyclin B1-Cdk1

    G Maryu, Q Yang

    Cell Reports 41, 111870 (2022).
    DOI: 10.1016/j.celrep.2022.111870 | Link 

  • In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density

    M Jin, F Tavella, S Wang, Q Yang

    PNAS 119, 6 (2022).
    DOI: 10.1073/pnas.2109547119 | Link 

  • Monitoring spontaneous quiescence and asynchronous proliferation-quiescence decisions in prostate cancer cells.

    A Pulianmackal, D Sun, K Yumoto, Z Li, Y Chen, M Patel, Y Wang, E Yoon, A Pearson, Q Yang, R Taichman, F Cackowski, L Buttitta

    Frontiers in Cell and Developmental Biology 9, 3494 (2021).
    DOI: 10.3389/fcell.2021.728663 | Link 

  • Plug-in tubes removing oil and packing droplets for time-controlled droplet-based assays.

    M Sun, G Maryu, S Wang, Q Yang, RC Bailey

    Biomicrofluidics 15, 024108 (2021).
    DOI: 10.1063/5.0047924 | Link 

  • Real-Time Monitoring of APC/C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts.

    J Kamenz, R Qiao, Q Yang, JE Ferrell

    Methods Mol Biol 2329, 29 (2021).
    DOI: 10.1007/978-1-0716-1538-6_3 | Link 

  • High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning.

    Z Li, S Wang, M Sun, M Jin, D Khain, Q Yang

    bioRxiv (2021).
    DOI: 10.1101/2021.05.10.442602 | Link 

  • Engineering spatiotemporal organization and dynamics in synthetic cells.

    A. Groaz, H. Moghimianavval, F. Tavella, T. Giessen, A. Vecchiarelli, Q. Yang, A. Liu

    WIREs Nanomedicine and Nanobiotechnology e1685 (2020).
    DOI: 10.1002/wnan.1685 | Link 

  • Building Dynamic Cellular Machineries in Droplet-Based Artificial Cells with Single-Droplet Tracking and Analysis.

    M. Sun, Z. Li, S. Wang, G. Maryu, and Q. Yang

    Analytical Chemistry 91, 9813 (2019).
    DOI: 10.1021/acs.analchem.9b01481 | Link 

  • μdroPi: A Hand-Held Microfluidic Droplet Imager and Analyzer Built on Raspberry Pi.

    M. Sun, Z. Li, and Q. Yang

    Journal of Chemical Education 96, 1152 (2019).
    DOI: 10.1021/acs.jchemed.8b00975 | Link 

  • The Rise of Ultrafast Waves.

    O. Puls and Q. Yang.

    Developmental Cell 47, 532 (2018).
    DOI: 10.1016/j.devcel.2018.11.026 | Link 

  • Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts.

    Y. Guan, S. Wang, M. Jin, H. Xu, and Q. Yang

    J. Vis. Exp. 139, e58240 (2018).
    DOI: 10.3791/58240 | Link | News 

  • A robust and tunable mitotic oscillator in artificial cells.

    Y. Guan*, Z. Li*, S. Wang, P. Barnes, X. Liu, H. Xu, M. Jin, A.P. Liu, and Q. Yang

    eLife 7, e33549 (2018).
    DOI: 10.7554/eLife.33549 | Link 

  • Systems and synthetic biology approaches in understanding biological oscillators.

    Z. Li and Q. Yang

    Quantitative Biology 6, 1 (2018).
    DOI: 10.1007/s40484-017-0120-7 | Link 

  • Incoherent Inputs Enhance the Robustness of Biological Oscillators.

    Z. Li, S. Liu, and Q. Yang

    Cell Systems 5, 72 (2017).
    DOI: 10.1016/j.cels.2017.06.013 | Link 

  • 2014 and Earlier

  • The Cdk1-APC/C cell cycle oscillator circuit functions as a timedelayed, ultrasensitive switch.

    Q. Yang and J. E. Ferrell Jr.

    Nature Cell Biology 15, 519 (2013).
    PDF  | Link 

  • Modeling the cell cycle: why do certain circuits oscillate?

    J. E. Ferrell Jr., T. Tsai, and Q. Yang

    Cell 144, 874 (2011).
    PDF  | Link 

  • Circadian gating of the cell cycle revealed in single cyanobacterial cells.

    Q. Yang*, B. F. Pando*, G. Dong, S. S. Golden, and A. van Oudenaarden

    Science 327, 1522 (2010).
    PDF  | Link 

  • Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus.

    G. Dong, Q. Yang, Q. Wang, Y. Kim, T. L. Wood, K. W. Osteryoung, A. van Oudenaarden, and S. S. Golden

    Cell 140, 529 (2010).
    PDF  | Link | Editorial 

  • Heritable stochastic switching revealed by single-cell genealogy.

    B. B. Kaufmann*, Q. Yang*, J. T. Mettetal, and A. van Oudenaarden

    PLos Biology 5, e239 (2007).
    PDF  | Link 






  • Software Developed in the Yang Lab

    This web application facilitates user interaction with a cell cycle differential equation model we published in eLife 2018.

    A robust and tunable mitotic oscillator in artificial cells. Y. Guan*, Z. Li*, S. Wang, P. Barnes, X. Liu, H. Xu, M. Jin, A.P. Liu, and Q. Yang. eLife 7, e33549 (2018). PDF  | Link 

    The model simulates the cell cycle behavior, which is regulated by various proteins and signaling pathways. Developed using Plotly's Dash framework, the web application allows users to modify parameters and initial conditions and observe changes in cell cycle dynamics in real-time. We encourage users to explore, modify, and contribute to the development of the app. We hope that this app will be a valuable resource for those interested in understanding cell cycles via modeling using differential equations. Feel free to contact us with questions or feedback! Special acknowledgment to Franco Tavella for software development.