Publications

Preprints

Mechanistic origins of temperature scaling in the early embryonic cell cycle
J. Rombouts*, F.Tavella*, A. Vandervelde, C. Phong, J. Ferrell, Q. Yang, L. Gelens
BioRxiv (2025)
DOI: 10.1101/2024.12.24.630245 | Link

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Substrate rigidity modulates segmentation clock dynamics in isolated presomitic mesoderm cells
C.-Y. Sung*, U. Kadiyala*, O. Blanchard*, L. Yourston, D. Walker, L. Li, J. Fu, Q. Yang
BioRxiv (2024)
DOI: 10.1101/2024.07.02.601712 | Link

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Publications

Spatial heterogeneity accelerates phase-to-trigger wave transitions in frog egg extracts
O. Puls*, D. R. Reynés*, F. Tavella, M. Jin, Y. Kim, L. Gelens, Q. Yang
Nature Communications (2024)
DOI: 10.1038/s41467-024-54752-7 | Link

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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 (2024)
DOI: 10.1016/j.stem.2024.06.004 | Link

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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

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Nuclear-cytoplasmic compartmentalization of cyclin B1-Cdk1 promotes robust timing of mitotic events
G. Maryu and Q. Yang
Cell Reports (2022)
DOI: 10.1016/j.celrep.2022.111870 | Link

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In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
M. Jin*, F. Tavella*, S. Wang, Q. Yang
Proceedings of the National Academy of Sciences (2022)
DOI: 10.1073/pnas.2109547119 | Link

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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 (2021)
DOI: 10.3389/fcell.2021.728663 | Link

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Plug-in tubes removing oil and packing droplets for time-controlled droplet-based assays
M. Sun, G. Maryu, S. Wang, Q. Yang, R. C. Bailey
Biomicrofluidics (2021)
DOI: 10.1063/5.0047924 | Link

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Real-time monitoring of APC/C-Mediated substrate degradation using Xenopus laevis egg extracts
J. Kamenz, R. Qiao, Q. Yang, J. E. Ferrell Jr.
Methods in Molecular Biology (2021)
DOI: 10.1007/978-1-0716-1538-6_3 | Link

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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 (2020)
DOI: 10.1002/wnan.1685 | Link

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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 (2019)
DOI: 10.1021/acs.analchem.9b01481 | Link

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μdroPi: a hand-held microfluidic droplet imager and analyzer built on Raspberry Pi
M. Sun, Z. Li, and Q. Yang
Journal of Chemical Education (2019)
DOI: 10.1021/acs.jchemed.8b00975 | Link

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The rise of ultrafast waves
O. Puls and Q. Yang
Developmental Cell (2018)
DOI: 10.1016/j.devcel.2018.11.026 | Link

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Reconstitution of cell-cycle oscillations in microemulsions of cell-free Xenopus egg extracts
Y. Guan, S. Wang, M. Jin, H. Xu, and Q. Yang
Journal of Visualized Experiments (2018)
DOI: 10.3791/58240 | Link

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

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Systems and synthetic biology approaches in understanding biological oscillators
Z. Li and Q. Yang
Quantitative Biology (2018)
DOI: 10.1007/s40484-017-0120-7 | Link

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Incoherent inputs enhance the robustness of biological oscillators
Z. Li, S. Liu, and Q. Yang
Cell Systems (2017)
DOI: 10.1016/j.cels.2017.06.013 | Link

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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 (2013)
DOI: 10.1038/ncb2737 | Link

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Modeling the cell cycle: why do certain circuits oscillate?
J. E. Ferrell Jr., T. Tsai, and Q. Yang
Cell (2011)
DOI: 10.1016/j.cell.2011.03.006 | Link

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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 (2010)
DOI: 10.1126/science.1181759 | Link

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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 (2010)
DOI: 10.1016/j.cell.2009.12.042 | Link

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Heritable stochastic switching revealed by single-cell genealogy
B. B. Kaufmann*, Q. Yang*, J. T. Mettetal, and A. van Oudenaarden
PLoS Biology (2007)
DOI: 10.1371/journal.pbio.0050239 | Link

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Software Developed in the Yang Lab

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First plot: — B nullcline — C nullcline — Trajectory
Second plot: — Total Cyclin B1 (B) — Active Cdk1:Cyclin B1 (C)

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B0: Cyclin B1 initial value (nM)

C0: CyclinB1:Cdk1 initial value (nM)

kS: Cyclin B1 synthesis rate (nM/min)

rWT: Wee1 to Cdc25 activity ratio (a.u.)

aD: Basal degradation rate (1/min)

bD: Cdk1-based degradation rate (1/min)

KD: Half-max degradation rate (nM)

nD: Hill exponent for degradation (a.u.)

aT: Basal Cdc25 activation rate (1/min)

bT: Cdk1-based Cdc25 rate (1/min)

KT: Half-max Cdc25 rate (nM)

nT: Hill exponent for Cdc25 (a.u.)

aW: Basal Wee1 activation rate (1/min)

bW: Cdk1-based Wee1 rate (1/min)

KW: Half-max Wee1 rate (nM)

nW: Hill exponent for Wee1 (a.u.)

Number of datapoints to simulate

Final simulation time

Reset parameters

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Credit: Interactive Cell Cycle Model - Yang Lab by Franco Tavella