John J. Tyson Home Lectures Curriculum Vitae Research Publications Family Photos
[Systems Biology]
[Network Dynamics]
[Yeast Cell Cycles]
[Stochastic Models]
[Bifurcation Theory]
[Cancer Biology]
[T Cell Differentiation] [Misc. Lectures]
Lectures Systems Biology of Cell Cycle Regulation in Eukaryotes Back to Lectures
Molecular Mechanisms and Mathematical Models of the Eukaryotic Cell Cycle Regulation Lecture given at VBI Research Symposium, Blacksburg, Va. March 27, 2012.
The eukaryotic cell cycle: molecules, mechanisms and mathematical models.
Open slides first and then video.
A Systems Biology View of the Cell Cycle Control Mechanisms a review to appear in Handbook of Systems Biology (edit by A. J. Marian Walhout, Marc Vidal and Job Dekker), @Elsevier, San Diego, CA, 2012.
Irreversible transitions, bistability and checkpoint controls in the eukaryotic cell cycle: a systems-level understanding.
pdf
Cell Cycle Vignettes Five excerpts from an article to appear in the Encyclopedia of Systems Biology (Edit by W. Dubitszky, O. Wolkenhauer, K.-H. Cho and H. Yokota), @Springer Verlag, Heidelberg, DE, 2011.
1. The cell cycle of budding yeast.
pdf
2. Irreversible transitions in the cell cycle.
pdf
3. Cell cycle modeling by differential equations.
pdf
4. Bistability and oscillations.
pdf
5. Analysis of cell cycle dynamics by bifurcation theory.
pdf
Information Processing in Living Cells Back to Lectures
Functional Motifs in Cellular Networks a review published in Annu. Rev Phys. Chem. 61:219-240 (2010).
Functional motifs in biochemical reaction networks.
pdf
Network Dynamics and Cell Physiology given at Institute for Mathematics and Its Applications (IMA), Univ. of Minnesota, St. Paul, MN, April 17-18, 2008.
Cell physiology, molecular biology and modeling.
video
Network motifs: sniffers, buzzers, toggles and blinkers.
video
Cell cycle regulation.
video
Biological Switches and Clocks given at Kavli Institute for Theoretical Physics (KITP) program, UC Santa Barbara, CA, Jul 2 - Aug 10, 2007.
Biological switches.
video
Cell cycle regulation.
video
Cell Cycle Regulation in Budding Yeast and Fission Yeast Cells Back to Lectures
Control of Cell Growth, Division and Death given at Mathematical Biosciences Institute (MBI), Ohio State Univerisity, Columbus, OH, Sep 29 - Oct 3, 2003
Modeling the cell cycle engine and checkpoints in yeast cells.
slides
Modeling cell growth, diviions and morphology in fission yeast.
slides
Stochastic Models of Cell Cycle Regulation in Eukaryotes Back to Lectures
Stochastic Models of the Budding Yeast Cell Cycle given on Nov 5, 2008, at VBI, Virginia Tech, Blacksburg, VA.
Why do we need stochastic models for cell cycle regulation?
slides and audio
Stochastic models of cell cycle control in budding yeast.
slides and audio
A model of yeast cell cycle regulation based on multisite posphorylation. Mol. Syst. Biol. 6:405 (2010).
pdf
Exploring the roles of noise in eukaryotic cell cycle. Proc. Natl. Acad. Sci. 106:6471-6476 (2009).
pdf
Stochastic simulation of enzyme catalyzed reactions with disparate time scales. Biophys. J. 95: 3563-3574 (2008).
pdf
Bifurcation Theory Back to Lectures
A Primer in Bifurcation Theory for Computational Cell Biologists Fall Semester, 2010.
1: Bifurcation Diagram=Signal/Response Curve.
slides and audio
2: Saddle Node Bifurcation.
slides and audio
3: Hopf Bifurcation.
slides and audio
4: Global Bifurcations.
slides and audio
5: Two-Parameter Bifurcation Diagrams.
slides and audio
6: Takens-Bogdanov Bifurcation.
slides and audio
7: Fold-Hopf Bifurcation.
slides and audio
Practical Bifurcation Theory 8 lectures given weekly at Virginia Tech, Blacksburg, VA. (Oct. 6-Dec. 1, 2008)
1: Local Bifurcations--saddle node bifurcations.
slides and audio
2: Hopf bifurcations.
slides and audio
3A: Floquet multipliers--period doubling, torus and cyclic fold bifurcations.
slides and audio
3B: Global bifurcations--homoclinic and heteroclinic orbits.
slides and audio
4A: Codimension Two bifurcations--Cusp, Takens Bogdanov, Degenerate Hopf.
slides and audio
4B: How do 1-p bifurcation diagrams fit together at DH and TB points.
slides and audio
5: An example by Guckenheimer on multiple bifurcations for chemical reactors.
slides and audio
6A: More on Codimension Two bifurcations--TB and Saddle-NodeLoop.
slides and audio
6B: Fold-Hopf bifurcations.
slides and audio
7: Fold-Hopf bifurcations continued. Case 1 and 2.
slides and audio
8: Fold-Hopf bifurcations, Case 3 and 4.
slides and (no audio)
Estrogen Receptor Signalling Network in Breast Cancer Cells Back to Lectures
Cell Fate Decision in Breast Cancer Cells a review appears in Nature Rev Cancer.
Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nature Rev. Cancer 11:523-532 (2011)
pdf
T Cell Differentiation Back to Lectures
Cell Fate Determination in T Cell Differentiation. Use bifurcation analysis to study T cell differentiation.
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. BMC Syst. Biol. 6:66 (2012).
pdf
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comp. Biol. 7:21002122 (201l).
pdf
Miscellaneous Lectures 2008. New frontiers in system biology. (slides) 2008. How do cells compute? (slides) 2006. Network dynamics and cell physiology. (slides) 1999. Coping with complexity. (slides)
1998. Commencement speech at Virginia Tech, Dec. 18. (pdf or html)
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