[Systems Biology] [Network Dynamics] [Yeast Cell Cycles] [Stochastic Models]
[Bifurcation Theory] [Cancer Biology] [T Cell Differentiation] [Misc. Lectures]


Systems Biology of Cell Cycle Regulation in Eukaryotes

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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.

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.

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.
2. Irreversible transitions in the cell cycle.
3. Cell cycle modeling by differential equations.
4. Bistability and oscillations.
5. Analysis of cell cycle dynamics by bifurcation theory.

Information Processing in Living Cells

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Functional Motifs in Cellular Networks

a review published in Annu. Rev Phys. Chem. 61:219-240 (2010).

Functional motifs in biochemical reaction networks.

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.
Network motifs: sniffers, buzzers, toggles and blinkers.
Cell cycle regulation.

Biological Switches and Clocks

given at Kavli Institute for Theoretical Physics (KITP) program, UC Santa Barbara, CA, Jul 2 - Aug 10, 2007.

Biological switches.
Cell cycle regulation.

Cell Cycle Regulation in Budding Yeast and Fission Yeast Cells

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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.
Modeling cell growth, diviions and morphology in fission yeast.

Stochastic Models of Cell Cycle Regulation in Eukaryotes

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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?
Stochastic models of cell cycle control in budding yeast.
A model of yeast cell cycle regulation based on multisite posphorylation. Mol. Syst. Biol. 6:405 (2010).
Exploring the roles of noise in eukaryotic cell cycle. Proc. Natl. Acad. Sci. 106:6471-6476 (2009).
Stochastic simulation of enzyme catalyzed reactions with disparate time scales. Biophys. J. 95: 3563-3574 (2008).

Bifurcation Theory

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A Primer in Bifurcation Theory for Computational Cell Biologists

Fall Semester, 2010.

1: Bifurcation Diagram=Signal/Response Curve.
2: Saddle Node Bifurcation.
3: Hopf Bifurcation.
4: Global Bifurcations.
5: Two-Parameter Bifurcation Diagrams.
6: Takens-Bogdanov Bifurcation.
7: Fold-Hopf Bifurcation.

Practical Bifurcation Theory

8 lectures given weekly at Virginia Tech, Blacksburg, VA. (Oct. 6-Dec. 1, 2008)

1: Local Bifurcations--saddle node bifurcations.
2: Hopf bifurcations.
3A: Floquet multipliers--period doubling, torus and cyclic fold bifurcations.
3B: Global bifurcations--homoclinic and heteroclinic orbits.
4A: Codimension Two bifurcations--Cusp, Takens Bogdanov, Degenerate Hopf.
4B: How do 1-p bifurcation diagrams fit together at DH and TB points.
5: An example by Guckenheimer on multiple bifurcations for chemical reactors.
6A: More on Codimension Two bifurcations--TB and Saddle-Node-Loop.
6B: Fold-Hopf bifurcations.
7: Fold-Hopf bifurcations continued. Case 1 and 2.
8: Fold-Hopf bifurcations, Case 3 and 4.

Estrogen Receptor Signalling Network in Breast Cancer Cells

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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)


T Cell Differentiation

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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).
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comp. Biol. 7:21002122 (201l).

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)