[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 
Molecular Mechanisms and Mathematical Models of the Eukaryotic Cell Cycle RegulationLecture 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 Mechanismsa 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 systemslevel understanding. 
Cell Cycle VignettesFive 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 
Functional Motifs in Cellular Networksa review published in Annu. Rev Phys. Chem. 61:219240 (2010). 
Functional motifs in biochemical reaction networks. 
Network Dynamics and Cell Physiologygiven at Institute for Mathematics and Its Applications (IMA), Univ. of Minnesota, St. Paul, MN, April 1718, 2008. 
Cell physiology, molecular biology and modeling.  video 
Network motifs: sniffers, buzzers, toggles and blinkers.  video 
Cell cycle regulation.  video 
Biological Switches and Clocksgiven 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 
Control of Cell Growth, Division and Deathgiven 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 
Stochastic Models of the Budding Yeast Cell Cyclegiven 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).  
Exploring the roles of noise in eukaryotic cell cycle. Proc. Natl. Acad. Sci. 106:64716476 (2009).  
Stochastic simulation of enzyme catalyzed reactions with disparate time scales. Biophys. J. 95: 35633574 (2008). 
Bifurcation Theory 
A Primer in Bifurcation Theory for Computational Cell BiologistsFall 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: TwoParameter Bifurcation Diagrams.  slides and audio 
6: TakensBogdanov Bifurcation.  slides and audio 
7: FoldHopf Bifurcation.  slides and audio 
Practical Bifurcation Theory8 lectures given weekly at Virginia Tech, Blacksburg, VA. (Oct. 6Dec. 1, 2008) 
1: Local Bifurcationssaddle node bifurcations.  slides and audio 
2: Hopf bifurcations.  slides and audio 
3A: Floquet multipliersperiod doubling, torus and cyclic fold bifurcations.  slides and audio 
3B: Global bifurcationshomoclinic and heteroclinic orbits.  slides and audio 
4A: Codimension Two bifurcationsCusp, Takens Bogdanov, Degenerate Hopf.  slides and audio 
4B: How do 1p 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 bifurcationsTB and SaddleNodeLoop.  slides and audio 
6B: FoldHopf bifurcations.  slides and audio 
7: FoldHopf bifurcations continued. Case 1 and 2.  slides and audio 
8: FoldHopf bifurcations, Case 3 and 4.  slides and (no audio) 
Estrogen Receptor Signalling Network in Breast Cancer Cells 
Cell Fate Decision in Breast Cancer Cellsa review appears in Nature Rev Cancer. 
Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nature Rev. Cancer 11:523532 (2011) 
T Cell Differentiation 
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) 