|[Systems Biology]||[Network Dynamics]||[Yeast Cell Cycles]||[Stochastic Models]|
|[Bifurcation Theory]||[Cancer Biology]||[T Cell Differentiation]||[Misc. 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 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.|
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.||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.
|Cell cycle regulation.||video|
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 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).|
|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).|
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-Node-Loop.||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)|
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)|
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).|
|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)|