| [Systems Biology] | [Network Dynamics] | [Yeast Cell Cycles] | [Stochastic Models] |
| [Bifurcation Theory] | [Cancer Biology] | [T Cell Differentiation] | [Misc. Lectures] |
Lectures
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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 systems-level 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. |
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Information Processing in Living Cells |
Functional Motifs in Cellular Networksa review published in Annu. Rev Phys. Chem. 61:219-240 (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 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 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 |
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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 |
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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. 106:6471-6476 (2009). | |
| Stochastic simulation of enzyme catalyzed reactions with disparate time scales. Biophys. J. 95: 3563-3574 (2008). |
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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: Two-Parameter Bifurcation Diagrams. | slides and audio |
| 6: Takens-Bogdanov Bifurcation. | slides and audio |
| 7: Fold-Hopf Bifurcation. | slides and audio |
Practical Bifurcation Theory8 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) |
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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 11:523-532 (2011) |
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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 |
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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) |
