Course materials
From UBCMATH WIKI
Contents |
References
Below is a list of papers from which you can select for your "Friday-paper-presentation". Those in bold have already been selected by someone for presentation in class.
General
- Mogilner, A., Allard, J., & Wollman, R. (2012). Cell polarity: quantitative modeling as a tool in cell biology. Science, 336(6078), 175.
Week 1 - Gene regulation networks
- Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767), 335.
- Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767), 339.
Week 2 - (Reaction-)Diffusion
- Meyers, J., Craig, J., & Odde, D. J. (2006). Potential for control of signaling pathways via cell size and shape. Curr. Biol., 16(17), 1685.
- Tostevin, F., ten Wolde, P. R., & Howard, M. (2007). Fundamental limits to position determination by concentration gradients. PLoS Comput. Biol., 3(4), 78.
Week 3 - Reaction-Diffusion
- Lewis, J., Slack, J. M., & Wolpert, L. (1977). Thresholds in development. J. Theor. Biol., 65(3), 579.
- Holmes, W. R., Carlsson, A. E., & Edelstein-Keshet, L. (2012). Regimes of wave type patterning driven by refractory actin feedback: transition from static polarization to dynamic wave behaviour. Phys. Biol., 9, 046005.
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- Turing, A. M. (1952). The chemical basis of morphogenesis. , B 237(641), 37.
- Turing, A. M. (1990). The chemical basis of morphogenesis. 1953. Bull. Math. Biol., 52(1-2), 153. (reprinted)
- Huang, K. C., Meir, Y., & Wingreen, N. S. (2003). Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones. Proc. Natl. Acad. Sci. U.S.A., 100(22), 12724.
- Andrews, S. S. (2009). Accurate particle-based simulation of adsorption, desorption and partial transmission. Phys Biol, 6(4), 046015.
Week 4 - Polymer dynamics
- Holy, T. E., & Leibler, S. (1994). Dynamic instability of microtubules as an efficient way to search in space. Proc. Natl. Acad. Sci. U.S.A., 91(12), 5682.
- Gardner, M. K., Pearson, C. G., Sprague, B. L., Zarzar, T. R., Bloom, K., Salmon, E. D., & Odde, D. J. (2005). Tension-dependent regulation of microtubule dynamics at kinetochores can explain metaphase congression in yeast. Mol. Biol. Cell, 16(8), 3764.
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- Cytrynbaum, E. N., Rodionov, V., & Mogilner, A. (2004). Computational model of dynein-dependent self-organization of microtubule asters. J. Cell. Sci., 117(Pt 8), 1381.
- Malikov, V., Cytrynbaum, E. N., Kashina, A., Mogilner, A., & Rodionov, V. (2005). Centering of a radial microtubule array by translocation along microtubules spontaneously nucleated in the cytoplasm. Nat. Cell Biol., 7(12), 1213.
- Cytrynbaum, E. N., Rodionov, V., & Mogilner, A. (2006). Nonlocal mechanism of self-organization and centering of microtubule asters. Bull. Math. Biol., 68(5), 1053.
- Allard, J. F., Wasteneys, G. O., & Cytrynbaum, E. N. (2010). Mechanisms of self-organization of cortical microtubules in plants revealed by computational simulations. Mol. Biol. Cell, 21(2), 278.
Week 5 - Polymer force balance
- Grill, S. W., Howard, J., Schaffer, E., Stelzer, E. H., & Hyman, A. A. (2003). The distribution of active force generators controls mitotic spindle position. Science, 301(5632), 518.
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- Allard, J. F., & Cytrynbaum, E. N. (2009). Force generation by a dynamic Z-ring in Escherichia coli cell division. Proc. Natl. Acad. Sci. U.S.A., 106(1), 145.
- Lan, G., Daniels, B. R., Dobrowsky, T. M., Wirtz, D., & Sun, S. X. (2009). Condensation of FtsZ filaments can drive bacterial cell division. Proc. Natl. Acad. Sci. U.S.A., 106(1), 121.
Week 6 - Brownian ratchets
- Peskin, C. S., Odell, G. M., & Oster, G. F. (1993). Cellular motions and thermal fluctuations: the Brownian ratchet. Biophys. J., 65(1), 316.
- Mogilner, A., & Oster, G. (1996). Cell motility driven by actin polymerization. Biophys. J., 71(6), 3030.
Week 7 - Mechanics of linear polymers
- Andrews, S. S., & Arkin, A. P. (2007). A mechanical explanation for cytoskeletal rings and helices in bacteria. Biophys. J., 93(6), 1872.
- Mogilner, A., & Rubinstein, B. (2005). The physics of filopodial protrusion. Biophys. J., 89(2), 782.
- Rubinstein, B., Larripa, K., Sommi, P., & Mogilner, A. (2009). The elasticity of motor-microtubule bundles and shape of the mitotic spindle. Phys Biol, 6(1), 016005.
Week 8 -
- Cytrynbaum, E. N., Li, Y. D., Allard, J. F., & Mehrabian, H. (2012). Estimating the bending modulus of a FtsZ bacterial-division protein filament. Phys Rev E Stat Nonlin Soft Matter Phys, 85(1 Pt 1), 011902.
Supplemental material
- Lac operon
- Michaelis-Menten kinetics
- Microtubule centering forces
- Slides shown in class.