Course materials

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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

  1. 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

  1. Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767), 335.
  2. 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

  1. Meyers, J., Craig, J., & Odde, D. J. (2006). Potential for control of signaling pathways via cell size and shape. Curr. Biol., 16(17), 1685.
  2. 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

  1. Lewis, J., Slack, J. M., & Wolpert, L. (1977). Thresholds in development. J. Theor. Biol., 65(3), 579.
  2. 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.
    1. Turing, A. M. (1952). The chemical basis of morphogenesis. , B 237(641), 37.
    2. Turing, A. M. (1990). The chemical basis of morphogenesis. 1953. Bull. Math. Biol., 52(1-2), 153. (reprinted)
  3. 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.
  4. Andrews, S. S. (2009). Accurate particle-based simulation of adsorption, desorption and partial transmission. Phys Biol, 6(4), 046015.

Week 4 - Polymer dynamics

  1. 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.
  2. 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.
    1. 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.
    2. 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.
    3. Cytrynbaum, E. N., Rodionov, V., & Mogilner, A. (2006). Nonlocal mechanism of self-organization and centering of microtubule asters. Bull. Math. Biol., 68(5), 1053.
  3. 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

  1. 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.
    1. 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.
    2. 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

  1. Peskin, C. S., Odell, G. M., & Oster, G. F. (1993). Cellular motions and thermal fluctuations: the Brownian ratchet. Biophys. J., 65(1), 316.
  2. Mogilner, A., & Oster, G. (1996). Cell motility driven by actin polymerization. Biophys. J., 71(6), 3030.

Week 7 - Mechanics of linear polymers

  1. Andrews, S. S., & Arkin, A. P. (2007). A mechanical explanation for cytoskeletal rings and helices in bacteria. Biophys. J., 93(6), 1872.
  2. Mogilner, A., & Rubinstein, B. (2005). The physics of filopodial protrusion. Biophys. J., 89(2), 782.
  3. 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 -

  1. 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.


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