Readings

To facilitate interactions during class between students, there are short required questions about the reading that will be due before class.

Required Texts

[UA] = Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall / CRC, 2006. ISBN: 9781584886426. [Preview with Google Books]

[MN] = Nowak, M. A. Evolutionary Dynamics: Exploring the Equations of Life. Belknap Press, 2006. ISBN: 9780674023383. [Preview with Google Books]

Supplementary Reading

[BA] = Alberts, B., et al. Essential Cell Biology. 3rd ed. Garland Science, 2009. ISBN: 9780815341291.

[SS] = Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Westview Press, 2014. ISBN: 9780813349107. [Preview with Google Books]

SES #	TOPICS	READINGS
1	Introduction to the class and overview of topics. Basic concepts in networks and chemical reactions.	### Optional [BA] Chapter 1.
2	Input function of a gene, Michaelis-Menten kinetics, and cooperativity	### Required [UA] Chapters 1 and 2. [UA] Appendix A. ### Optional [BA] Chapter 3, pp. 98–103. [BA] Chapter 7: “From DNA to Protein: How Cells Read the Genome.”  [BA] Chapter 8, pp. 269–80.
3	Autoregulation, feedback and bistability	### Required [UA] Chapter 3. ### Optional [SS] Chapters 1 and 2. Becskei, A., and L. Serrano. “Engineering Stability in Gene Networks by Autoregulation.” Nature 405 (2000): 590–3.
4	Introduction to synthetic biology and stability analysis in the toggle switch	### Required Hasty, J., D. McMillen, et al. “Engineered Gene Circuits.” Nature 420 (2002): 224–30. Supplementary notes on Stability Analysis (PDF) written by Alexander van Oudenaarden. ### Optional [SS] Chapters 5 and 6. Gardner, T. S., C. R. Cantor, et al. “Construction of a Genetic Toggle Switch in Escherichia Coli.” Nature 403 (2000): 339–42.
5	Oscillatory genetic networks	### Required Elowitz, M. B., and S. Leibler. “A Synthetic Oscillatory Network of Transcriptional Regulators.” Nature 403 (2000): 335–38. ### Optional [SS] Chapter 7. Stricker, J., S. Cookson, et al. “A Fast, Robust and Tunable Synthetic Gene Oscillator.” Nature 456 (2008): 516–19.
6	Graph properties of transcription networks	### Required [UA] Appendix C. [UA] Chapters 4.1–4.3 Barabasi, A. L., and R. Alpert. “Emergence of Scaling in Random Networks.” Science 286, no. 5439 (1999): 509–12.
7	Feed-forward loop network motif	### Required [UA] Chapter 4.
8	Introduction to stochastic gene expression	### Required [UA] Appendix D. Yu, J., J. Xiao, et al. “Probing Gene Expression in Live Cells, One Protein Molecule at a Time.” Science 311, no. 5767 (2006): 1600–3.
9	Causes and consequences of stochastic gene expression	### Required Raj, A., and A. van Oudenaarden. “Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences.” Cell 135, no. 2 (2008): 216–26. ### Optional Elowitz, M. B., A. J. Levine, et al. “Stochastic Gene Expression in a Single Cell.” Science 297, no. 5584 (2002): 1183–86.
10	Stochastic modeling—The master equation, Fokker-Planck Equation, and the Gillespie algorithm	### Required Supplementary notes on the Master Equation and Fokker Plank Equation (PDF), by Alexander van Oudenaarden. ### Optional Gillespie, D. T. “Exact Stochastic Simulation of Coupled Chemical Reactions.” The Journal of Physical Chemistry 81, no. 25 (1977): 2340–61.
11	Life at low Reynold’s number	### Required Purcell, E. M. “Life at Low Reynolds Number.” American Journal of Physics 45, no. 3 (1977): 3–11. ### Optional Berg, H. C., and E. M. Purcell. “Physics of Chemoreception.” Biophysical Journal 20, no. 2 (1977): 193–219.
12	Robustness and bacterial chemotaxis	### Required [UA] Chapter 7. ### Optional Barkai, N., and S. Leibler. “Robustness in Simple Biochemical Networks.” Nature 387, no. 6636 (1997): 913–17. Alon, U., M. G. Surette, et al. “Robustness in Bacterial Chemotaxis.” Nature 397 (1999): 168–71.
13	Robustness in development and pattern formation	### Required [UA] Chapter 8. Supplementary notes on Fick’s Law (PDF) by Alexander van Oudenaarden. Kondo, S., and T. Miura. “Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation.” Science 329, no. 5999 (2010): 1616–20. ### Optional Loose, M., E. Fischer-Friedrich, et al. “Spatial Regulators for Bacterial Cell Division Self Organize into Surface Waves in Vitro.” Science 320, no. 5877 (2008): 789–92.
14	Introduction to microbial evolution experiments, and optimal gene circuit design	### Required [MN] Chapters 1–2. Dekel, E., and U. Alon. “Optimality and Evolutionary Tuning in the Expression Level of a Protein.” Nature 436 (2005): 588–92. ### Optional [UA] Chapter 10. Elena, S. F., and R. E. Lenski. “Evolution Experiments with Micro-organisms: The Dynamics and Genetic Bases of Adaptation.” Nature Reviews Genetics 4 (2003): 457–69.
15	Evolution in finite populations, genetic drift, and the theory of neutral molecular evolution	### Required Duret, L. “Neutral Theory: The Null Hypothesis of Molecular Evolution.” Nature Education 1, no. 1 (2008). [MN] Chapter 6.
16	Clonal interference and the distribution of beneficial mutations	### Required Hegreness, M., N. Shoresh, et al. “An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations.” Science 311, no. 5767 (2006): 1615–17. ### Optional Orr, H. A. “The Genetic Theory of Adaptation: A Brief History.” Nature Reviews Genetics 6 (2005): 119–27. Desai, M., D. S. Fisher, et al. “The Speed of Evolution and Maintenance of Variation in Asexual Populations.” Current Biology 17, no. 5 (2007): 385–94. Weissman, D. B., M. M. Desai, et al. “The Rate at which Asexual Populations Cross Fitness Valleys.” Theoretical Population Biology 75, no. 4 (2009): 286–300.
17	Fitness landscapes and sequence spaces	### Required [MN] Chapter 3. Weinreich, D. M., N. F. Delaney, et al. “Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins.” Science 312, no. 5770 (2006): 111–4.
18	Evolutionary games	### Required [MN] Chapter 4. ### Optional Turner, P. E., and L. Chao. “Prisoner’s Dilemma in an RNA Virus.” Nature 398 (1999): 441–43.
19	Survival in fluctuating environments	### Required Mitchell, A., G. H. Romano, et al. “Adaptive Prediction of Environmental Change by Micro-Organisms.” Nature 460 (2009): 220–24. Kussell, E., and S Leibler. “Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments.” Science 309, no. 5743 (2005): 2075–78.
20	Parasites, the evolution of virulence and sex	### Required [MN] Chapter 11. Morran, L., O. Schmidt, et al. “Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex.” Science 333, no. 6039 (2011): 216–18. ### Optional Lloyd-Smith, J. O., S. J. Schreiber, et al. “Superspreading and the Effect of Individual Variation on Disease Emergence.” Nature 438 (2005): 355–59.
21	Interspecies interactions, the Lotka-Volterra model, and predator-prey oscillations	### Required Edelstein-Keshet, L. Sections 6.2, 6.6, and 6.7 in Mathematical Models in Biology. Society for Industrial and Applied Mathematics, 2005. ISBN: 9780898715545. Yoshida, T., L. E. Jones, et al. “Rapid Evolution Drives Ecological Dynamics in a Predator-prey System.” Nature 424 (2003): 303–06. ### Optional McKane, A. J., and T. J. Newman. “Predator-Prey Cycles from Resonant Amplification of Demographic Stochasticity.” Physical Review Letters 94 (2010): 218102.
22	Ecosystem stability, critical transitions, and the maintenance of biodiversity	### Required Scheffer, M., J. Bascompte, et al. “Early-warning Signals for Critical Transitions.” Nature 461 (2009): 53–59. ### Optional [SS] Chapter 3. Dai, L., D. Vorselen, et al. “Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse.” Science 336, no. 6085 (2012): 1175–77.
23	Dynamics of populations in space	### Required Hallatschek, O., and D. R. Nelson. “Population Genetics and Range Expansions.” Physics Today 62, no. 7 (2009): 42. Kerr, B., M. A. Riley, et al. “Local Dispersal Promotes Biodiversity in a Real-Life Game of Rock-Paper-Scissors.” Nature 418, no. 6894 (2002): 171–74.
24	The neutral theory of ecology	### Required Whitfield, J. “Ecology: Neutrality Versus the Niche.” Nature 417 (2002): 480–81. Volkov, I., J. Banavar, et al. “Neutral Theory and Relative Species Abundance in Ecology.” Nature 424 (2003): 1035–37.