Systems Biology

Readings

• [UA] = Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits . Chapman and Hall / CRC, 2006. ISBN: 9781584886426. [Preview with Google Books ] ↗
  Required
• [MN] = Nowak, M. A. Evolutionary Dynamics: Exploring the Equations of Life . Belknap Press, 2006. ISBN: 9780674023383. [Preview with Google Books ] ↗
  Required
• [BA] = Alberts, B., et al. Essential Cell Biology . 3rd ed. Garland Science, 2009. ISBN: 9780815341291.
  Listed reading
• [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 ] ↗
  Listed reading
• [BA] Chapter 1.
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• [UA] Chapters 1 and 2.
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• [BA] Chapter 3, pp. 98–103.
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• [BA] Chapter 7: “From DNA to Protein: How Cells Read the Genome.”
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• [BA] Chapter 8, pp. 269–80.
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• [UA] Chapter 3.
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• [SS] Chapters 1 and 2.
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• Becskei, A., and L. Serrano. “ Engineering Stability in Gene Networks by Autoregulation .” Nature 405 (2000): 590–3. ↗
  Listed reading
• Hasty, J., D. McMillen, et al. “ Engineered Gene Circuits .” Nature 420 (2002): 224–30. ↗
  Listed reading
• [SS] Chapters 5 and 6.
  Listed reading
• Gardner, T. S., C. R. Cantor, et al. “ Construction of a Genetic Toggle Switch in Escherichia Coli .” Nature 403 (2000): 339–42. ↗
  Listed reading
• Elowitz, M. B., and S. Leibler. “ A Synthetic Oscillatory Network of Transcriptional Regulators .” Nature 403 (2000): 335–38. ↗
  Listed reading
• [SS] Chapter 7.
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• Stricker, J., S. Cookson, et al. “ A Fast, Robust and Tunable Synthetic Gene Oscillator .” Nature 456 (2008): 516–19. ↗
  Listed reading
• [UA] Chapters 4.1–4.3
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• Barabasi, A. L., and R. Alpert. “ Emergence of Scaling in Random Networks .” Science 286, no. 5439 (1999): 509–12. ↗
  Listed reading
• [UA] Chapter 4.
  Listed reading
• 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. ↗
  Listed reading
• Raj, A., and A. van Oudenaarden. “ Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences .” Cell 135, no. 2 (2008): 216–26. ↗
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• Elowitz, M. B., A. J. Levine, et al. “ Stochastic Gene Expression in a Single Cell .” Science 297, no. 5584 (2002): 1183–86. ↗
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• Gillespie, D. T. “ Exact Stochastic Simulation of Coupled Chemical Reactions .” The Journal of Physical Chemistry 81, no. 25 (1977): 2340–61. ↗
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• Purcell, E. M. “ Life at Low Reynolds Number .” American Journal of Physics 45, no. 3 (1977): 3–11. ↗
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• Berg, H. C., and E. M. Purcell. “ Physics of Chemoreception .” Biophysical Journal 20, no. 2 (1977): 193–219. ↗
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• [UA] Chapter 7.
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• Barkai, N., and S. Leibler. “ Robustness in Simple Biochemical Networks .” Nature 387, no. 6636 (1997): 913–17. ↗
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• Alon, U., M. G. Surette, et al. “ Robustness in Bacterial Chemotaxis .” Nature 397 (1999): 168–71. ↗
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• [UA] Chapter 8.
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• Kondo, S., and T. Miura. “ Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation .” Science 329, no. 5999 (2010): 1616–20. ↗
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• 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. ↗
  Listed reading
• [MN] Chapters 1–2.
  Listed reading
• Dekel, E., and U. Alon. “ Optimality and Evolutionary Tuning in the Expression Level of a Protein .” Nature 436 (2005): 588–92. ↗
  Listed reading
• [UA] Chapter 10.
  Listed reading
• 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. ↗
  Listed reading
• Duret, L. “ Neutral Theory: The Null Hypothesis of Molecular Evolution .” Nature Education 1, no. 1 (2008). ↗
  Listed reading
• [MN] Chapter 6.
  Listed reading
• 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. ↗
  Listed reading
• Orr, H. A. “ The Genetic Theory of Adaptation: A Brief History .” Nature Reviews Genetics 6 (2005): 119–27. ↗
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• 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. ↗
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• 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. ↗
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• [MN] Chapter 3.
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• 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. ↗
  Listed reading
• [MN] Chapter 4.
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• Turner, P. E., and L. Chao. “ Prisoner’s Dilemma in an RNA Virus .” Nature 398 (1999): 441–43. ↗
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• Mitchell, A., G. H. Romano, et al. “ Adaptive Prediction of Environmental Change by Micro-Organisms .” Nature 460 (2009): 220–24. ↗
  Listed reading
• Kussell, E., and S Leibler. “ Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments .” Science 309, no. 5743 (2005): 2075–78. ↗
  Listed reading
• [MN] Chapter 11.
  Listed reading
• 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. ↗
  Listed reading
• Lloyd-Smith, J. O., S. J. Schreiber, et al. “ Superspreading and the Effect of Individual Variation on Disease Emergence .” Nature 438 (2005): 355–59. ↗
  Listed reading
• 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.
  Listed reading
• Yoshida, T., L. E. Jones, et al. “ Rapid Evolution Drives Ecological Dynamics in a Predator-prey System .” Nature 424 (2003): 303–06. ↗
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• McKane, A. J., and T. J. Newman. “ Predator-Prey Cycles from Resonant Amplification of Demographic Stochasticity .” Physical Review Letters 94 (2010): 218102. ↗
  Listed reading
• Scheffer, M., J. Bascompte, et al. “ Early-warning Signals for Critical Transitions .” Nature 461 (2009): 53–59. ↗
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• [SS] Chapter 3.
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• 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. ↗
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• Hallatschek, O., and D. R. Nelson. “ Population Genetics and Range Expansions .” Physics Today 62, no. 7 (2009): 42. ↗
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• 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. ↗
  Listed reading
• Whitfield, J. “ Ecology: Neutrality Versus the Niche .” Nature 417 (2002): 480–81. ↗
  Listed reading
• Volkov, I., J. Banavar, et al. “ Neutral Theory and Relative Species Abundance in Ecology .” Nature 424 (2003): 1035–37. ↗
  Listed reading
• Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits . Chapman & Hall / CRC, 2006. ISBN: 9781584886426. [Preview with Google Books ] ↗
  Required
• Nowak, M. A. Evolutionary Dynamics: Exploring the Equations of Life . Belknap Press, 2006. ISBN: 9780674023383. [Preview with Google Books ] ↗
  Required
• Alberts, Bruce. Essential Cell Biology . Garland Science, 2009. ISBN: 9780815341291.
  Listed reading
• Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering . Westview Press, 2014. ISBN: 9780813349107. [Preview with Google Books ] ↗
  Listed reading