Catalog

Systems Biology

Physics MIT CC BY-NC-SA 4.0 24 lectures

This course provides an introduction to cellular and population-level systems biology with an emphasis on synthetic biology, modeling of genetic networks, cell-cell interactions, and evolutionary dynamics. Cellular systems include genetic switches and oscillators, network motifs, genetic network evolution, and cellular decision-making. Population-level systems include models of pattern formation, cell-cell communication, and evolutionary systems biology.

Syllabus

  1. 1 Introduction to the Class and Overview of Topics
  2. 2 Input Function, Michaelis-Menten kinetics, and Cooperativity
  3. 3 Autoregulation, Feedback and Bistability
  4. 4 Synthetic Biology and Stability Analysis in the Toggle Switch
  5. 5 Oscillatory Genetic Networks
  6. 6 Graph Properties of Transcription Networks
  7. 7 Feed-forward Loop Network Motif
  8. 8 Introduction to Stochastic Gene Expression
  9. 9 Causes and Consequences of Stochastic Gene Expression
  10. 10 Stochastic Modeling
  11. 11 Life at Low Reynolds Number
  12. 12 Robustness and Bacterial Chemotaxis
  13. 13 Robustness in Development and Pattern Formation
  14. 14 Microbial Evolution Experiments and Optimal Gene Circuit Design
  15. 15 Evolution in Finite Populations
  16. 16 Clonal Interference and the Distribution of Beneficial Mutations
  17. 17 Fitness Landscapes and Sequence Spaces
  18. 18 Evolutionary Games
  19. 19 Survival in Fluctuating Environments
  20. 20 Parasites, the Evolution of Virulence and Sex
  21. 21 Interspecies Interactions
  22. 22 Ecosystem Stability, Critical Transitions, and Biodiversity
  23. 23 Dynamics of Populations in Space
  24. 24 The Neutral Theory of Ecology

Course materials