Systems Biology

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.

Introduction to the class and overview of topics.
Input function, Michaelis-Menten kinetics, and cooperativity.
Autoregulation, feedback and bistability.
Synthetic biology and stability analysis in the toggle switch.
Oscillatory genetic networks.
Graph properties of transcription networks.
Feed-forward loop network motif.
Introduction to stochastic gene expression.
Causes and consequences of stochastic gene expression.
Stochastic modeling.
Life at low Reynolds number.
Robustness and bacterial chemotaxis.
Robustness in development and pattern formation.
Microbial evolution experiments and optimal gene circuit design.
Evolution in finite populations.
Clonal interference and the distribution of beneficial mutations.
Fitness landscapes and sequence spaces.
Evolutionary games.
Survival in fluctuating environments.
Parasites, the evolution of virulence and sex.
Interspecies interactions.
Ecosystem stability, critical transitions, and biodiversity.
Dynamics of populations in space.
The neutral theory of ecology.