Systems biology



  1. Introduction.
    Introduction of the scope and approach of the course. Some basic biological concepts: DNA transcription and translation.
  2. Transcription Networks.
    Basic concepts: activators and repressors. Michaelis-Menten kinetics and Hill input functions. Elements of transcription networks. Dynamics of simple gene regulatory systems. Michaelis-Menten kinetics and Hill input functions. Elements of Transcription Networks. Dynamics of simple gene regulation.
  3. Network Motifs I.
    Autoregulation: negative and positive.
  4. Network Motifs II.
    Feed-forward loop gene circuits: coherent and incoherent. Single-input modules. The multi- output feed-forward loop.
  5. Network Motifs at work.
    Developmental transcription networks. Signal transduction networks. Motifs for information processing: multi-layer perceptrons. Negative feedback and oscillator motifs.
  6. Stochastic aspects of biological systems
    Noise induced by low copy numbers in biological systems. Effects of noise on gene circuits and cellular decision making. Mathematical description and computer modelling.
  7. Oscillations in biological systems
    Design principles of biological oscillators. Delayed negative feedback. The segmentation clock.
  8. Robustness of biological circuits
    An example: bacterial chemotaxis. Response and exact adaptation. Robust patterning and precision in development.
  9. Biological systems in changing environments
    Models of biological systems in changing environments; bed-hedging and phenotypic switching.
  10. Kinetic Proofreading
    Kinetic proofreading of the genetic code. Recognizing self and non-self by the immune system.
  11. Demand Rules for Gene Regulation
    Evidence of demand rules. The selection pressure for optimal regulation.
  12. Optimal Gene Circuit Design
    Cost, benefit and fitness functions of biological circuits.