- Course code: 11010
- Semester: 2nd
- Credits (ECTS): 3 credits
- Teaching hours:
- Teaching guide: Teaching Guide (PDF)
Introduction of the scope and approach of the course. Some basic biological concepts: DNA
transcription and translation.
- 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.
- Network Motifs I.
Autoregulation: negative and positive.
- Network Motifs II.
Feed-forward loop gene circuits: coherent and incoherent. Single-input modules. The multi-
output feed-forward loop.
- Network Motifs at work.
Developmental transcription networks. Signal transduction networks. Motifs for information
processing: multi-layer perceptrons. Negative feedback and oscillator motifs.
- 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.
- Oscillations in biological systems
Design principles of biological oscillators. Delayed negative feedback. The segmentation clock.
- Robustness of biological circuits
An example: bacterial chemotaxis. Response and exact adaptation. Robust patterning and
precision in development.
- Biological systems in changing environments
Models of biological systems in changing environments; bed-hedging and phenotypic
- Kinetic Proofreading
Kinetic proofreading of the genetic code. Recognizing self and non-self by the immune system.
- Demand Rules for Gene Regulation
Evidence of demand rules. The selection pressure for optimal regulation.
- Optimal Gene Circuit Design
Cost, benefit and fitness functions of biological circuits.