29544 - MODELS OF BIOLOGICAL SYSTEMS

Learning outcomes

"Course aims: The aim of this course is to offer an introduction to Systems Biology. At the end of the course, students will be able to: - understand networks and their graph representation - understand and work with elements of transcription networks and its dynamics and response time - understand and design simple gene circuits "

Course contents

INTRODUCTION TO SYSTEMS BIOLOGY
Biological Systems
Experimental Techniques
Genomics, Proteomics, Interactomics, Transcriptomics, Metabolomics
Basics on Model
Mathematical Methods: Networks
Mathematical Methods: Differential equations (Basics)
Mathematical Methods: Process Algebra (Basics)


A MODEL SYSTEM: THE TRANSCRIPTION NETWORK IN PROKARYOTS
-Elements of Transcription Networks
-Dynamics and Response Time of Simple Gene Circuits

AUTO-REGULATION, A NETWORK MOTIF
-Patterns, Randomized Networks and Network Motifs
-Autoregulation is a Network Motif
-Negative Auto-Regulation Speeds the Response Time of Gene Circuits
-Negative Auto-Regulation Promotes Robustness to Fluctuations in Production
-Positive auto-regulation speeds responses and widens cell-cell variability

THE FEEDFORWARD LOOP NETWORK MOTIF
-The Number of Appearances of a Subgraph in Random Networks
-The Feedforward Loop (FFL) is a Network Motif
-The Structure of the Feedforward Loop Circuit
-Dynamics of the Coherent FFL with AND-Logic
-The C1-FFL is a Sign-Sensitive Delay Element
-The Incoherent FFL: a pulse generator and response accelerator

OPTIMAL GENE CIRCUIT DESIGN
-Cost and Benefit Analysis of Gene circuits
-Optimal Expression Level of a Protein Under Constant Conditions
-Optimal Regulation in Variable Environments
-Environmental Selection of the Feedforward Loop Network Motif

Readings/Bibliography

Klipp, E., Herwig, R., Kowald, A., Wierling, C. and Lehrach, H. 2005. Systems Biology in Practice: Concepts, Implementation and Application. Wiley-VCH , Weinheim. ISBN 3-527-31078-9

Aron U. 2006. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC Mathematical and  Computational Biology (Vol. 10). ISBN-13: 9781584886426

Teaching methods

Lectures

Assessment methods

Written and oral exams

Office hours

See the website of Pier Luigi Martelli