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Systems Biology

Teacher: Clément Nizak (clement.nizak@espci.fr)

Schedule: 7 Sessions of 2 hours lecture + 1 hour discussion, 3 Sessions of 3h classwork.

Evaluation: The evaluation is based on 2 marks, activity during discussion sessions (30%), and an exam in common with the synthetic biology and computational biology courses (70%).

 

Overview of the class:

Most of the biological functions cannot be associated to a single protein, a single gene, a single cell, or a single organism. Rather, the ability of living matter to perform amazing tasks relies on an ensemble of actors acting collectively. Those tasks, like decision making or information processing, can thus be understood only at the system level. In this course, we will first introduce basic concepts of statistical physics and engineering that have been very successful in solving such problems in other disciplines. We will then show how they apply to the description of biological systems. The examples we will cover span from the molecular to the ecological scale, and will include:

  1. self-organized subcellular systems
  2. cell functions such as regulation of protein expression, division and circadian cycles
  3. evolution of bio-molecules, cells, and populations

The course will be grounded in quantitative biology and modeling motivated by examples coming from biological systems.

 

Course objectives:

  1. To become familiar with basic concepts and models of statistical physics and engineering: systems of many interacting (Ising) or non-interacting (perfect gas) particles, modularity, robustness…
  2. To be able to describe biological systems that have already been studied at the system level (examples we will study during this course), as a list of units and their interactions, or as a combination of modules, and the resulting dynamics.
  3. Finally, to be able to describe any biological process at the system level.

 

Requirements: the bootcamp will be an ideal preparation to this course, there are no specific requirements otherwise. Above all, you need to be ready to look at biology with a different, highly interdisciplinary perspective, integrating most of what you will learn in other courses.

 

Strongly suggested readings:

– From molecular to modular cell biology. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. Nature. 1999

– A new biology for a new century. Carl R Woese. Microbiol Mol Biol Rev. 2004

– An Introduction to Systems Biology – Design Principles of Biological Circuits. Uri Alon 2007

 

The course will be based on and/or inspired from many other papers that will be made available.