Systems Biology

Systems Biology

Coordinators
Ana Teixeira and Claudine Chaouiya

Instructors
Ana Teixeira, Claudine Chaouiya, Daniel Sobral, Nuno Mendes

Objectives
This unit is meant to provide to the students an overview of Systems Biology, one of the most competitive and fast evolving areas in Biology. It will particularly focus on the analysis of biological sequences and on biological networks.

Syllabus

1. What is Systems Biology? a brief overview.
2. High Throughput Sequencing: sequence data generation and analysis; Introduction to HTS and its applications: genomics, transcriptomics, epigenomics. Practical hands-on data session.
3. Genome Sequence Analysis: Challenges of coding and non-coding gene finding; Motif finding in cis-regulatory regions. Practical hands-on data session.
4. Metabolic network modelling. Genome-scale metabolic models, kinetic and stoichiometric models, metabolic pathway analysis, flux balance analysis. Exercises on metabolic flux analysis.
5. Regulatory and signalling networks: from structure to dynamics; ODE and logical models. Practical session with GINsim (http://ginsim.org).

Evaluation
Evaluation will be done by presentation and discussion of two papers (in group) and an individual review report on one of the papers.

Main bibliography

• Klipp, E et al. (2006) Systems Biology in Practice. John Wyley, Weinheim
• Bower, JM and Bolouri H. Eds (2000) Computational Modeling of Genetic and Biochemical Networks. MIT Press
• Palsson, BO (2006) Systems Biology. Cambridge Univ. Press, Cambridge
• Neil C Jones and Pavel A Pevzner (2004). An introduction to bioinformatics algorithms. MIT Press.

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