This 2-day course will introduce the basics concepts of a “network”, and how this is used to describe biological processes occurring within the cell, in the framework of Systems Biology.
The course will be particularly focused on teaching participants how to use “reverse-engineering” computational algorithms to analyze large-scale experimental data, such as gene expression profiles, to identify the gene regulatory network in which a gene of interest is embedded.
Participants will learn how to use state-of-the-art reverse engineering methods based on Bayesian Networks, Mutual Information and Differential Equations.
The course is aimed at participants with a biological, or computational background. For biologists ,it will provide an understanding of the theory and practical application of systems biology in order to help them use these news tools in their research. For participants from engineering, physics, mathematics, informatics and related sciences, it will provide a thorough understanding of both the biological and computational aspects of reverse-engineering, with direct application to the analysis of biological data.
|Venue||Bologna (Italy) - EuroMediterranean University Centre of Ronzano|
Diego di Bernardo ( Naples, Italy)
D. di Bernardo ( Naples, Italy)
V. Belcastro ( Naples, Italy)
F. Iorio ( Naples, Italy)
A. Honkela ( Helsinki, Finland)
N. Lawrence ( Manchester, UK)
S. Lebre ( Strasbourg, France)
9 October, 2010
14:00 – 15:00 D. di Bernardo Theory: Introduction to Biological Networks
15:00- 15:30 Coffee Break
15:30 – 16:30 D. Di Bernardo Theory: Introduction to Reverse Engineering approaches
16:30-18:30 V. Belcastro and R. Iorio: Computer Lab Practice: Using reverse-engineered networks to understand gene function, drug mode of action and for gene signature analysis.
10 October, 2010
9:30 – 10:30 S. Lebre:Reverse engineering genetic networks using dynamic Bayesian networks
10:30- 11:00 Coffee Break
11:00 – 12:00 S. Lebre : Recovering the time-varying structure of gene-regulation
12:00 – 13:00 N. Lawrence: Bayesian approaches to transcription factor target identification
13:00 – 14:30 Lunch
14:30- 15:30 N. Lawrence and A. Honkela Theory: Bayesian approaches to transcription factor target identification
15:30 – 18:30 N. Lawrence , S. Lebre, A. Honkela Computer Lab Practice: R packages to reverse-engineer gene networks from gene expression data using Bayesian Networks and for Transcription Factor Target identification
11 October, 2010
9:30 – 10:30 F. Iorio : Reverse Engineering using Differential Equations
10:30- 11:00 Coffee Break
11:00 – 12:00 V. Belcastro : Reverse Engineering using Mutual Information
12:00 – 13:00 V. Belcastro Computer Lab Practice: How to use ARACNE to reverse-engineer gene networks from gene expression data
13:00 – 14:00 Lunch
14:00- 15:00 F. Iorio Computer Lab Practice: How to use NIR/TSNI to reverse-engineer gene networks from gene expression data