Data integration in systems biology:
characterization of biological
phenomena from structural and
functional information
Ronaldo Fumio Hashimoto (IME-USP)
David Correa Martins Jr (CMCC-UFABC)
Roberto Marcondes Cesar Jr (IME-USP)
Marie-Anne Van Sluys (IB-USP)
Helena Brentani (IPq-USP)
The main goals
http://genomics.energy.gov/gallery/
Challenges
• Inference of gene regulatory networks
from expression profiles: great challenge
in systems biology
– thousands of variables (genes) for dozens of
experiments (number of samples)
– intrinsic noise
– use of biological knowledge available in public
databases
– high complexity of biological networks
• significant estimation error
The keys
• Integration of several sources of
biological data in order to improve the
quality of estimation
– genomics, transcriptomics, proteomics,
metabolomics and other omics...
• Incorporation of network topology
information (local and global network
properties)
– random, scale-free, small-world, geographic...
• Analysis of the system dynamics
– System trajectories can be drawn from the
inferred topology and relationships
The project
Something already going on...
Engaged Institutions
IME-USP
UFABC
CTBE
IB-USP
IPq-USP
UTFPR
TAMU
TGEN
Research Team
• Main investigators
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Ronaldo Fumio Hashimoto (IME-USP)
David Correa Martins Jr (CMCC-UFABC)
Roberto Marcondes Cesar Jr (IME-USP/CTBE)
Marie-Anne Van Sluys (IB-USP)
Helena Brentani (IPq-USP)
• Main collaborators
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Fabrício Martins Lopes (UTFPR)
Marcos Buckeridge (IB-USP/CTBE)
Edward Russell Dougherty (TAMU/TGEN)
Ulisses Braga-Neto (TAMU)