Better Network Modules: New tools for protein network analysis
People
Faculty: Carl Kingsford
Students: Saket Navlakha,
Guillaume Marçais
Funding
This work is supported by the NSF through grant
ABI-0849899
to Carl Kingsford
Graph clustering as a tool for understanding
protein interaction networks
Recently developed high-throughput techniques are being used to sample
protein-protein interactions from many organisms and are creating a wealth of
data that must be analyzed computationally. A central challenge in the study of
these networks is finding biologically meaningful and interpretable modules
within them. We will develop new algorithms and a suite of software tools based
on a general and flexible definition of a "network module" in order
to extract meaningful biological clusters from noisy and incomplete interaction
data.
The new tools and algorithms will be used to improve visualization of
protein interaction networks, identify protein complexes and biological
processes embedded within the network data, and to discover redundant pathways
from synthetic lethal interaction data. They will also be applied to comparing
the interaction networks of several different species. The resulting network
analysis software will expand the capabilities of both systems biologists and
biologists working on particular protein complexes and pathways to make better
use of noisy network data, and the proposed visualization software will vastly
improve researchers’ capability to interactively explore these networks. Our
predictions will be deposited in a public database that we will create in order
to collect computationally predicted annotations made by us and other
groups.
The tools will strengthen our understanding of the organization of
biological networks, and it will have broader impact by increasing the
information technology infrastructure available for the analysis of interaction
data, providing better transfer of hypotheses between computational biologists
and biologists, and by the training of undergraduates in a summer internship
program.
Research Sub-projects
To be written soon.
Software
Coming soon!
Publications
Papers supported by the project:
Preliminary and prior work related to the project:
Any opinions, findings, and conclusions or recommendations expressed
in this material are those of the author(s) and do not necessarily
reflect the views of the National Science Foundation
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