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Briefings in Bioinformatics Advance Access originally published online on August 29, 2007
Briefings in Bioinformatics 2007 8(5):318-332; doi:10.1093/bib/bbm038
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Current progress in network research: toward reference networks for key model organisms

Balaji S. Srinivasan, Nigam H. Shah, Jason A. Flannick, Eduardo Abeliuk, Antal F. Novak and Serafim Batzoglou

Corresponding author. Balaji S. Srinivasan, 318 Campus Drive, Clark Center S251, Stanford, CA 94305, USA. Tel: (650) 380-0695; Fax: (650) 725-1449; E-mail: balajis{at}stanford.edu

The collection of multiple genome-scale datasets is now routine, and the frontier of research in systems biology has shifted accordingly. Rather than clustering a single dataset to produce a static map of functional modules, the focus today is on data integration, network alignment, interactive visualization and ontological markup. Because of the intrinsic noisiness of high-throughput measurements, statistical methods have been central to this effort. In this review, we briefly survey available datasets in functional genomics, review methods for data integration and network alignment, and describe recent work on using network models to guide experimental validation. We explain how the integration and validation steps spring from a Bayesian description of network uncertainty, and conclude by describing an important near-term milestone for systems biology: the construction of a set of rich reference networks for key model organisms.

Keywords: pathways, reference networks, systems biology, data integration, network alignment, machine learning

Submitted: May 21, 2007. Received (in revised form): July 22, 2007.


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[Abstract] [Full Text] [PDF]


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