Nature Biotechnology 24, 427 - 433 (2006)
Published online: 6 April 2006; | doi:10.1038/nbt1196
Modeling cellular machinery through biological network comparisonRoded Sharan1
& Trey Ideker21
School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. 2
Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
Correspondence should be addressed to Roded Sharan roded@post.tau.ac.il Molecular networks represent the backbone of molecular activity within the cell. Recent studies have taken a comparative approach toward interpreting these networks, contrasting networks of different species and molecular types, and under varying conditions. In this review, we survey the field of comparative biological network analysis and describe its applications to elucidate cellular machinery and to predict protein function and interaction. We highlight the open problems in the field as well as propose some initial mathematical formulations for addressing them. Many of the methodological and conceptual advances that were important for sequence comparison will likely also be important at the network level, including improved search algorithms, techniques for multiple alignment, evolutionary models for similarity scoring and better integration with public databases.
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