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Modeling cellular machinery through biological network comparison

Nature Biotechnology volume 24, pages 427–433 (2006)Cite this article

Abstract

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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Figure 1: Network alignment.
Figure 2: A gamut of network comparative approaches.
Figure 3: Evolutionary processes shaping protein interaction networks.
Figure 4: Parallels between sequence and network comparison on a timeline.

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Acknowledgements

R.S. is supported by an Alon Fellowship; T.I., by the David and Lucille Packard Foundation. This work was also supported by the National Center for Research Resources (RR018627) and the National Science Foundation (NSF 0425926).

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Authors and Affiliations

  1. School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel

    Roded Sharan

  2. Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Trey Ideker

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Correspondence to Roded Sharan.

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Sharan, R., Ideker, T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 24, 427–433 (2006). https://doi.org/10.1038/nbt1196

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