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Computational Reconstruction of Protein–Protein Interaction Networks: Algorithms and Issues

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Computational Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 541))

Abstract

Accurate mapping of protein–protein interaction networks in model organisms is a crucial first step toward subsequent quantitative study of the organization and evolution of biological systems. Data quality of experimental interactome maps can be assessed and improved by integrating multiple sources of evidence using machine learning methods. Here we describe the commonly used algorithms for predicting protein–protein interaction by genome data integration, and discuss several important yet often overlooked issues in computational reconstruction of protein–protein interaction networks.

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Acknowledgments

Y.X. thanks Mark Gerstein for advice and support.

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Authors and Affiliations

  1. Bioinformatics Program, Boston University, Boston, MA, USA

    Eric Franzosa & Bolan Linghu

  2. Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, National Institutes of Health, Boston, MA, USA

    Yu Xia

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  1. Eric Franzosa
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  2. Bolan Linghu
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  3. Yu Xia
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    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

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    Franzosa, E., Linghu, B., Xia, Y. (2009). Computational Reconstruction of Protein–Protein Interaction Networks: Algorithms and Issues. In: Ireton, R., Montgomery, K., Bumgarner, R., Samudrala, R., McDermott, J. (eds) Computational Systems Biology. Methods in Molecular Biology, vol 541. Humana Press. https://doi.org/10.1007/978-1-59745-243-4_5

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    • DOI: https://doi.org/10.1007/978-1-59745-243-4_5

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