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NEMo: An Evolutionary Model with Modularity for PPI Networks

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Bioinformatics Research and Applications (ISBRA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9683))

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Abstract

Modelling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events include addition and removal of vertices and edges, but also duplication of vertices and their associated edges. Since duplication is viewed as a primary driver of genomic evolution, recent work has focused on duplication-based models. Missing from these models is any embodiment of modularity, a widely accepted attribute of biological networks. Some models spontaneously generate modular structures, but none is known to maintain and evolve them.

We describe NEMo (Network Evolution with Modularity), a new model that embodies modularity. NEMo allows modules to emerge and vanish, to fission and merge, all driven by the underlying edge-level events using a duplication-based process. We introduce measures to compare biological networks in terms of their modular structure and use them to compare NEMo and existing duplication-based models and to compare both generated and published networks.

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Acknowledgments

MY wishes to thank Mingfu Shao for many helpful discussions.

Author information

Authors and Affiliations

  1. School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland

    Min Ye & Bernard M. E. Moret

  2. Department of Mathematics, University of Zagreb, Zagreb, Croatia

    Gabriela C. Racz

  3. Department of Electrical and Computer Engineering, Stanford University, Palo Alto, USA

    Qijia Jiang

  4. European Bioinformatics Institute (EMBL-EBI), Cambridge, UK

    Xiuwei Zhang

Authors
  1. Min Ye
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  2. Gabriela C. Racz
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  3. Qijia Jiang
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  4. Xiuwei Zhang
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  5. Bernard M. E. Moret
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Corresponding author

Correspondence to Bernard M. E. Moret .

Editor information

Editors and Affiliations

  1. Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA

    Anu Bourgeois

  2. Centre for Disease Control & Prevention, Atlanta, Georgia, USA

    Pavel Skums

  3. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Xiang Wan

  4. Georgia State University, Atlanta, Georgia, USA

    Alex Zelikovsky

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Ye, M., Racz, G.C., Jiang, Q., Zhang, X., Moret, B.M.E. (2016). NEMo: An Evolutionary Model with Modularity for PPI Networks. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_19

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_19

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38781-9

  • Online ISBN: 978-3-319-38782-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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