NEMo: An Evolutionary Model with Modularity for PPI Networks

  • Min Ye
  • Gabriela C. Racz
  • Qijia Jiang
  • Xiuwei Zhang
  • Bernard M. E. Moret
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9683)

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.

Keywords

Generative model Evolutionary model PPI network Evolutionary event Modularity Network topology 

Notes

Acknowledgments

MY wishes to thank Mingfu Shao for many helpful discussions.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Min Ye
    • 1
  • Gabriela C. Racz
    • 2
  • Qijia Jiang
    • 3
  • Xiuwei Zhang
    • 4
  • Bernard M. E. Moret
    • 1
  1. 1.School of Computer and Communication SciencesEPFLLausanneSwitzerland
  2. 2.Department of MathematicsUniversity of ZagrebZagrebCroatia
  3. 3.Department of Electrical and Computer EngineeringStanford UniversityPalo AltoUSA
  4. 4.European Bioinformatics Institute (EMBL-EBI)CambridgeUK

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