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 

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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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