NEMo: An Evolutionary Model with Modularity for PPI Networks

• Published in: Bioinformatics Research and Applications pp. 224 - 236
• Main Authors: Ye, Min, Racz, Gabriela C., Jiang, Qijia, Zhang, Xiuwei, Moret, Bernard M. E.
• Format: Book Chapter
• Language: English
• Published: Cham Springer International Publishing 2016
• Series: Lecture Notes in Computer Science
• Subjects: Evolutionary event; Evolutionary model; Generative model; Modularity; Network topology; PPI network
• ISBN: 9783319387819; 3319387812
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-319-38782-6_19

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.