title: NEMo: An Evolutionary Model With Modularity for PPI Networks.
abstract: Modeling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events not only 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 network evolution with modularity (NEMo), a new model that embodies modularity. NEMo allows modules to appear and disappear and to fission and to merge, all driven by the underlying edge-level events using a duplication-based process. We also introduce measures to compare biological networks in terms of their modular structure; we present comparisons between NEMo and existing duplication-based models and run our measuring tools on both generated and published networks.
authors.forename: Min
authors.initials: M
authors.lastname: Ye
authors.forename: Xiuwei
authors.initials: X
authors.lastname: Zhang
authors.forename: Gabriela C
authors.initials: GC
authors.lastname: Racz
authors.forename: Qijia
authors.initials: Q
authors.lastname: Jiang
authors.forename: Bernard M E
authors.initials: BME
authors.lastname: Moret
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D011506:Proteins