NEMo: An Evolutionary Model With Modularity for PPI Networks
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. Index indicates
WOS:000399943600008
2017
Piscataway
9
16
2
131
139
REVIEWED
Event name | Event place | Event date |
Belorussian State Univ, Minsk, BYELARUS | JUN 05-08, 2016 | |