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

Published in:
Ieee Transactions On Nanobioscience, 16, 2, 131-139
Presented at:
12th International Symposium on Bioinformatics Research and Applications (ISBRA), Belorussian State Univ, Minsk, BYELARUS, JUN 05-08, 2016
Piscataway, IEEE Press

 Record created 2017-05-30, last modified 2018-09-13

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