NEMo: An Evolutionary Model with Modularity for PPI Networks

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.

Bourgeois, A
Skums, P
Wan, X
Zelikovsky, A
Published in:
Proceedings of the 12th International Symposium on Bioinformatics Research And Applications ISBRA 2016, 9683, 224-236
Presented at:
12th International Symposium on Bioinformatics Research and Applications (ISBRA)', u'12th International Symposium on Bioinformatics Research and Applications (ISBRA)'], 2016
Cham, Springer Int Publishing Ag
978-3-319-38782-6; 978-3-319-38781-9

 Record created 2016-11-21, last modified 2018-03-17

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