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Journal Articles Trends in Microbiology Year : 2016

Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

Eduardo Corel
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Philippe Lopez
Eric Bapteste

Abstract

The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families–genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.
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Dates and versions

hal-01300043 , version 1 (08-04-2016)

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Attribution - NonCommercial - NoDerivatives

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Eduardo Corel, Philippe Lopez, Raphaël Méheust, Eric Bapteste. Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends in Microbiology, 2016, 24 (3), pp.224-237. ⟨10.1016/j.tim.2015.12.003⟩. ⟨hal-01300043⟩
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