3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

Weighill, Deborah A.; Jacobson, Daniel A.

doi:10.1371/journal.pcbi.1004079

Title: 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

Journal Article · 27 March 2015 · PLoS Computational Biology (Online)

DOI: https://doi.org/10.1371/journal.pcbi.1004079 · OSTI ID:1260601

Weighill, Deborah A. ^[1]; Jacobson, Daniel A. ^[2]

Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Herein we present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC05-00OR22725; AC05-00OR22725

OSTI ID:: 1260601

Journal Information:: PLoS Computational Biology (Online), Journal Name: PLoS Computational Biology (Online) Journal Issue: 3 Vol. 11; ISSN 1553-7358

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Coupling functions: Universal insights into dynamical interaction mechanisms Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E. Reviews of Modern Physics, Vol. 89, Issue 4 https://doi.org/10.1103/revmodphys.89.045001	journal	November 2017
Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype Bonito, Gregory; Benucci, Gian Maria Niccolò; Hameed, Khalid Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00481	journal	March 2019

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