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 · Fri Mar 27 00:00:00 EDT 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)

In this paper, we present and develop the theory 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)

Grant/Contract Number:: PS02-06ER64304; AC05-00OR22725

OSTI ID:: 1260601

Alternate ID(s):: OSTI ID: 1265407

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

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 9 works

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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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