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

Abstract

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.

Authors:
 [1];  [2]
  1. Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1260601
Alternate Identifier(s):
OSTI ID: 1265407
Grant/Contract Number:  
PS02-06ER64304; AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 11; Journal Issue: 3; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats

Weighill, Deborah A., and Jacobson, Daniel A. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. United States: N. p., 2015. Web. doi:10.1371/journal.pcbi.1004079.
Weighill, Deborah A., & Jacobson, Daniel A. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. United States. doi:10.1371/journal.pcbi.1004079.
Weighill, Deborah A., and Jacobson, Daniel A. Fri . "3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics". United States. doi:10.1371/journal.pcbi.1004079. https://www.osti.gov/servlets/purl/1260601.
@article{osti_1260601,
title = {3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics},
author = {Weighill, Deborah A. and Jacobson, Daniel A.},
abstractNote = {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.},
doi = {10.1371/journal.pcbi.1004079},
journal = {PLoS Computational Biology (Online)},
number = 3,
volume = 11,
place = {United States},
year = {Fri Mar 27 00:00:00 EDT 2015},
month = {Fri Mar 27 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 1 work
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Works referenced in this record:

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2