skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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.

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 Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
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 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. https://doi.org/10.1371/journal.pcbi.1004079
Weighill, Deborah A., and Jacobson, Daniel A. 2015. "3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics". United States. https://doi.org/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 = {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.},
doi = {10.1371/journal.pcbi.1004079},
url = {https://www.osti.gov/biblio/1260601}, journal = {PLoS Computational Biology (Online)},
issn = {1553-7358},
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
Publisher's Version of Record

Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

A comparative genomic view of clostridial sporulation and physiology
journal, October 2005


Decomposition of Flux Distributions into Metabolic Pathways
journal, July 2013


Use of ternary similarities in graph based clustering for protein structural family classification
conference, January 2010

  • Santini, Guillaume; Soldano, Henry; Pothier, Joël
  • Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10
  • https://doi.org/10.1145/1854776.1854856

Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
journal, February 2009


Bayesian evolutionary hypergraph learning for predicting cancer clinical outcomes
journal, June 2014


Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
journal, April 2009


An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957


A multiple-site similarity measure
journal, October 2006


Basic local alignment search tool
journal, October 1990


Network biology: understanding the cell's functional organization
journal, February 2004


Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
journal, January 2013


MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996


An efficient algorithm for large-scale detection of protein families
journal, April 2002


Handbook of Graph Theory
book, December 2003


The Logic of Inductive Inference
journal, January 1935


OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003


Feature Correlation Hypergraph: Exploiting High-order Potentials for Multimodal Recognition
journal, August 2014


Similarity indices, sample size and diversity
journal, September 1981


A comparative genomic view of clostridial sporulation and physiology
journal, October 2005


Preterm infants with isolated cerebellar hemorrhage show bilateral cortical alterations at term equivalent age
journal, March 2020


An efficient algorithm for large-scale detection of protein families
journal, April 2002


NCBI BLAST: a better web interface
journal, May 2008


A multiple-site similarity measure
journal, October 2006


OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003


MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996


Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
journal, January 2013


An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957


Works referencing / citing this record:

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
journal, March 2019