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

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:

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)

Publication Date:: Fri Mar 27 00:00:00 EDT 2015

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:: 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.

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                    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

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                    Weighill, Deborah A., and Jacobson, Daniel A. Fri .  
"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.

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@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},

  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}

}

Copy to clipboard

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Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria
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Works referencing / citing this record:

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

Bonito, Gregory; Benucci, Gian Maria Niccolò; Hameed, Khalid
Frontiers in Microbiology, Vol. 10
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Title: 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

Abstract

Citation Formats

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

Decomposition of Flux Distributions into Metabolic Pathways journal, July 2013

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

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A multiple-site similarity measure journal, October 2006

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal, November 2003

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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

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria journal, April 2006

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

Characterization of a Polysaccharide Deacetylase Gene Homologue (pdaB) on Sporulation of Bacillus subtilis journal, September 2004

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

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

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

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants journal, July 2021

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

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal, November 2003

A Polysaccharide Deacetylase Gene (pdaA) Is Required for Germination and for Production of Muramic δ-Lactam Residues in the Spore Cortex of Bacillus subtilis journal, November 2002

MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS journal, December 1996

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria journal, April 2006

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

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

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

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
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journal, November 2003

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
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Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria
journal, April 2006

An efficient algorithm for large-scale detection of protein families
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Handbook of Graph Theory
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The Logic of Inductive Inference
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Similarity indices, sample size and diversity
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A comparative genomic view of clostridial sporulation and physiology
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journal, July 2021

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journal, May 2008

A multiple-site similarity measure
journal, October 2006

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

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003

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journal, December 1996

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journal, April 2006

Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
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journal, February 1957

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