CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape

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Abstract

Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.
Original languageEnglish
Article number20170014
JournalJournal of Integrative Bioinformatics
Volume14
Issue number2
Number of pages8
ISSN1613-4516
DOIs
Publication statusPublished - 2017
Event13th Annual Meeting of the International Symposium on Integrative Bioinformatics - University of Southern Denmark, Campusvej 55 5230 Odense, Odense, Denmark
Duration: 22. Jun 201724. Jun 2017
Conference number: 13
http://www.imbio.de/ib2017/program.php

Conference

Conference13th Annual Meeting of the International Symposium on Integrative Bioinformatics
Number13
LocationUniversity of Southern Denmark, Campusvej 55 5230 Odense
CountryDenmark
CityOdense
Period22/06/201724/06/2017
Internet address

Cite this

@inproceedings{72b77d8118dd4ad39615ac9862387575,
title = "CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape",
abstract = "Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.",
author = "Simon Larsen and Jan Baumbach",
year = "2017",
doi = "10.1515/jib-2017-0014",
language = "English",
volume = "14",
journal = "Journal of Integrative Bioinformatics",
issn = "1613-4516",
publisher = "IMBIO e.V.",
number = "2",

}

CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. / Larsen, Simon; Baumbach, Jan.

In: Journal of Integrative Bioinformatics, Vol. 14, No. 2, 20170014, 2017.

Research output: Contribution to journalConference articleResearchpeer-review

TY - GEN

T1 - CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape

AU - Larsen, Simon

AU - Baumbach, Jan

PY - 2017

Y1 - 2017

N2 - Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.

AB - Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.

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JO - Journal of Integrative Bioinformatics

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