Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks

BackgroundThe alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variable...

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Detalles Bibliográficos
Autores: Llabres, Merce, Riera, Gabriel, Rossello, Francesc, Valiente, Gabriel
Tipo de recurso: artículo
Fecha de publicación:2020
País:España
Institución:Conselleria de Salut i Consum del Govern de les Illes Balears
Repositorio:Docusalut
Idioma:inglés
OAI Identifier:oai:docusalut.com:20.500.13003/19432
Acceso en línea:https://hdl.handle.net/20.500.13003/19432
Access Level:acceso abierto
Palabra clave:Software
Protein Interaction Maps
Programming, Linear
Algorithms
Models, Theoretical
Modelos Teóricos
Algoritmos
Programas Informáticos
Mapas de Interacción de Proteínas
Programación Lineal
Systems biology
Virus-host protein-protein interaction
Integer linear programming
Network alignment
Graph matching
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spelling Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networksLlabres, MerceRiera, GabrielRossello, FrancescValiente, GabrielSoftwareProtein Interaction MapsProgramming, LinearAlgorithmsModels, TheoreticalModelos TeóricosAlgoritmosProgramas InformáticosMapas de Interacción de ProteínasProgramación LinealSystems biologyVirus-host protein-protein interactionInteger linear programmingNetwork alignmentGraph matchingBackgroundThe alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use.ResultsWe present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful.ConclusionsThe implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.BMC20202020-11-1820202020-11-18research articlehttp://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/20.500.13003/19432reponame:Docusalutinstname:Conselleria de Salut i Consum del Govern de les Illes BalearsInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:docusalut.com:20.500.13003/194322026-06-22T12:44:07Z
dc.title.none.fl_str_mv Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
title Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
spellingShingle Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
Llabres, Merce
Software
Protein Interaction Maps
Programming, Linear
Algorithms
Models, Theoretical
Modelos Teóricos
Algoritmos
Programas Informáticos
Mapas de Interacción de Proteínas
Programación Lineal
Systems biology
Virus-host protein-protein interaction
Integer linear programming
Network alignment
Graph matching
title_short Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
title_full Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
title_fullStr Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
title_full_unstemmed Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
title_sort Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
dc.creator.none.fl_str_mv Llabres, Merce
Riera, Gabriel
Rossello, Francesc
Valiente, Gabriel
author Llabres, Merce
author_facet Llabres, Merce
Riera, Gabriel
Rossello, Francesc
Valiente, Gabriel
author_role author
author2 Riera, Gabriel
Rossello, Francesc
Valiente, Gabriel
author2_role author
author
author
dc.contributor.none.fl_str_mv
dc.subject.none.fl_str_mv Software
Protein Interaction Maps
Programming, Linear
Algorithms
Models, Theoretical
Modelos Teóricos
Algoritmos
Programas Informáticos
Mapas de Interacción de Proteínas
Programación Lineal
Systems biology
Virus-host protein-protein interaction
Integer linear programming
Network alignment
Graph matching
topic Software
Protein Interaction Maps
Programming, Linear
Algorithms
Models, Theoretical
Modelos Teóricos
Algoritmos
Programas Informáticos
Mapas de Interacción de Proteínas
Programación Lineal
Systems biology
Virus-host protein-protein interaction
Integer linear programming
Network alignment
Graph matching
description BackgroundThe alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use.ResultsWe present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful.ConclusionsThe implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-11-18
2020
2020-11-18
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/20.500.13003/19432
url https://hdl.handle.net/20.500.13003/19432
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv reponame:Docusalut
instname:Conselleria de Salut i Consum del Govern de les Illes Balears
instname_str Conselleria de Salut i Consum del Govern de les Illes Balears
reponame_str Docusalut
collection Docusalut
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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