BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

dc.contributor.authorAlkan, Ferhat
dc.contributor.authorErten, Cesim
dc.date.accessioned2019-06-27T08:03:02Z
dc.date.available2019-06-27T08:03:02Z
dc.date.issued2014
dc.departmentFakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Bilgisayar Mühendisliği Bölümüen_US
dc.description.abstractMotivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks the informal goal is to group together related nodes. For the case of protein-protein interaction networks such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships in predicting the functions of proteins with unknown functions and in verifying those with estimated functions. Results: A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity usually determined via sequence similarities and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show through experiments based on biological significance tests that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms.en_US]
dc.identifier.citation54
dc.identifier.doi10.1093/bioinformatics/btt713en_US
dc.identifier.endpage539
dc.identifier.issn1367-4803en_US
dc.identifier.issn1460-2059en_US
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.issue4
dc.identifier.pmid24336414en_US
dc.identifier.scopus2-s2.0-84894559216en_US
dc.identifier.scopusqualityN/A
dc.identifier.startpage531en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12469/728
dc.identifier.urihttps://doi.org/10.1093/bioinformatics/btt713
dc.identifier.volume30en_US
dc.identifier.wosWOS:000332032100011en_US
dc.identifier.wosqualityQ1
dc.institutionauthorAlkan, Ferhaten_US
dc.institutionauthorErten, Cesimen_US
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.relation.journalBioinformaticsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.titleBEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networksen_US
dc.typeArticleen_US
dspace.entity.typePublication

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