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DC Field | Value | Language |
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dc.contributor.author | Abaka, Gamze | - |
dc.contributor.author | Bıyıkoğlu, Türker | - |
dc.contributor.author | Erten, Cesim | - |
dc.date.accessioned | 2017-04-11T08:28:45Z | |
dc.date.available | 2017-04-11T08:28:45Z | |
dc.date.issued | 2013-07 | |
dc.identifier.citation | Abaka, G., Bıyıkoğlu, T., and Erten, C. (2013). CAMPways: Constrained alignment framework for the comparative analysis of a pair of metabolic pathways. Bioinformatics, 29(13), i145-i153. doi.10.1093/bioinformatics/btt235 | en_US |
dc.identifier.issn | 1367-4803 | |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://doi.org/10.1093/bioinformatics/btt235 | |
dc.identifier.uri | http://hdl.handle.net/11147/5283 | |
dc.description.abstract | Motivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism.Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. © The Author 2013. | en_US |
dc.description.sponsorship | TUBITAK (112E137); TÜBA GEBIP 2009 and ESF EUROCORES TUBITAK (210T173) | en_US |
dc.language.iso | en | en_US |
dc.publisher | Oxford University Press | en_US |
dc.relation.ispartof | Bioinformatics | en_US |
dc.rights | info:eu-repo/semantics/openAccess | en_US |
dc.subject | Algorithms | en_US |
dc.subject | Metabolic engineering | en_US |
dc.subject | Metabolism | en_US |
dc.subject | Metabolic pathways | en_US |
dc.subject | Metabolic networks | en_US |
dc.title | Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways | en_US |
dc.type | Article | en_US |
dc.institutionauthor | Bıyıkoğlu, Türker | - |
dc.department | İzmir Institute of Technology. Mathematics | en_US |
dc.identifier.volume | 29 | en_US |
dc.identifier.issue | 13 | en_US |
dc.identifier.startpage | i145 | en_US |
dc.identifier.endpage | i153 | en_US |
dc.identifier.wos | WOS:000321746100017 | en_US |
dc.identifier.scopus | 2-s2.0-84879975686 | en_US |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
dc.identifier.doi | 10.1093/bioinformatics/btt235 | - |
dc.identifier.pmid | 23812978 | en_US |
dc.relation.doi | 10.1093/bioinformatics/btt235 | en_US |
dc.coverage.doi | 10.1093/bioinformatics/btt235 | en_US |
dc.identifier.wosquality | Q1 | - |
dc.identifier.scopusquality | Q1 | - |
item.fulltext | With Fulltext | - |
item.openairetype | Article | - |
item.openairecristype | http://purl.org/coar/resource_type/c_18cf | - |
item.languageiso639-1 | en | - |
item.cerifentitytype | Publications | - |
item.grantfulltext | open | - |
crisitem.author.dept | 04.02. Department of Mathematics | - |
Appears in Collections: | Mathematics / Matematik PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection |
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