Rednemo: Topology-Based Ppi Network Reconstruction Via Repeated Diffusion With Neighborhood Modifications

dc.contributor.author Alkan, Ferhat
dc.contributor.author Erten, Cesim
dc.contributor.author Erten, Cesim
dc.date.accessioned 2019-06-27T08:01:23Z
dc.date.available 2019-06-27T08:01:23Z
dc.date.issued 2017
dc.department Fakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Bilgisayar Mühendisliği Bölümü en_US
dc.description.abstract Motivation: Analysis of protein-protein interaction (PPI) networks provides invaluable insight into several systems biology problems. High-throughput experimental techniques together with computational methods provide large-scale PPI networks. However a major issue with these networks is their erroneous nature en_US]
dc.description.abstract they contain false-positive interactions and usually many more false-negatives. Recently several computational methods have been proposed for network reconstruction based on topology where given an input PPI network the goal is to reconstruct the network by identifying false-positives/-negatives as correctly as possible. Results: We observe that the existing topology-based network reconstruction algorithms suffer several shortcomings. An important issue is regarding the scalability of their computational requirements especially in terms of execution times with the network sizes. They have only been tested on small-scale networks thus far and when applied on large-scale networks of popular PPI databases the executions require unreasonable amounts of time or may even crash without producing any output for some instances even after several months of execution. We provide an algorithm RedNemo for the topology-based network reconstruction problem. It provides more accurate networks than the alternatives as far as biological qualities measured in terms of most metrics based on gene ontology annotations. The recovery of a high-confidence network modified via random edge removals and rewirings is also better with RedNemo than with the alternatives under most of the experimented removal/rewiring ratios. Furthermore through extensive tests on databases of varying sizes we show that RedNemo achieves these results with much better running time performances. en_US]
dc.identifier.citationcount 7
dc.identifier.doi 10.1093/bioinformatics/btw655 en_US
dc.identifier.endpage 544
dc.identifier.issn 1367-4803 en_US
dc.identifier.issn 1460-2059 en_US
dc.identifier.issn 1367-4803
dc.identifier.issn 1460-2059
dc.identifier.issue 4
dc.identifier.pmid 27797764 en_US
dc.identifier.scopus 2-s2.0-85028354842 en_US
dc.identifier.startpage 537 en_US
dc.identifier.uri https://hdl.handle.net/20.500.12469/366
dc.identifier.uri https://doi.org/10.1093/bioinformatics/btw655
dc.identifier.volume 33 en_US
dc.identifier.wos WOS:000397264100010 en_US
dc.identifier.wosquality Q1
dc.institutionauthor Erten, Cesim en_US
dc.language.iso en en_US
dc.publisher Oxford University Press en_US
dc.relation.journal Bioinformatics en_US
dc.relation.publicationcategory Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı en_US
dc.rights info:eu-repo/semantics/openAccess en_US
dc.scopus.citedbyCount 10
dc.title Rednemo: Topology-Based Ppi Network Reconstruction Via Repeated Diffusion With Neighborhood Modifications en_US
dc.type Article en_US
dc.wos.citedbyCount 8
dspace.entity.type Publication
relation.isAuthorOfPublication ba94d962-58f9-4c10-bdc8-667be0ec3b67
relation.isAuthorOfPublication.latestForDiscovery ba94d962-58f9-4c10-bdc8-667be0ec3b67

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