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Article: Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

TitleUnidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps
Authors
Liao, HNg, MFung, ESham, PC
KeywordsHapmap
LD
Linkage equilibrium
Matrix-vector multiplication
Nonnegativity
Parallel computation
Single nucleotide polymorphisms
SNPs
Unidimensional scaling
Issue Date2008
PublisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbra
Citation
International Journal Of Bioinformatics Research And Applications, 2008, v. 4 n. 4, p. 417-434 How to Cite?
DOI: http://dx.doi.org/10.1504/IJBRA.2008.021177
AbstractThe main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation. Copyright © 2008 Inderscience Enterprises Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/175976
ISSN
1744-5485
2023 SCImago Journal Rankings: 0.138
References
References in Scopus

 

DC FieldValueLanguage
dc.contributor.authorLiao, Hen_US
dc.contributor.authorNg, Men_US
dc.contributor.authorFung, Een_US
dc.contributor.authorSham, PCen_US
dc.date.accessioned2012-11-26T09:03:10Z-
dc.date.available2012-11-26T09:03:10Z-
dc.date.issued2008en_US
dc.identifier.citationInternational Journal Of Bioinformatics Research And Applications, 2008, v. 4 n. 4, p. 417-434en_US
dc.identifier.issn1744-5485en_US
dc.identifier.urihttp://hdl.handle.net/10722/175976-
dc.description.abstractThe main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation. Copyright © 2008 Inderscience Enterprises Ltd.en_US
dc.languageengen_US
dc.publisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbraen_US
dc.relation.ispartofInternational Journal of Bioinformatics Research and Applicationsen_US
dc.subjectHapmap-
dc.subjectLD-
dc.subjectLinkage equilibrium-
dc.subjectMatrix-vector multiplication-
dc.subjectNonnegativity-
dc.subjectParallel computation-
dc.subjectSingle nucleotide polymorphisms-
dc.subjectSNPs-
dc.subjectUnidimensional scaling-
dc.subject.meshChromosome Mapping - Statistics & Numerical Dataen_US
dc.subject.meshComputational Biologyen_US
dc.subject.meshDatabases, Geneticen_US
dc.subject.meshGenomics - Statistics & Numerical Dataen_US
dc.subject.meshHumansen_US
dc.subject.meshLinkage Disequilibriumen_US
dc.subject.meshModels, Geneticen_US
dc.subject.meshPolymorphism, Single Nucleotideen_US
dc.subject.meshSoftwareen_US
dc.titleUnidimensional nonnegative scaling for genome-wide Linkage Disequilibrium mapsen_US
dc.typeArticleen_US
dc.identifier.emailSham, PC: pcsham@hku.hken_US
dc.identifier.authoritySham, PC=rp00459en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1504/IJBRA.2008.021177en_US
dc.identifier.pmid19008184-
dc.identifier.scopuseid_2-s2.0-55849093648en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-55849093648&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume4en_US
dc.identifier.issue4en_US
dc.identifier.spage417en_US
dc.identifier.epage434en_US
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLiao, H=25641487600en_US
dc.identifier.scopusauthoridNg, M=34571761900en_US
dc.identifier.scopusauthoridFung, E=7005440799en_US
dc.identifier.scopusauthoridSham, PC=34573429300en_US
dc.identifier.issnl1744-5485-

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