GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda
Wang S, Kim J, Jiang X, Brunner S, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Medical Genomics 2014, 7: s9. PMID: 25077821, PMCID: PMC4101446, DOI: 10.1186/1755-8794-7-s1-s9.Peer-Reviewed Original ResearchConceptsCompute Unified Device ArchitectureGraphics processing unitsHigh performance computeParallel computingNVIDIA Compute Unified Device ArchitectureUnified Device ArchitectureMultiple test datasetsGiga cell updatesTimes performance gainsSmith-Waterman algorithmGPU developersSW implementationSource codeExecution timeGHz CPUIntel XeonLong reference sequencesProcessing unitTarget identification algorithmCell updatesTest datasetProjects/Such large scalePerformance gainsBiomedical research communityHUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads
Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. Journal Of The American Medical Informatics Association 2014, 21: 363-373. PMID: 24368726, PMCID: PMC3932469, DOI: 10.1136/amiajnl-2013-002147.Peer-Reviewed Original ResearchConceptsBase quality valuesCompression algorithmStorage savingsGenome compressionSequence Alignment/Map (SAM) formatCompression ratioNovel compression algorithmComparable compression ratioCompression mechanismK-means clusteringDifferent reference genomesQuality valuesDecompression qualityLossless compressionExecution timeCompression rateAligned readsMap formatAlgorithmBiomedical communityDifferent quality valuesExperimental datasetsAdaptive schemeStorage capabilityArchiving