2017
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 2017, 33: 3716-3725. PMID: 29036461, PMCID: PMC5860319, DOI: 10.1093/bioinformatics/btx470.Peer-Reviewed Original ResearchChildFamilyGenetic PrivacyGenome-Wide Association StudyHumansLinkage DisequilibriumParentsPolymorphism, Single NucleotideSoftwareWhole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
Kim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.Peer-Reviewed Original ResearchConceptsWhole genome sequencesGenome-wide association studiesToll-like receptor 6Single nucleotide variantsCommon disease-rare variant hypothesisExpression quantitative trait loci (eQTL) analysisDifferential expressionQuantitative trait locus (QTL) analysisCommon disease–common variantPathogen-associated molecular pattern recognitionIntegrative genomics approachIntronic single nucleotide variantsComplex genetic diseasesSequence quality scoresMolecular pattern recognitionWhole-genome sequencingGenomic approachesTranscriptome dataGenome sequenceSequence variationLocus analysisGenome sequencingAssociation studiesFunction of genotypeNucleotide variants
2014
Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery
Zhao Y, Wang X, Jiang X, Ohno-Machado L, Tang H. Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. Journal Of The American Medical Informatics Association 2014, 22: 100-108. PMID: 25352565, PMCID: PMC4433380, DOI: 10.1136/amiajnl-2014-003043.Peer-Reviewed Original ResearchMeSH KeywordsConfidentialityDatasets as TopicDNAGenetic MarkersGenome, HumanGenome-Wide Association StudyHumansPolymorphism, Single NucleotideConceptsData ownersData usersHuman genomic datasetsHuman genomic dataPatient privacyPrivacyGeneration approachUsersData selectionReal dataDatasetGenomic datasetsPrivate solicitationDNA datasetsScientific discoveryNew approachGenomic dataHigh confidencePilot versionEvaluation methodRight choiceOwnersAlgorithmNew techniqueDisease marker discovery
2006
Approximation properties of haplotype tagging
Vinterbo S, Dreiseitl S, Ohno-Machado L. Approximation properties of haplotype tagging. BMC Bioinformatics 2006, 7: 8. PMID: 16401341, PMCID: PMC1395335, DOI: 10.1186/1471-2105-7-8.Peer-Reviewed Original ResearchConceptsApproximation propertiesCombinatorial optimization problemsOptimization problemImplementable algorithmComputational effortSolution qualityTerms of complexitySimple algorithmSize m.Population membersSingle processor machineAlgorithmProblemAsymptoticsApproximationProcessor machineHaplotype taggingNPsUnique identification