2021
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation
Kim M, Harmanci A, Bossuat J, Carpov S, Cheon J, Chillotti I, Cho W, Froelicher D, Gama N, Georgieva M, Hong S, Hubaux J, Kim D, Lauter K, Ma Y, Ohno-Machado L, Sofia H, Son Y, Song Y, Troncoso-Pastoriza J, Jiang X. Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation. Cell Systems 2021, 12: 1108-1120.e4. PMID: 34464590, PMCID: PMC9898842, DOI: 10.1016/j.cels.2021.07.010.Peer-Reviewed Original ResearchConceptsHomomorphic encryption techniqueResource-intensive computationsSecure outsourcingGenomic data analysisData securityEncryption modelEncryption techniquePrivacy concernsSource codeMemory requirementsGenetic data analysisData analysisComparable accuracyFundamental stepGenotype imputationImputationDownloadSecurityOutsourcingComputationCodeServicesRequirementsAccuracyMethod
2019
Evaluating and sharing global genetic ancestry in biomedical datasets
Harismendy O, Kim J, Xu X, Ohno-Machado L. Evaluating and sharing global genetic ancestry in biomedical datasets. Journal Of The American Medical Informatics Association 2019, 26: 457-461. PMID: 30869786, PMCID: PMC6433181, DOI: 10.1093/jamia/ocy194.Peer-Reviewed Original ResearchConceptsGenetic diversity measurementsGenetic ancestryAvailable molecular datasetsHuman genetics researchCancer Genome Atlas (TCGA) datasetContinental resolutionGenetic diversityPhenotype-genotype associationsMolecular datasetsGlobal genetic ancestryAncestry informationGenetic researchAtlas datasetDiversity measurementsAncestryTraitsGlobal scaleDiversityBiomedical datasetsAvailable datasetsData repositoryDisease riskAccess datasetDatasetAvailable cohorts
2014
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Doan S, Lin K, Conway M, Ohno-Machado L, Hsieh A, Feupe S, Garland A, Ross M, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal Of The American Medical Informatics Association 2014, 21: 31-36. PMID: 23989082, PMCID: PMC3912702, DOI: 10.1136/amiajnl-2013-001882.Peer-Reviewed Original ResearchConceptsNew information retrieval systemInformation retrieval systemsInformation retrieval toolsDatabase of GenotypesText processing toolsRetrieval systemSearch scenariosDiscovery systemRetrieval toolsAuthorized usersNon-standardized wayCross-study validationSearch comparisonProcessing toolsPromising performanceUsersPhenotype informationDatabaseInformationBiotechnology InformationQueriesMetadataEntrezResourcesSystem
2012
Selecting cases for whom additional tests can improve prognostication.
Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L. Selecting cases for whom additional tests can improve prognostication. AMIA Annual Symposium Proceedings 2012, 2012: 1260-8. PMID: 23304404, PMCID: PMC3540468.Peer-Reviewed Original Research
2003
Microarrays and clinical dentistry
Kuo W, Whipple M, Jenssen T, Todd R, Epstein J, Ohno-Machado L, Sonis S, Park P. Microarrays and clinical dentistry. The Journal Of The American Dental Association 2003, 134: 456-462. PMID: 12733779, DOI: 10.14219/jada.archive.2003.0195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsAdvanced microarray technologiesEntire human genomeActivity of genesGene expression patternsHuman Genome ProjectGenome levelHuman genomeGenetic approachesCellular developmentDNA sequencesGenome ProjectExciting biologyCandidate genesExpression patternsMicroarray technologyMicroarrayNumber of cancersGenesMolecular profileAnalysis of diseasesMolecular behaviorGenomeBiologyTissue samplesProtein