2023
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia
Ohno-Machado L, Jiang X, Kuo T, Tao S, Chen L, Ram P, Zhang G, Xu H. A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia. Journal Of Biomedical Informatics 2023, 139: 104322. PMID: 36806328, PMCID: PMC10975485, DOI: 10.1016/j.jbi.2023.104322.Peer-Reviewed Original ResearchConceptsPrivacy of individualsAppropriate privacy protectionData-driven modelsPrivacy protectionPrivacy risksData Coordination CenterData hubData repositoryHierarchical strategyPrivacyBiomedical discoveryData setsRecord linkageData Coordinating CenterRepositoryComplex strategiesCoordination centerTechnologyTechniqueDataPartiesSetHierarchy
2022
The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition
Kuo T, Jiang X, Tang H, Wang X, Harmanci A, Kim M, Post K, Bu D, Bath T, Kim J, Liu W, Chen H, Ohno-Machado L. The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. Journal Of The American Medical Informatics Association 2022, 29: 2182-2190. PMID: 36164820, PMCID: PMC9667175, DOI: 10.1093/jamia/ocac165.Peer-Reviewed Original ResearchConceptsSensitive personal informationGenomic data analysisPotential future research directionsPersonal informationSecurity concernsGenomics data repositoryData repositoryReport lessonsProtection techniquesFuture research directionsPrivacyResearch directionsData usePractical challengesGenomic dataData analysisAnonymizationCommunity effortsRepositorySecurityBiomedical researchInformationDataChallenges
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
2017
Finding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineDataInformation retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
Roberts K, Gururaj A, Chen X, Pournejati S, Hersh W, Demner-Fushman D, Ohno-Machado L, Cohen T, Xu H. Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database 2017, 2017: bax068. DOI: 10.1093/database/bax068.Peer-Reviewed Original ResearchBiomedical datasetsRetrieval challengesInformation retrieval techniquesAdvanced query processingBiomedical data repositoriesAdvanced retrieval methodsQuery processingInformation retrievalTest queriesRetrieval systemRank frameworkRetrieval approachRetrieval techniquesData repositoryRetrieval methodTop precisionDatasetQueriesRepositoryChallengesRetrievalTaskLearningSystemCorpus
2015
Preserving Genome Privacy in Research Studies
Wang S, Jiang X, Fox D, Ohno-Machado L. Preserving Genome Privacy in Research Studies. 2015, 425-441. DOI: 10.1007/978-3-319-23633-9_16.Peer-Reviewed Original ResearchGenome privacyPrivacy researchBetter privacy protectionObfuscation of dataSecure data repositoryLoss of privacyData use agreementsPrivacy challengesPrivacy problemsPrivacy protectionAttack modelIndividual privacyData sharingMassive collectionPrivacyData repositoryTraditional clinical informationScientific discoveryGenomic dataData analysis methodsBig challengeUse agreementsBiomedical communityTechnical aspects
2013
Identifying inference attacks against healthcare data repositories.
Vaidya J, Shafiq B, Jiang X, Ohno-Machado L. Identifying inference attacks against healthcare data repositories. AMIA Joint Summits On Translational Science Proceedings 2013, 2013: 262-6. PMID: 24303279, PMCID: PMC3845790.Peer-Reviewed Original Research
2012
Privacy-preserving Biometric System for Secure Fingerprint Authentication
Wang S, Jiang X, Ohno-Machado L, Cui L, Cheng S, Xiong H. Privacy-preserving Biometric System for Secure Fingerprint Authentication. 2012, 1: 128-128. DOI: 10.1109/hisb.2012.53.Peer-Reviewed Original ResearchSecure Fingerprint AuthenticationBiometric systemsFingerprint authenticationElectronic health recordsPrivacy-preserving mannerSecure biometric systemsHigh authentication accuracySlepian-Wolf codesRe-identify individualsAuthentication systemSensitive informationAuthentication accuracyBiometric featuresMobile devicesResearch Data RepositoryPersonal privacyBiometricsData repositoryAuthenticationHealth recordsPrivacyExperimental resultsSuch informationImportant concernAttackerData Locked Inside Databases: A Text Classification In The Database Of Genotypes And Phenotypes (dbGaP) To Address Challenges In Retrieving Clinical Information From Public Data Repositories
Ross M, Kim J, Lin K, Ohno-Machado L, Finn P, Kim H. Data Locked Inside Databases: A Text Classification In The Database Of Genotypes And Phenotypes (dbGaP) To Address Challenges In Retrieving Clinical Information From Public Data Repositories. 2012, a5777-a5777. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5777.Peer-Reviewed Original Research
1999
Using Boolean reasoning to anonymize databases
Øhrn A, Ohno-Machado L. Using Boolean reasoning to anonymize databases. Artificial Intelligence In Medicine 1999, 15: 235-254. PMID: 10206109, DOI: 10.1016/s0933-3657(98)00056-6.Peer-Reviewed Original ResearchConceptsBoolean reasoningMedical data repositoriesMeasure of anonymitySensitive dataPrivacy issuesDatabase fieldAmount of trustConfidential informationDegree of anonymityData repositoryDeterministic inferenceIndividual objectsAnonymityParticular pieceAlgorithmElectronic medical recordsSpecific needsReasoningDatabasePossible misuseAnonymizationInformationRepositoryOutside worldIssues