2024
Privacy-Enhancing Technologies in Biomedical Data Science
Cho H, Froelicher D, Dokmai N, Nandi A, Sadhuka S, Hong M, Berger B. Privacy-Enhancing Technologies in Biomedical Data Science. Annual Review Of Biomedical Data Science 2024, 7: 317-343. PMID: 39178425, PMCID: PMC11346580, DOI: 10.1146/annurev-biodatasci-120423-120107.Peer-Reviewed Original ResearchConceptsPrivacy-enhancing technologiesAdoption of privacy-enhancing technologiesBiomedical data scienceData scienceAnalyze sensitive dataBiomedical data repositoriesPrivacy protectionSensitive dataPrivacy concernsData silosProtect privacyHuman subject dataBiomedical domainData repositoriesPrivacySubjective dataConventional frameworkSecure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets
Hong M, Froelicher D, Magner R, Popic V, Berger B, Cho H. Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. Lecture Notes In Computer Science 2024, 14758: 308-313. PMID: 39027313, PMCID: PMC11257153, DOI: 10.1007/978-1-0716-3989-4_19.Peer-Reviewed Original ResearchIdentity-by-descentMultiparty homomorphic encryptionGenomic datasetsPairwise sequence comparisonsPrivacy-preserving solutionsDegree of relatednessEffective hash functionsGenetic relationPairs of individualsRelatedness coefficientsSequence comparisonCryptographic techniquesHomomorphic encryptionPrivacy guaranteesHash functionPrivate dataFederated algorithmPrivacy concernsGenetic sequencesData silosRelation detectionEfficient algorithmMultiple entitiesBurden of operatorsPrivacy
2023
sfkit: a web-based toolkit for secure and federated genomic analysis.
Mendelsohn S, Froelicher D, Loginov D, Bernick D, Berger B, Cho H. sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic Acids Research 2023, 51: w535-w541. PMID: 37246709, PMCID: PMC10320181, DOI: 10.1093/nar/gkad464.Peer-Reviewed Original ResearchConceptsCommand line interfaceGroup of collaboratorsCryptographic techniquesPrivacy concernsCollaborative workflowsUse casesWeb-based toolkitWeb serverComputational environmentCollaborative toolsMultiple partiesEssential taskDatasetServerPrivacyGenomic data collectionPrincipal component analysisToolkitData collectionWorkflowToolTaskComponent analysisRecent workComplexity
2022
Mechanisms for Hiding Sensitive Genotypes With Information-Theoretic Privacy
Ye F, Cho H, Rouayheb S. Mechanisms for Hiding Sensitive Genotypes With Information-Theoretic Privacy. IEEE Transactions On Information Theory 2022, 68: 4090-4105. PMID: 37283781, PMCID: PMC10243750, DOI: 10.1109/tit.2022.3156276.Peer-Reviewed Original ResearchInformation-theoretic privacyGenomic data sharingOptimal greedy algorithmCritical health-related informationEfficient algorithmic implementationPrivacy leakagePrivacy mechanismsPrivacy problemsPersonal genomics servicesData sharingPrivacyGreedy algorithmStandard modeling approachesComplexity polynomialOptimal utilityAlgorithmic implementationProcessing orderHealth-related informationStraightforward solutionMarkov modelGenomic dataNearby positionsModeling approachGenomic servicesUsers
2020
Mechanisms for Hiding Sensitive Genotypes with Information-Theoretic Privacy
Ye F, Cho H, Rouayheb S. Mechanisms for Hiding Sensitive Genotypes with Information-Theoretic Privacy. 2020, 00: 902-907. DOI: 10.1109/isit44484.2020.9174492.Peer-Reviewed Original ResearchInformation-theoretic privacyGenomic data sharingCritical health-related informationEfficient algorithmic implementationHidden Markov ModelPersonal genomics servicesData sharingGenomic privacyPrivacyAlgorithmic implementationSuch servicesHealth-related informationStraightforward solutionMarkov modelGenomic dataServicesGenomic servicesInformationSharingImplementationCorrelation structureDataPrivacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs
Cho H, Simmons S, Kim R, Berger B. Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. Cell Systems 2020, 10: 408-416.e9. PMID: 32359425, DOI: 10.1016/j.cels.2020.03.006.Peer-Reviewed Original ResearchConceptsDifferential privacySensitive individual-level dataFormal privacy guaranteesQuery-answering systemPrivacy-utility tradePrivacy guaranteesQuery answersCount queriesCohort discoveryDatabase queriesUtility functionUse casesProof of optimalityResearch workflowAggregate insightsBiomedical databasesAccuracy improvementPrivate informationQueriesPrivacyGeneral utility functionDatabaseMore general utility functionsNew theoretical resultsLookup
2019
Emerging technologies towards enhancing privacy in genomic data sharing
Berger B, Cho H. Emerging technologies towards enhancing privacy in genomic data sharing. Genome Biology 2019, 20: 128. PMID: 31262363, PMCID: PMC6604426, DOI: 10.1186/s13059-019-1741-0.Commentaries, Editorials and Letters
2018
Realizing private and practical pharmacological collaboration
Hie B, Cho H, Berger B. Realizing private and practical pharmacological collaboration. Science 2018, 362: 347-350. PMID: 30337410, PMCID: PMC6519716, DOI: 10.1126/science.aat4807.Peer-Reviewed Original ResearchConceptsArt DTI prediction methodsDrug-target interactionsDTI prediction methodsIntellectual property concernsCryptographic toolsData privacyData sharingMultiple entitiesReal datasetsOpen sharingProperty concernsPrediction methodSharingDatasetPredictive modelPrivacyProtocolConfidentialityBiomedical researchCollaborationToolDataEntities