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
2021
Privacy-preserving genotype imputation in a trusted execution environment
Dokmai N, Kockan C, Zhu K, Wang X, Sahinalp S, Cho H. Privacy-preserving genotype imputation in a trusted execution environment. Cell Systems 2021, 12: 983-993.e7. PMID: 34450045, PMCID: PMC8542641, DOI: 10.1016/j.cels.2021.08.001.Peer-Reviewed Original ResearchConceptsTrusted Execution EnvironmentExecution environmentHardware-based solutionsSide-channel attacksIntel SGXEnhanced securityPrivacy concernsAnalysis servicesImputation ServerServer limitData resourcesImputation algorithmSGXServerImputation softwareGenomic data resourcesImputation accuracyGenotype imputationImputation strategiesServicesDownstream analysisScalabilityImputationEssential toolSecurity
2020
Privacy-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
Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks
Cho H, Berger B, Peng J. Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks. Cell Systems 2018, 7: 185-191.e4. PMID: 29936184, PMCID: PMC6469860, DOI: 10.1016/j.cels.2018.05.017.Peer-Reviewed Original Research