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 ResearchMeSH KeywordsBiomedical ResearchComputer SecurityConfidentialityData ScienceHumansInformation DisseminationPrivacyConceptsPrivacy-enhancing technologiesAdoption of privacy-enhancing technologiesBiomedical data scienceData scienceAnalyze sensitive dataBiomedical data repositoriesPrivacy protectionSensitive dataPrivacy concernsData silosProtect privacyHuman subject dataBiomedical domainData repositoriesPrivacySubjective dataConventional framework
2023
Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing
Smajlović H, Shajii A, Berger B, Cho H, Numanagić I. Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing. Genome Biology 2023, 24: 5. PMID: 36631897, PMCID: PMC9832703, DOI: 10.1186/s13059-022-02841-5.Peer-Reviewed Original ResearchConceptsSecure multiparty computationHigh-performance frameworkMultiparty computationMPC applicationsSensitive biomedical dataRapid application developmentPython programming languageCompile-time optimizationBiomedical data sharingCryptographic toolsApplication developmentInvolved entitiesProgramming languageBioinformatics tasksData sharingBiomedical dataPrivate informationComputationFrameworkUsabilitySharingApplicationsSyntaxPerformanceTask
2021
Bayesian information sharing enhances detection of regulatory associations in rare cell types
Wu A, Peng J, Berger B, Cho H. Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics 2021, 37: i349-i357. PMID: 34252956, PMCID: PMC8275330, DOI: 10.1093/bioinformatics/btab269.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremGene Expression ProfilingInformation DisseminationSequence Analysis, RNASingle-Cell AnalysisSoftwareConceptsScRNA-seq datasetsRegulatory associationsCell typesRegulatory networksCell type-specific gene regulatory networksCell-type specific gene regulationSingle-cell RNA sequencing technologyCell-type specific networksBenchmark scRNA-seq datasetsDiverse cellular contextsGene regulatory network inference methodRNA sequencing technologyGene regulatory networksRare cell typesSingle-cell datasetsSpecific cell typesNetwork inference methodsDynamic biological processesTranscriptional statesGene regulationCellular contextNetwork inference algorithmsComplex rewiringBiological processesGene associations
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
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 ResearchMeSH KeywordsComputer SimulationConfidentialityDatabases, PharmaceuticalDrug Delivery SystemsHumansInformation DisseminationPharmacologyConceptsArt DTI prediction methodsDrug-target interactionsDTI prediction methodsIntellectual property concernsCryptographic toolsData privacyData sharingMultiple entitiesReal datasetsOpen sharingProperty concernsPrediction methodSharingDatasetPredictive modelPrivacyProtocolConfidentialityBiomedical researchCollaborationToolDataEntitiesSecure genome-wide association analysis using multiparty computation
Cho H, Wu D, Berger B. Secure genome-wide association analysis using multiparty computation. Nature Biotechnology 2018, 36: 547-551. PMID: 29734293, PMCID: PMC5990440, DOI: 10.1038/nbt.4108.Peer-Reviewed Original ResearchMeSH KeywordsBiotechnologyComputer SecurityConfidentialityCrowdsourcingGenetic PrivacyGenome-Wide Association StudyHumansInformation DisseminationPrincipal Component AnalysisQuality Control