2024
Secure 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. Genome Research 2024, 34: gr.279057.124. PMID: 39111815, PMCID: PMC11529841, DOI: 10.1101/gr.279057.124.Peer-Reviewed Original ResearchMultiparty homomorphic encryptionIdentity-by-descentEffective hash functionsGenomic datasetsHomomorphic encryptionHash functionPrivate dataFederated algorithmBucketing strategyData holdersData silosDegree of relatednessRelation detectionGenetic relationEfficient algorithmMultiple entitiesRelatedness coefficientsPairs of individualsGenomic studiesDatasetIdentification of relationsRuntimeGenetic sequencesAccurate detectionAlgorithm
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
Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Froelicher D, Troncoso-Pastoriza J, Raisaro J, Cuendet M, Sousa J, Cho H, Berger B, Fellay J, Hubaux J. Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption. Nature Communications 2021, 12: 5910. PMID: 34635645, PMCID: PMC8505638, DOI: 10.1038/s41467-021-25972-y.Peer-Reviewed Original ResearchConceptsMultiparty homomorphic encryptionHomomorphic encryptionPrivacy-preserving analysisNecessary key stepMultiple healthcare institutionsFederated analyticsFederated settingAnalysis tasksAnalytics systemIntermediate dataEncryptionCentralized studiesPatient dataBiomedical insightsScientific collaborationAccurate resultsIndispensable complementAnalyticsHealthcare institutionsDatasetTaskSystemBiomedical researchAccessCollaboration
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 researchCollaborationToolDataEntitiesGeneralizable 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