2024
Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review
Lacson R, Yu Y, Kuo T, Ohno-Machado L. Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review. Journal Of The American Medical Informatics Association 2024, 31: 1423-1435. PMID: 38726710, PMCID: PMC11105130, DOI: 10.1093/jamia/ocae084.Peer-Reviewed Original ResearchConceptsElectronic health recordsSystematic reviewData sharingMedical data sharingSpeed metricsPreferred Reporting ItemsCertificate storageDecentralized InternetNetwork permissionsBlockchain platformBlockchain applicationsEvaluation metricsBiomedical domainBlockchainBiomedical data managementHealth recordsData managementData storageReporting ItemsHealth sectorQuantitative metricsMedical facilitiesMetricsTrial managementClinical trial management
2022
Codesigning a community-based participatory research project to assess tribal perspectives on privacy and health data sharing: A report from the Strong Heart Study
Triplett C, Fletcher B, Taitingfong R, Zhang Y, Ali T, Ohno-Machado L, Bloss C. Codesigning a community-based participatory research project to assess tribal perspectives on privacy and health data sharing: A report from the Strong Heart Study. Journal Of The American Medical Informatics Association 2022, 29: 1120-1127. PMID: 35349678, PMCID: PMC9093024, DOI: 10.1093/jamia/ocac038.Peer-Reviewed Original Research
2021
Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track
Kuo T, Bath T, Ma S, Pattengale N, Yang M, Cao Y, Hudson C, Kim J, Post K, Xiong L, Ohno-Machado L. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. International Journal Of Medical Informatics 2021, 154: 104559. PMID: 34474309, PMCID: PMC9933142, DOI: 10.1016/j.ijmedinf.2021.104559.Peer-Reviewed Original ResearchConceptsSecure genome analysis competitionData retrieval queriesBlockchain-based methodData sharing methodReal-world problemsQuery indexType of sharingRetrieval queriesBlockchain technologyLedger technologySource codeBlockchain utilizationBlockchain strategyHealthcare applicationsInteraction recordsSharing methodTest datasetSharing recordsBiomedical research applicationsConsortium resourcesNew platformPatient recordsBlockchainQueriesTechnology
2020
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles
Zuo X, Chen Y, Ohno-Machado L, Xu H. How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. Briefings In Bioinformatics 2020, 22: 800-811. PMID: 33757278, PMCID: PMC7799277, DOI: 10.1093/bib/bbaa331.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsUse of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers
Madhavan S, Bastarache L, Brown J, Butte A, Dorr D, Embi P, Friedman C, Johnson K, Moore J, Kohane I, Payne P, Tenenbaum J, Weiner M, Wilcox A, Ohno-Machado L. Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. Journal Of The American Medical Informatics Association 2020, 28: 393-401. PMID: 33260207, PMCID: PMC7665546, DOI: 10.1093/jamia/ocaa287.Commentaries, Editorials and LettersMeSH KeywordsAcademic Medical CentersCOVID-19Electronic Health RecordsHumansInformation DisseminationInformation SystemsPublic Health PracticeRegistriesUnited StatesPrivacy challenges and research opportunities for genomic data sharing
Bonomi L, Huang Y, Ohno-Machado L. Privacy challenges and research opportunities for genomic data sharing. Nature Genetics 2020, 52: 646-654. PMID: 32601475, PMCID: PMC7761157, DOI: 10.1038/s41588-020-0651-0.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2019
Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research
Kim J, Kim H, Bell E, Bath T, Paul P, Pham A, Jiang X, Zheng K, Ohno-Machado L. Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research. JAMA Network Open 2019, 2: e199550. PMID: 31433479, PMCID: PMC6707015, DOI: 10.1001/jamanetworkopen.2019.9550.Peer-Reviewed Original ResearchFair compute loads enabled by blockchain: sharing models by alternating client and server roles
Kuo T, Gabriel R, Ohno-Machado L. Fair compute loads enabled by blockchain: sharing models by alternating client and server roles. Journal Of The American Medical Informatics Association 2019, 26: 392-403. PMID: 30892656, PMCID: PMC7787356, DOI: 10.1093/jamia/ocy180.Peer-Reviewed Original Research
2018
Sharing data from electronic health records within, across, and beyond healthcare institutions: Current trends and perspectives
Ohno-Machado L. Sharing data from electronic health records within, across, and beyond healthcare institutions: Current trends and perspectives. Journal Of The American Medical Informatics Association 2018, 25: 1113-1113. PMID: 30184157, PMCID: PMC7646901, DOI: 10.1093/jamia/ocy116.Commentaries, Editorials and Letters
2017
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop
Jagodnik K, Koplev S, Jenkins S, Ohno-Machado L, Paten B, Schurer S, Dumontier M, Verborgh R, Bui A, Ping P, McKenna N, Madduri R, Pillai A, Ma'ayan A. Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. Journal Of Biomedical Informatics 2017, 71: 49-57. PMID: 28501646, PMCID: PMC5545976, DOI: 10.1016/j.jbi.2017.05.006.Peer-Reviewed Original ResearchMeSH KeywordsBiomedical ResearchDatasets as TopicHumansInformation DisseminationKnowledgeNational Institutes of Health (U.S.)Translational Research, BiomedicalUnited StatesConceptsBig dataDigital objectsBig data scienceNIH Big DataDiversity of dataComputational infrastructureData scienceData sharingVirtual environmentSecure processK frameworkDiverse datasetsKnowledge initiativesKnowledge commonsSuch dataBiomedical researchObjectsInteroperabilityFrameworkDiscoverabilityRecent yearsSharingDatasetInfrastructurePilot projectAddressing Beacon re-identification attacks: quantification and mitigation of privacy risks
Raisaro J, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux J. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. Journal Of The American Medical Informatics Association 2017, 24: 799-805. PMID: 28339683, PMCID: PMC5881894, DOI: 10.1093/jamia/ocw167.Peer-Reviewed Original ResearchPrerequisites for International Exchanges of Health Information for Record Research: Comparison of Australian, Austrian, Finnish, Swiss, and US Policies.
Suominen H, Müller H, Ohno-Machado L, Salanterä S, Schreier G, Hanlen L. Prerequisites for International Exchanges of Health Information for Record Research: Comparison of Australian, Austrian, Finnish, Swiss, and US Policies. 2017, 245: 1312. PMID: 29295395.Peer-Reviewed Original ResearchAustraliaAustriaConfidentialityFinlandHealth Information SystemsHumansInformation DisseminationPrivacySwitzerland
2016
Biospecimen Sharing Among Hispanic Women in a Safety-Net Clinic: Implications for the Precision Medicine Initiative
Nodora J, Komenaka I, Bouton M, Ohno-Machado L, Schwab R, Kim H, Farcas C, Perez G, Martinez M. Biospecimen Sharing Among Hispanic Women in a Safety-Net Clinic: Implications for the Precision Medicine Initiative. Journal Of The National Cancer Institute 2016, 109: djw201. PMID: 27688295, PMCID: PMC5040829, DOI: 10.1093/jnci/djw201.Peer-Reviewed Original ResearchConceptsSafety-net clinicsPrecision Medicine InitiativeHispanic womenUnderserved populationsMedicine InitiativeSafety-net hospitalUS Hispanic populationPatient's physicianIndividualized careConsent ratesBreast biopsyBiospecimen donationHispanic populationClinicHospitalResearch assistantsPhysiciansWomenPersonalized medicineBiospecimenPopulationBiopsyiCONCUR: informed consent for clinical data and bio-sample use for research
Kim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe S, Ohno-Machado L. iCONCUR: informed consent for clinical data and bio-sample use for research. Journal Of The American Medical Informatics Association 2016, 24: 380-387. PMID: 27589942, PMCID: PMC5391727, DOI: 10.1093/jamia/ocw115.Peer-Reviewed Original ResearchMeSH KeywordsBiomedical ResearchElectronic Health RecordsFeasibility StudiesFemaleHumansInformation DisseminationInformed ConsentMalePatient PreferenceSocioeconomic FactorsConceptsPatient preferencesClinical dataHuman immunodeficiency virus clinicInternal medicine clinicElectronic health record dataHealth record dataAcademic medical centerElectronic health recordsDe-identified dataOutpatient clinicMedicine clinicFamily historyMedical CenterInformed Consent ToolClinical settingClinicHealth recordsRecord dataInformed consent systemPatientsConsent toolRecipientsConsentE-consentParticipants
2015
WebDISCO: a web service for distributed cox model learning without patient-level data sharing
Lu C, Wang S, Ji Z, Wu Y, Xiong L, Jiang X, Ohno-Machado L. WebDISCO: a web service for distributed cox model learning without patient-level data sharing. Journal Of The American Medical Informatics Association 2015, 22: 1212-1219. PMID: 26159465, PMCID: PMC5009917, DOI: 10.1093/jamia/ocv083.Peer-Reviewed Original ResearchA system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research
Meeker D, Jiang X, Matheny M, Farcas C, D’Arcy M, Pearlman L, Nookala L, Day M, Kim K, Kim H, Boxwala A, El-Kareh R, Kuo G, Resnic F, Kesselman C, Ohno-Machado L. A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. Journal Of The American Medical Informatics Association 2015, 22: 1187-1195. PMID: 26142423, PMCID: PMC4639714, DOI: 10.1093/jamia/ocv017.Peer-Reviewed Original ResearchConceptsFederated networkData sharing policiesParallel computation methodSharing policiesPolicy management systemData exchange policiesData storage requirementsWeb servicesNetwork queriesQuery functionalityComputation resourcesFederated modelGraphical interfaceData transportCentralized networkStorage requirementsNetwork participantsManagement systemQueriesNetworkComputation methodNew featuresMultivariate statistical estimationDifferent state lawsImportant new featureComparison of consumers’ views on electronic data sharing for healthcare and research
Kim K, Joseph J, Ohno-Machado L. Comparison of consumers’ views on electronic data sharing for healthcare and research. Journal Of The American Medical Informatics Association 2015, 22: 821-830. PMID: 25829461, PMCID: PMC5009901, DOI: 10.1093/jamia/ocv014.Peer-Reviewed Original ResearchConceptsElectronic data sharingData sharingHealth information exchangeData networksHealth informationTechnology infrastructureInformation exchangePrivacyHealth Insurance PortabilitySharingAccountability ActUse of dataInsurance PortabilitySecurityNetworkInformationHealthcareIndividual controlHealthcare deliveryMere relianceDepth studyPortabilityAccessInfrastructureComparison of consumersGrid multi-category response logistic models
Wu Y, Jiang X, Wang S, Jiang W, Li P, Ohno-Machado L. Grid multi-category response logistic models. BMC Medical Informatics And Decision Making 2015, 15: 10. PMID: 25886151, PMCID: PMC4342889, DOI: 10.1186/s12911-015-0133-y.Peer-Reviewed Original ResearchMeSH KeywordsClinical Decision-MakingConfidentialityHumansInformation DisseminationLogistic ModelsModels, StatisticalConceptsGrid modelLikelihood estimation problemClassification performance evaluationReal data setsGrid computingEstimation problemTypes of modelsGrid computationGrid methodPrivacyResponse modelCentralized modelMulti-center dataSuch decompositionsFit assessmentFitting methodLinear modelPerformance evaluationModel constructionData setsModel assumptionsIndividual observationsPractical solutionComputationResultsSimulation results
2014
A community assessment of privacy preserving techniques for human genomes
Jiang X, Zhao Y, Wang X, Malin B, Wang S, Ohno-Machado L, Tang H. A community assessment of privacy preserving techniques for human genomes. BMC Medical Informatics And Decision Making 2014, 14: s1. PMID: 25521230, PMCID: PMC4290799, DOI: 10.1186/1472-6947-14-s1-s1.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsBiomedical dataPrivacy preserving techniquesPrivacy protection techniquesData privacyBiomedical computingHuman genomic dataData donorsDissemination techniquesPersonal Genome ProjectRaw dataProtection techniquesRigorous protectionPrivacyGenomic dataFinal resultsComputingCommunity effortsAnalysis outcomesChallengesTechniqueDataProjectSharing my health data: a survey of data sharing preferences of healthy individuals.
Bell E, Ohno-Machado L, Grando M. Sharing my health data: a survey of data sharing preferences of healthy individuals. AMIA Annual Symposium Proceedings 2014, 2014: 1699-708. PMID: 25954442, PMCID: PMC4419941.Peer-Reviewed Original Research