2023
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia
Ohno-Machado L, Jiang X, Kuo T, Tao S, Chen L, Ram P, Zhang G, Xu H. A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia. Journal Of Biomedical Informatics 2023, 139: 104322. PMID: 36806328, PMCID: PMC10975485, DOI: 10.1016/j.jbi.2023.104322.Peer-Reviewed Original ResearchConceptsPrivacy of individualsAppropriate privacy protectionData-driven modelsPrivacy protectionPrivacy risksData Coordination CenterData hubData repositoryHierarchical strategyPrivacyBiomedical discoveryData setsRecord linkageData Coordinating CenterRepositoryComplex strategiesCoordination centerTechnologyTechniqueDataPartiesSetHierarchy
2022
Achieving a Representative Sample of Asian Americans in Biomedical Research Through Community-Based Approaches: Comparing Demographic Data in the All of Us Research Program With the American Community Survey
Randal F, Lozano P, Qi S, Maene C, Shah S, Mo Y, Ratsimbazafy F, Boerwinkle E, Cicek M, Clark C, Cohn E, Gebo K, Loperena R, Mayo K, Mockrin S, Ohno-Machado L, Schully S, Ramirez A, Aschebrook-Kilfoy B, Ahsan H, Lam H, Kim K. Achieving a Representative Sample of Asian Americans in Biomedical Research Through Community-Based Approaches: Comparing Demographic Data in the All of Us Research Program With the American Community Survey. Journal Of Transcultural Nursing 2022, 34: 59-67. PMID: 36398985, DOI: 10.1177/10436596221130796.Peer-Reviewed Original ResearchMeSH KeywordsAsianBiomedical ResearchEducational StatusHumansPopulation HealthSurveys and QuestionnairesUnited StatesCodesigning 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
Hypertension prevalence in the All of Us Research Program among groups traditionally underrepresented in medical research
Chandler P, Clark C, Zhou G, Noel N, Achilike C, Mendez L, Ramirez A, Loperena-Cortes R, Mayo K, Cohn E, Ohno-Machado L, Boerwinkle E, Cicek M, Qian J, Schully S, Ratsimbazafy F, Mockrin S, Gebo K, Dedier J, Murphy S, Smoller J, Karlson E. Hypertension prevalence in the All of Us Research Program among groups traditionally underrepresented in medical research. Scientific Reports 2021, 11: 12849. PMID: 34158555, PMCID: PMC8219813, DOI: 10.1038/s41598-021-92143-w.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultBiomedical ResearchFemaleHumansHypertensionMaleMiddle AgedMinority GroupsPrevalenceUnited StatesYoung AdultConceptsPrevalence of hypertensionHTN prevalenceUs Research ProgramMajor public health concernBlood pressure medicationsPopulation-based studyNutrition Examination SurveyBlood pressure measurementsPopulation-based surveyEHR dataPatient measurementsPublic health concernAntihypertensive medicationsEHR cohortHTN medicationsHypertension prevalenceCrude prevalenceHypertension casesHypertension treatmentExamination SurveyNational HealthHypertensionBilling codesMedicationsCohort
2020
Coronavirus: indexed data speed up solutions
Ohno-Machado L, Xu H. Coronavirus: indexed data speed up solutions. Nature 2020, 584: 192-192. PMID: 32782375, DOI: 10.1038/d41586-020-02331-3.Commentaries, Editorials and LettersEngaging heart failure patients from a clinical data research network: A survey on willingness to participate in different types of research.
Choi Y, López J, Meeker D, Ohno-Machado L, Kim K. Engaging heart failure patients from a clinical data research network: A survey on willingness to participate in different types of research. AMIA Annual Symposium Proceedings 2020, 2019: 305-312. PMID: 32308823, PMCID: PMC7153117.Peer-Reviewed Original ResearchConceptsClinical Data Research NetworkHeart failure patientsLarge cohort studyResearch participationResearch NetworkCohort studyFailure patientsOne-time surveyPatient cohortObservational studyPatient motivationWeight controlSignificant associationClinical researchPatientsPrecision medicineHealth dataRecruitment effortsNational effortsActivity interestsSurgeryCohort
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 Research
2018
Data science and artificial intelligence to improve clinical practice and research
Ohno-Machado L. Data science and artificial intelligence to improve clinical practice and research. Journal Of The American Medical Informatics Association 2018, 25: 1273-1273. PMID: 30312446, PMCID: PMC7646927, DOI: 10.1093/jamia/ocy136.Commentaries, Editorials and LettersA Scalable Privacy-preserving Data Generation Methodology for Exploratory Analysis.
Vaidya J, Shafiq B, Asani M, Adam N, Jiang X, Ohno-Machado L. A Scalable Privacy-preserving Data Generation Methodology for Exploratory Analysis. AMIA Annual Symposium Proceedings 2018, 2017: 1695-1704. PMID: 29854240, PMCID: PMC5977652.Peer-Reviewed Original ResearchConceptsPrivacy-preserving approachData management systemBig dataBiomedical datasetsClassification taskBiomedical dataContext of regressionManagement systemSynthetic dataGeneration methodologyEssential problemResearch tasksAdditional datasetsDatasetTaskSignificant effortsDirect accessFirstorder approximationDataParticular typeAccessPrecision medicineFinding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge
Wei W, Ji Z, He Y, Zhang K, Ha Y, Li Q, Ohno-Machado L. Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge. Database 2018, 2018: bay017. PMID: 29688374, PMCID: PMC5861401, DOI: 10.1093/database/bay017.Peer-Reviewed Original Research
2017
Finding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesBiomedical ResearchComputational BiologyDatabases, FactualHumansMetadataSoftwareSystems IntegrationConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineDataDeveloping 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 ResearchConceptsBig dataDigital objectsBig data scienceNIH Big DataDiversity of dataComputational infrastructureData scienceData sharingVirtual environmentSecure processK frameworkDiverse datasetsKnowledge initiativesKnowledge commonsSuch dataBiomedical researchObjectsInteroperabilityFrameworkDiscoverabilityRecent yearsSharingDatasetInfrastructurePilot projectAdvancing healthcare and biomedical research via new data-driven approaches
Ohno-Machado L. Advancing healthcare and biomedical research via new data-driven approaches. Journal Of The American Medical Informatics Association 2017, 24: 471-471. PMID: 28403381, PMCID: PMC7651977, DOI: 10.1093/jamia/ocx036.Commentaries, Editorials and LettersA publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge
Cohen T, Roberts K, Gururaj A, Chen X, Pournejati S, Alter G, Hersh W, Demner-Fushman D, Ohno-Machado L, Xu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database 2017, 2017: bax061. PMID: 29220453, PMCID: PMC5737202, DOI: 10.1093/database/bax061.Peer-Reviewed Original Research
2016
iCONCUR: 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 ResearchConceptsPatient 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-consentParticipantsSecure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE)
Shi H, Jiang C, Dai W, Jiang X, Tang Y, Ohno-Machado L, Wang S. Secure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE). BMC Medical Informatics And Decision Making 2016, 16: 89. PMID: 27454168, PMCID: PMC4959358, DOI: 10.1186/s12911-016-0316-1.Peer-Reviewed Original ResearchConceptsData sharingPatient privacySecure multi-party computationModel learning phaseMulti-party computationBiomedical data sharingInformation leakageModel learningIntermediary informationInformation exchangeSecondary usePrivacyBig concernPractical solutionLogistic regression frameworkExperimental resultsSharingRegression frameworkFrameworkMultiple institutionsPrevious workComputationLearningBiomedical researchInformation
2015
Trends in biomedical informatics: automated topic analysis of JAMIA articles
Han D, Wang S, Jiang C, Jiang X, Kim H, Sun J, Ohno-Machado L. Trends in biomedical informatics: automated topic analysis of JAMIA articles. Journal Of The American Medical Informatics Association 2015, 22: 1153-1163. PMID: 26555018, PMCID: PMC5009912, DOI: 10.1093/jamia/ocv157.Peer-Reviewed Original ResearchMeSH KeywordsBibliometricsBiomedical ResearchMedical InformaticsMedical Subject HeadingsPeriodicals as TopicSocieties, MedicalConceptsTensor decompositionA 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 feature
2014
Sharing 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 ResearchNIH's Big Data to Knowledge initiative and the advancement of biomedical informatics
Ohno-Machado L. NIH's Big Data to Knowledge initiative and the advancement of biomedical informatics. Journal Of The American Medical Informatics Association 2014, 21: 193-193. PMID: 24509598, PMCID: PMC3932475, DOI: 10.1136/amiajnl-2014-002666.Commentaries, Editorials and Letters