2019
Comparison of blockchain platforms: a systematic review and healthcare examples
Kuo T, Rojas H, Ohno-Machado L. Comparison of blockchain platforms: a systematic review and healthcare examples. Journal Of The American Medical Informatics Association 2019, 26: 462-478. PMID: 30907419, PMCID: PMC7787359, DOI: 10.1093/jamia/ocy185.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsBlockchain platformPopular blockchain platformsBlockchain applicationsSuitable blockchain platformDifferent blockchain platformsClinical informatics researchersTechnical featuresSoftware engineersHealth informatics applicationsHealthcare applicationsInformatics applicationsHealthcare exampleInformatics researchersPlatformBiomedical research applicationsHealthcareBlockchainImportant technical featuresKey featuresApplicationsResearch applicationsFeaturesBrief introductionTechnologyRequirements
2017
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 2017, 33: 3716-3725. PMID: 29036461, PMCID: PMC5860319, DOI: 10.1093/bioinformatics/btx470.Peer-Reviewed Original ResearchFinding 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 ResearchConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineData
2016
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS
Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp S, Shimizu C, Burns J, Wright V, Png E, Hibberd M, Lloyd D, Yang H, Telenti A, Bloss C, Fox D, Lauter K, Ohno-Machado L. PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinformatics 2016, 33: 871-878. PMID: 28065902, PMCID: PMC5860394, DOI: 10.1093/bioinformatics/btw758.Peer-Reviewed Original ResearchConceptsSoftware Guard ExtensionsHomomorphic encryptionDistributed ComputationCollaboration frameworkTrustworthy computationCollaboration modelSupplementary dataNetwork collaborationEncryptionExperimental resultsHealth informationAlternative solutionComputationInternational collaboration frameworkHardwareAccurate analysisPerformanceBioinformaticsImplementationFrameworkDataExtensionInformationCollaboration
2015
A 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
Privacy Preserving RBF Kernel Support Vector Machine
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy Preserving RBF Kernel Support Vector Machine. BioMed Research International 2014, 2014: 827371. PMID: 25013805, PMCID: PMC4071990, DOI: 10.1155/2014/827371.Peer-Reviewed Original ResearchConceptsPrivate dataPrivacy-preserving data disseminationKernel support vector machineRBF kernel support vector machinePublic dataSupport vector machineSupport vector machine modelVector machine modelData disseminationData sharingBiomedical dataPrivacy standardsVector machineRBF kernelPerformance metricsSVMMachine modelFull usePrivacyFinal outputSeparable caseAvailable informationMachineSharingMetricsMAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics 2014, 30: 2826-2827. PMID: 24907367, PMCID: PMC4173015, DOI: 10.1093/bioinformatics/btu377.Peer-Reviewed Original ResearchConceptsWeb servicesWeb reportsLarge input filesNovel feature extractionEnd performance improvementsExploration of resultsGPU infrastructureInteractive visualizationJavaScript frameworkParallel computingGPU devicesHypertext PreprocessorCUDA CFeature extractionDrop operationInput filesPlot generationSalient featuresPerformance improvementInfrastructureNodesServicesData analysisComputingBrowsermiRIAD—integrating microRNA inter- and intragenic data
Hinske L, França G, Torres H, Ohara D, Lopes-Ramos C, Heyn J, Reis L, Ohno-Machado L, Kreth S, Galante P. miRIAD—integrating microRNA inter- and intragenic data. Database 2014, 2014: bau099. PMID: 25288656, PMCID: PMC4186326, DOI: 10.1093/database/bau099.Peer-Reviewed Original ResearchConceptsProtein-coding genesIntragenic miRNAsHost genesGene expressionProtein-protein interaction dataSmall non-coding RNAsHost gene functionHost gene expressionMiRNA binding sitesNon-coding RNAsMajority of miRNAsGene functionGenomic contextFunctional annotationFunctional network analysisTarget mRNAsExpression correlationExonic regionsGenesMiRNAsDifferent tissuesInteraction dataBinding sitesGenomic classificationSilico validation
2013
DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique
Li P, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X. DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique. PLOS ONE 2013, 8: e80377. PMID: 24282536, PMCID: PMC3840021, DOI: 10.1371/journal.pone.0080377.Peer-Reviewed Original ResearchConceptsReference-free compressionDisk storage capacityCompression algorithmDecompression costData transferringArt algorithmsCompression performanceFile sizeGenome compressionCompression rateBit rateAlgorithmDNA compressionBiomedical researchersPerformance advantagesGenome dataModeling techniquesContextual modelImportant concernResearch purposesCompressionPerformanceStorage capacityBitsReference sequenceWebGLORE: a Web service for Grid LOgistic REgression
Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: a Web service for Grid LOgistic REgression. Bioinformatics 2013, 29: 3238-3240. PMID: 24072732, PMCID: PMC3842761, DOI: 10.1093/bioinformatics/btt559.Peer-Reviewed Original ResearchConceptsWeb servicesHypertext Transfer Protocol SecurePrivacy-preserving constructionFree Software FoundationGNU General Public LicenseUse web serviceFree web serviceGeneral Public LicenseDistributed datasetsTrusted serverProtocol SecureSoftware FoundationPublic LicensePHP technologyInformation exchangeBiomedical researchersLocal statisticsServicesServletsServerSecureAjaxGlobal logistic regression modelDatasetGlobal modelPrivacy Technology to Support Data Sharing for Comparative Effectiveness Research
Jiang X, Sarwate A, Ohno-Machado L. Privacy Technology to Support Data Sharing for Comparative Effectiveness Research. Medical Care 2013, 51: s58-s65. PMID: 23774511, PMCID: PMC3728160, DOI: 10.1097/mlr.0b013e31829b1d10.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsData sharingPrivacy-preserving data sharingPrivacy-preserving technologiesEffective data sharingPrivacy technologiesData miningNetwork dataData typesThird-party expertsData tablesSpecific scenariosSharingInappropriate disclosurePractical evaluationPractical impactPatient dataNew technologiesTechnologyPrivacyComparative effectiveness researchMiningPractical toolCER studiesTextTime series
2012
SHARE: system design and case studies for statistical health information release
Gardner J, Xiong L, Xiao Y, Gao J, Post A, Jiang X, Ohno-Machado L. SHARE: system design and case studies for statistical health information release. Journal Of The American Medical Informatics Association 2012, 20: 109-116. PMID: 23059729, PMCID: PMC3555328, DOI: 10.1136/amiajnl-2012-001032.Peer-Reviewed Original ResearchConceptsDifferential privacy frameworkPrivacy frameworkDifferential privacyMultidimensional histogramsReal medical datasetsMedical data warehouseOriginal data distributionInformation releaseHigh-dimensional dataBreast cancer datasetPattern queriesMedical datasetsElectronic medical record datasetHeterogeneous dataData warehouseUse casesElectronic health recordsMedical domainBiomedical dataThree-dimensional data cubeArt methodsData distributionMedical dataDimensional dataData cube
2011
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Kim J, Patel K, Jung H, Kuo W, Ohno-Machado L. AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics 2011, 12: 75. PMID: 21410990, PMCID: PMC3076267, DOI: 10.1186/1471-2105-12-75.Peer-Reviewed Original ResearchConfluence of Disciplines in Health Informatics: an International Perspective
Geissbuhler A, Kimura M, Kulikowski C, Murray P, Ohno-Machado L, Park H, Haux R. Confluence of Disciplines in Health Informatics: an International Perspective. Methods Of Information In Medicine 2011, 50: 545-555. PMID: 22146917, DOI: 10.3414/me11-06-0005.Commentaries, Editorials and LettersConceptsHealth informaticsCollaborative software developmentSoftware developmentConfluence of disciplinesUbiquitous healthcareHealth informatics expertsMobile technologyInformatics expertsDisaster situationsIntrinsic multidisciplinary natureSocial mediaInformaticsConvergence of disciplinesDiversity of contextsKey issuesSignificant challengeInformatics interventions
2010
DSGeo: Software tools for cross-platform analysis of gene expression data in GEO
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: Software tools for cross-platform analysis of gene expression data in GEO. Journal Of Biomedical Informatics 2010, 43: 709-715. PMID: 20435161, PMCID: PMC2934864, DOI: 10.1016/j.jbi.2010.04.007.Peer-Reviewed Original ResearchConceptsAggregation of dataData loaderRelational databaseGene expression dataUser preferencesData browserData browsingCross-platform dataSoftware toolsSeamless integrationCross-platform analysisGroups of dataQueriesExpression dataPublic gene expression dataSpecific sample characteristicsLarge resourcesBrowserToolBrowsingAnnotatingUsersRetrievalApplicationsPlatform
2009
Towards large-scale sample annotation in gene expression repositories
Pitzer E, Lacson R, Hinske C, Kim J, Galante P, Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics 2009, 10: s9. PMID: 19761579, PMCID: PMC2745696, DOI: 10.1186/1471-2105-10-s9-s9.Peer-Reviewed Original Research
2007
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
Galante P, Trimarchi J, Cepko C, de Souza S, Ohno-Machado L, Kuo W. Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data. Bioinformatics 2007, 23: 903-905. PMID: 17277333, DOI: 10.1093/bioinformatics/btm023.Peer-Reviewed Original Research
2006
Approximation properties of haplotype tagging
Vinterbo S, Dreiseitl S, Ohno-Machado L. Approximation properties of haplotype tagging. BMC Bioinformatics 2006, 7: 8. PMID: 16401341, PMCID: PMC1395335, DOI: 10.1186/1471-2105-7-8.Peer-Reviewed Original ResearchConceptsApproximation propertiesCombinatorial optimization problemsOptimization problemImplementable algorithmComputational effortSolution qualityTerms of complexitySimple algorithmSize m.Population membersSingle processor machineAlgorithmProblemAsymptoticsApproximationProcessor machineHaplotype taggingNPsUnique identification
2005
Monitoring Device Safety in Interventional Cardiology
Matheny M, Ohno-Machado L, Resnic F. Monitoring Device Safety in Interventional Cardiology. Journal Of The American Medical Informatics Association 2005, 13: 180-187. PMID: 16357356, PMCID: PMC1447549, DOI: 10.1197/jamia.m1908.Peer-Reviewed Original ResearchSmall, fuzzy and interpretable gene expression based classifiers
Vinterbo S, Kim E, Ohno-Machado L. Small, fuzzy and interpretable gene expression based classifiers. Bioinformatics 2005, 21: 1964-1970. PMID: 15661797, DOI: 10.1093/bioinformatics/bti287.Peer-Reviewed Original Research