2014
Differentially private distributed logistic regression using private and public data
Ji Z, Jiang X, Wang S, Xiong L, Ohno-Machado L. Differentially private distributed logistic regression using private and public data. BMC Medical Genomics 2014, 7: s14. PMID: 25079786, PMCID: PMC4101668, DOI: 10.1186/1755-8794-7-s1-s14.Peer-Reviewed Original ResearchMeSH KeywordsAccess to InformationAlgorithmsBreast NeoplasmsData MiningHumansLogistic ModelsMedical InformaticsPatient DischargePrivacyConceptsPrivate dataDifferential privacyPublic datasetsPublic dataRigorous privacy guaranteeData privacy researchPrivate data setsData mining modelsData setsProvable privacyPrivacy guaranteesMining modelPrivacy researchDifferent data setsArt frameworksMedical informaticsPrivacyAmount of noisePrivate methodsAuxiliary informationBetter utilityNew algorithmUpdate stepAvailable public dataAlgorithm
2012
Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration
Jiang X, Menon A, Wang S, Kim J, Ohno-Machado L. Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration. PLOS ONE 2012, 7: e48823. PMID: 23139819, PMCID: PMC3490990, DOI: 10.1371/journal.pone.0048823.Peer-Reviewed Original ResearchSelecting cases for whom additional tests can improve prognostication.
Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L. Selecting cases for whom additional tests can improve prognostication. AMIA Annual Symposium Proceedings 2012, 2012: 1260-8. PMID: 23304404, PMCID: PMC3540468.Peer-Reviewed Original ResearchSHARE: 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
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Galante P, Parmigiani R, Zhao Q, Caballero O, de Souza J, Navarro F, Gerber A, Nicolás M, Salim A, Silva A, Edsall L, Devalle S, Almeida L, Ye Z, Kuan S, Pinheiro D, Tojal I, Pedigoni R, de Sousa R, Oliveira T, de Paula M, Ohno-Machado L, Kirkness E, Levy S, da Silva W, Vasconcelos A, Ren B, Zago M, Strausberg R, Simpson A, de Souza S, Camargo A. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research 2011, 39: 6056-6068. PMID: 21493686, PMCID: PMC3152357, DOI: 10.1093/nar/gkr221.Peer-Reviewed Original ResearchConceptsTumor genomesSomatic alterationsProtein-protein interaction analysisSynonymous substitutionsKEGG analysisEndogenous mutagensGenomeTumorigenic transformationNucleotide substitutionsBreast tumor cell linesReplication errorsTumor cell linesGenetic alterationsFrequency of mutationsCell linesTumorigenesisMutationsSynergistic functionDistinct patternsInteraction analysisLymphoblastoidAlterationsGenesSame individualPathwayTwist1-Induced Invadopodia Formation Promotes Tumor Metastasis
Eckert M, Lwin T, Chang A, Kim J, Danis E, Ohno-Machado L, Yang J. Twist1-Induced Invadopodia Formation Promotes Tumor Metastasis. Cancer Cell 2011, 19: 372-386. PMID: 21397860, PMCID: PMC3072410, DOI: 10.1016/j.ccr.2011.01.036.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Vesicular TransportAnimalsBase SequenceBreast NeoplasmsCell LineCell Line, TumorCell MovementCell Surface ExtensionsElectrophoresis, Polyacrylamide GelEpithelial-Mesenchymal TransitionFemaleHEK293 CellsHumansMiceMice, NudeNeoplasm MetastasisNeoplasmsNuclear ProteinsReceptor, Platelet-Derived Growth Factor alphaReverse Transcriptase Polymerase Chain ReactionRNA InterferenceSignal TransductionSrc Homology DomainsTwist-Related Protein 1ConceptsInvadopodia formationTumor metastasisFormation of invadopodiaDirect transcriptional targetTwist1 transcription factorEMT-inducing signalsMatrix degradationPromotes Tumor MetastasisMembrane protrusionsExtracellular matrix degradationTranscriptional targetsTranscription factorsInvadopodiaPDGFRα expressionMesenchymal transitionTwist1Central mediatorPDGFRαKey functionsSnail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis
Casas E, Kim J, Bendesky A, Ohno-Machado L, Wolfe C, Yang J. Snail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis. Cancer Research 2011, 71: 245-254. PMID: 21199805, PMCID: PMC3025803, DOI: 10.1158/0008-5472.can-10-2330.Peer-Reviewed Original Research
2001
Finding appropriate clinical trials: evaluating encoded eligibility criteria with incomplete data.
Ash N, Ogunyemi O, Zeng Q, Ohno-Machado L. Finding appropriate clinical trials: evaluating encoded eligibility criteria with incomplete data. AMIA Annual Symposium Proceedings 2001, 27-31. PMID: 11825151, PMCID: PMC2243370.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremBreast NeoplasmsClinical ProtocolsClinical Trials as TopicComputer SystemsExpert SystemsHumansPatient Selection
1999
Decision support for clinical trial eligibility determination in breast cancer.
Ohno-Machado L, Wang S, Mar P, Boxwala A. Decision support for clinical trial eligibility determination in breast cancer. AMIA Annual Symposium Proceedings 1999, 340-4. PMID: 10566377, PMCID: PMC2232554.Peer-Reviewed Original ResearchConceptsClinical trial eligibility determinationPhysician Data Query databaseEligibility criteriaClinical trialsBreast cancerMetastatic breast cancerPrimary care providersClinical trial protocolTrial protocolFree-text eligibility criteriaCare providersClinical informationEligibility informationPatientsEligibility determinationPatient informationPhase IICancerTrialsOrder of likelihoodNumerical scoreCriteria
1998
Diagnosing breast cancer from FNAs: variable relevance in neural network and logistic regression models.
Ohno-Machado L, Bialek D. Diagnosing breast cancer from FNAs: variable relevance in neural network and logistic regression models. 1998, 52 Pt 1: 537-40. PMID: 10384515.Peer-Reviewed Original ResearchMeSH KeywordsAnalysis of VarianceBiopsy, NeedleBreast NeoplasmsFemaleHumansLogistic ModelsMultivariate AnalysisNeural Networks, Computer