2018
A Novel Stakeholder Engagement Approach for Patient-centered Outcomes Research
Kim K, Khodyakov D, Marie K, Taras H, Meeker D, Campos H, Ohno-Machado L. A Novel Stakeholder Engagement Approach for Patient-centered Outcomes Research. Medical Care 2018, 56: s41-s47. PMID: 30074950, PMCID: PMC6143220, DOI: 10.1097/mlr.0000000000000790.Peer-Reviewed Original ResearchConceptsClinical Data Research NetworkPatient-centered outcomes researchEngagement of patientsOutcomes research studiesConditions of focusStakeholder advisory boardPatient-centered outcomes research studiesKawasaki diseaseHeart failurePatient advocatesPatientsClinical sitesOutcomes researchSignificant differencesHealth researchCliniciansResearch NetworkResearch prioritiesSetting of prioritiesEngagement strategiesAdvisory BoardFavorable opinionObesityEngagement principlesDisease
2017
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
Kim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.Peer-Reviewed Original ResearchConceptsWhole genome sequencesGenome-wide association studiesToll-like receptor 6Single nucleotide variantsCommon disease-rare variant hypothesisExpression quantitative trait loci (eQTL) analysisDifferential expressionQuantitative trait locus (QTL) analysisCommon disease–common variantPathogen-associated molecular pattern recognitionIntegrative genomics approachIntronic single nucleotide variantsComplex genetic diseasesSequence quality scoresMolecular pattern recognitionWhole-genome sequencingGenomic approachesTranscriptome dataGenome sequenceSequence variationLocus analysisGenome sequencingAssociation studiesFunction of genotypeNucleotide variants
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 ResearchMeSH KeywordsComputer SecurityGenetic Association StudiesGenomicsHumansMucocutaneous Lymph Node SyndromePrivacyRare DiseasesSoftwareConceptsSoftware Guard ExtensionsHomomorphic encryptionDistributed ComputationCollaboration frameworkTrustworthy computationCollaboration modelSupplementary dataNetwork collaborationEncryptionExperimental resultsHealth informationAlternative solutionComputationInternational collaboration frameworkHardwareAccurate analysisPerformanceBioinformaticsImplementationFrameworkDataExtensionInformationCollaborationBuilding a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes
Doan S, Maehara C, Chaparro J, Lu S, Liu R, Graham A, Berry E, Hsu C, Kanegaye J, Lloyd D, Ohno‐Machado L, Burns J, Tremoulet A, Group T. Building a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. Academic Emergency Medicine 2016, 23: 628-636. PMID: 26826020, PMCID: PMC5031359, DOI: 10.1111/acem.12925.Peer-Reviewed Original ResearchMeSH KeywordsChildData MiningElectronic Health RecordsEmergency Service, HospitalHumansMucocutaneous Lymph Node SyndromeNatural Language ProcessingSensitivity and SpecificityConceptsDiagnosis of KDKawasaki diseaseED notesHigh suspicionPediatric ED patientsSerious cardiac complicationsHigh clinical suspicionEmergency department patientsManual chart reviewCardiac complicationsChart reviewClinical suspicionFebrile illnessDepartment patientsED patientsElectronic health record systemsEmergency departmentClinical signsDiagnostic criteriaHealth record systemsPatientsClinical termsSuspicionDiagnosisRecord system
2013
Differential Expression of miR-145 in Children with Kawasaki Disease
Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau H, Akers J, Chen C, Kanegaye J, Tremoulet A, Ohno-Machado L, Burns J. Differential Expression of miR-145 in Children with Kawasaki Disease. PLOS ONE 2013, 8: e58159. PMID: 23483985, PMCID: PMC3590129, DOI: 10.1371/journal.pone.0058159.Peer-Reviewed Original ResearchMeSH KeywordsArteriesBase SequenceChildChild, PreschoolCluster AnalysisGene Expression RegulationHumansInfantMicroRNAsModels, BiologicalMolecular Sequence DataMucocutaneous Lymph Node SyndromeReal-Time Polymerase Chain ReactionSequence AlignmentSequence Analysis, DNASignal TransductionTransforming Growth Factor betaConceptsTGF-β pathwayGene expressionMiR-145Small non-coding RNAsKawasaki disease pathogenesisExtracellular vesiclesSmall RNA speciesPost-transcriptional levelDiscovery of microRNAsKawasaki diseaseNon-coding RNAsExpression of genesDisease pathogenesisSmall extracellular vesiclesSmall RNAsRNA speciesTarget genesTop pathwaysVascular smooth muscle cellsPathway analysisDifferentiation of neutrophilsDifferential expressionMicroRNAsArterial wallGeneration of myofibroblasts