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
2008
Improving calibration of logistic regression models by local estimates.
Osl M, Ohno-Machado L, Baumgartner C, Tilg B, Dreiseitl S. Improving calibration of logistic regression models by local estimates. AMIA Annual Symposium Proceedings 2008, 2008: 535-9. PMID: 18998878, PMCID: PMC2656048.Peer-Reviewed Original Research
2005
Small, 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
2004
The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer
Jaroszewicz S, Simovici D, Kuo W, Ohno-Machado L. The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer. IEEE Transactions On Biomedical Engineering 2004, 51: 1095-1102. PMID: 15248526, DOI: 10.1109/tbme.2004.827267.Peer-Reviewed Original ResearchGenomic Analysis of Mouse Retinal Development
Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo W, Weber G, Lee K, Fraioli R, Cho S, Yung R, Asch E, Ohno-Machado L, Wong W, Cepko C. Genomic Analysis of Mouse Retinal Development. PLOS Biology 2004, 2: e247. PMID: 15226823, PMCID: PMC439783, DOI: 10.1371/journal.pbio.0020247.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBromodeoxyuridineCell LineageChromosome MappingCluster AnalysisComputational BiologyDatabases, GeneticExpressed Sequence TagsGene Expression RegulationGene Expression Regulation, DevelopmentalGene LibraryGenomeIn Situ HybridizationInterneuronsMiceMitosisMolecular Sequence DataNeurogliaOpen Reading FramesRetinaRNA, MessengerStem CellsTime FactorsConceptsMitotic progenitor cellsRetinal cell typesGene expressionCell typesExpression patternsRetinal developmentDevelopmental gene expression patternsGene expression patternsMajor retinal cell typesOpen reading frameProgenitor cellsMüller gliaPhotoreceptor-enriched genesGene expression profilesMouse retinal developmentMajor cell typesRetinal disease genesGenomic analysisMultiple retinal cell typesChromosomal intervalMolecular atlasMultiple transcriptsReading frameTaxonomic classificationDisease genes
2003
A neural network-based similarity index for clustering DNA microarray data
Sawa T, Ohno-Machado L. A neural network-based similarity index for clustering DNA microarray data. Computers In Biology And Medicine 2003, 33: 1-15. PMID: 12485626, DOI: 10.1016/s0010-4825(02)00032-x.Peer-Reviewed Original Research
2002
Analysis of matched mRNA measurements from two different microarray technologies
Kuo W, Jenssen T, Butte A, Ohno-Machado L, Kohane I. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18: 405-412. PMID: 11934739, DOI: 10.1093/bioinformatics/18.3.405.Peer-Reviewed Original ResearchVisualization and evaluation of clusters for exploratory analysis of gene expression data
Kim J, Kohane I, Ohno-Machado L. Visualization and evaluation of clusters for exploratory analysis of gene expression data. Journal Of Biomedical Informatics 2002, 35: 25-36. PMID: 12415724, DOI: 10.1016/s1532-0464(02)00001-1.Peer-Reviewed Original ResearchConceptsClustering algorithmDifferent clustering algorithmsPopular clustering algorithmNew clustering algorithmComprehensive data visualizationGene expression data analysisData visualization strategiesExpression data analysisEvaluation of clustersData visualizationSoftware toolsCluster qualityCluster consistencyAlgorithmActual implementationData setsGene expression dataQuality measuresVisualizationPromising resultsFrameworkData analysisObjective evaluationUsersExpression data
2000
Unsupervised learning from complex data: the matrix incision tree algorithm.
Kim J, Ohno-Machado L, Kohane I. Unsupervised learning from complex data: the matrix incision tree algorithm. Biocomputing 2000, 30-41. PMID: 11262950, DOI: 10.1142/9789814447362_0004.Peer-Reviewed Original ResearchConceptsHigh-dimensional spaceTree algorithmComplex high-dimensional spacesPredictive model buildingData setsLarge-scale gene expression dataLow-dimensional spaceKnowledge discoveryUnsupervised learningData structureComplex dataNovel methodMeaningful structuresMicroarray data setsDNA microarray data setsAlgorithm