2012
SPLOOCE
Kroll J, Galante P, Ohara D, Navarro F, Ohno-Machado L, de Souza S. SPLOOCE. RNA Biology 2012, 9: 1339-1343. PMID: 23064119, PMCID: PMC3597574, DOI: 10.4161/rna.22182.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingComputational BiologyDatabases, Nucleic AcidHumansInternetOligonucleotide Array Sequence AnalysisRNA Splice Sites
2011
A Primer on the Current State of Microarray Technologies
Trachtenberg A, Robert J, Abdalla A, Fraser A, He S, Lacy J, Rivas-Morello C, Truong A, Hardiman G, Ohno-Machado L, Liu F, Hovig E, Kuo W. A Primer on the Current State of Microarray Technologies. Methods In Molecular Biology 2011, 802: 3-17. PMID: 22130870, DOI: 10.1007/978-1-61779-400-1_1.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsDatabases, Nucleic AcidDNA PrimersEquipment DesignFluorescent DyesGene Expression ProfilingHumansOligonucleotide Array Sequence AnalysisConceptsMicroarray technologyGenome-wide gene expression studiesAvailability of microarraysVariety of genesThousands of genesDNA microarray technologyDisease-specific genesGene expression studiesGene discoveryMolecular functioningExpression studiesGene expressionMolecular geneticsGenesComputer science analysisMicroarrayComplicated networkDisease statesDrug developmentNormal functioningMassive levelsDisease diagnosisGeneticsField of microarraysHigh levelsAnyExpress: 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 ResearchMeSH KeywordsAlgorithmsGene Expression ProfilingHumansOligonucleotide Array Sequence AnalysisSoftware
2010
Effect of data combination on predictive modeling: a study using gene expression data.
Osl M, Dreiseitl S, Kim J, Patel K, Baumgartner C, Ohno-Machado L. Effect of data combination on predictive modeling: a study using gene expression data. AMIA Annual Symposium Proceedings 2010, 2010: 567-71. PMID: 21347042, PMCID: PMC3041313.Peer-Reviewed Original Research
2008
Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses
Fu S, Zhao H, Shi J, Abzhanov A, Crawford K, Ohno-Machado L, Zhou J, Du Y, Kuo W, Zhang J, Jiang M, Jin J. Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses. BMC Genomics 2008, 9: 369. PMID: 18673543, PMCID: PMC2529314, DOI: 10.1186/1471-2164-9-369.Peer-Reviewed Original ResearchMeSH KeywordsAdultAtherosclerosisFemoral ArteryGene Expression ProfilingGene Expression RegulationGenes, MHC Class IIHumansInflammationMaleMiddle AgedOligonucleotide Array Sequence AnalysisPeripheral Vascular DiseasesReverse Transcriptase Polymerase Chain ReactionTranscription, GeneticUp-RegulationVasculitisConceptsAdvanced lesionsInflammatory responseDisease progressionArterial diseaseGene OntologyIntermediate lesionsInflammatory genesGenome-wide gene expression profilingReal-time RT-PCR validationGlobal gene expression analysisToll-like receptor signalingBackgroundPeripheral arterial diseaseFemoral artery samplesSignificant cardiovascular morbidityNatural killer cellsFalse discovery rateNormal femoral arteryRT-PCR validationGene expression analysisGene expression profilingAffymetrix microarray platformCardiovascular morbidityKiller cellsFemoral arteryKyoto EncyclopediaValidation of oligoarrays for quantitative exploration of the transcriptome
Nygaard V, Liu F, Holden M, Kuo W, Trimarchi J, Ohno-Machado L, Cepko C, Frigessi A, Glad I, van de Wiel M, Hovig E, Lyng H. Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 2008, 9: 258. PMID: 18513391, PMCID: PMC2430212, DOI: 10.1186/1471-2164-9-258.Peer-Reviewed Original ResearchAnimalsExpressed Sequence TagsGene Expression ProfilingMiceOligonucleotide Array Sequence AnalysisRetinaRNA, Messenger
2007
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
Liu F, Jenssen T, Trimarchi J, Punzo C, Cepko C, Ohno-Machado L, Hovig E, Patrick Kuo W. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007, 8: 153. PMID: 17555589, PMCID: PMC1899500, DOI: 10.1186/1471-2164-8-153.Peer-Reviewed Original ResearchMeSH KeywordsAnalysis of VarianceAnimalsGene Expression ProfilingGene LibraryMiceMice, Inbred C57BLNucleic Acid HybridizationOligonucleotide Array Sequence AnalysisSequence Analysis, DNAConceptsDNA microarray platformMicroarray platformSequencing-based approachesSequencing-based technologiesGene expression technologyGene expression profilingTranscriptome profilingBiological replicatesExpression profilingExpression technologyGene expressionDifferential expressionBiomarker discoveryProfilingExpressionMicroarrayImportant tool
2006
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
Kuo W, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple M, Maysuria M, Serikawa K, Lee S, McCrann D, Kang J, Shearstone J, Burke J, Park D, Wang X, Rector T, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim J, Short G, Freeman M, Seed B, Jensen R, Church G, Hovig E, Cepko C, Park P, Ohno-Machado L, Jenssen T. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotechnology 2006, 24: 832-840. PMID: 16823376, DOI: 10.1038/nbt1217.Peer-Reviewed Original ResearchChromosome MappingDNA ProbesGene Expression ProfilingMicroarray AnalysisOligonucleotide Array Sequence AnalysisReproducibility of Results
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 ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceBiomarkers, TumorCluster AnalysisFuzzy LogicGene Expression ProfilingHumansNeoplasm ProteinsNeoplasmsOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedSoftware
2004
A primer on gene expression and microarrays for machine learning researchers
Kuo W, Kim E, Trimarchi J, Jenssen T, Vinterbo S, Ohno-Machado L. A primer on gene expression and microarrays for machine learning researchers. Journal Of Biomedical Informatics 2004, 37: 293-303. PMID: 15465482, DOI: 10.1016/j.jbi.2004.07.002.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAlgorithmsArtificial IntelligenceComputational BiologyGene Expression ProfilingGene Expression RegulationHumansModels, BiologicalOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedResearch DesignConceptsNew algorithmSupervised learning modelUCI machineLearning modelMicroarray data analysisAlgorithmic developmentsTypes of dataMachineData setsMain challengesGene expression dataMain motivationAlgorithmData analysisBiomedical experimentsLarge numberExpression dataMicroarray dataResearchersRepositoryWebMicroarray experimentsNew waveDataSetThe 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 ResearchMeSH KeywordsAlgorithmsCluster AnalysisDiagnosis, Computer-AssistedGenetic TestingHumansNeoplasmsOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificityMultivariate selection of genetic markers in diagnostic classification
Weber G, Vinterbo S, Ohno-Machado L. Multivariate selection of genetic markers in diagnostic classification. Artificial Intelligence In Medicine 2004, 31: 155-167. PMID: 15219292, DOI: 10.1016/j.artmed.2004.01.011.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceDiagnosisDiagnosis, DifferentialGene Expression ProfilingGenetic MarkersHumansMultivariate AnalysisOligonucleotide Array Sequence AnalysisConceptsClassification performanceBetter classification performanceLogistic regression algorithmUser-friendly implementationDifferent data setsSophisticated algorithmsRegression algorithmAlgorithmNew algorithmParticular classificationUnivariate algorithmsData setsGene expression dataClassificationNumber of variablesGene selectionSetInternetExpression dataNew setViable choiceMachinePerformanceImplementationSelectionDeciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine
Kuo W, Whipple M, Epstein J, Jenssen T, Santos G, Ohno-Machado L, Sonis S. Deciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine. Oral Surgery Oral Medicine Oral Pathology And Oral Radiology 2004, 97: 584-591. PMID: 15153870, DOI: 10.1016/j.tripleo.2003.11.016.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsBiomarkersGene Expression ProfilingGenesHumansMouth DiseasesOligonucleotide Array Sequence AnalysisOral MedicinePrognosisConceptsGene expression profilesTranscriptional mappingDNA microarraysExpression profilesGenome-wide monitoringThousands of genesApplication of microarraysTypical microarray experimentTranscription levelsBiological processesGenetic changesMicroarray technologyMicroarray experimentsDiseased cellsMicroarrayRelative expressionDisease etiologyNew therapeutic toolsWidespread hopeCellsGenesNew biomarkersTherapeutic toolExpressionDiscovery
2003
An Epicurean learning approach to gene-expression data classification
Albrecht A, Vinterbo S, Ohno-Machado L. An Epicurean learning approach to gene-expression data classification. Artificial Intelligence In Medicine 2003, 28: 75-87. PMID: 12850314, DOI: 10.1016/s0933-3657(03)00036-8.Peer-Reviewed Original ResearchMicroarrays and clinical dentistry
Kuo W, Whipple M, Jenssen T, Todd R, Epstein J, Ohno-Machado L, Sonis S, Park P. Microarrays and clinical dentistry. The Journal Of The American Dental Association 2003, 134: 456-462. PMID: 12733779, DOI: 10.14219/jada.archive.2003.0195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAnti-Bacterial AgentsDisease ProgressionGene Expression ProfilingGenetic VariationGenotypeHuman Genome ProjectHumansMouth DiseasesMouth NeoplasmsOligonucleotide Array Sequence AnalysisPrecancerous ConditionsProteinsRNA, MessengerTooth DiseasesConceptsAdvanced microarray technologiesEntire human genomeActivity of genesGene expression patternsHuman Genome ProjectGenome levelHuman genomeGenetic approachesCellular developmentDNA sequencesGenome ProjectExciting biologyCandidate genesExpression patternsMicroarray technologyMicroarrayNumber of cancersGenesMolecular profileAnalysis of diseasesMolecular behaviorGenomeBiologyTissue samplesProteinClassification and identification of genes associated with oral cancer based on gene expression profiles. A preliminary study.
Kuo W, Hasina R, Ohno-Machado L, Lingen M. Classification and identification of genes associated with oral cancer based on gene expression profiles. A preliminary study. Dental Journal 2003, 69: 23-6. PMID: 12703240.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Squamous CellGene Expression ProfilingGene Expression Regulation, NeoplasticHuman Genome ProjectHumansMatched-Pair AnalysisMouth NeoplasmsOligonucleotide Array Sequence AnalysisConceptsGene expression profilesHuman Genome ProjectOral squamous cell carcinomaExpression profilesIdentification of genesGenome ProjectDNA microarraysMolecular networksFive-year survival rateSquamous cell carcinomaCurrent treatment strategiesGenesAggressive malignancyCell carcinomaOral cancerPreliminary studyTreatment strategiesCytologic changesEarly diagnosisSurvival rateCancerMicroarrayStatistical algorithmsCarcinomaMalignancyA 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
Gene expression profiling by DNA microarrays and its application to dental research
Kuo W, Whipple M, Sonis S, Ohno-Machado L, Jenssen T. Gene expression profiling by DNA microarrays and its application to dental research. Oral Oncology 2002, 38: 650-656. PMID: 12353490, DOI: 10.1016/s1368-8375(02)00013-1.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsCarcinoma, Squamous CellComputational BiologyDental ResearchDNA, CircularGene Expression ProfilingHead and Neck NeoplasmsHumansIn Situ HybridizationMouth NeoplasmsOligonucleotide Array Sequence AnalysisOligonucleotidesRNA, MessengerConceptsGenome-wide gene expression studiesMicroarray technologyThousands of genesVariety of genesDNA microarray technologyGene expression studiesDisease-specific genesGene expression profilingGenetic profileGene discoveryMolecular functioningSpecific genesExpression profilingDNA microarraysExpression studiesMolecular geneticsIncorporation of DNAGenesIndividual patient's genetic profileDNAComplicated networkDisease statesDrug developmentNormal functioningMRNA expressionAnalysis 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 ResearchMeSH KeywordsAlgorithmsCell CycleCluster AnalysisComputational BiologyData Interpretation, StatisticalDatabases, FactualFibroblastsGene Expression ProfilingHumansIris PlantLeukemiaOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeConceptsClustering 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