2012
Selecting 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 ResearchMeSH KeywordsArea Under CurveBreast NeoplasmsFemaleGene ExpressionGene Expression ProfilingGenotypeHumansLogistic ModelsPhenotypePrognosisTranscriptome
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 Research
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 ResearchAssessing the quality of annotations in asthma gene expression experiments
Lacson R, Mbagwu M, Yousif H, Ohno-Machado L. Assessing the quality of annotations in asthma gene expression experiments. BMC Bioinformatics 2010, 11: s8. PMID: 21044366, PMCID: PMC2967749, DOI: 10.1186/1471-2105-11-s9-s8.Peer-Reviewed Original ResearchAsthmaDatabases, GeneticGene ExpressionGene Expression ProfilingHumansMolecular Sequence AnnotationResearch DesignDSGeo: 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 ResearchEvaluation of a large-scale biomedical data annotation initiative
Lacson R, Pitzer E, Hinske C, Galante P, Ohno-Machado L. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics 2009, 10: s10. PMID: 19761564, PMCID: PMC2745681, DOI: 10.1186/1471-2105-10-s9-s10.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyDatabases, GeneticGene Expression ProfilingInformation Storage and Retrieval
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, MessengerAngiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications
Hasina R, Whipple M, Martin L, Kuo W, Ohno-Machado L, Lingen M. Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications. Laboratory Investigation 2008, 88: 342-353. PMID: 18283272, PMCID: PMC2614382, DOI: 10.1038/labinvest.2008.6.Peer-Reviewed Original Research
2007
MODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS
STRANSKY B, BARRERA J, OHNO-MACHADO L, DE SOUZA S. MODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS. Journal Of Bioinformatics And Computational Biology 2007, 5: 977-986. PMID: 17787066, DOI: 10.1142/s0219720007002990.Peer-Reviewed Original ResearchComparison 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 toolAutomatic 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
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 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
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 StatementsConceptsNew algorithmSupervised learning modelUCI machineLearning modelMicroarray data analysisAlgorithmic developmentsTypes of dataMachineData setsMain challengesGene expression dataMain motivationAlgorithmData analysisBiomedical experimentsLarge numberExpression dataMicroarray dataResearchersRepositoryWebMicroarray experimentsNew waveDataSetMultivariate 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 Research