2015
Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data
Kroll J, Kim J, Ohno-Machado L, de Souza S. Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. PeerJ 2015, 3: e1419. PMID: 26618088, PMCID: PMC4655094, DOI: 10.7717/peerj.1419.Peer-Reviewed Original ResearchAlternative splicing eventsSequencing dataAlternative splicing analysisNext-generation DNA sequencing technologiesTranscriptome sequencing dataUCSC Genome BrowserDNA sequencing technologiesRNA-seq dataNext-generation sequencing dataDNA sequencing platformsSoftware suiteHuman Body MapEukaryotic speciesSplicing eventsTranscriptome dataGene coordinatesSplicing analysisGenome browserUNIX-like systemsNext-generation DNA sequencing platformsSequencing technologiesBioinformatics skillsAvailable speciesExpression profilesBioinformatics background
2010
TGF-beta1 interactome: metastasis and beyond.
Perera M, Tsang C, Distel R, Lacy J, Ohno-Machado L, Ricchiuti V, Samaranayake L, Smejkal G, Smith M, Trachtenberg A, Kuo W. TGF-beta1 interactome: metastasis and beyond. Cancer Genomics & Proteomics 2010, 7: 217-29. PMID: 20656987.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsDifferential expression profilesCancer therapeuticsPersonalized cancer therapeuticsRegulation of tumorEffective cancer therapeuticsNovel cancer biomarkersGenomic dataExpression profilesMetastatic attributesInteractomeUbiquitous cytokineTumor progressionCancer biomarkersPolarity changeTherapeuticsValuable insightsImmense valueRegulationInsightsInducerImportant stepMappingGrowth
2004
Deciphering 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 StatementsConceptsGene 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
Classification 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 ResearchConceptsGene 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 algorithmsCarcinomaMalignancy