Featured Publications
Phosphoproteomic Screen Identifies Potential Therapeutic Targets in Melanoma
Tworkoski K, Singhal G, Szpakowski S, Zito CI, Bacchiocchi A, Muthusamy V, Bosenberg M, Krauthammer M, Halaban R, Stern DF. Phosphoproteomic Screen Identifies Potential Therapeutic Targets in Melanoma. Molecular Cancer Research 2011, 9: 801-812. PMID: 21521745, PMCID: PMC3117976, DOI: 10.1158/1541-7786.mcr-10-0512.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCell Line, TumorCell MovementCell ProliferationErbB ReceptorsGene Expression Regulation, NeoplasticGene Knockdown TechniquesHEK293 CellsHumansInfant, NewbornMelanocytesMelanomaPhosphoproteinsPhosphorylationProteomicsReceptor Protein-Tyrosine KinasesReceptor, IGF Type 2RNA, Small InterferingSignal TransductionSkin NeoplasmsSTAT3 Transcription FactorConceptsTherapeutic targetReceptor tyrosine kinasesMelanoma cellsPotential therapeutic targetIdentifies potential therapeutic targetsActive receptor tyrosine kinasesTyrosine kinaseMelanoma cell migrationReceptor expressionBreast cancerAxl knockdownAutocrine circuitTherapeutic interventionsCancer subtypesReceptor tyrosine kinase activationTyrosine kinase activationNovel targetActivated receptorsAxlRNA knockdownMelanomaCell migrationHER3KnockdownIGF1R
2017
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Klein MI, Stern DF, Zhao H. GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics 2017, 18: 317. PMID: 28651562, PMCID: PMC5485588, DOI: 10.1186/s12859-017-1711-z.Peer-Reviewed Original ResearchConceptsGene expression profilesExpression profilesIndividual gene expression profilesTissue-specific functionalityEnrichment-based methodsPathway scoresGene expression levelsBatch effectsPathway genesPresent genesPerturbed pathwaysPathway expressionExpression levelsIndividual samplesTissue typesPathwayGenesTCGA subtypesAbnormal pathwaysIndependent datasetsBreast cancer subtypesNon-competitive approachIndividual tumorsCancer subtypesGrapes