2021
Identifying modules of cooperating cancer drivers
Klein MI, Cannataro VL, Townsend JP, Newman S, Stern DF, Zhao H. Identifying modules of cooperating cancer drivers. Molecular Systems Biology 2021, 17: msb20209810. PMID: 33769711, PMCID: PMC7995435, DOI: 10.15252/msb.20209810.Peer-Reviewed Original ResearchConceptsCancer typesNRAS-mutant melanomaCombination of alterationsMultiple cancer typesClinical outcomesNFE2L2 mutationsIndividual patientsDriver alterationsEffective personalized treatmentPathway inhibitionTherapeutic potentialCancer etiologyPersonalized treatmentTumor formationTCGA cancer typesAlterationsPatientsCancer driversEtiologyMelanomaCancer
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
2016
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data
Huang X, Stern DF, Zhao H. Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data. Scientific Reports 2016, 6: 20567. PMID: 26837275, PMCID: PMC4738355, DOI: 10.1038/srep20567.Peer-Reviewed Original ResearchConceptsPatient survivalTumor cell contaminationField cancerization effectNormal samplesCancer patient survivalNormal tissue samplesSitu immunizationCancer Genome AtlasCancer patientsPatient progressionNormal controlsTumorsNormal tissuesPan-cancer dataTissue samplesGenome AtlasCancer studiesDisease etiologyCell contaminationPatientsPathway analysisTCGA pan-cancer dataSurvivalTranscriptional profilesPotential benefits
2005
Phosphoproteomics for oncology discovery and treatment
Stern DF. Phosphoproteomics for oncology discovery and treatment. Expert Opinion On Therapeutic Targets 2005, 9: 851-860. PMID: 16083347, DOI: 10.1517/14728222.9.4.851.Peer-Reviewed Original ResearchConceptsPhosphoproteomic analysisProtein phosphorylationReversible protein phosphorylationSignal transduction pathwaysCellular regulationProtein kinaseTransduction pathwaysHuman cancersDevelopment of drugsPathwayPhosphorylationGood targetImportant insightsCancer therapyCancer drugsPhosphoproteomicsCellsIndividual tumorsPowerful toolKinaseRegulationIntermediary levelDiscoveryTargetIdentification
2001
Phosphoproteomics
Stern D. Phosphoproteomics. Experimental And Molecular Pathology 2001, 70: 327-331. PMID: 11418011, DOI: 10.1006/exmp.2001.2370.Peer-Reviewed Original Research
1994
The biology of erbB-2/nue/HER-2 and its role in cancer
Hynes N, Stern D. The biology of erbB-2/nue/HER-2 and its role in cancer. Biochimica Et Biophysica Acta 1994, 1198: 165-184. PMID: 7819273, DOI: 10.1016/0304-419x(94)90012-4.Peer-Reviewed Original Research