2020
Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis
Brown K, Diez-Roux A, Smith J, Needham B, Mukherjee B, Ware E, Liu Y, Cole S, Seeman T, Kardia S. Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis. Psychoneuroendocrinology 2020, 117: 104654. PMID: 32387875, PMCID: PMC7685527, DOI: 10.1016/j.psyneuen.2020.104654.Peer-Reviewed Original ResearchConceptsGene expressionMulti-Ethnic Study of AtherosclerosisGene set enrichment testGene Ontology databaseGene expression dataMulti-Ethnic StudyLifetime discriminationStudy of AtherosclerosisDifferential gene expressionInflammation-related genesExpression dataGene setsChronic burdenSocial factorsGene transcriptionRelated gene expressionOntology databaseGenesInflammatory responseTranscriptionGlobal analysisElastic net penalized regressionAdverse social factorsGlobal expressionExpression of inflammation-related genes
2012
Incorporating auxiliary information for improved prediction in high-dimensional datasets: an ensemble of shrinkage approaches
Boonstra P, Taylor J, Mukherjee B. Incorporating auxiliary information for improved prediction in high-dimensional datasets: an ensemble of shrinkage approaches. Biostatistics 2012, 14: 259-272. PMID: 23087411, PMCID: PMC3590922, DOI: 10.1093/biostatistics/kxs036.Peer-Reviewed Original ResearchConceptsHigh-dimensional datasetsAuxiliary informationRidge estimatorBayesian alternativeOutcome YSimulation studyEstimates of BShrinkage approachBiological processesRidge regressionGene expression datasetsDatasetGenomic technologiesMicroarray technologyOptimal choiceBalance efficiencyX.EstimationPrediction errorPolymerase chain reactionBiological phenomenaInformationTechnologyQuantitative real-time polymerase chain reaction
2011
MRE11 Deficiency Increases Sensitivity to Poly(ADP-ribose) Polymerase Inhibition in Microsatellite Unstable Colorectal Cancers
Vilar E, Bartnik C, Stenzel S, Raskin L, Ahn J, Moreno V, Mukherjee B, Iniesta M, Morgan M, Rennert G, Gruber S. MRE11 Deficiency Increases Sensitivity to Poly(ADP-ribose) Polymerase Inhibition in Microsatellite Unstable Colorectal Cancers. Cancer Research 2011, 71: 2632-2642. PMID: 21300766, PMCID: PMC3407272, DOI: 10.1158/0008-5472.can-10-1120.Peer-Reviewed Original ResearchMeSH KeywordsAcid Anhydride HydrolasesBenzimidazolesCell Line, TumorColorectal NeoplasmsDNA DamageDNA Repair EnzymesDNA-Binding ProteinsEnzyme InhibitorsGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockdown TechniquesHumansMicrosatellite InstabilityMRE11 Homologue ProteinMutationPoly (ADP-Ribose) Polymerase-1Poly(ADP-ribose) Polymerase InhibitorsPoly(ADP-ribose) PolymerasesRad51 RecombinaseRecombination, GeneticConceptsPoly(ADP-riboseDouble strand breaksColorectal cancer cell linesPARP-1 inhibitionCell linesPARP-1ABT-888PARP-1 inhibitorsColorectal cancerPoly(ADP-ribose) polymeraseRepetitive DNA sequencesWild-type cell linesMSI cell linesMicrosatellite instabilityConcept of synthetic lethalityMicrosatellite instability colorectal tumorsSensitivity to poly(ADP-riboseMutant Mre11Short hairpin RNAPoly(ADP-ribose) polymerase inhibitionDNA sequencesDNA mismatch repairCell line modelsSecondary to mutationsSynthetic lethality
2009
Gene Expression Patterns in Mismatch Repair-Deficient Colorectal Cancers Highlight the Potential Therapeutic Role of Inhibitors of the Phosphatidylinositol 3-Kinase-AKT-Mammalian Target of Rapamycin Pathway
Vilar E, Mukherjee B, Kuick R, Raskin L, Misek D, Taylor J, Giordano T, Hanash S, Fearon E, Rennert G, Gruber S. Gene Expression Patterns in Mismatch Repair-Deficient Colorectal Cancers Highlight the Potential Therapeutic Role of Inhibitors of the Phosphatidylinositol 3-Kinase-AKT-Mammalian Target of Rapamycin Pathway. Clinical Cancer Research 2009, 15: 2829-2839. PMID: 19351759, PMCID: PMC3425357, DOI: 10.1158/1078-0432.ccr-08-2432.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAntineoplastic AgentsBenzoquinonesCell CycleCell Line, TumorChromonesColorectal NeoplasmsComputational BiologyDNA Mismatch RepairDrug Evaluation, PreclinicalEnzyme InhibitorsGene Expression ProfilingHumansHydroxamic AcidsImmunosuppressive AgentsLactams, MacrocyclicMicrosatellite InstabilityMorpholinesPhosphoinositide-3 Kinase InhibitorsProto-Oncogene Proteins c-aktSirolimusConceptsGene expression informationColorectal cancerCell linesExpression informationGene expression dataSystems biology toolsLY-294002Gene expression patternsLow molecular weight compoundsPhosphatidylinositol 3-kinase-Akt-mammalian target of rapamycin pathwayMutant cellsBioinformatics approachTarget of rapamycin pathwayExpression dataMismatch repair-deficient colorectal cancerMolecular weight compoundsGroup of patientsCell cycleBiology toolsApoptosis effectExpression patternsPotential therapeutic roleTrichostatin AMSI-HWeight compounds