2023
A Synthetic Data Integration Framework to Leverage External Summary-Level Information from Heterogeneous Populations
Gu T, Taylor J, Mukherjee B. A Synthetic Data Integration Framework to Leverage External Summary-Level Information from Heterogeneous Populations. Biometrics 2023, 79: 3831-3845. PMID: 36876883, PMCID: PMC10480346, DOI: 10.1111/biom.13852.Peer-Reviewed Original ResearchConceptsCovariate effectsStatistical inferenceHeterogeneity of covariate effectsRegression coefficient estimatesSummary-level informationImprove statistical inferenceInternational studiesOutcome YCovariate informationData integration frameworkStatistical efficiencyCoefficient estimatesPartial informationExternal populationGeneral frameworkIndividual-level dataRisk prediction modelExternal modelPrediction problemInternational study populationMultiple imputation
2022
Predicting cumulative lead (Pb) exposure using the Super Learner algorithm
Wang X, Bakulski K, Mukherjee B, Hu H, Park S. Predicting cumulative lead (Pb) exposure using the Super Learner algorithm. Chemosphere 2022, 311: 137125. PMID: 36347347, PMCID: PMC10160242, DOI: 10.1016/j.chemosphere.2022.137125.Peer-Reviewed Original ResearchConceptsPatella leadNational Health and Nutrition Examination SurveyHealth and Nutrition Examination SurveyNutrition Examination SurveyLong-term health effectsPopulation-based studyK-shell X-ray fluorescenceNormative Aging StudyCumulative lead exposureEvaluate health effectsExamination SurveyLead concentrationsBone lead measurementsAging StudyTibia leadPositive associationStudy populationHealth effectsRegression-based predictive modelBone lead concentrationsBlood pressureFlexible machine learning approachCorrelation coefficientX-ray fluorescence techniqueLead measurements
2021
Bayesian hierarchical models for high‐dimensional mediation analysis with coordinated selection of correlated mediators
Song Y, Zhou X, Kang J, Aung M, Zhang M, Zhao W, Needham B, Kardia S, Liu Y, Meeker J, Smith J, Mukherjee B. Bayesian hierarchical models for high‐dimensional mediation analysis with coordinated selection of correlated mediators. Statistics In Medicine 2021, 40: 6038-6056. PMID: 34404112, PMCID: PMC9257993, DOI: 10.1002/sim.9168.Peer-Reviewed Original Research
2018
Selection of nonlinear interactions by a forward stepwise algorithm: Application to identifying environmental chemical mixtures affecting health outcomes
Narisetty N, Mukherjee B, Chen Y, Gonzalez R, Meeker J. Selection of nonlinear interactions by a forward stepwise algorithm: Application to identifying environmental chemical mixtures affecting health outcomes. Statistics In Medicine 2018, 38: 1582-1600. PMID: 30586682, PMCID: PMC7134269, DOI: 10.1002/sim.8059.Peer-Reviewed Original Research
2017
Complete hazard ranking to analyze right-censored data: An ALS survival study
Huang Z, Zhang H, Boss J, Goutman S, Mukherjee B, Dinov I, Guan Y, . Complete hazard ranking to analyze right-censored data: An ALS survival study. PLOS Computational Biology 2017, 13: e1005887. PMID: 29253881, PMCID: PMC5749893, DOI: 10.1371/journal.pcbi.1005887.Peer-Reviewed Original Research
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
2010
Missing Exposure Data in Stereotype Regression Model: Application to Matched Case–Control Study with Disease Subclassification
Ahn J, Mukherjee B, Gruber S, Sinha S. Missing Exposure Data in Stereotype Regression Model: Application to Matched Case–Control Study with Disease Subclassification. Biometrics 2010, 67: 546-558. PMID: 20560931, PMCID: PMC3119773, DOI: 10.1111/j.1541-0420.2010.01453.x.Peer-Reviewed Original ResearchConceptsStereotype regression modelSubtypes of casesDeletion of observationsExpectation/conditional maximization algorithmBaseline category logit modelEstimation of model parametersMissingness mechanismData mechanismCase-control dataProportional oddsBayesian approachCategorical responsesCase-control studyCase-control study of colorectal cancerMissingnessMaximization algorithmCategorical outcomesMonte CarloModel assumptionsRegression modelsStudy of colorectal cancerModel parametersNonidentifiabilityDisease subclassificationMultinomial logit model
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
2008
Inference of the Haplotype Effect in a Matched Case-Control Study Using Unphased Genotype Data
Sinha S, Gruber S, Mukherjee B, Rennert G. Inference of the Haplotype Effect in a Matched Case-Control Study Using Unphased Genotype Data. The International Journal Of Biostatistics 2008, 4: article 6. PMID: 20231916, PMCID: PMC2835450, DOI: 10.2202/1557-4679.1079.Peer-Reviewed Original ResearchConceptsCase-control studyUnphased genotype dataHardy-Weinberg equilibriumLocus-specific genotype dataGenotype dataBeta-Carotene Cancer Prevention StudyCancer Prevention StudyCase-control study designStudy of breast cancer patientsMatched case-control studyCase-control designPhasing of haplotypesDisease risk modelsBreast cancer patientsPrevention StudyHaplotype effectsStudy designGametic phasePolymorphic lociHaplotype frequenciesCancer patientsLociConditional likelihood approachAssociationHaplotypes
2006
A Score Test for Determining Sample Size in Matched Case‐Control Studies with Categorical Exposure
Sinha S, Mukherjee B. A Score Test for Determining Sample Size in Matched Case‐Control Studies with Categorical Exposure. Biometrical Journal 2006, 48: 35-53. PMID: 16544811, DOI: 10.1002/bimj.200510200.Peer-Reviewed Original ResearchConceptsCase-control studyCategorical exposureMatched case-control studyScore testDichotomous exposureNull hypothesisExposure variablesOdds ratioNatural orderDisease-gene associationsMatched setsDisease riskColorectal cancerPower functionSample sizeAssociationOddsGeneralizationDiseaseSetsScoresEstimationExposureStudyRisk
2004
Bayesian Semiparametric Modeling for Matched Case–Control Studies with Multiple Disease States
Sinha S, Mukherjee B, Ghosh M. Bayesian Semiparametric Modeling for Matched Case–Control Studies with Multiple Disease States. Biometrics 2004, 60: 41-49. PMID: 15032772, DOI: 10.1111/j.0006-341x.2004.00169.x.Peer-Reviewed Original ResearchConceptsSemiparametric Bayesian frameworkBayesian semiparametric modelSemiparametric modelDirichlet processStratum effectsConditional likelihoodProbability of disease developmentBayesian approachNumerical integration schemeBayesian frameworkSample sizeDirichletActual estimationMLEMissingnessMarkovIntegration schemeExposure distributionBayesianEstimationRegression modelsMultiple disease statesDistributionProbabilityDisease states