Featured Publications
Methods for mediation analysis with high-dimensional DNA methylation data: Possible choices and comparisons
Clark-Boucher D, Zhou X, Du J, Liu Y, Needham B, Smith J, Mukherjee B. Methods for mediation analysis with high-dimensional DNA methylation data: Possible choices and comparisons. PLOS Genetics 2023, 19: e1011022. PMID: 37934796, PMCID: PMC10655967, DOI: 10.1371/journal.pgen.1011022.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremDNA MethylationEnvironmental ExposureHumansLinear ModelsMediation AnalysisConceptsBayesian Sparse Linear Mixed ModelMediation analysisHigh-dimensional mediation analysisMulti-ethnic cohortEpigenetic researchHealth outcomesHigh-dimensional DNA methylation dataLinear mixed modelsDNA methylation dataContinuous outcomesEvaluate DNA methylationDNA methylationMethylation dataDNAm dataMixed modelsDiverse simulationsSeamless implementationModern statistical methodsMediation effectR packageUnited StatesOutcomes
2021
Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI)
Aung M, Bakulski K, Feinberg J, Dou J, Meeker J, Mukherjee B, Loch-Caruso R, Ladd-Acosta C, Volk H, Croen L, Hertz-Picciotto I, Newschaffer C, Fallin M. Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI). Epigenetics 2021, 17: 253-268. PMID: 33794742, PMCID: PMC8920182, DOI: 10.1080/15592294.2021.1897059.Peer-Reviewed Original ResearchConceptsBlood metal concentrationsDNA methylation sitesDNA methylationMetal concentrationsWhole blood DNA methylationK arrayMethylation sitesBlood DNA methylationIllumina 450K arrayGene ontology analysisPotential biomarkers of exposurePrenatal metal exposureCellular metabolic pathwaysDownstream gene pathwaysCell type compositionCalcium ion bindingEarly Autism Risk Longitudinal InvestigationBiomarkers of exposureInductively coupled plasma mass spectrometryNervous system developmentAssociated with hypermethylationMetal exposureIndividual metalsPlasma mass spectrometryOntology analysis
2019
Bayesian Shrinkage Estimation of High Dimensional Causal Mediation Effects in Omics Studies
Song Y, Zhou X, Zhang M, Zhao W, Liu Y, Kardia S, Roux A, Needham B, Smith J, Mukherjee B. Bayesian Shrinkage Estimation of High Dimensional Causal Mediation Effects in Omics Studies. Biometrics 2019, 76: 700-710. PMID: 31733066, PMCID: PMC7228845, DOI: 10.1111/biom.13189.Peer-Reviewed Original ResearchConceptsMediation analysisEffect of socioeconomic statusPotential mediatorsMulti-Ethnic StudyCausal mediation analysisCardiometabolic outcomesDNA methylation regionsSocioeconomic statusHigh-throughput technologiesMediation effectGenomic dataEpidemiological dataMethylation regionsHigh-dimensional mediatorsBayesian inference methodsContinuous shrinkage priorsHigh-dimensional settingsBayesian shrinkage estimatorsJoint analysisOutcomesShrinkage priorsPathwayNull caseInference methodsBiomedical studiesTargeted Assessment of G0S2 Methylation Identifies a Rapidly Recurrent, Routinely Fatal Molecular Subtype of Adrenocortical Carcinoma
Mohan D, Lerario A, Else T, Mukherjee B, Almeida M, Vinco M, Rege J, Mariani B, Zerbini M, Mendonca B, Latronico A, Marie S, Rainey W, Giordano T, Fragoso M, Hammer G. Targeted Assessment of G0S2 Methylation Identifies a Rapidly Recurrent, Routinely Fatal Molecular Subtype of Adrenocortical Carcinoma. Clinical Cancer Research 2019, 25: 3276-3288. PMID: 30770352, PMCID: PMC7117545, DOI: 10.1158/1078-0432.ccr-18-2693.Peer-Reviewed Original ResearchConceptsUpregulation of cell cycleDNA damage response programsAdrenocortical carcinomaTargeted bisulfite sequencingCancer Genome Atlas projectBisulfite sequencingCpG island hypermethylation phenotypeHypermethylation phenotypeAggressive adrenocortical carcinomasCell cycleMolecular markersBiological processesHypermethylationMolecular diagnosticsShorter disease-freeCancers of patientsBiomarker methylationAtlas projectEfficacious adjuvant therapyLocoregional diseaseOverall survivalAdjuvant therapyAdrenocortical tumorsDismal outcomeSilencing
2017
Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis
Smith J, Zhao W, Wang X, Ratliff S, Mukherjee B, Kardia S, Liu Y, Roux A, Needham B. Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis. Epigenetics 2017, 12: 662-673. PMID: 28678593, PMCID: PMC5687339, DOI: 10.1080/15592294.2017.1341026.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisMulti-Ethnic StudyStudy of AtherosclerosisSocioeconomic disadvantageIndividual-level socioeconomic factorsEtiology of health disparitiesAssociated with poor health outcomesPopulation-based sample of US adultsSocioeconomic factorsNeighborhood conditionsNeighborhood socioeconomic disadvantageSample of US adultsNeighborhood social environmentHigher socioeconomic disadvantagePoor health outcomesIndividual socioeconomic factorsPopulation-based sampleDimensions of neighborhood contextHealth disparitiesInfluence methylation levelsHealth outcomesUS adultsSocial environmentDisadvantaged neighborhoodsNeighborhood characteristics
2015
Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis
Needham B, Smith J, Zhao W, Wang X, Mukherjee B, Kardia S, Shively C, Seeman T, Liu Y, Roux A. Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis. Epigenetics 2015, 10: 958-969. PMID: 26295359, PMCID: PMC4844216, DOI: 10.1080/15592294.2015.1085139.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisAssociated with DNA methylationSocioeconomic statusStress-related genesMulti-Ethnic StudyStudy of AtherosclerosisDNA methylationLow adult socioeconomic statusLife course socioeconomic statusLow childhood socioeconomic statusMeasures of socioeconomic statusAdult socioeconomic statusSocial patterning of diseaseChildhood socioeconomic statusGene expressionLow socioeconomic statusLife course measuresAssociated with gene expressionInflammation-related genesFunctional consequences of alterationsDNA methylation measurementsNon-HispanicHispanic participantsPotential functional consequencesEpigenetic data