2024
LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information
Dong Z, Jiang W, Li H, DeWan A, Zhao H. LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information. Briefings In Bioinformatics 2024, 25: bbae335. PMID: 38980374, PMCID: PMC11232466, DOI: 10.1093/bib/bbae335.Peer-Reviewed Original ResearchConceptsHuman complex traitsComplex traitsGene-environment interactionsGene-environmentLinkage disequilibriumPhenotypic variance componentsPhenotypic varianceProportion of phenotypic varianceSummary statisticsEuropean ancestry subjectsUK Biobank dataAssociation summary statisticsComplete linkage disequilibriumControlled type I error ratesLD informationLD matrixVariance componentsBiobank dataType I error rateEuropean ancestrySample size increaseGenetic effectsTraitsE-I pairsSimulation study
2019
Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
Zeng L, Warren J, Zhao H. Phylogeny-based tumor subclone identification using a Bayesian feature allocation model. The Annals Of Applied Statistics 2019, 13: 1212-1241. DOI: 10.1214/18-aoas1223.Peer-Reviewed Original ResearchCopy number variationsCourse of evolutionSubgroup of cellsWhole-genome sequencing samplesTumor subclonesBayesian feature allocation modelPhylogenetic structureDifferent genetic alterationsPhylogeny structureSequencing depthFeature allocation modelNumber variationsSequencing samplesTree sizeDistinct genotypesGenetic alterationsSubclonesResult of competitionTumor progressionBayesian modelEstimation accuracySifADrug resistanceCellsSimulation study
2017
On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
Lin Z, Wang T, Yang C, Zhao H. On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data. Biometrics 2017, 73: 769-779. PMID: 28099997, PMCID: PMC5515703, DOI: 10.1111/biom.12650.Peer-Reviewed Original ResearchConceptsGaussian graphical modelsTemporal dataGraphical modelsComplex data structuresJoint estimationMarkov random field modelRandom field modelParallel computingSelection consistencyData structureStatistical inferenceNeighborhood selection methodTemporal dependenciesEfficient algorithmIndividual networksMultiple groupsSpatial dataModel convergesNetwork estimationField modelSelection methodNetworkPosterior probabilitySimulation studyImproved estimationGraphical model selection with latent variables
Wu C, Zhao H, Fang H, Deng M. Graphical model selection with latent variables. Electronic Journal Of Statistics 2017, 11: 3485-3521. DOI: 10.1214/17-ejs1331.Peer-Reviewed Original ResearchGraphical model selectionModel selection consistencyEfficient ADMM algorithmSparse precision matrixGraphical modelsGaussian graphical modelsGenetical genomics dataSelection consistencyPenalized estimationStatistical inferencePrecision matrixLatent variablesParameter estimationTheoretical propertiesIdentifiability conditionsADMM algorithmModel selectionSimulation studyConditional dependenceEstimationTrace lossSuperior performanceEstimatorGraphVariables
2016
Estimating a sparse reduction for general regression in high dimensions
Wang T, Chen M, Zhao H, Zhu L. Estimating a sparse reduction for general regression in high dimensions. Statistics And Computing 2016, 28: 33-46. DOI: 10.1007/s11222-016-9714-6.Peer-Reviewed Original ResearchOn high-dimensional misspecified mixed model analysis in genome-wide association study
Jiang J, Li C, Paul D, Yang C, Zhao H. On high-dimensional misspecified mixed model analysis in genome-wide association study. The Annals Of Statistics 2016, 44: 2127-2160. DOI: 10.1214/15-aos1421.Peer-Reviewed Original ResearchREML estimatorsAsymptotic resultsAsymptotic conditional varianceReal data applicationRandom effectsMaximum likelihood estimatorExtensive simulation studyAsymptotic analysisConvergence rateLikelihood estimatorLinear mixed modelsEstimatorSimulation studyConvergenceData applicationsTrue varianceConditional varianceImportant genetic implicationsCertain limits
2012
Time course RNA-seq: A potential avenue with somewhat different approach in tandem of differential analysis
Oh S, Zhao H, Noonan J. Time course RNA-seq: A potential avenue with somewhat different approach in tandem of differential analysis. 2012, 1: 580-587. DOI: 10.1109/cisis.2012.204.Peer-Reviewed Original ResearchMonte Carlo simulation studySimulation studyReal data setsStatistical frameworkDifferential expression methodsStatistical approachDependent dataMarkov model approachInherent dependenciesTime seriesModel approachHidden Markov Model ApproachStandard approachTime-series RNA-seq dataData setsIntuitive solutionBiological systemsTrajectory indexTemporal complexityDifferential analysisDifferent approachesApproachConsiderable advantagesSolution
2011
Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
Luo R, Zhao H. Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data. The Annals Of Applied Statistics 2011, 5: 725-745. PMID: 22162986, PMCID: PMC3233205, DOI: 10.1214/10-aoas425.Peer-Reviewed Original ResearchMarkov chain Monte CarloReal data analysisBayesian hierarchical modeling frameworkHierarchical modelingHierarchical modeling frameworkBayesian hierarchical modelingStatistical inferencePosterior distributionMonte CarloNetwork sparsitySimulation studyIntrinsic noiseModeling frameworkMeasurement errorInterventional dataInferenceMultiple protein activitiesPathway inferenceCarloModelingInterventional experimentsSuch dataSparsityData analysisNoise
2008
Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Liu J, Yu W, Wu B, Zhao H. Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios. Cancer Informatics 2008, 6: 117693510800600006. DOI: 10.4137/117693510800600006.Peer-Reviewed Original Research
2000
Transmission/Disequilibrium Tests Using Multiple Tightly Linked Markers
Zhao H, Zhang S, Merikangas K, Trixler M, Wildenauer D, Sun F, Kidd K. Transmission/Disequilibrium Tests Using Multiple Tightly Linked Markers. American Journal Of Human Genetics 2000, 67: 936-946. PMID: 10968775, PMCID: PMC1287895, DOI: 10.1086/303073.Peer-Reviewed Original Research