Featured Publications
Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data
Jiang W, Chen L, Girgenti M, Zhao H. Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data. Nature Communications 2024, 15: 24. PMID: 38169469, PMCID: PMC10762162, DOI: 10.1038/s41467-023-44009-0.Peer-Reviewed Original ResearchA fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics
Zhou G, Zhao H. A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics. PLOS Genetics 2021, 17: e1009697. PMID: 34310601, PMCID: PMC8341714, DOI: 10.1371/journal.pgen.1009697.Peer-Reviewed Original ResearchConceptsBayesian nonparametric methodParameter tuningNonparametric methodsExternal reference panelSummary statisticsComputational resourcesParallel algorithmBlock structureExplicit assumptionsExisting methodsStatisticsSeparate validation dataAccurate risk prediction modelsAssumptionPrediction modelPredictionAlgorithm
2023
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy
Deng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. Briefings In Bioinformatics 2023, 24: bbac616. PMID: 36631398, PMCID: PMC9851324, DOI: 10.1093/bib/bbac616.Peer-Reviewed Original Research
2022
phyloMDA: an R package for phylogeny-aware microbiome data analysis
Liu T, Zhou C, Wang H, Zhao H, Wang T. phyloMDA: an R package for phylogeny-aware microbiome data analysis. BMC Bioinformatics 2022, 23: 213. PMID: 35668363, PMCID: PMC9169257, DOI: 10.1186/s12859-022-04744-5.Peer-Reviewed Original ResearchConceptsHost-associated microbial communitiesShared evolutionary historyMicrobiome data analysisEvolutionary historyPhylogenetic informationPhylogenetic treeMicrobial communitiesR packageSequencing technologiesAbundance dataMicrobial compositionRelative abundanceMicrobiome dataSample sitesUser-friendly toolMultivariate abundance dataAbundanceUnique opportunityUnprecedented scaleDifferent patternsTrees
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 estimation
2013
Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies
Hou L, Chen M, Zhang CK, Cho J, Zhao H. Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies. Human Molecular Genetics 2013, 23: 2780-2790. PMID: 24381306, PMCID: PMC3990172, DOI: 10.1093/hmg/ddt668.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesWide association studyDisease-associated genesGWAS signalsNetwork rewiringAssociation studiesFunctional genomic informationGene expression networksCo-expression networkDisease-associated pathwaysExpression networksGene networksGenomic informationAssociation signalsGene prioritizationDisease genesDisease locusSusceptibility lociGenesAssociation principleRewiringDisease associationsLociMillions of candidatesDisease conditions
2012
iFad: an integrative factor analysis model for drug-pathway association inference†
Ma H, Zhao H. iFad: an integrative factor analysis model for drug-pathway association inference†. Bioinformatics 2012, 28: 1911-1918. PMID: 22581178, PMCID: PMC3389771, DOI: 10.1093/bioinformatics/bts285.Peer-Reviewed Original Research
2001
Comparisons of Two Methods for Haplotype Reconstruction and Haplotype Frequency Estimation from Population Data
Zhang S, Pakstis A, Kidd K, Zhao H. Comparisons of Two Methods for Haplotype Reconstruction and Haplotype Frequency Estimation from Population Data. American Journal Of Human Genetics 2001, 69: 906-912. PMID: 11536083, PMCID: PMC1226079, DOI: 10.1086/323622.Peer-Reviewed Original Research