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
2019
Prediction analysis for microbiome sequencing data
Wang T, Yang C, Zhao H. Prediction analysis for microbiome sequencing data. Biometrics 2019, 75: 875-884. PMID: 30994187, DOI: 10.1111/biom.13061.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBacteriaHumansLikelihood FunctionsMicrobiotaMonte Carlo MethodRegression AnalysisSequence AnalysisConceptsMonte Carlo expectation-maximization algorithmInverse regression modelReal data exampleTypes of covariatesNew statistical frameworkMaximum likelihood estimationExpectation-maximization algorithmDimension reduction structureInverse regressionStatistical frameworkData examplesStatistical challengesLikelihood estimationMicrobiome sequencing dataHuman microbiome studiesHuman microbiome compositionDifferent library sizesZerosPredictive analysisModelEstimationAlgorithmSimulationsRegression modelsFramework
2017
A Dirichlet-Tree Multinomial Regression Model for Associating Dietary Nutrients with Gut Microorganisms
Wang T, Zhao H. A Dirichlet-Tree Multinomial Regression Model for Associating Dietary Nutrients with Gut Microorganisms. Biometrics 2017, 73: 792-801. PMID: 28112797, PMCID: PMC5587402, DOI: 10.1111/biom.12654.Peer-Reviewed Original ResearchMeSH KeywordsDietGastrointestinal MicrobiomeHumansLikelihood FunctionsPhylogenyRegression AnalysisStatistical Distributions
2013
Improving genetic risk prediction by leveraging pleiotropy
Li C, Yang C, Gelernter J, Zhao H. Improving genetic risk prediction by leveraging pleiotropy. Human Genetics 2013, 133: 639-650. PMID: 24337655, PMCID: PMC3988249, DOI: 10.1007/s00439-013-1401-5.Peer-Reviewed Original ResearchMeSH KeywordsGenetic PleiotropyGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansRegression Analysis