Tao Wang, PhD
Assistant Professor Adjunct of BiostatisticsCards
About
Research
Publications
2026
Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap
Deng C, Ma X, Lu H, Zhao H, Ming J, Wang T. Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap. Proceedings Of The National Academy Of Sciences Of The United States Of America 2026, 123: e2505182123. PMID: 41650244, PMCID: PMC12890892, DOI: 10.1073/pnas.2505182123.Peer-Reviewed Original Research
2025
PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata
Zhang Z, Zhao H, Wang T. PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata. Nucleic Acids Research 2025, 54: d255-d263. PMID: 41171140, PMCID: PMC12807763, DOI: 10.1093/nar/gkaf1057.Peer-Reviewed Original ResearchConceptsTaxonomic abundance profilesAmplicon sequencing dataSequence dataRead countsTaxonomic levelsManual curationMicrobiome dataSequencing protocolPhenotypic referenceRelative abundanceBody sitesProgrammatic accessReference databasePhenotypic categoriesR packageAbundance profilesWeb interfaceCross-study analysisAbundanceComprehensive metadataMicrobiomeSequenceSitesDisease statusProbabilistic exponential family inverse regression and its applications
Pang D, Zhu R, Zhao H, Wang T. Probabilistic exponential family inverse regression and its applications. Biometrics 2025, 81: ujaf065. PMID: 40407023, DOI: 10.1093/biomtc/ujaf065.Peer-Reviewed Original ResearchConceptsExponential familyDouble exponential familyHigh-dimensional regressionLow-dimensional reductionHierarchical likelihoodData exampleInverse regressionDiscrete predictorsSimulation studyDiscrete dataHigh-dimensional dataParallelizable algorithmContinuous predictorsPresence–absence recordsDimension reductionResponse variablesAccumulation of high dimensional dataHigh-throughput sequencing technologyFactor model frameworkLatent factorsRecords of speciesSequence readsSingle-cell studiesSequencing technologiesCommunity ecology
2024
mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data
Tan X, Xue F, Zhang C, Wang T. mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data. Briefings In Bioinformatics 2024, 25: bbae580. PMID: 39526854, PMCID: PMC11551971, DOI: 10.1093/bib/bbae580.Peer-Reviewed Original ResearchmbDecoda: a debiased approach to compositional data analysis for microbiome surveys
Zong Y, Zhao H, Wang T. mbDecoda: a debiased approach to compositional data analysis for microbiome surveys. Briefings In Bioinformatics 2024, 25: bbae205. PMID: 38701410, PMCID: PMC11066923, DOI: 10.1093/bib/bbae205.Peer-Reviewed Original ResearchConceptsComposition of microbiomesCompositional biasMicrobiome datasetsMicrobiome studiesProbiotic microbesMicrobiome surveysMicrobiome compositionMicrobial loadMicrobiomeMaximum likelihood estimationAbundance analysisAbundance levelsAbsolute abundanceAbundance dataAbundanceClinical phenotypeFeature tableLikelihood estimation of model parametersEnvironmental factorsMaximum likelihood estimation of model parametersEstimation of model parametersMicrobesState-of-the-art methodsOver-dispersionState-of-the-art
2023
Data-driven slicing for dimension reduction in regressions: A likelihood-ratio approach
Xu P, Wang T, Zhu L. Data-driven slicing for dimension reduction in regressions: A likelihood-ratio approach. Science China Mathematics 2023, 67: 647-664. DOI: 10.1007/s11425-022-2088-x.Peer-Reviewed Original ResearchLikelihood ratio criterionDimension reductionLikelihood ratio approachAsymptotic propertiesCentral subspaceSlicing schemeInverse regressionConcrete compressive strengthSimulation studyLog-likelihood ratio criterionOptimal propertiesCompressive strengthData-driven schemeRegression-based methodsAd hocLikelihood ratioDimensionsEstimationSchemeSubspaceDiscretizationFactor Augmented Inverse Regression and its Application to Microbiome Data Analysis
Pang D, Zhao H, Wang T. Factor Augmented Inverse Regression and its Application to Microbiome Data Analysis. Journal Of The American Statistical Association 2023, 119: 1957-1967. DOI: 10.1080/01621459.2023.2231577.Peer-Reviewed Original ResearchInverse regressionCount vectorsLow-dimensional summariesAsymptotic propertiesVariational expectation-maximization algorithmExpectation-maximization algorithmGroup lassoVariational approximationApproximate inferenceSupplementary materialsCount dataModel selectionInformation criterionAbundance of featuresVectorPrediction of host phenotypeOverdispersionLatent factorsApproximationAuthor Correction: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis
Zeng Y, Li J, Wei C, Zhao H, Wang T. Author Correction: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis. Genome Biology 2023, 24: 84. PMID: 37085916, PMCID: PMC10120140, DOI: 10.1186/s13059-023-02940-x.Peer-Reviewed Original ResearchPGNneo: A Proteogenomics-Based Neoantigen Prediction Pipeline in Noncoding Regions
Tan X, Xu L, Jian X, Ouyang J, Hu B, Yang X, Wang T, Xie L. PGNneo: A Proteogenomics-Based Neoantigen Prediction Pipeline in Noncoding Regions. Cells 2023, 12: 782. PMID: 36899918, PMCID: PMC10000440, DOI: 10.3390/cells12050782.Peer-Reviewed Original ResearchConceptsTumor mutational burdenHepatocellular carcinomaColorectal cancerLow tumor mutational burdenNeoantigen prediction pipelineCancer immunotherapyMutational burdenHLA typingPersonalized vaccinesTumor typesNeoantigen predictionImmune targetsNeoantigensGenes associated with hepatocellular carcinomaVaccine designCancer typesTumorVaccine potentialCancerCohortVaccineNoncoding regionsImmunotherapyCarcinomaCoding region
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
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