2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
2022
microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data
Dahl E, Neer E, Bowie K, Leung E, Karstens L. microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data. Microbiology Resource Announcements 2022, 11: e00795-22. PMID: 36314910, PMCID: PMC9670991, DOI: 10.1128/mra.00795-22.Peer-Reviewed Original ResearchDifferential richness inference for 16S rRNA marker gene surveys
Kumar M, Slud E, Hehnly C, Zhang L, Broach J, Irizarry R, Schiff S, Paulson J. Differential richness inference for 16S rRNA marker gene surveys. Genome Biology 2022, 23: 166. PMID: 35915508, PMCID: PMC9344657, DOI: 10.1186/s13059-022-02722-x.Peer-Reviewed Original ResearchConceptsMarker gene surveysRRNA marker gene surveysGene surveysMicrobial assemblagesSpecies discoveryMicrobial taxaMicrobial communitiesMicrobiome surveysRichness estimationSequencing readsDiversity measuresTaxaGenus abundanceMicrobiome dataR packageAbundanceRichnessDiscoveryDiversityReadsAssemblagesObserved numberExperimental evidenceAccumulationInferencephyloMDA: 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 patternsTreesA Zero-Inflated Logistic Normal Multinomial Model for Extracting Microbial Compositions
Zeng Y, Pang D, Zhao H, Wang T. A Zero-Inflated Logistic Normal Multinomial Model for Extracting Microbial Compositions. Journal Of The American Statistical Association 2022, 118: 2356-2369. DOI: 10.1080/01621459.2022.2044827.Peer-Reviewed Original ResearchMaximum likelihood estimationEfficient iterative algorithmProbabilistic PCA modelsEmpirical Bayes approachApproximation estimatorVariational approximationExcessive zerosM-estimationAsymptotic normalityIterative algorithmLikelihood estimationBayes approachCount dataHigh dimensionalityRaw count dataMultinomial modelExtensive simulationsZerosSupplementary materialMicrobiome dataCompositional natureEstimationPCA modelComposition estimationApproximation
2021
Multivariate log‐contrast regression with sub‐compositional predictors: Testing the association between preterm infants' gut microbiome and neurobehavioral outcomes
Liu X, Cong X, Li G, Maas K, Chen K. Multivariate log‐contrast regression with sub‐compositional predictors: Testing the association between preterm infants' gut microbiome and neurobehavioral outcomes. Statistics In Medicine 2021, 41: 580-594. PMID: 34897772, DOI: 10.1002/sim.9273.Peer-Reviewed Original ResearchConceptsLinear log-contrast modelLog-contrast modelGut microbiomeGut microbiome of preterm infantsHypothesis testing procedureInfant gut microbiomeLinear constraintsCompositional covariatesInference proceduresMultivariate responsePenalization approachSimulation studyGroup structureMicrobiome dataIdentified microbesMicrobiome analysisTaxonomic hierarchyInference methodsPreterm infant studyTest procedureMicrobiomeMicrobesBiological understandingCovariatesFeature matrixStatistical Methods for Analyzing Tree-Structured Microbiome Data
Wang T, Zhao H. Statistical Methods for Analyzing Tree-Structured Microbiome Data. Frontiers In Probability And The Statistical Sciences 2021, 193-220. DOI: 10.1007/978-3-030-73351-3_8.Peer-Reviewed Original ResearchStatistical methodsOnly relative informationMicrobiome data analysisMicrobiome dataEmpirical Bayes estimationCompositional predictorsBayes estimationComputational challengesRelative informationDimension reductionAbundance matrixTaxa countsMultinomial modelMicrobiome datasetsPhylogenetic informationMicrobial taxaPhylogenetic treeSequencing technologiesOriginal ecosystemMicrobial compositionOrders of magnitudeMatrixExperimental methodsLibrary sizeZeros
2020
microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
Williams J, Bravo H, Tom J, Paulson J. microbiomeDASim: Simulating longitudinal differential abundance for microbiome data. F1000Research 2020, 8: 1769. PMID: 32148761, PMCID: PMC7047923, DOI: 10.12688/f1000research.20660.2.Peer-Reviewed Original Research
2019
microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
Williams J, Bravo H, Tom J, Paulson J. microbiomeDASim: Simulating longitudinal differential abundance for microbiome data. F1000Research 2019, 8: 1769. DOI: 10.12688/f1000research.20660.1.Peer-Reviewed Original Research
2017
Constructing Predictive Microbial Signatures at Multiple Taxonomic Levels
Wang T, Zhao H. Constructing Predictive Microbial Signatures at Multiple Taxonomic Levels. Journal Of The American Statistical Association 2017, 112: 1022-1031. DOI: 10.1080/01621459.2016.1270213.Peer-Reviewed Original ResearchBacterial taxaTaxonomic levelsMultiple taxonomic levelsDifferent taxonomic levelsDNA sequencing technologiesHuman microbiome studiesPhylogenetic treeHost phenotypeSequencing technologiesNormal human physiologyTaxaHuman microbiomeMicrobial signaturesMicrobiome studiesMicrobiome data analysisImportant groupMicrobiome dataHigh-dimensional compositional dataHuman physiologyRecent advancesMicrobesRapid advancesMajor goalMicrobiomePhenotype
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