Featured Publications
Differential 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 evidenceAccumulationInference
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
2021
Vaginal microbiome topic modeling of laboring Ugandan women with and without fever
Movassagh M, Bebell L, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar S, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga B, Weeks A, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts D, Meier F, Irizarry R, Broach J, Schiff S, Paulson J. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. Npj Biofilms And Microbiomes 2021, 7: 75. PMID: 34508087, PMCID: PMC8433417, DOI: 10.1038/s41522-021-00244-1.Peer-Reviewed Original ResearchConceptsIntrapartum feverClinical variablesHigh prevalenceVaginal microbiomeUgandan womenLonger labour durationMaternal clinical featuresYoung maternal ageDuration of pregnancyOnset of laborMicrobial communitiesVaginal microbial communitiesAfebrile mothersFebrile mothersPeripartum courseMaternal feverNeonatal outcomesLabor durationClinical featuresMaternal ageVaginal microbesFeverOutcome riskVeillonella genusMicrobiome influences
2020
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities
Reeder J, Huang M, Kaminker J, Paulson J. MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities. Bioinformatics 2020, 37: 1317-1318. PMID: 32960962, PMCID: PMC8193707, DOI: 10.1093/bioinformatics/btaa838.Peer-Reviewed Original ResearchmicrobiomeDASim: 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
2018
Metaviz: interactive statistical and visual analysis of metagenomic data
Wagner J, Chelaru F, Kancherla J, Paulson J, Zhang A, Felix V, Mahurkar A, Elmqvist N, Bravo H. Metaviz: interactive statistical and visual analysis of metagenomic data. Nucleic Acids Research 2018, 46: gky136-. PMID: 29529268, PMCID: PMC5887897, DOI: 10.1093/nar/gky136.Peer-Reviewed Original ResearchConceptsWeb servicesInteractive exploratory data analysisMetagenomic shotgun sequencingState-of-the-artState-of-the-art analysis toolsMetagenomic samplesShotgun sequencingUser navigationMicrobial communitiesCommunity profilesData featuresData valuesDisease phenotypeMarker genesMetavizUsersData resourcesProcess dataVisual analysisAnalysis toolsHierarchical structureSignificant effortBioconductorMetagenomicsMicrobiome