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 evidenceAccumulationInferenceDifferential abundance analysis for microbial marker-gene surveys
Paulson J, Stine O, Bravo H, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nature Methods 2013, 10: 1200-1202. PMID: 24076764, PMCID: PMC4010126, DOI: 10.1038/nmeth.2658.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArea Under CurveCluster AnalysisComputer SimulationDatabases, GeneticGene Expression ProfilingGenetic MarkersGenetic VariationHumansIntestinesMetagenomicsMiceMicrobiotaModels, GeneticModels, StatisticalNormal DistributionPhenotypeRNA, Ribosomal, 16SSequence Analysis, DNASoftware
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 ResearchMeSH KeywordsAdultBacteriaBiodiversityCluster AnalysisFemaleHumansLabor, ObstetricLactobacillusMicrobiotaPregnancyRNA, Ribosomal, 16SUgandaVaginaConceptsIntrapartum 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
2018
An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila
Shapiro L, Paulson J, Arnold B, Scully E, Zhaxybayeva O, Pierce N, Rocha J, Klepac-Ceraj V, Holton K, Kolter R. An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. MBio 2018, 9: 10.1128/mbio.01307-18. PMID: 30279283, PMCID: PMC6168856, DOI: 10.1128/mbio.01307-18.Peer-Reviewed Original ResearchConceptsTemperate eastern North AmericaEastern North AmericaErwinia tracheiphila</i>,Host plant speciesPlant speciesCrop plantsCausal agent of bacterial wiltAgent of bacterial wiltVirulence gene repertoireLow genetic heterogeneityLarge-scale sequencingSusceptible to isolatesNorth AmericaDriving diversificationPhylogenomic analysisPopulation bottlenecksGenetic clustersEcological traitsIsolate collectionGene repertoirePopulation expansionGeographic rangeEvolutionary trajectoriesGenetic heterogeneityCausal agent
2017
Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing
Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson J, Almeida M, Domman D, Thomson N, Alonso P, Stine O. Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLOS Neglected Tropical Diseases 2017, 11: e0005671. PMID: 28622368, PMCID: PMC5489214, DOI: 10.1371/journal.pntd.0005671.Peer-Reviewed Original ResearchConceptsMultilocus variable-number tandem-repeat analysisWhole-genome sequencingTandem repeat analysisGenome sequenceMultilocus variable number tandem repeat analysisVariable number tandem repeat analysisVariable-number tandem repeat analysisCholera toxin geneVibrio cholerae isolatesPresence of recombinationMinimal genetic changeMLVA lociCholerae isolatesSeventh pandemicGenetic relatednessClonal complexesToxin genesMolecular clockVibrio choleraeClinical isolatesIdentical isolatesGenetic changesRepeat analysisEnvironmental reservoirsIsolates