2021
Multivariable association discovery in population-scale meta-omics studies
Mallick H, Rahnavard A, McIver L, Ma S, Zhang Y, Nguyen L, Tickle T, Weingart G, Ren B, Schwager E, Chatterjee S, Thompson K, Wilkinson J, Subramanian A, Lu Y, Waldron L, Paulson J, Franzosa E, Bravo H, Huttenhower C. Multivariable association discovery in population-scale meta-omics studies. PLOS Computational Biology 2021, 17: e1009442. PMID: 34784344, PMCID: PMC8714082, DOI: 10.1371/journal.pcbi.1009442.Peer-Reviewed Original ResearchConceptsMicrobial community measurementsMeta-omics studiesMicrobial community featuresMulti-omics datasetsControlling false discoveriesLandscape of inflammatory bowel diseaseHuman microbiomeMaAsLinMulti-omicsOmics profilesFalse discoveriesCommunity measuresMicrobiomeEnvironmental conditionsInflammatory bowel diseaseCommunity featuresHealth outcomesAssociation discoveryMultivariate associationsMultiple covariatesEpidemiological studiesLongitudinal designObservational studyStatistical powerZero-inflation
2017
Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik K, Reid M, Smyth E, Hittle L, Paulson J, Cruz-Cano R, Pop M, Buehler S, Clark P, Sapkota A, Mongodin E. Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens. Microbiome 2017, 5: 22. PMID: 28202080, PMCID: PMC5312438, DOI: 10.1186/s40168-017-0235-0.Peer-Reviewed Original ResearchConceptsQuantitative Insights Into Microbial EcologyResistant to harsh environmental conditionsBacterial pathogensHarsh environmental conditionsV3-V4 hypervariable regionIllumina MiSeq platformHuman bacterial pathogensBacterial community profilesBacterial community richnessPotential bacterial pathogensEnvironmental conditionsRRNA geneMiSeq platformAbundant generaBacterial microbiotaBacterial communitiesMicrobial ecologyGenomic DNACommunity richnessBacterial compositionHypervariable regionPCR amplificationCommunity profilesPseudomonas putidaLysis protocol