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
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