2020
Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water
Kulkarni P, Olson N, Bui A, Bradshaw R, Del Collo L, Hittle L, Handy E, Paulson J, Ghurye J, Nasko D, East C, Van Kessel J, Kniel K, Chiu P, Mongodin E, Pop M, Sharma M, Sapkota A. Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water. Frontiers In Environmental Science 2020, 8: 541921. DOI: 10.3389/fenvs.2020.541921.Peer-Reviewed Original ResearchProportion of open reading framesNitrogen-fixing bacterial generaZVI-sand filtrationPlant pathogenic genusPlant growth-promoting bacteriaPlant pathogenic bacteriaRRNA gene sequencesOpen reading frameMetagenomic shotgun sequencingExploratory functional analysisAntimicrobial susceptibility testingGrowth-promoting bacteriaBacterial community structureTetracycline-resistant E. coliReclaimed waterOxidative stress responseShotgun sequencingReading frameZVI-sandGene sequencesBacterial generaPathogenic generaBacterial communitiesIron-rich environmentsPromoting bacteriamicrobiomeDASim: 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