2022
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Skoufos G, Almodaresi F, Zakeri M, Paulson J, Patro R, Hatzigeorgiou A, Vlachos I. AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. Genome Biology 2022, 23: 39. PMID: 35101114, PMCID: PMC8802518, DOI: 10.1186/s13059-022-02610-4.Peer-Reviewed Original Research
2019
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
Carrión V, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes L, van Ijcken W, Gomez-Exposito R, Elsayed S, Mohanraju P, Arifah A, van der Oost J, Paulson J, Mendes R, van Wezel G, Medema M, Raaijmakers J. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 2019, 366: 606-612. PMID: 31672892, DOI: 10.1126/science.aaw9285.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaBacterial Physiological PhenomenaBacteroidetesBeta vulgarisBiodiversityChitinasesDisease ResistanceEndophytesFlavobacteriumGenes, BacterialGenome, BacterialMetagenomeMicrobiotaMutagenesis, Site-DirectedPeptide SynthasesPlant DiseasesPlant RootsPolyketide SynthasesRhizoctoniaSoil MicrobiologyConceptsEndophytic root microbiomeNonribosomal peptide synthetasesGene clusterPolyketide synthaseRoot microbiomeBiosynthetic gene clusterInfection of plant rootsFungal root diseasesSite-directed mutagenesisPromote plant growthGenome reconstructionPeptide synthetasesRoot endosphereFunctional traitsNRPS-PKSFunctional diversityChitinase geneEndophytic consortiaFungal infectionsDisease suppressionRoot diseasePlant growthNetwork inferenceDisease-suppressive functionsPlant roots
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
2016
Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
Pop M, Paulson J, Chakraborty S, Astrovskaya I, Lindsay B, Li S, Bravo H, Harro C, Parkhill J, Walker A, Walker R, Sack D, Stine O. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 2016, 17: 440. PMID: 27277524, PMCID: PMC4898365, DOI: 10.1186/s12864-016-2777-0.Peer-Reviewed Original ResearchConceptsGene sequencesBackgroundEnterotoxigenic Escherichia coliHuman gut microbiotaRRNA gene sequencesEnterotoxigenic Escherichia coliHuman intestinal microbiotaFecal E. coliCiprofloxacin treatmentETEC infectionETEC diarrheaRibosomal RNAGut microbiotaFecal microbiotaIntestinal microbiotaE. coliMicrobiotaMonthly follow-up visitsCompared to variationsETECFollow-up visitQuantitative PCRHuman challenge studiesCiprofloxacinQuantitative culturesSequence