Featured Publications
Differential 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
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
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 culturesSequencePrivacy-preserving microbiome analysis using secure computation
Wagner J, Paulson J, Wang X, Bhattacharjee B, Corrada Bravo H. Privacy-preserving microbiome analysis using secure computation. Bioinformatics 2016, 32: 1873-1879. PMID: 26873931, PMCID: PMC4908319, DOI: 10.1093/bioinformatics/btw073.Peer-Reviewed Original ResearchConceptsDNA of micro-organismsMicrobiome research communityPrivacy concernsSensitive attributesResearch participant dataFeature countsSharing dataSupplementary dataMetagenomic analysisResearch datasetsMicrobiome sequencingSequencing studiesMicrobial DNAHuman DNAResearch communityMicrobiome analysisMicrobiomeDNAAnalysis toolsDatasetComputerMicro-organismsBioinformaticsImplementationIndividual collections
2014
Reply to: "A fair comparison"
Paulson J, Bravo H, Pop M. Reply to: "A fair comparison". Nature Methods 2014, 11: 359-360. PMID: 24681718, DOI: 10.1038/nmeth.2898.Peer-Reviewed Original Research