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 ResearchMeSH KeywordsComputational BiologyComputer SimulationGastrointestinal MicrobiomeHumansInflammatory Bowel DiseasesMultivariate AnalysisConceptsMicrobial 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
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat
Damgaard M, Pærregaard S, Søgaard I, Agerholm M, Paulson J, Treebak J, Sina C, Holm J, Kristiansen K, Jensen B. Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. The Journal Of Nutritional Biochemistry 2017, 54: 66-76. PMID: 29268121, DOI: 10.1016/j.jnutbio.2017.09.026.Peer-Reviewed Original ResearchConceptsGlucose homeostasisGut microbial alterationsGene amplicon sequencingInfluence of dietary fat sourceLow-fat dietAmplicon sequencingFatty acidsGut microbiotaResponse to insulinDietary fat sourceMicrobial alterationsAssessed glucose homeostasisMetabolic homeostasisDietary fatGlucose clearanceGlucose regulationLFD-fed miceFat sourcesHomeostasisFish oilGroups of miceInsulin tolerance testWeek 8 to weekSoybean oilSevere nonalcoholic steatohepatitis
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