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
2020
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 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
Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo)
Shapiro L, Andrade A, Scully E, Rocha J, Paulson J, Kolter R. Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo). Microbiology Resource Announcements 2018, 7: 10.1128/mra.01058-18. PMID: 30533754, PMCID: PMC6256489, DOI: 10.1128/mra.01058-18.Peer-Reviewed Original ResearchInfected muskmelonDraft genome sequenceBacterial plant pathogensCucumis meloChromosome contigPlasmid contigsEastern North AmericaGenome sequencePlant pathogensE. tracheiphilaGenetic variationErwinia tracheiphilaContigsGenomeCucumisNorth AmericaMuskmelonBacteriophageErwiniaPlasmidPathogensSequenceIsolates
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