2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
2022
Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus
Hehnly C, Shi A, Ssentongo P, Zhang L, Isaacs A, Morton S, Streck N, Erdmann-Gilmore P, Tolstoy I, Townsend R, Limbrick D, Paulson J, Ericson J, Galperin M, Schiff S, Broach J. Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. MBio 2022, 13: e02688-22. PMID: 36374038, PMCID: PMC9765702, DOI: 10.1128/mbio.02688-22.Peer-Reviewed Original ResearchConceptsPostinfectious hydrocephalusClinical isolatesVirulence factorsCritical virulence factorPotential virulence factorsPoor long-term outcomesPrevention of hydrocephalusLong-term outcomesBacterial pathogensDevastating sequelaeNeonatal sepsisMiddle-income countriesNeonatal infectionSurgical interventionReference strainsNovel bacterial pathogensAfrican cohortBeta-lactamase genesChildhood mortalityHydrocephalusTherapeutic targetInfectionVirulent strainDevastating diseaseWhole-genome sequencing
2020
Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156
Hehnly C, Zhang L, Paulson J, Almeida M, von Bredow B, Wijetunge D, Galperin M, Sheldon K, Schiff S, Broach J. Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156. Microbiology Resource Announcements 2020, 9: 10.1128/mra.00181-20. PMID: 32273361, PMCID: PMC7380522, DOI: 10.1128/mra.00181-20.Peer-Reviewed Original Research
2017
Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing
Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson J, Almeida M, Domman D, Thomson N, Alonso P, Stine O. Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLOS Neglected Tropical Diseases 2017, 11: e0005671. PMID: 28622368, PMCID: PMC5489214, DOI: 10.1371/journal.pntd.0005671.Peer-Reviewed Original ResearchConceptsMultilocus variable-number tandem-repeat analysisWhole-genome sequencingTandem repeat analysisGenome sequenceMultilocus variable number tandem repeat analysisVariable number tandem repeat analysisVariable-number tandem repeat analysisCholera toxin geneVibrio cholerae isolatesPresence of recombinationMinimal genetic changeMLVA lociCholerae isolatesSeventh pandemicGenetic relatednessClonal complexesToxin genesMolecular clockVibrio choleraeClinical isolatesIdentical isolatesGenetic changesRepeat analysisEnvironmental reservoirsIsolates