Featured Publications
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants
Paulson J, Williams B, Hehnly C, Mishra N, Sinnar S, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge D, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell L, Burgoine K, Couto-Rodriguez M, Ericson J, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs A, Kaaya B, Kangere S, Kulkarni A, Kumbakumba E, Li X, Limbrick D, Magombe J, Morton S, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson M, Roy F, Sheldon K, Townsend R, Weeks A, Whalen A, Quackenbush J, Ssenyonga P, Galperin M, Almeida M, Atkins H, Warf B, Lipkin W, Broach J, Schiff S. Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Science Translational Medicine 2020, 12 PMID: 32998967, PMCID: PMC7774825, DOI: 10.1126/scitranslmed.aba0565.Peer-Reviewed Original ResearchConceptsPostinfectious hydrocephalusCSF samplesPIH casesPotential causative organismsCerebrospinal fluid accumulationCytomegalovirus coinfectionUgandan infantsNeonatal sepsisSurgical palliationNeonatal infectionInfant casesOptimal treatmentInfant cohortCommon causeCausative organismPediatric hydrocephalusFluid accumulationHydrocephalusAnaerobic bacterial isolatesControl casesInfectionFacultative anaerobic bacterial isolatesInfantsParasitic DNADisease
2023
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours
Nabbi A, Beck P, Delaidelli A, Oldridge D, Sudhaman S, Zhu K, Yang S, Mulder D, Bruce J, Paulson J, Raman P, Zhu Y, Resnick A, Sorensen P, Sill M, Brabetz S, Lambo S, Malkin D, Johann P, Kool M, Jones D, Pfister S, Jäger N, Pugh T. Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours. Genome Medicine 2023, 15: 67. PMID: 37679810, PMCID: PMC10486055, DOI: 10.1186/s13073-023-01219-x.Peer-Reviewed Original ResearchConceptsChimeric antigen receptorNervous system tumorsImmune clustersImmunogenomic analysisSystem tumorsCancer typesImmune checkpoint inhibitorsT-cell therapyPaediatric solid tumoursTumor mutational burdenImmune cell frequenciesPotential immune biomarkersImmune infiltration levelsB cell repertoireDeterminants of immune responseVariable response ratesBackgroundCancer immunotherapyImmunogenomic profilingMyeloid predominanceCheckpoint inhibitorsImmunotherapeutic strategiesImmunotherapy approachesImmune compositionImmune neutralizationImmune desertMultimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab
Nabbi A, Danesh A, Espin-Garcia O, Pedersen S, Wellum J, Fu L, Paulson J, Geoerger B, Marshall L, Trippett T, Rossato G, Pugh T, Hutchinson K. Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab. Nature Cancer 2023, 4: 502-515. PMID: 37038005, PMCID: PMC10132976, DOI: 10.1038/s43018-023-00534-x.Peer-Reviewed Original ResearchConceptsPediatric patientsAssociated with progression-free survivalCD8+ T cellsT cell receptor repertoireProgression-free survivalImmune-checkpoint inhibitionB cell infiltrationTertiary lymphoid structuresBiomarker analysisAtezolizumab therapyAntitumor immunityStable diseasePD-L1Partial responseTumor neoantigensRefractory tumorsPatient tumorsLymphoid structuresT cellsB cellsReceptor repertoireClinical trialsClinical activityTumorImmune response
2021
Normal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid
Peterson M, Cherukuri V, Paulson J, Ssentongo P, Kulkarni A, Warf B, Monga V, Schiff S. Normal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid. Journal Of Neurosurgery Pediatrics 2021, 28: 458-468. PMID: 34243147, PMCID: PMC8594737, DOI: 10.3171/2021.2.peds201006.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAlgorithmsAnalysis of VarianceAnthropometryBody WeightBrainCerebrospinal FluidChildChild DevelopmentChild, PreschoolCohort StudiesFemaleFunctional LateralityHumansHydrocephalusInfantInfant, NewbornMagnetic Resonance ImagingMaleOrgan SizePopulationReference StandardsSex CharacteristicsConceptsBrain growthBrain volumeFluid accumulationRatio of brainHealthy pediatric subjectsTotal brain volumeAge 18 yearsYears of ageRegional brain volumesNormal brain growthAge-dependent relationshipCSF accumulationPediatric subjectsChildhood diseasesCerebrospinal fluidCSF volumeCongenital disorderVolume trajectoriesEarly childhoodNormative growth curvesNumerous conditionsSexMagnetic resonanceBrain size
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
2013
Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
Lindsay B, Pop M, Antonio M, Walker A, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine M, Kotloff K, Li S, Magder L, Paulson J, Liu B, Ikumapayi U, Ebruke C, Dione M, Adeyemi M, Rance R, Stares M, Ukhanova M, Barnes B, Lewis I, Ahmed F, Alam M, Amin R, Siddiqui S, Ochieng J, Ouma E, Juma J, Mailu E, Omore R, O'Reilly C, Hannis J, Manalili S, DeLeon J, Yasuda I, Blyn L, Ranken R, Li F, Housley R, Ecker D, Hossain M, Breiman R, Morris J, McDaniel T, Parkhill J, Saha D, Sampath R, Stine O, Nataro J. Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. Journal Of Clinical Microbiology 2013, 51: 3263-3269. PMID: 23884998, PMCID: PMC3811648, DOI: 10.1128/jcm.01342-13.Peer-Reviewed Original ResearchConceptsEnteroaggregative Escherichia coliEnteropathogenic E. coliEnterotoxigenic E. coliDNA samplesShigella sppGoldenGate assaySequencing of 16S rRNA genesRRNA gene sequencesBiosensor assayCultivation-based assaysMolecular technologiesStool samplesIdentification of pathogensBacterial pathogen detectionDetect bacterial pathogensEnzyme-linked immunosorbent assay (ELISA)-based methodVirulence genesRRNA geneVirulence factorsGene sequencesBacterial pathogensDiarrheal pathogensEnteric pathogensPathogen detectionDNA