Joseph N Paulson, PhD
Assistant Professor AdjunctCards
About
Research
Publications
Featured Publications
Differential richness inference for 16S rRNA marker gene surveys
Kumar M, Slud E, Hehnly C, Zhang L, Broach J, Irizarry R, Schiff S, Paulson J. Differential richness inference for 16S rRNA marker gene surveys. Genome Biology 2022, 23: 166. PMID: 35915508, PMCID: PMC9344657, DOI: 10.1186/s13059-022-02722-x.Peer-Reviewed Original ResearchConceptsMarker gene surveysRRNA marker gene surveysGene surveysMicrobial assemblagesSpecies discoveryMicrobial taxaMicrobial communitiesMicrobiome surveysRichness estimationSequencing readsDiversity measuresTaxaGenus abundanceMicrobiome dataR packageAbundanceRichnessDiscoveryDiversityReadsAssemblagesObserved numberExperimental evidenceAccumulationInferencePaenibacillus 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 DNADiseaseNeoantigens in Patients with De Novo Follicular Lymphoma: Results from the PRIMA Study
Henneges C, Jin D, Venstrom J, Trabucco S, Nielsen T, Penuel E, Huet S, Salles G, Paulson J. Neoantigens in Patients with De Novo Follicular Lymphoma: Results from the PRIMA Study. Blood 2020, 136: 25-26. DOI: 10.1182/blood-2020-134795.Peer-Reviewed Original ResearchDiffuse large B-cell lymphomaDe novo diffuse large B-cell lymphomaProgression-free survivalTumor mutational burdenComprehensive genomic profilingCurrent equity holderAssociated with progression-free survivalFollicular lymphomaF. Hoffmann-La RocheFoundation MedicinePrognostic valueClinical outcomesMedian tumor mutation burdenProgression-free survival eventsPooled analysis of patientsLarge B-cell lymphomaResponse to induction treatmentCalculate tumor mutational burdenAssociated with clinical outcomesEZH2 mutation statusComprehensive genomic profiling dataB-cell lymphomaGenetic mutational landscapeAnalysis of patientsProportion of patientsDifferential 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
2024
Lubricating gel influence on vaginal microbiome sampling
Amitai Komem D, Hadar R, Paulson J, Mordechai Y, Eskandarian H, Efroni G, Amir A, Haberman Y, Tsur A. Lubricating gel influence on vaginal microbiome sampling. Scientific Reports 2024, 14: 18223. PMID: 39107405, PMCID: PMC11303677, DOI: 10.1038/s41598-024-68948-w.Peer-Reviewed Original ResearchConceptsMicrobial compositionVaginal samplesVaginal microbiome samplesBeta diversityVaginal microbiome studiesMicrobiome studiesMicrobiome samplesTaxa abundanceGynecological examinationPregnant womenLubricant gelReduce painMicrobial dataGel exposureEmergency roomSterile swabsEffect of gelMicrobial analysisPrediction of Benefit From Adjuvant Pertuzumab by 80-Gene Signature in the APHINITY (BIG 4-11) Trial
Krop I, Mittempergher L, Paulson J, Andre F, Bonnefoi H, Loi S, Loibl S, Gelber R, Caballero C, Bhaskaran R, Dreezen C, Menicucci A, Bernards R, van ’t Veer L, Piccart M. Prediction of Benefit From Adjuvant Pertuzumab by 80-Gene Signature in the APHINITY (BIG 4-11) Trial. JCO Precision Oncology 2024, 8: e2200667. PMID: 38237097, DOI: 10.1200/po.22.00667.Peer-Reviewed Original ResearchConceptsInvasive disease-free survivalHER2 typeLuminal typeInvasive disease-free survival eventsHazard ratioEarly-stage breast cancerLuminal-type tumorsMolecular subtype signaturesAnti-HER2 therapyHER2-positive tumorsDisease-free survivalStandard adjuvant chemotherapyBasal-type tumorsBasal typePredictive of benefitAdjuvant pertuzumabAPHINITY trialHER2-typeHER2-positiveInferior prognosisAdjuvant chemotherapyTumor subtypesNo significant differenceAnti-HER2Breast tumors
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 desertmbQTL: 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 packageAbundanceTranscriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia
Al-Sawaf O, Zhang C, Jin H, Robrecht S, Choi Y, Balasubramanian S, Kotak A, Chang Y, Fink A, Tausch E, Schneider C, Ritgen M, Kreuzer K, Chyla B, Paulson J, Pallasch C, Frenzel L, Peifer M, Eichhorst B, Stilgenbauer S, Jiang Y, Hallek M, Fischer K. Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia. Nature Communications 2023, 14: 2147. PMID: 37072421, PMCID: PMC10113251, DOI: 10.1038/s41467-023-37648-w.Peer-Reviewed Original ResearchConceptsProgression-free survivalChronic lymphocytic leukemiaUntreated chronic lymphocytic leukemiaLymphocytic leukemiaAssociated with longer progression-free survivalParallel-group phase 3 studyProgression-free survival ratesTreatment of chronic lymphocytic leukemiaLonger progression-free survivalDepth of remissionMedian follow-upPhase 3 studyAssociated with increased expressionLong-term efficacyLong-term outcomesExploratory post hoc analysisPost hoc analysisMRD statusBCL2 inhibitionOverall survivalPrimary endpointSecondary endpointsInflammatory response pathwaysVenetoclax-obinutuzumabFollow-upMultimodal 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