Adjunct Faculty
Adjunct faculty typically have an academic or research appointment at another institution and contribute or collaborate with one or more School of Medicine faculty members or programs.
Adjunct rank detailsJoseph N Paulson, PhD
Assistant Professor AdjunctAbout
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: eaba0565. 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 DNADiseaseDifferential 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
2026
538TiP A first-in-human, phase I study of XB010, a 5T4-MMAE ADC, in patients with advanced breast cancer and other solid tumors
Kang I, Choudhury N, Fontana E, O'Shaughnessy J, Powderly J, Ahnert J, Salkeni M, Thistlethwaite F, Ulahannan S, Vandross A, Weiss M, Bernardi R, Paulson J, McGoldrick S, Walsh E. 538TiP A first-in-human, phase I study of XB010, a 5T4-MMAE ADC, in patients with advanced breast cancer and other solid tumors. ESMO Open 2026, 11: 107560. DOI: 10.1016/j.esmoop.2026.107560.Peer-Reviewed Original Research220eTiP A first-in-human, phase I study of XB010, a 5T4-MMAE ADC, in patients with non-small cell lung cancer (NSCLC) and other solid tumors
Salkeni M, Larijani F, Benyounes A, Choudhury N, Kang I, O'Shaughnessy J, Powderly J, Ahnert J, Thistlethwaite F, Ulahannan S, Walsh E, Weiss M, Paulson J, Rasooli S, Bernardi R, Johnson M. 220eTiP A first-in-human, phase I study of XB010, a 5T4-MMAE ADC, in patients with non-small cell lung cancer (NSCLC) and other solid tumors. ESMO Open 2026, 11: 106526. DOI: 10.1016/j.esmoop.2026.106526.Peer-Reviewed Original ResearchA unified framework for pre-screening and screening tools in oncology clinical trials
Horgan D, Paulson J, Loaiza-Bonilla A, Svedman C, Malapelle U, Penault-Llorca F, Rahsheed H, Hofman P, Kachnowski S, Schneider D, Subbiah V. A unified framework for pre-screening and screening tools in oncology clinical trials. Npj Precision Oncology 2026, 10: 143. PMID: 41611789, PMCID: PMC13056990, DOI: 10.1038/s41698-026-01306-3.Peer-Reviewed Original Research
2025
Poor surgical outcomes following Paenibacillus infant infectious hydrocephalus
Ericson J, Natukwatsa D, Ssenyonga P, Onen J, Mugamba J, Mulondo R, Morton S, Movassagh M, Templeton K, Hehnly C, Mbabazi-Kabachelor E, Kulkarni A, Warf B, Broach J, Paulson J, Schiff S. Poor surgical outcomes following Paenibacillus infant infectious hydrocephalus. Journal Of Neurosurgery Pediatrics 2025, 36: 145-156. PMID: 40378477, PMCID: PMC12211056, DOI: 10.3171/2025.1.peds24254.Peer-Reviewed Original ResearchPostinfectious hydrocephalusPP patientsPN patientsEndoscopic diversionHydrocephalus surgeryPositive CSF polymerase chain reactionPrimary outcomeMedian follow-up periodCSF polymerase chain reactionFailure-free survivalPoor surgical outcomesPrimary event rateFollow-up periodOverall survivalCSF diversionHydrocephalic infantsSurgical outcomesNeurosurgical evaluationPolymerase chain reactionCompare outcomesSecondary outcomesPatientsEvent ratesInfantsChain reaction
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 analysisbacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria
Guerrero-Egido G, Pintado A, Bretscher K, Arias-Giraldo L, Paulson J, Spaink H, Claessen D, Ramos C, Cazorla F, Medema M, Raaijmakers J, Carrión V. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nature Communications 2024, 15: 2072. PMID: 38453959, PMCID: PMC10920822, DOI: 10.1038/s41467-024-46302-y.Peer-Reviewed Original ResearchConceptsPhytopathogenic lifestylePlant pathogenic lifestylePseudomonas syringae pvBacteria-host interactionsSite-directed mutagenesisExtracellular binding proteinsComputational workflowGenome annotationEukaryotic hostsComparative genomicsNiche adaptationPathogenic lifestyleHypothetical proteinsHomoserine dehydrogenaseGenomic analysisBurkholderia plantariiPseudomonas genusHost growthGenomeBinding proteinGenesGeneration of hypothesesBacteriaPlant bioassaysProteinPrediction 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