Featured Publications
The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2
Townsend JP, Hassler HB, Sah P, Galvani AP, Dornburg A. The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2204336119. PMID: 35858382, PMCID: PMC9351502, DOI: 10.1073/pnas.2204336119.Peer-Reviewed Original ResearchThe durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study
Townsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet Microbe 2021, 2: e666-e675. PMID: 34632431, PMCID: PMC8486316, DOI: 10.1016/s2666-5247(21)00219-6.Peer-Reviewed Original ResearchConceptsDurability of immunitySARS-CoV-2Human-infecting coronavirusesProbability of reinfectionAntibody levelsMERS-CoVSARS-CoVLong-term immune responsePeak antibody responsePublic health decision makingCOVID-19 pandemic continuesEndemic conditionsCOVID-19 morbidityPublic health measuresVirus SARS-CoVHealth decision makingOptical density levelsDevastating COVID-19 pandemicAntibody declineLikely reinfectionAntibody responseEndemic coronavirusesHCoV-NL63Immune responseHuman coronavirusesQuarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study
Wells CR, Pandey A, Fitzpatrick MC, Crystal WS, Singer BH, Moghadas SM, Galvani AP, Townsend JP. Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. The Lancet Regional Health - Europe 2022, 14: 100304. PMID: 35036981, PMCID: PMC8743228, DOI: 10.1016/j.lanepe.2021.100304.Peer-Reviewed Original ResearchShorter quarantineContacts of casesQuarantine durationCOVID-19 infectionLarge socioeconomic burdenCOVID-19 pandemicRisk stratificationSocioeconomic burdenInfection rateRT-PCRThree daysCanadian InstitutePandemic diseaseNational InstituteHealth researchLonger quarantineEpidemic situationTesting strategiesTesting for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing
Wells CR, Gokcebel S, Pandey A, Galvani AP, Townsend JP. Testing for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing. International Journal Of Public Health 2022, 67: 1604659. PMID: 35967267, PMCID: PMC9363582, DOI: 10.3389/ijph.2022.1604659.Peer-Reviewed Original ResearchComparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation
Wells CR, Pandey A, Moghadas SM, Singer BH, Krieger G, Heron RJL, Turner DE, Abshire JP, Phillips KM, Michael Donoghue A, Galvani AP, Townsend JP. Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation. Communications Medicine 2022, 2: 84. PMID: 35822105, PMCID: PMC9271059, DOI: 10.1038/s43856-022-00147-y.Peer-Reviewed Original ResearchRT-PCR testingRT-PCR testAntigen testRA testRT-PCRSerial testingSingle RT-PCR testSARS-CoV-2 infectionRapid antigen testEmergency use authorizationUnited States FoodExtent of transmissionDrug AdministrationCOVID-19 infectiousnessEffective reproduction numberStates FoodCOVID-19 quarantineQuarantine durationTest specificitySpread of diseaseDiagnostic characteristicsTesting strategiesReproduction numberFalse positive rateQuarantineAPOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma
Cannataro VL, Kudalkar S, Dasari K, Gaffney SG, Lazowski HM, Jackson LK, Yildiz I, Das RK, Rothberg BE, Anderson KS, Townsend JP. APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma. Lung Cancer 2022, 171: 34-41. PMID: 35872531, PMCID: PMC10126952, DOI: 10.1016/j.lungcan.2022.07.004.Peer-Reviewed Original ResearchConceptsCytidine deaminationMutagenic processesDefective homologous recombinationGenomic sequencesHomologous recombinationAttractive potential targetAPOBEC mutagenesisLung squamous cell carcinomaDeamination activityCancer cell growthAPOBEC proteinsAPOBEC activityCell growthCellular proliferationNFE2L2MutationsMolecular investigationsCancer effectsPotential targetMolecular variantsAPOBECSurvival of cancerSquamous cell carcinomaDeaminationVariantsAttribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes
Cannataro VL, Mandell JD, Townsend JP. Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Molecular Biology And Evolution 2022, 39: msac084. PMID: 35580068, PMCID: PMC9113445, DOI: 10.1093/molbev/msac084.Peer-Reviewed Original ResearchConceptsBurden of cancerPublic health strategiesWhole-exome sequencingTobacco exposureLung cancerProstate adenocarcinomaBreast cancerCancer effectsHealth strategiesOncogenic driversCancer originCancer typesCancer cell lineagesCancerPathogen exposureExogenous mutational processesMajority of mutationsTumorsSingle nucleotide variantsPreventable processActivity accountsSurvivalOncogenic variantsCell lineagesProliferationPremetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma
Fisk JN, Mahal AR, Dornburg A, Gaffney SG, Aneja S, Contessa JN, Rimm D, Yu JB, Townsend JP. Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma. Cancer Letters 2021, 526: 346-351. PMID: 34780851, PMCID: PMC8702484, DOI: 10.1016/j.canlet.2021.11.011.Peer-Reviewed Original ResearchConceptsMutational processesSingle ancestral lineageAncestral lineageProgression of cancerMetastatic lineagesPhylogenetic analysisGenetic resistanceEvolutionary processesExogenous mutational processesCancer evolutionConsolidative therapyMutational signature analysisEGFR-positive non-small cell lung cancerNon-small cell lung cancerKey eventsLineagesCell populationsTherapeutic resistanceLocal consolidative therapyClinical time courseCell lung cancerDisease etiologyTherapeutic decision makingCisplatin therapyLung cancerHeavy mutagenesis by tobacco leads to lung adenocarcinoma tumors with KRAS G12 mutations other than G12D, leading KRAS G12D tumors—on average—to exhibit a lower mutation burden
Tan C, Mandell JD, Dasari K, Cannataro VL, Alfaro-Murillo JA, Townsend JP. Heavy mutagenesis by tobacco leads to lung adenocarcinoma tumors with KRAS G12 mutations other than G12D, leading KRAS G12D tumors—on average—to exhibit a lower mutation burden. Lung Cancer 2021, 166: 265-269. PMID: 34736794, DOI: 10.1016/j.lungcan.2021.10.008.Peer-Reviewed Original ResearchThe Prognostic Value of an RT-PCR Test for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Contingent on Timing across Disease Time Course in addition to Assay Sensitivity
Townsend JP, Wells CR. The Prognostic Value of an RT-PCR Test for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Contingent on Timing across Disease Time Course in addition to Assay Sensitivity. Journal Of Molecular Diagnostics 2021, 24: 101-103. PMID: 34974875, PMCID: PMC8717055, DOI: 10.1016/j.jmoldx.2021.10.002.Peer-Reviewed Original ResearchEnvironmental and sex-specific molecular signatures of glioma causation
Claus EB, Cannataro VL, Gaffney SG, Townsend JP. Environmental and sex-specific molecular signatures of glioma causation. Neuro-Oncology 2021, 24: 29-36. PMID: 33942853, PMCID: PMC8730771, DOI: 10.1093/neuonc/noab103.Peer-Reviewed Original ResearchConceptsIDH wild-type tumorsWild-type tumorsEnvironmental risk factorsIDH-mutant tumorsRisk factorsCases of gliomaMolecular signaturesPIK3CA mutationsPossible risk exposuresMutation subtypesCancer effectsExogenous exposureAdult gliomasTumorsWhole-exome sequencing dataGliomasKinase domainMutational signaturesCancer-causing mutationsMalesFemalesNon-coding regionsPIK3R1SexCancer mutational signaturesOptimal COVID-19 quarantine and testing strategies
Wells CR, Townsend JP, Pandey A, Moghadas SM, Krieger G, Singer B, McDonald RH, Fitzpatrick MC, Galvani AP. Optimal COVID-19 quarantine and testing strategies. Nature Communications 2021, 12: 356. PMID: 33414470, PMCID: PMC7788536, DOI: 10.1038/s41467-020-20742-8.Peer-Reviewed Original ResearchThe landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment
Gaffney SG, Perry EB, Chen PM, Greenstein A, Kaech SM, Townsend JP. The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment. Oncotarget 2019, 10: 4532-4545. PMID: 31360302, PMCID: PMC6642048, DOI: 10.18632/oncotarget.27027.Peer-Reviewed Original ResearchJot: guiding journal selection with suitability metrics
Gaffney S, Townsend J. Jot: guiding journal selection with suitability metrics. Journal Of The Medical Library Association 2022, 110: 376-380. PMID: 36589304, PMCID: PMC9782573, DOI: 10.5195/jmla.2022.1499.Commentaries, Editorials and LettersPairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis
Alfaro-Murillo J, Townsend J. Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis. Mathematical Biosciences 2023, 366: 109091. PMID: 37996064, PMCID: PMC10847963, DOI: 10.1016/j.mbs.2023.109091.Peer-Reviewed Original ResearchStrength of selectionEpistatic effectsSelection coefficientsMutation rateHigher-order epistatic effectsLarge mutation ratesLarge selection coefficientsSomatic cancer mutationsUncontrolled cell growthSomatic evolutionMultiple somatic mutationsDriver genesCancer mutationsCancer research communityGenesSomatic genotypeCell growthOncogenesisMutationsSomatic mutationsEvolutionary modelsConsequent trajectoriesCancer genotypesPersonalized cancer therapyMutual exclusivitySeasonality of endemic COVID-19
Townsend J, Hassler H, Lamb A, Sah P, Nishio A, Nguyen C, Tew A, Galvani A, Dornburg A. Seasonality of endemic COVID-19. MBio 2023, 14: e01426-23. PMID: 37937979, PMCID: PMC10746271, DOI: 10.1128/mbio.01426-23.Peer-Reviewed Original ResearchPublic health interventionsSARS-CoV-2Health interventionsSARS-CoV-2 infectionCOVID-19SARS-CoV-2 circulationEffective public health policiesLocal public health effortsEndemic COVID-19Public health effortsPublic healthPublic health policyLong-term dataCOVID-19 transmissionHealth effortsMedical preparednessVaccination driveHealth policyVaried interventionsEndemic diseaseSeasonal surgesInterventionInfectionEffective healthcareEndemic pathogensInfection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments
Townsend J, Hassler H, Emu B, Dornburg A. Infection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments. Journal Of The National Cancer Institute 2023, 115: 1626-1628. PMID: 37599438, PMCID: PMC10699797, DOI: 10.1093/jnci/djad158.Peer-Reviewed Original ResearchConceptsReinfection riskAntineoplastic therapyAntibody dataSARS-CoV-2 infectionSARS-CoV-2 vaccinesChemotherapy-immunotherapy combinationsPfizer-BioNTech BNT162b2COVID-19 vaccinationHigh infection riskFrequent boostingRituximab therapyBreakthrough infectionsVaccination scheduleAntibody levelsBooster scheduleVaccination frequencyImmune responseAdditional interventionsReduced riskHigh riskHormonal treatmentGeneral populationNecessitating assessmentPatientsInfection riskCancer Relevance of Human Genes
Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.Peer-Reviewed Original ResearchConceptsCore cancer genesHuman genesFunctional importanceSomatic mutation frequencySelection pressureGene/protein networksCancer genesHigher somatic mutation frequencyNegative selection pressureGene-gene interaction networksMutation frequencyProtein-truncating variantsGenomic contextCell viabilityGenes decreasesCancer Genome AtlasInteraction networksProtein networkCancer relevanceCancer cell viabilityCell survivalGenesCancer biologyGenome AtlasSearch toolsGEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software
Gaffney SG, Ad O, Smaga S, Schepartz A, Townsend JP. GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software. ACS Central Science 2019, 5: 1159-1169. PMID: 31404233, PMCID: PMC6661976, DOI: 10.1021/acscentsci.9b00111.Peer-Reviewed Original ResearchSoftware infrastructureMulti-institution teamOpen source codeCollaboration softwareCode editingData sharingSource codeTask managementCustom applicationsCollaborative documentInfrastructureCommunicationMultiple fieldsInternal communicationUsersUniversity campusSchedulingSecuritySharingSoftwareTeamCodeImplementationDocumentsGoalOptimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets
Dornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Systematic Biology 2018, 68: 145-156. PMID: 29939341, DOI: 10.1093/sysbio/syy047.Peer-Reviewed Original ResearchConceptsPhylogenetic experimental designOptimal rateExperimental design decisionsGenome-scale data setsTheoretical conditionsSite rate heterogeneityData setsComprehensive theoryAccurate predictionTheoryInferenceExperimental designPhylogenetic problemsOptimalityExistence of charactersPredictionRate heterogeneitySetPhylogenetic inferenceData scrutiny