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 ResearchOptimal 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 Research
2016
PhyloOncology: Understanding cancer through phylogenetic analysis
Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica Et Biophysica Acta (BBA) - Reviews On Cancer 2016, 1867: 101-108. PMID: 27810337, PMCID: PMC9583457, DOI: 10.1016/j.bbcan.2016.10.006.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAdaptation, PhysiologicalAlgorithmsAnimalsBiomarkers, TumorCell Transformation, NeoplasticEvolution, MolecularGene Expression Regulation, NeoplasticGenetic FitnessGenetic Predisposition to DiseaseGenomicsHeredityHumansModels, GeneticMutationNeoplasmsPedigreePhenotypePhylogenySignal TransductionSystems BiologyTime FactorsConceptsDr. Robert A. GatenbyGenome-scale dataSystems biology approachPowerful systems biology approachUse of phylogeneticsPhylogenetic analysisBiology approachPhylogenetic applicationsSubclonal evolutionCancer biologyCancer progressionSuite of algorithmsPhylogeneticsCancer data setsCancer samplesImproved therapeutic interventionRobust approachDecades of researchFundamental insightsNew toolBiologyDiverse fieldsGatenbyData setsTherapeutic interventionsClimatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14601-14608. PMID: 27791071, PMCID: PMC5187705, DOI: 10.1073/pnas.1604985113.Peer-Reviewed Original ResearchConceptsPlague resistanceEnvironmental driversIntense natural selectionWild host populationsIntense selective pressureEvolutionary driversPossible evolutionary basisHost evolutionNatural selectionDisease resistanceEvolutionary selectionFlea population dynamicsEvolutionary basisSelective pressureEvolutionary processesPopulation dynamicsHost populationsWildlife hostsLocal persistencePlague dynamicsCommensal ratsDisease agentsPowerful insightsDisease transmissionEcologyEarly and multiple origins of metastatic lineages within primary tumors
Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2140-2145. PMID: 26858460, PMCID: PMC4776530, DOI: 10.1073/pnas.1525677113.Peer-Reviewed Original ResearchConceptsMetastatic lineagesGenetic changesEarly genetic divergenceMolecular evolutionary modelsSingle genetic changeDivergent lineagesTumor phylogeneticsDivergence timesAncestral stateGenetic divergenceCancer lineagesPhylogenetic analysisEvolutionary processesLineagesCancer evolutionMultiple originsDriver genesCancer biologyCancer progressionSomatic mutationsTumor developmentEvolutionary modelsDriver mutationsChronogramMutations
2014
Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa
Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLOS ONE 2014, 9: e110398. PMID: 25329823, PMCID: PMC4203796, DOI: 10.1371/journal.pone.0110398.Peer-Reviewed Original ResearchConceptsNeurospora crassaSexual reproductionN. crassaGenetic basisThree-dimensional fruiting bodiesSexual spore productionN. crassa geneBody developmentDiverse life historiesGenome-wide transcriptomicsSexual developmentStudy of meiosisGene expression differencesList of genesGene expression levelsMeiotic machineryMeiosis genesOrthologous genesSporulation genesNeurospora speciesGlomerella graminicolaEvolutionary timeAnimal taxaPerithecium formationLife history
2012
RBE controls microRNA164 expression to effect floral organogenesis
Huang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development 2012, 139: 2161-2169. PMID: 22573623, DOI: 10.1242/dev.075069.Peer-Reviewed Original ResearchConceptsCUP-SHAPED COTYLEDON1Zinc finger transcriptional repressorKey transcriptional regulatorMiR164 expressionPetal organogenesisArabidopsis flowersPetal developmentPlant developmentEffector genesTranscriptional regulatorsTranscriptional repressorFloral organogenesisGene productsDevelopmental eventsConcomitant regulationGenesOrgan boundariesOrganogenesisExpressionMiR164cCUC2RepressorBoundary specificationPromoterFlowersDifferential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa
Wang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics And Biology 2012, 49: 405-413. PMID: 22469835, PMCID: PMC3397380, DOI: 10.1016/j.fgb.2012.03.004.Peer-Reviewed Original ResearchConceptsCarrot agarPerithecial developmentNeurospora crassaNutritional resourcesCore metabolic genesDifferent fungiSexual developmentDiverse environmental stimuliMetabolic gene expressionKey regulatory roleDevelopmental programMetabolic genesMicroarray hybridizationTranscriptional profilesAnabolic pathwaysExpression patternsGene expressionBody sizeMetabolic differentiationRegulatory roleBody developmentEffects of nutritionNutritional environmentEnvironmental stimuliBody morphology
2011
Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods
Mathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. Methods In Molecular Biology 2011, 722: 61-77. PMID: 21590413, DOI: 10.1007/978-1-61779-040-9_5.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsExpensive softwareData generationMultiple platformsGenomic data generationEfficient waySuch dataPossible informationGenome sequencing technologiesKind of analysisData analysisFungal dataUsersDifferent environmentsMicroarray dataBioinformaticistsCostExperimental costSoftwareProtocolBottleneckPlatformTaskTechnologyDataAcademia
2010
Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
Townsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology 2010, 59: 446-457. PMID: 20547780, DOI: 10.1093/sysbio/syq025.Peer-Reviewed Original ResearchConceptsPhylogenetic experimental designOptimal rateAsymptotic impactAnalytical predictionsAddition of charactersOptimal selectionObvious applicationApproximate ideaEstimation of ratesCurrent phylogenetic studiesOptimal efficiencyTheoryDeep internodesTaxon additionRate of evolutionExperimental designNew taxonPhylogenetic informativenessPhylogenetic relationships