Featured Publications
Optimal 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
2016
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
Dornburg A, Fisk JN, Tamagnan J, Townsend JP. PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Ecology And Evolution 2016, 16: 262. PMID: 27905871, PMCID: PMC5134231, DOI: 10.1186/s12862-016-0837-3.Peer-Reviewed Original ResearchConceptsParallel processingOpen-source software packageBayesian posterior distributionLack of softwareOpen-source programPhylogenetic experimental designProbability of resolutionUser hardwareData explorationData visualizationNext-generation sequence datasetsInformation contentSource programNovel visualizationPosterior distributionBayesian settingAdditional sample dataPower usersDataset partitionsBayesian approachSequence data setsSoftware packageDatasetGenomic information contentSoftware
2011
Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference
Townsend JP, Leuenberger C. Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference. Systematic Biology 2011, 60: 358-365. PMID: 21303824, DOI: 10.1093/sysbio/syq097.Peer-Reviewed Original Research
2004
Monitoring and modeling horizontal gene transfer
Nielsen KM, Townsend JP. Monitoring and modeling horizontal gene transfer. Nature Biotechnology 2004, 22: 1110-1114. PMID: 15340481, DOI: 10.1038/nbt1006.Peer-Reviewed Original ResearchConceptsHorizontal gene transfer eventsPopulation genetic approachesGene transfer eventsStrength of selectionHorizontal gene transferPopulation genetic modelsWild-type bacteriaLarge bacterial populationsHGT hypothesisBacterial generation timesHGT eventsTransgenic plantsGenetic approachesBacterial communitiesBacterial transformantsBacterial populationsPopulation sizeCurrent monitoring effortsGene transferTransfer eventsYears of growthGeneration timeGenetic modelsBacteriaTime of sampling
2003
Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
Townsend JP. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 2003, 4: 41. PMID: 14525623, PMCID: PMC239860, DOI: 10.1186/1471-2164-4-41.Peer-Reviewed Original Research