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
2022
Placing human gene families into their evolutionary context
Dornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.Peer-Reviewed Original ResearchConceptsHuman gene familyGene familyHuman genomeEvolutionary contextGene family evolutionNon-model organismsFirst human genomeGenome biologyComparative genomicsFamily evolutionDistant speciesDraft sequenceGenomic studiesGene expressionGenome sequencingSequence complexityGenomeCancer biologyUnprecedented insightsNovel discoveriesCritical roleOrganismsBiologyComparative approachFamily
2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomology
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
2013
Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
2012
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13: 43. PMID: 22435713, PMCID: PMC3368730, DOI: 10.1186/1471-2105-13-43.Peer-Reviewed Original ResearchConceptsCodon usage biasNucleotide compositionUsage biasGenome evolutionGene functionProtein functionCodon usageNatural selectionCodon positionsTranslational efficiencySelective pressureSequence compositionGene expressionSequence analysisSimulated sequencesSequenceGenomeGenesFundamental importanceMutationsInformative estimationExpression
2005
Horizontal gene transfer, genome innovation and evolution
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 2005, 3: 679-687. PMID: 16138096, DOI: 10.1038/nrmicro1204.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHorizontal gene transferHGT eventsImportance of HGTLife historyConcatenation of genesGene transferTypes of genesGroups of organismsGene historiesReticulation eventsPhylogenetic signalTaxonomic samplingMicrobial evolutionSelective sweepsGenome innovationPhylogenetic reconstructionEvolutionary biologyProkaryotic genomesSuch genesMicrobial communitiesPhylogenetic analysisGene swappingHorizontal transferTaxonomic classificationGenes
2004
Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster
Townsend JP, Rand DM. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 2004, 93: 98-103. PMID: 15138453, DOI: 10.1038/sj.hdy.6800484.Peer-Reviewed Original ResearchConceptsMtDNA length variationNew World samplesDrosophila melanogasterFounder eventsMitochondrial genome size variationLength variationMtDNA length variantsGenome size variationDifferent mutational pressureOld World populationsD-loop regionNew World populationsMutation-selection dynamicsPatterns of variationLevel of heteroplasmyMitochondrial genomeRelaxed selectionMutational pressureControl regionGenetic variationRange expansionLength variantsMutational dynamicsNew WorldLinkage relationships