2017
New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset
Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics And Evolution 2017, 110: 27-38. PMID: 28254474, DOI: 10.1016/j.ympev.2017.02.017.Peer-Reviewed Original Research
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
2010
Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny
Ohenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 2010, 102: 1089-1095. PMID: 20943508, DOI: 10.3852/09-317.Peer-Reviewed Original Research
2006
Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions Of The Royal Society B Biological Sciences 2006, 361: 1947-1963. PMID: 17062413, PMCID: PMC1764934, DOI: 10.1098/rstb.2006.1923.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGlobal geographic rangeGeographic rangeSpecies recognitionFungal speciesGenetic isolationEukaryotic microbesSmall organismsNon-exclusive reasonsPhylogenetic species recognitionEndemic speciesRecognizable morphological changesEukaryotic speciesMorphological changesPhylogenetic speciesGeographic limitsReproductive isolationMorphological speciesKingdom FungiMorphological charactersMicrobial organismsGenetic changesSpeciesMorphological differencesOrganismsFungiPhase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii
Johannesson H, Kasuga T, Schaller RA, Good B, Gardner MJ, Townsend JP, Cole GT, Taylor JW. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics And Biology 2006, 43: 545-559. PMID: 16697669, DOI: 10.1016/j.fgb.2006.02.003.Peer-Reviewed Original ResearchConceptsGene expressionPhase-specific gene expressionPathogenic phaseNumber of genesConsistent differential expressionOpen reading frameDimorphic fungal pathogenDimorphic human pathogenic fungusHuman pathogenic fungiTranscriptional profilingEntire speciesEnvironmental stressReading frameComparative hybridizationMorphological adaptationsFungal pathogensCandidate genesSaprobic phasePathogenic fungiMetabolism of lipidsDifferential expressionGenesFungal isolatesElevated expressionDevelopmental phases
2005
Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii
Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics 2005, 171: 109-117. PMID: 15965255, PMCID: PMC1456504, DOI: 10.1534/genetics.105.040923.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, FungalCoccidioidesCoccidioidomycosisDNA, FungalEvolution, MolecularGene ConversionGenetic VariationHumansMembrane GlycoproteinsMutationPhylogenyPolymorphism, GeneticRecombination, GeneticRepetitive Sequences, Nucleic AcidSequence Analysis, DNASpecies SpecificityTandem Repeat SequencesConceptsPathogenic fungus Coccidioides immitisConcerted evolutionProtein-coding genesC. posadasiiGenetic distance analysisPoint mutation rateHost-pathogen interactionsCell surface proteinsGenome dynamicsPathogen's benefitMultigene familyUnequal crossingGeographic rangeFungus Coccidioides immitisRepetitive domainEntire geneMutation rateRepetitive arraysSurface proteinsDistance analysisGenesHost immune systemImmune systemImmunodominant proteinsParasitic phaseDesigning Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species
Townsend JP, Taylor JW. Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species. Methods In Enzymology 2005, 395: 597-617. PMID: 15865986, DOI: 10.1016/s0076-6879(05)95031-3.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsDNA, ComplementaryGene Expression RegulationNucleic Acid HybridizationOligonucleotide Array Sequence AnalysisRNA, MessengerSpecies SpecificityConceptsGene expressionGenome-wide gene expressionGene regulation differencesDifferential gene expressionMultiple developmental stagesMultiple environmental conditionsMultiple speciesDevelopmental stagesRegulation differencesSpeciesEnvironmental conditionsMultiple individualsMicroarrayExpressionSuch studiesStatistical powerExperimental protocol
2002
Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 2002, 3: research0071.1. PMID: 12537560, PMCID: PMC151173, DOI: 10.1186/gb-2002-3-12-research0071.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremDNA-Binding ProteinsEthanolGene DeletionGene Expression ProfilingGene Expression Regulation, FungalGenotypeModels, GeneticNuclear ProteinsOligonucleotide Array Sequence AnalysisRNA, FungalRNA, MessengerSaccharomyces cerevisiae ProteinsSpecies SpecificityTranscription FactorsZincConceptsGene of interestExpression levelsGene expression levelsTwofold thresholdGene basisTranscriptional responseMicroarray comparisonsMinimal mediumExpression differencesBiological insightsMicroarray analysisEthanol shockMicroarray dataRelative mRNA levelsGenesMRNA levelsMultiple strainsBayesian analysisDevelopmental state