2009
Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover
2008
Sleuthing the difference a nucleotide can make
Townsend JP. Sleuthing the difference a nucleotide can make. Molecular Ecology 2008, 17: 2793-2795. PMID: 18565029, DOI: 10.1111/j.1365-294x.2008.03824.x.Peer-Reviewed Original ResearchConceptsGene expression polymorphismsExpression polymorphismsGenetic variationGene expressionGenome-wide gene expressionPotential evolutionary impactCis-regulatory regionsAmino acid sensorsDifferential gene expressionSingle nucleotide insertionEcological genomicsEvolutionary impactNatural populationsDifferential fitnessYeast SaccharomycesTranscription factorsGenetic basisNatural isolatesHomonucleotide repeatsNatural variationNucleotide insertionEnvironment interactionPolymorphismAcid sensorsSSY1
2006
Population structure and gene evolution in Saccharomyces cerevisiae
Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 2006, 6: 702-715. PMID: 16879422, DOI: 10.1111/j.1567-1364.2006.00059.x.Peer-Reviewed Original ResearchConceptsPopulation genetic variationPopulation structureS. cerevisiaeDistinct population structureSaccharomyces sensu strictoSulfur-based fungicidesSulfite exporterGene evolutionGene treesGene SSU1Historical selectionTranscription factorsHigh polymorphismNatural isolatesProtein productsCerevisiaeSequence analysisSSU1Oak forestsGreater polymorphismSensu strictoWine yeastSequence studiesFZF1Expression levels