2023
Chapter 5 Measurement and meaning in gene expression evolution
Diaz R, Wang Z, Townsend J. Chapter 5 Measurement and meaning in gene expression evolution. 2023, 111-129. DOI: 10.1016/b978-0-323-91810-7.00008-x.ChaptersGene expressionPhenotypic evolutionGene expression evolutionMessenger RNAEffects of epistasisIndividual gene expressionRibonucleic acid sequencingExpression evolutionNonmodel speciesFunctional genomicsGenomic scaleTranscriptional networksGene functionRelative mRNA abundancePhenotypic variationPopulation geneticsReference genomeTranscriptome profilingBiological traitsMolecular adjustmentsQuantitative traitsPhenotypic varianceGene interactionsGenetic controlExpression variation
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