2025
Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes
Wang Y, Wang F, Meng G, Lopez-Giraldez F, Dong C, Wang Z, Townsend J. Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes. Molecular Biology And Evolution 2025, 42: msaf131. PMID: 40452442, PMCID: PMC12203517, DOI: 10.1093/molbev/msaf131.Peer-Reviewed Original ResearchConceptsRate of gene expression evolutionGene expression evolutionExpression evolutionGene expressionPhenotypic evolutionHeterogeneous rates of evolutionNonsynonymous to synonymous substitution ratesRates of phenotypic evolutionDevelopmental stagesSingle-copy orthologsGene sequence evolutionSynonymous substitution ratesRate of evolutionExpression of genesFunctional pathway analysisCarbon metabolismEvolutionary forcesConsequent phenotypesSexual reproductionSequence evolutionConserved pathwaysMeiosis pathwaysSubstitution ratesCell cyclePathway analysis
2023
Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts
Dighe A, Maziarz J, Ibrahim-Hashim A, Gatenby R, Kshitiz, Levchenko A, Wagner G. Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts. IScience 2023, 27: 108593. PMID: 38174318, PMCID: PMC10762354, DOI: 10.1016/j.isci.2023.108593.Peer-Reviewed Original ResearchGene expression changesGene expression evolutionEndometrial stromal fibroblastsExpression evolutionExpression changesCell typesGene expressionSimilar gene expression changesSubstantial gene expression changesGene expression profilesSkin fibroblastsMultiple cell typesEvolutionary correlationPhylogenetic evidenceEvolutionary changeDermal skin fibroblastsMammalian speciesExpression profilesPlacental invasivenessComparative datasetCancer growthCultured skin fibroblastsStromal fibroblastsFibroblastsMouse strainsChapter 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
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