2017
Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana
Park B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP. Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017, 206: 2105-2117. PMID: 28550014, PMCID: PMC5560809, DOI: 10.1534/genetics.116.199190.Peer-Reviewed Original ResearchConceptsMutation accumulation dataDirectional selectionNatural selectionMutational effectsPhenotypic traitsDirectional natural selectionQuantitative trait lociDivergent lineagesRosette diameterTrait lociHistorical selectionQuantitative traitsLineagesArabidopsisTraitsDensity traitsAccumulation dataDivergenceKey roleUltimate sourceLociSelectionOrganismsKey componentMutations
2012
RBE controls microRNA164 expression to effect floral organogenesis
Huang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development 2012, 139: 2161-2169. PMID: 22573623, DOI: 10.1242/dev.075069.Peer-Reviewed Original ResearchConceptsCUP-SHAPED COTYLEDON1Zinc finger transcriptional repressorKey transcriptional regulatorMiR164 expressionPetal organogenesisArabidopsis flowersPetal developmentPlant developmentEffector genesTranscriptional regulatorsTranscriptional repressorFloral organogenesisGene productsDevelopmental eventsConcomitant regulationGenesOrgan boundariesOrganogenesisExpressionMiR164cCUC2RepressorBoundary specificationPromoterFlowersCodon 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