2022
Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides
Gortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. Journal Of Fungi 2022, 8: 854. PMID: 36012842, PMCID: PMC9410309, DOI: 10.3390/jof8080854.Peer-Reviewed Original ResearchPolar growthTranscript abundanceConidial germinationGlucanase-encoding geneOnset of germinationTranscriptional hubsTranscriptional programsTrichoderma asperelloidesHyphal growthTranscriptional profilesDevelopmental eventsChitin synthaseHost recognitionDifferential expressionGerminationSpecific membersDormant conidiaFirst branchingGenomeGenesInitial branchingAbundanceNetwork analysisExpressionMorphological progression
2013
Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection
McBride RC, Boucher N, Park DS, Turner PE, Townsend JP. Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection. FEMS Yeast Research 2013, 13: 162-179. PMID: 23122216, DOI: 10.1111/1567-1364.12019.Peer-Reviewed Original ResearchConceptsGlobal gene expressionGene expressionFungal hostUnusual life historyHost gene expressionAsexual modeAsexual reproductionFungal communitiesYeast responseReproductive successLife historyFungal cellsUbiquitous distributionLA virusFungal growthMycoviral infectionFungiViral infectionHostExpressionFitnessImportant roleDeleterious impactSaccharomycesVirus
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
2009
Evolving gene expression: from G to E to G×E
Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to G×E. Trends In Ecology & Evolution 2009, 24: 649-658. PMID: 19699549, PMCID: PMC2805859, DOI: 10.1016/j.tree.2009.06.011.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene expressionMode of evolutionGene expression data setsTerms of geneticsExpression data setsGenetic variationBreadth of conclusionsEnvironmental responsesGxE interactionsMultiple individualsGeneticsExpressionSingle strainEnvironmental controlEvolutionEnvironmental effectsKey componentSpeciesG×EInteractionStrains
2005
Designing 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 StatementsConceptsGene expressionGenome-wide gene expressionGene regulation differencesDifferential gene expressionMultiple developmental stagesMultiple environmental conditionsMultiple speciesDevelopmental stagesRegulation differencesSpeciesEnvironmental conditionsMultiple individualsMicroarrayExpressionSuch studiesStatistical powerExperimental protocol