2018
Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development
Wang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend J. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. Fungal Biology Reviews 2018, 32: 249-264. DOI: 10.1016/j.fbr.2018.02.001.ChaptersModel speciesFungal developmentGenome-wide gene expression dataEvolutionary developmental biologyEvo-devo researchGenome-wide analysisSystems biology strategiesGene expression dataEvolutionary genomicsSpecies phylogenyGenetic screenDevelopmental biologyDevelopmental traitsGene networksRegulatory networksFungal modelCell biologyModern biologyFossil recordKnockout strategiesDevelopmental processesMultiple speciesSystems biologyMolecular geneticsExpression data
2012
Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae
Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology And Evolution 2012, 4: 1061-1079. PMID: 23019066, PMCID: PMC3514956, DOI: 10.1093/gbe/evs084.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisCopperDNA-Binding ProteinsDose-Response Relationship, DrugGene Expression ProfilingGene Expression Regulation, FungalGene-Environment InteractionGenes, FungalGenetic VariationMetabolic Networks and PathwaysMicroarray AnalysisNuclear ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsTranscriptomeConceptsPopulation variationReaction normsGene expression reaction normsGene expressionNovel ecological contextsGenome-wide mRNA levelsGenetic backgroundRelevant copper concentrationsAbundance of variationMitotic fitnessSulfur homeostasisPlastic phenotypesDownstream metabolic consequencesPlastic variationMost genesCopper stressPhenotypic variationGene networksAbundant genesGenetic variationCopper gradientExpression variationEcological contextDifferential expressionGenes