2017
Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology And Evolution 2017, 34: 3006-3022. PMID: 28962009, PMCID: PMC5850860, DOI: 10.1093/molbev/msx213.Peer-Reviewed Original ResearchConceptsPoisson random fieldRandom fieldsEnsemble of modelsRandom field frameworkField frameworkClustering modelHistorical demographic trendsAmino acid-altering substitutionsSelection intensityEnsembleHigh powerUniform selectionProtein-coding genesProtein coding genesHeterogeneity of selectionDNA sequence polymorphismsComparison of polymorphisms
2014
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3: Genes, Genomes, Genetics 2014, 4: 1731-1745. PMID: 25053707, PMCID: PMC4169166, DOI: 10.1534/g3.114.012617.Peer-Reviewed Original ResearchConceptsNeurospora crassaRNA-seqFilamentous fungus Neurospora crassaGenome-wide characterizationProtein coding genesFungus Neurospora crassaPrevious microarray studyRibosome biogenesisCoding genesTranscriptional responseRRNA metabolismCellular metabolismMicroarray studiesGenesCrassaSignificant oxidative stressRNA levelsOrganismsMRNA levelsOxidative stressMRNAMetabolismBiogenesisTranscriptsMycelium