2016
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae
Neymotin B, Ettorre V, Gresham D. Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics 2016, 6: 3475-3483. PMID: 27633789, PMCID: PMC5100846, DOI: 10.1534/g3.116.032276.Peer-Reviewed Original ResearchMRNA degradation ratesGreen fluorescent proteinGC contentRibosome densityTranscriptional propertiesVariants of green fluorescent proteinThird position of codonsTranscriptome-wide variationGenome-wide variationSaccharomyces cerevisiae</i>Positions of codonsProperties of transcriptionIncreasing GC contentTranslation start siteDecreased ribosome densityRate of mRNA degradationThird positionCoding sequence variantsDegradation of mRNABudding YeastSynonymous sitesCodon usageSaccharomyces cerevisiaeTranscript lengthStart site
2006
The Role of Selection in the Evolution of Human Mitochondrial Genomes
Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. The Role of Selection in the Evolution of Human Mitochondrial Genomes. Genetics 2006, 172: 373-387. PMID: 16172508, PMCID: PMC1456165, DOI: 10.1534/genetics.105.043901.Peer-Reviewed Original ResearchConceptsHuman mitochondrial genomeMitochondrial genomeNegative Tajima's D valuesMutation rateHeavy strand DNAMammalian mitochondrial DNATajima's D valuesRole of selectionAmino acid replacementsNonsynonymous base substitutionsHigh mutation rateSynonymous sitesPhylogenetic treeMitochondrial DNAPhylogenetic analysisCodon usageCoalescent timesCold adaptationNonsynonymous changesAcid replacementsSynonymous transitionsDivergent poolValine codonNonsynonymous mutationsBase substitutions
1997
Evolution of codon usage bias in Drosophila
Powell J, Moriyama E. Evolution of codon usage bias in Drosophila. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 7784-7790. PMID: 9223264, PMCID: PMC33704, DOI: 10.1073/pnas.94.15.7784.Peer-Reviewed Original ResearchConceptsCodon usage biasHigher codon usage biasUsage biasBiased genesMutation biasSynonymous sitesCodon biasAmino acidsLow codon usage biasDrosophila genesDNA evolutionEffect of recombinationSmall geneIndividual amino acidsLong genesSynonymous substitutionsTRNA poolPreferred codonsSynonymous polymorphismWobble positionDrosophilaSame nucleotideSelection hypothesisGenesLines of evidence
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