The availability of viral genomes provides unprecedented opportunities for studying the viral evolutionary process. Codon-substitution models aim to model the evolutionary process of viral genes by explicitly incorporating mutational biases and selective pressure. In this project the student will participate in development of mutation-selection models of codon substitution, and compile and analyze alignments of viral sequences, to infer changes in selection profile of viral genes, such as changes in selection when the virus jumps hosts or under drug treatments.
The project provides training in computer/bioinformatics skills, and quantitative skills of statistical data analysis.
Yang, Z. 2019. Adaptive molecular evolution. Pages 369-395 in Handbook of Statistical Genomics (D. Balding, I. Moltke, and J. Marioni, eds.). Wiley, New York.
Tamuri, A. U., N. Goldman, and M. dos Reis. 2014. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics 197:257–271.
Tamuri, A. U., M. Dos Reis, A. J. Hay, and R. A. Goldstein. 2009. Identifying changes in selective constraints: host shifts in influenza. PLoS Comput. Biol. 5:e1000564.
Yang, Z., and R. Nielsen. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol. Biol. Evol. 25:568-579.
Yang, Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.