PhD, North Carolina State University
Postdoc, Pennsylvania State University
Office: 305 Ricks Hall
Website: Visit my Homepage
My research centers on the development of statistical methods and software for studying processes of molecular evolution. Historically, my work has explored a variety of applications where simple stochastic models of sequence evolution were not sufficient, and that theme continues to this day. My current work includes: (i) model selection techniques and multi-model inferential procedures to estimate evolutionary parameters; (ii) modeling heterogeneity of silent substitution rates across genes, sites, and lineages; and (iii) continued development of the HyPhy molecular evolutionary analysis platform.
Kosakovsky Pond SL, Delport W, Muse SV, and Schffler K. (2010). Correcting the bias of empirical frequency parameter estimators in codon models. PLoS ONE. 5:e11230.
Gibson GG, and Muse SV. (2009). A Primer of Genome Science–3rd edition. Sinauer
Kosakovsky Pond SL, and Muse SV. (2005). Modeling heterogeneity of synonymous and nonsynonymous nucleotide substitution rates across sites. Mol. Biol. Evol. 22(12):2375–2385.
Muse SV. (1996). Estimating synonymous and nonsynonymous nucleotide substitution rates. Mol. Biol. Evol. 13:105–114.
Muse SV, and Gaut BS. (1994). A likelihood approach for comparing synonymous and nonsysnonymous nucleotide substitution rates with application to the chloroplast genome. Mol. Biol. Evol. 11:715–724.