Premal Shah

Epistasis and the dynamics of reversion in molecular evolution

The paper analyzes how reversion rates of amino acid substitutions decrease over time in the presence of epistasis, showing that longer absence leads to lower reversion probability.

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

The paper improves ribosome-footprint and mRNA measurements in yeast, revealing new insights into translation dynamics and regulation.

Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data alone.

This paper introduces a Bayesian model to estimate gene expression, codon-specific translational efficiencies, mutation biases, and selection coefficients from genomic data without requiring gene expression measurements.

A codon model of nucleotide substitution with selection on synonymous codon usage

The paper introduces a new codon substitution model that incorporates selection on synonymous codon usage and tests its performance on yeast genes, finding it provides better fit in most cases.