Alexander L. Cope

This paper models nonsense error rates in protein synthesis using ribosome profiling data and finds codon-specific variation in error rates and evidence of selection against nonsense errors.

This study estimates biophysical parameters of gene expression in multiple vertebrate species and finds coordinated evolution under evolutionary systems drift and additional constraints on transcriptional bursting.

The paper quantifies natural selection and mutation biases on a per-codon basis across budding yeast species, showing how changes in the tRNA pool influence codon usage bias and macroevolutionary variation.

This study uses a phylogenetic model to analyze multi-species data and finds that protein abundances are under strong stabilizing selection, while mRNA abundances adapt more quickly due to mutational opportunity.

riboviz 2 provides a flexible and robust workflow for analyzing and visualizing Ribo-seq data with improved functionality and usability.