A. L. Cope

Phylogenetic analysis reveals how selection and mutation shape the coevolution of mRNA and protein abundances

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.

Determining the effects of temperature on the evolution of bacterial tRNA pools

This study investigates how environmental temperature influences the evolution of bacterial tRNA pools and finds that thermophiles have more anticodons, which may increase translation errors.

Decoupling of evolutionary changes in mRNA and protein levels

The paper develops a theoretical model to study coevolution of mRNA and protein levels, finding that stabilizing selection leads to compensatory evolution, while directional selection causes negative correlation across lineages and positive correlation across genes.

Re-examining supposed correlations between synonymous codon usage and protein bond angles in E. coli

The paper re-examines a correlation between synonymous codon usage and protein bond angles in E. coli, finding that the original results may be confounded by gene expression and methodological noise.

Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage

The paper assesses how intragenomic variation in mutation bias affects estimates of selection on synonymous codon usage in yeast, finding that ignoring this variation can underestimate selection signals.

Tracking extracellular vesicle (EV) cargo as a platform for studying EVomics, signaling, and targeting in vivo

The paper presents a platform using C. elegans to track extracellular vesicles and identify their cargo, demonstrating animal-to-animal EV targeting during mating.

Quantifying shifts in natural selection on codon usagebetween protein regions: A population genetics approach

This study quantifies shifts in natural selection on codon usage between protein regions using a population genetics approach, revealing a weak relationship between codon usage and protein structure.

Gene Expression of Functionally-Related Genes Coevolves Across Fungal Species: Detecting Coevolution of Gene Expression Using Phylogenetic Comparative Methods

This study uses phylogenetic comparative methods to detect coevolution of gene expression across 18 fungal species, finding that physically interacting proteins show stronger coevolution signals.

Quantifying Codon Usage in Signal Peptides: Gene Expression and Amino Acid Usage Explain Apparent Selection for Inefficient Codons

The paper investigates codon usage in E. coli signal peptides and finds that apparent selection for inefficient codons is explained by amino acid usage and gene expression, not selection.