2024

The Importance of Nonsense Errors: Estimating the Rate and Implications of Drop-Off Errors during Protein Synthesis

Cope et al. 2024. bioRxiv

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

Cope et al. 2024. bioRxiv

Evolutionary principles underpinning codon usage bias: patterns, functions, and mechanisms

Cope et al. 2024. EcoEvoRxiv

Examining the Effects of Temperature on the Evolution of Bacterial tRNA Pools

Jain and Cope, Gen. Biol. and Evol.

Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli

Akeju and Cope, Gen. Biol. and Evol.

2023

On the Decoupling of Evolutionary Changes in mRNA and Protein Levels

Jiang et al. Mol. Biol. and Evol.

2022

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

Favate et al. 2022. eLife.

Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage

Cope and Shah 2022. Plos Genetics.

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

Cope and Gilchrist 2022. BMC Genomics.

Isolation, profiling, and tracking of extracellular vesicle cargo in Caenorhabditis elegans

Nikonorova et al. 2022. Current Biology.

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Cope et al. 2022. Bioinformatics.

2021

Exploring ribosome-positioning on translating transcripts with ribosome profiling

Cope et al. 2021. Methods in Molecular Biology.

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Skalenko et al. 2021. PNAS.

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Poudel et al. 2021. Biotechnology for Biofuels.

2020

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Cope et al. 2020. BMC Genomics

2018

Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons

Cope et al. 2018. Biochimica et Biophysica Acta (BBA) - Biomembranes.

AnaCoDa: analyzing codon data with Bayesian mixture models

Landerer et al. 2018. Bioinformatics.