Shifts in gene expression are a major contributor to phenotypic variation within and across species, Gene expression is the result of multiple regulatory elements (REs) that span transcription to post-translation, leading to a complex interplay in the evolution of different REs. Phylogenetic studies of gene expression have emerged as a powerful approach to test if variation in gene expression across species is consistent with non-adaptive or adaptive evolution. Although useful, phylogenetic studies of are gene expression are often detached from the evolution of the underlying gene regulation. Building off my expertise in evolutionary genetics, transcriptomics, and proteomics, I study gene expression evolution at multiple regulatory levels using a combination of bioinformatics and phylogenetic.

Publications

Phylogenetic analysis reveals how selection and mutation shape the coevolution of mRNA and protein abundances Cope et al. 2024. bioRxiv

On the Decoupling of Evolutionary Changes in mRNA and Protein Levels Jiang et al. Mol. Biol. and Evol.

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow Cope et al. 2022. Bioinformatics.

Exploring ribosome-positioning on translating transcripts with ribosome profiling Cope et al. 2021. Methods in Molecular Biology.

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.

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