Alex Cope

Postdoctoral researcher
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alexander.copeobfuscate@rutgers.edu

I received my undergraduate degrees in mathematics and computer science from Centre College (Danville, Kentucky) in 2011. I went on to receive my PhD in the Genome Science and Technology graduate program at the University of Tennessee, Knoxville and Oak Ridge National Laboratory, whereI was advised by Dr. Michael Gilchrist and Dr. Robert Hettich. During this time, I developed and applied evolutionary models to omics-scale data for the purposes of testing biological hypotheses related to codon usage, protein localization and folding, and gene expression coevolution. I'm also a maintainer for the AnaCoDa R package found on CRAN, which includes various models for analyzing codon usage patterns and ribosome profiling data.

I am currently working on the effects of “extreme” environments on the dynamics of protein synthesis and how extremophilic microbes have adapted to maintain protein synthesis in these environments.

When not researching, I'm usually in the gym or playing guitar.

Previous publications

  1. Cope AL, O'Meara B, Gilchrist MA. 2020. Gene Expression of Functionally- Related Genes Coevolves Across Fungal Species: Detecting Coevolution of Gene Expression Using Phylogenetic Comparative Methods. BMC Genomics, 21:370 DOI

  2. Poudel S, Cope AL (Co-first author), O'Dell K, Guss AM, and Hettich RL. (In Review - mSystems). An integrated approach to characterize proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 as potential genetic engineering targets.

  3. Cope AL, Hettich RL, and Gilchrist MA. 2018. Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons. Biochimica et Biophysica Acta – Biomembranes 1860(12):2479-2485 DOI

  4. Landerer C, Cope AL, Zaretzki R, Gilchrist MA. 2018. AnaCoDa: analyzing codon data with Bayesian mixture models. Bioinformatics, 34(14):2496-2498 DOI