Intro

My research interests include phylogenetics, viral genomics, host-virus molecular interactions and genome compositional biases. My current research involves exploring the evolutionary history of SARS-CoV-2 and its related Sarbecoviruses in their respective bat hosts, and determining genomic signatures of virus-host arms race evolution especially relating to interferon immunity. I received my BSc in Evolutionary Biology from the University of Edinburgh in 2019, doing my dissertation project on the determinants of codon usage bias in Schistosoma mansoni.

Current Projects

DinuQ: The dinucleotide quantification Python3 package

The DinuQ (Dinucleotide Quantification) Python3 package provides a range of metrics for quantifying nucleotide, dinucleotide representation and synonymous codon usage in a DNA/RNA sequence. These include the recently developed corrected Synonymous Dinucleotide Usage (SDUc) and corrected Relative Synonymous Dinucleotide Usage (RSDUc).

Code and documentation at the DinuQ GitHub repository.

Selected Publications

MacLean, O., Lytras, S., et al. (2020) Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen. bioRxiv. doi: 10.1101/2020.05.28.122366 [preprint]

Lytras, S., Hughes, J. (2020) Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses. Viruses. doi: 10.3390/v12040462