My research group focusses on the development of bioinformatics methods and their application to open questions in biology. These falls into two main areas i) the functional annotation of proteins and ii) investigating how genetic variation alters these functions. In this talk I will initially discuss our recent work on functional annotation of the minimal bacterial genome. In 2016 Craig Venter and colleagues published a minimal bacterial cell, a synthetic version of Mycoplasma mycoides, with a genome that contained only 473 genes. Surprisingly the function of 149 of these genes was unknown, highlighting our limited understanding of essential biological functions. Using a wide range of computational methods we obtained evidence to assign functions to 66 of the proteins of unknown function. Further, many of the genes encoded transporters that reflect that the minimal genome cells were grown in a nutrient rich medium. Our findings highlight that the environment shapes the nature of a minimal genome, with a set of genes that are truly essential for all life and a further set that are essential depending on the environment in which the cells grow.
Finally, I will talk about our research on comparative virus genomics. There are many closely related species of virus that exhibit different phenotypes, for example pathogenicity or transmissibility. We have developed an approach that combines protein sequence and structural analyses to identify positions that are differentially conserved between species and that may be associated with these phenotypes. I will present our work on Ebolavirus pathogenicity and our most recent findings comparing SARS-coronavirus-2 (the virus that causes COVID-19) with SARS-coronavirus (which caused SARS in 2002-2003).