Research
My PhD was part of an EU-wide programme designed to understand marine processes, particularly in relation to the cycling of carbon, a topic of even more relevance now. On completion of my PhD, I worked on a “Natural Products Drug Discovery” project to understanding the diversity of Lithistid sponges, in particular those sponges thought to be closely related to Discodermia dissoluta, which produces the potent inhibitor of tumour cell growth, Discodermolide. This was funded in the UK by BBSRC and carried out at the Natural History Museum, London.
I started my bioinformatics research group in 1999 with a view to working on the evolution of prokaryotic genomes. I developed multivariate analysis software and found that bacteria can have two significantly different codon usage patterns on their lagging- and leading-strands of replication (1). My group has played a significant role in understanding the origin of Eukaryotes (2-6). We have developed several programs for phylogenetic model selection and computing phylogenetic trees in a distributed computing environment (7-9). We have shown lateral gene flows into Halophiles (10), the origins of major clades of archaea were facilitated by introgression from bacteria (11), we have developed a method of identifying reassortment in influenza (12) and we have shown gene replacement in fatty acid metabolism in Mycobacterium tuberculosis (13). We have collaborated on major international population genomic efforts, such as the worldwide study of polar bear population genomics (14). Most recently we have focussed on prokaryotic pangenomes (15-17). I have been part of more than €40 Million in programme grants, as well as several project grants and studentships directly awarded to the lab over the last two decades.
PAPERS CITED
1. McInerney, J. O. Proc Natl Acad Sci USA 95, 10698-10703 (1998).
2. McInerney et al., Nat Rev. Microbiol. 12, 449-455 (2014).
3. Cotton & McInerney Proc Natl Acad Sci USA 107, 17252-17255 (2010).
4. Alvarez-Ponce & McInerney Genome Biol Evol 3, 782-790 (2011).
5. Alvarez-Ponce, et al. Proc Natl Acad Sci USA 110 (2013).
6. Ku et al. Nature 524, 427-432 (2015).
7. Keane et al BMC Evol Biol 6, 29, doi:1471-2148-6-29 (2006).
8. Keane et al Nucleic Acids Res 35, W33-37 (2007).
9. Keane et al Bioinformatics 21, 969-974 (2005).
10. Nelson-Sathi, et al. Proc Natl Acad Sci USA 109, 20537-20542 (2012).
11. Nelson-Sathi et al. Nature 517(7532):77-80 (2014).
12. Svinti, et al BMC Evol Biol 13, 1 (2013).
13. Kinsella, & McInerney. Trends Genet 19, 687-689 (2003).
14. Liu et al Cell 157(4)785-794 (2014).
15. McInerney, et al Nat Microbiol 2, 17040 (2017).
16. Domingo-Sananes & McInerney Trends in Micro 29 (6), 493-503 (2021)
17. Beavan, et al Proc Natl Acad Sci USA 121 (1), e2304934120 (2024)