James O. McInerney

James O. McInerney is an Irish-born microbiologist, computational evolutionary biologist, professor, and former head of the School of Life Sciences^[1] at the University of Nottingham. He is an elected Fellow of the American Society for Microbiology and elected Fellow of the Linnean Society. In June 2020 he was elected president-designate of the Society for Molecular Biology and Evolution and in 2022 he took up the role of President.

James McInerney at the School of Life Sciences, University of Nottingham.

Early life and education

McInerney completed his bachelor's degree at NUI Galway.^[2] In 1994, he was awarded a PhD (also from NUI Galway).^[2] In 2013, he was awarded a Doctor of Science (DSc) degree from the National University of Ireland.^{[citation needed]}

Career and research

After completing his PhD, McInerney worked as a postdoctoral researcher at the National Diagnostics Centre in Galway and in the Department of Zoology at The Natural History Museum, London. In 1999, McInerney returned to Ireland to set up the Bioinformatics Research Group at NUI Maynooth and became the Director of the Genetics and Bioinformatics degree course. In 2012-2013, he took a sabbatical at the Center for Communicable Disease Dynamics at Harvard University. In 2015, the McInerney research group moved to The University of Manchester where McInerney took up a Chair in Evolutionary Biology. In 2016, McInerney was appointed as the Director of the Research Domain of "Evolution, Systems and Genomics" in the Faculty of Biology, Medicine and Health at the University of Manchester. In 2018, McInerney moved from Manchester to the University of Nottingham, to take up the Chair in Evolutionary Biology and the position of Head of the School of Life Sciences.^[3]

McInerney's early research career focused on the study of codon usage in a variety of organisms including Trichomonas vaginalis and Borrelia burgdorferi. McInerney was the first to show that the leading strands of replication and the lagging strands of replication in a prokaryotic genome could have significantly different codon usage patterns, due to the way in which polymerases replicate DNA.^[4] One of his first software packages, GCUA,^[5] allowed for the accessible and reproducible analysis of codon usage by other biologists. Since then, the McInerney research group has published several bioinformatic software programs including Clann:^[6] Software for inferring phylogenetic supertrees, Crann:^[7] Software for inferring selection, Modelgenerator:^[8] Amino acid and nucleotide substitution model selection, PutGaps: DNA gapped file from amino acid alignment, and TIGER:^[9] Identifying rapidly-evolving characters in evolutionary data.

Currently, the McInerney lab focusses on understanding the origins of eukaryotes,^[10] and on understanding horizontal gene transfer, and prokaryotic pangenomes and the assemblage of genes within them^[11]

McInerney has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), The Templeton Foundation, The European Molecular Biology Organisation, and Science Foundation Ireland.

Awards and honours

• Appointed as Senior Editor for Evolution and Responses to Interventions for the journal Microbial Genomics.
• Elected President of the Society for Molecular Biology and Evolution (President-elect for 2021, President in 2022, Past-President for 2023).
• Elected Fellow of the Linnean Society of London (2016).
• Elected Fellow of the American Society for Microbiology (2015).
• Recognised by the Irish government with a conference ambassador award by the Minister for Tourism (2015).
• Elected secretary of the Society for Molecular Biology and Evolution (2013-2017).
• Associate Editor for Molecular Biology and Evolution (2009-2018)

Public outreach

• Synopsis of Nature Micro (2017) paper "Why Prokaryotes Have Pangenomes"^[12]
• Speaking on Virgin Births (parthenogenesis) for FBMH's science-themed advent calendar^[13]
• Synopsis of Nature (2015) paper "Endosymbiotic origin and differential loss of eukaryotic genes"^[14]
• Radio interview for RTE's "Bright Sparks" radio series^[15]
• Synopsis of polar bear paper Cell (2014) paper "Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears"^[16]

References

1. "James McInerney - The University of Nottingham". www.nottingham.ac.uk. Retrieved 19 July 2019.
2. "James McInerney". University of Nottingham. Retrieved 21 September 2019.
3. "Welcome to the School of Life Sciences - The University of Nottingham". www.nottingham.ac.uk. Retrieved 28 July 2019.
4. McInerney, J. O. (1 September 1998). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proceedings of the National Academy of Sciences of the United States of America. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. ISSN 0027-8424. PMC 27958. PMID 9724767.
5. McInerney, J. O. (1 January 1998). "GCUA: general codon usage analysis". Bioinformatics. 14 (4): 372–373. doi:10.1093/bioinformatics/14.4.372. ISSN 1367-4803. PMID 9632833.
6. Creevey, C. J.; McInerney, J. O. (1 February 2005). "Clann: investigating phylogenetic information through supertree analyses". Bioinformatics. 21 (3): 390–392. doi:10.1093/bioinformatics/bti020. ISSN 1367-4803. PMID 15374874.
7. McInerney, J. O.; Creevey, C. J. (1 September 2003). "CRANN: detecting adaptive evolution in protein-coding DNA sequences". Bioinformatics. 19 (13): 1726. doi:10.1093/bioinformatics/btg225. ISSN 1367-4803. PMID 15593409.
8. Keane, Thomas M.; Creevey, Christopher J.; Pentony, Melissa M.; Naughton, Thomas J.; Mclnerney, James O. (24 March 2006). "Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified". BMC Evolutionary Biology. 6 (1): 29. doi:10.1186/1471-2148-6-29. ISSN 1471-2148. PMC 1435933. PMID 16563161.
9. Cummins, Carla A.; McInerney, James O. (December 2011). "A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases". Systematic Biology. 60 (6): 833–844. doi:10.1093/sysbio/syr064. ISSN 1076-836X. PMID 21804093.
10. Martin, William F.; Landan, Giddy; McInerney, James O.; Hazkani-Covo, Einat; David Bryant; Lockhart, Peter J.; Sousa, Filipa L.; Roettger, Mayo; Nelson-Sathi, Shijulal (August 2015). "Endosymbiotic origin and differential loss of eukaryotic genes" (PDF). Nature. 524 (7566): 427–432. Bibcode:2015Natur.524..427K. doi:10.1038/nature14963. ISSN 1476-4687. PMID 26287458. S2CID 4411690.
11. O'Connell, Mary J.; McNally, Alan; McInerney, James O. (April 2017). "Why prokaryotes have pangenomes" (PDF). Nature Microbiology. 2 (4): 17040. doi:10.1038/nmicrobiol.2017.40. ISSN 2058-5276. PMID 28350002. S2CID 19612970.
12. "Short Video Explaining Pangenomes Paper". James McInerney's Lab Website. 29 March 2017. Retrieved 19 July 2019.
13. "Prof. McInerney Speaking About Virgin Births (Parthenogenesis)". James McInerney's Lab Website. 30 November 2016. Retrieved 19 July 2019.
14. "Short Video On Recent Paper In Nature". James McInerney's Lab Website. 25 August 2015. Retrieved 19 July 2019.
15. "Prof McInerney Interviewed for RTE "Bright Sparks" Radio Series". James McInerney's Lab Website. 1 June 2015. Retrieved 19 July 2019.
16. Maynooth University (9 May 2014), Prof James McInerney - A New Dawn for Polar Bear Genetics, retrieved 19 July 2019