Haggerty, Leanne S., Jachiet, Pierre-Alain, Hanage, William P., Fitzpatrick, David A., Lopez, Philippe, O'Connell, Mary J., Pisani, Davide, Wilkinson, Mark, Bapteste, Eric and McInerney, James O. (2014) A Pluralistic Account of Homology: Adapting the Models to the Data. Molecular Biology and Evolution, 31 (3). pp. 501-506. ISSN 0737-4038

O'Connell, Mary J. and McInerney, James O. (2005) Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses? Gene, 360 (2). pp. 151-159.

Creevey, Christopher J., Fitzpatrick, David A., Philip, Gayle K., Kinsella, Rhoda J., O'Connell, Mary J., Pentony, Melissa M., Travers, Simon A., Wilkinson, Mark and McInerney, James O. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of The Royal Society of London, Biology Series, 271 (1557). pp. 2551-2558.