Keane, Thomas M. and Page, Andrew J. and McInerney, James O. and Naughton, Thomas J. (2005) A high-throughput bioinformatics distributed computing platform. .

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.

Casey, Orla M. and Fitzpatrick, Richard and McInerney, James O. and Morris, Dermot G. and Powell, Richard and Sreenan, Joseph M. (2004) Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs. Biochimica et Biophysica Acta, 1679 (1). pp. 10-17.

Creevey, Christopher J. and Fitzpatrick, David A. and Philip, Gayle K. and Kinsella, Rhoda J. and O'Connell, Mary J. and Pentony, Melissa M. and Travers, Simon A. and 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.

Fitzpatrick, David A. and McInerney, James O. (2005) Evidence of Positive Darwinian Selection in Omp85, a Highly Conserved Bacterial Outer Membrane Protein Essential for Cell Viability. Journal of Molecular Evolution, 61 (1). pp. 90-98.

Mahony, Shaun and McInerney, James O. and Smith, Terry J. and Golden, Aaron (2004) Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics, 5 (1). p. 23.

Fitzpatrick, David A. and Creevey, Christopher J. and McInerney, James O. (2006) Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales. Molecular Biology and Evolution, 23 (1). pp. 74-85.

Keane, Thomas M. and Naughton, Thomas J. and McInerney, James O. (2007) MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Research, 35 (Web Server Issue). W33-W37. ISSN 0305-1048

McInerney, James O. and Wilkinson, Mark (2005) New methods ring changes for the tree of life. Trends in Ecology and Evolution, 20 (3). pp. 105-107.

McInerney, James O. and Wilkinson, Mark and Patching, John W. and Embley, T. Martin and Powell, Richard (1995) Recovery and Phylogenetic Analysis of Novel Archaeal rRNA Sequences from a Deep-Sea Deposit Feeder. Applied and Environmental Microbiology (AEM), 61 (4). pp. 1646-1648. ISSN 1098-5336

Martin, Fergal J. and McInerney, James O. (2009) Recurring cluster and operon assembly for Phenylacetate degradation genes. BMC Evolutionary Biology, 9 . p. 36. ISSN 1471-2148)

Wilkinson, Mark and Thorley, Joseph L. and Pisani, David E. and Lapointe, Francois-Joseph and McInerney, James O. (2004) Some Desiderata for Liberal Supertrees. In: UNSPECIFIED Kluwer Academic Publishers, p. 564.

McInerney, James O. (2006) The causes of protein evolutionary rate variation. Trends in Ecology and Evolution, 21 (5). pp. 230-232.

Philip, Gayle K. and Creevey, Christopher J. and McInerney, James O. (2005) The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa. Molecular Biology and Evolution, 22 . pp. 1175-1184.

Travers, Simon A. A. and Clewley, Jonathan P. and Glynn, Judith R. and Fine, Paul E. M. and Crampin, Amelia C. and Sibande, Felix and Mulawa, Dominic and McInerney, James O. and McCormack, Grace P. (2004) Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1. Journal of Virology, 78 (19). pp. 10501-10506.