GCUA: general codon usage analysis. - James O. McInerney (Bioinform., 1998)

Distributed Java Platform with Programmable MIMD Capabilities. - Thomas M. Keane; Richard Allen; Thomas J. Naughton; James O. McInerney; John Waldron (FIDJI, 2002)

Distributed computing for DNA analysis. - Thomas M. Keane; Richard Allen; Thomas J. Naughton; James O. McInerney; John Waldron (PPPJ/IRE, 2002)

A New Approach to Gene Prediction Using the Self-Organizing Map. - Shaun Mahony; Terry J. Smith; James O. McInerney; Aaron Golden (CSB, 2003)

CRANN: detecting adaptive evolution in protein-coding DNA sequences. - C. J. Creevey; James O. McInerney (Bioinform., 2003)

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. - Shaun Mahony; James O. McInerney; Terry J. Smith; Aaron Golden (BMC Bioinform., 2004)

A High-Throughput Bioinformatics Distributed Computing Platform. - Thomas M. Keane; Andrew J. Page; James O. McInerney; Thomas J. Naughton (CBMS, 2005)

Clann: investigating phylogenetic information through supertree analyses. - C. J. Creevey; James O. McInerney (Bioinform., 2005)

DPRml: distributed phylogeny reconstruction by maximum likelihood. - Thomas M. Keane; Thomas J. Naughton; Simon A. A. Travers; James O. McInerney; Grace P. McCormack (Bioinform., 2005)

Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. - Thomas M. Keane; Andrew J. Page; Thomas J. Naughton; Simon A. A. Travers; James O. McInerney (Algorithmica, 2006)

TOPD/FMTS: a new software to compare phylogenetic trees. - Pere Puigbò; Santiago Garcia-Vallvé; James O. McInerney (Bioinform., 2007)

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. - Thomas M. Keane; Thomas J. Naughton; James O. McInerney (Nucleic Acids Res., 2007)

Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes. - Orla Coleman; Ruth Hogan; Nicole McGoldrick; Niamh Rudden; James O. McInerney (Comput., 2015)

Endosymbiotic origin and differential loss of eukaryotic genes. - Chuan Ku; Shijulal Nelson-Sathi; Mayo Roettger; Filipa L. Sousa; Peter J. Lockhart; David Bryant; Einat Hazkani-Covo; James O. McInerney; Giddy Landan; William F. Martin (Nat., 2015)