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Keane, Thomas and Creevey, Christopher and Pentony, Melissa and Naughton, Thomas and McInerney, James (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. pp. 29-46.
Keane, Thomas and Page, Andrew and Naughton, Thomas and Travers, Simon and McInerney, James (2006) Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. Algorithmica, 45 (3). pp. 285-300.
Mooney, Aidan and Duffin, Joe and Naughton, Thomas and Monahan, Rosemary and Power, James F. and Maguire, Phil (2014) PACT: An initiative to introduce computational thinking to second-level education in Ireland. In: International Conference on Engaging Pedagogy 2014 (ICEP), 5th December 2014, Athlone Institute of Technology.