Publications

Journal Papers

Andrew J. Page, Thomas M. Keane and Thomas J. Naughton, Scheduling in a dynamic heterogeneous distributed system using estimation error, Journal of Parallel and Distributed Computing, Volume 68, Issue 11, November 2008, 1452-1462. link
Thomas M. Keane, Thomas J. Naughton, James O. McInerney (2007) MultiPhyl: A high-throughput phylogenomics webserver using distributed computing, Nucleic Acids Research, 35:W33-W37. link
Thomas M. Keane, Christopher J. Creevey, Melissa M. Pentony, Thomas J. Naughton, James O. McInerney (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, 6:29. link
McCormack G.P., Glynn, J.R., Clewley, J.P., Crampin, A.C., Travers, S.A.A., Redmond, H., Keane, T.M., Sibande, F., Mulawa D. and Fine P.E.M (2006) Emergence of a three codon deletion in gag p17 in HIV-1 subtype C long-term survivors, and general population spread, Aids Research & Human Retroviruses, 22(2):195-201.link
Keane, T.M., Page, A.J., Naughton, T.J., Travers, S.A.A., McInerney, J.O. (2005) Building large phylogenetic trees on coarse-grained parallel machines, Algorithmica (Special Issue on Coarse Grained Parallel Algorithms For Scientific Applications), 45(3):285-300.pdf link
Andrew J. Page, Thomas J. Naughton (2005) Framework for task scheduling in heterogeneous distributed computing using genetic algorithms, Artificial Intelligence Review, 24(3-4):415-429. link pdf
Keane, T.M., Naughton, T.J., Travers, S.A.A., McInerney, J.O., McCormack, G.P. (2005) DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood, Bioinformatics, 21(7):969-974.link
Keane, T.M. and Naughton, T.J. (2005) DSEARCH: sensitive database searching using distributed computing, Bioinformatics, 21(8):1705-1706. link

Book chapters

Keane, T., Allen, R., Naughton, T.J., McInerney, J., and Waldron, J. (2003) Distributed Java platform with programmable MIMD capabilities, Scientific Engineering for Distributed Java Applications, Nicolas Guelfi, Egidio Astesiano, and Gianna Reggio, Eds., Springer Lecture Notes in Computer Science, 2604:122-131 (Springer-Verlag).pdf
Thomas Keane, Richard Allen, Thomas J. Naughton, James McInerney, and John Waldron, "Distributed computing for DNA analysis," in James F. Power and John T. Waldron, Eds., Recent Advances in Java Technology: Theory, Application, Implementation, chap. 11, pp. 99-108, Computer Science Press, Trinity College Dublin, Ireland, 2002. ISBN: 0-9544145-0-0 pdf

Peer-Reviewed Conference papers

Andrew J. Page, Shirley Coyle, Thomas M. Keane, Thomas J. Naughton, Charles Markham and Tomas Ward, Distributed Monte Carlo Simulation of Light Transportation in Tissue, 8th International Workshop on Java for Parallel and Distributed Computing, proceedings of the 20th International Parallel & Distributed Processing Symposium, Rhodes, Greece, April 2006. IEEE Computer Society. pdf
Thomas M. Keane, James O. McInerney, Andrew J. Page, Thomas J. Naughton, A high-throughput bioinformatics distributed computing platform, Bioinformatics and its Medical Applications Special Track, The 18th IEEE International Symposium on Computer-Based Medical Systems, 377-382, Dublin, Ireland, June 2005.pdf
Andrew J. Page, Thomas J. Naughton, Dynamic task scheduling using genetic algorithms for heterogeneous distributed computing, 8th International Workshop on Nature Inspired Distributed Computing, IPDPS, Denver, Colorado, USA, April 2005. pdf
Andrew J. Page, Thomas M. Keane, Thomas J. Naughton, Bioinformatics on a Heterogeneous Java Distributed System, 7th International Workshop on Java for Parallel and Distributed Computing, IPDPS, 6(6):184a, Denver, Colorado, USA, April 2005. pdf
Andrew J. Page, Thomas J. Naughton, Framework for task scheduling in heterogeneous distributed computing using genetic algorithms, 15th Artificial Intelligence and Cognitive Science Conference, eds. Lorraine McGinty and Brian Crean, pp. 137-146, September 8th - 10th 2004, Castlebar, Ireland. ISBN 1-902277-89-9. pdf
Andrew Page, Thomas Keane, Thomas J. Naughton, Adaptive Scheduling Across a Distributed Computation Platform, Third International Symposium on Parallel and Distributed Computing, ed. John P. Morrisson, pp. 141-149, July 2004, Cork, Ireland. ISBN 0-7695-2210-6, IEEE Computer Society. pdf
Andrew Page, Thomas Keane, Richard Allen, Thomas J. Naughton, John Waldron, Multi-tiered distributed computing platform , 2nd International Conference on the Principles and Practice of Programming in Java, pp. 191-194, Kilkenny City, Ireland, June 2003. ISBN 0-9544145-1-9. pdf
Keane, T., Allen, R., Naughton, T.J., McInerney, J., and Waldron, J. (2002) Distributed Java platform with programmable MIMD capabilities, FIDJI'2002 International Workshop on Scientific Engineering of Distributed Java Applications, 153-162, Luxembourg-Kirchberg, Luxembourg. pdf
Thomas Keane, Richard Allen, Thomas J. Naughton, James McInerney, and John Waldron, "Distributed computing for DNA analysis," Principles and Practice of Programming in Java, James F. Power and John T. Waldron, Eds., pp. 65-70, Dublin, Ireland, 13-14 June 2002. ISBN: 0-901519-87-1 pdf

Contributed conference papers (peer reviewed, 2 pages or less)

Thomas M. Keane, Andrew Page, Thomas J. Naughton, Simon A.A. Travers, James O. McInerney, and Grace P. McCormack, "Heterogeneous distributed computing," IFIP Working Group 8.6 Conference on IT Innovation for Adaptability and Competitiveness, Leixlip, Ireland, 30 May - 2 June 2004.

Thesis

Keane, T.M. (2006) Computational Methods for Statistical Phylogenetic Inference, PhD Thesis, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland. pdf
Keane, T.M. (2004) A General-Purpose Heterogeneous Distributed Computing System, M.Sc. Thesis, Department of Computer Science, National University of Ireland, Maynooth, County Kildare, Ireland. pdf