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Haggerty, Leanne S. and Jachiet, Pierre-Alain and Hanage, William P. and Fitzpatrick, David A. and Lopez, Philippe and O'Connell, Mary J. and Pisani, Davide and Wilkinson, Mark and 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
Feuda, Roberto and Hamilton, Sinead C. and McInerney, James O. and Pisani, Davide (2012) Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences . ISSN 1091-6490
Bapteste, Eric and Lopez, Philippe and Bouchard, Frédéric and Baquero, Fernando and McInerney, James O. and Burian, Richard M. (2012) Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proceedings of the National Academy of Sciences, 109 (145). pp. 18266-8272. ISSN 1091-6490
Cotton, James A. and McInerney, James O. (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proceedings of the National Academy of Sciences , 107 (40). pp. 17252-17255. ISSN 1091-6490
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)
Haggerty, Leanne S. and Martin, Fergal J. and Fitzpatrick, David A. and McInerney, James O. (2009) Gene and genome trees conflict at many levels. Philosophical Transactions of the Royal Society B, 364 (1527). pp. 2209-2219. ISSN 0080-4622
McCann, Angela and Cotton, James A. and McInerney, James O. (2008) The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods. BMC Evolutionary Biology, 8 (312). pp. 1-3. ISSN 1471-2148
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
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.
McInerney, James O. (2006) The causes of protein evolutionary rate variation. Trends in Ecology and Evolution, 21 (5). pp. 230-232.
O'Halloran, Damien M. and Fitzpatrick, David A. and McCormack, Grace P. and McInerney, James O. and Burnell, Ann (2006) The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes. Journal of Molecular Evolution, 63 (1). pp. 87-94. ISSN 0022-2844
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.
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.
Fitzpatrick, David A. and Creevey, Christopher J. and McInerney, James O. (2005) Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens. Journal of Molecular Evolution, 61 (1). pp. 90-98. ISSN 0022-2844
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.
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.
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.
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.
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.
Enright, Michael R. and McInerney, James O. and Griffin, Christine (2003) Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov. International Journal of Systematic and Evolutionary Microbiology, 53. pp. 435-441. ISSN 1466-5026
Kinsella, Rhoda J. and Fitzpatrick, David A. and Creevey, Christopher J. and McInerney, James O. (2003) Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication. Proceedings of the National Academy of Sciences, 100 (18). pp. 10320-10325. ISSN 1091-6490
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
Keane, Thomas M. and Page, Andrew J. and McInerney, James O. and Naughton, Thomas J. (2005) A high-throughput bioinformatics distributed computing platform. In: Proceedings. 18th IEEE Symposium on Computer-Based Medical Systems, 2005. IEEE, pp. 377-382. ISBN 0769523552
Wilkinson, Mark and Thorley, Joseph L. and Pisani, Davide and Lapointe, Francois-Joseph and McInerney, James O. (2004) Some Desiderata for Liberal Supertrees. In: Phylogenetic Supertrees. Computational Biology book series (COBO) (4). Springer, pp. 227-246. ISBN 9781402023293
Keane, Thomas M. and Allen, Richard and Naughton, Thomas J. and McInerney, James O. and Waldron, John (2003) Distributed Java Platform with Programmable MIMD Capabilities. In: FIDJI 2002: Scientific Engineering for Distributed Java Applications. Lecture Notes in Computer Science (LNCS) (2604). Springer, pp. 122-131. ISBN 3540006796
Keane, Thomas M. and Allen, Richard and Naughton, Thomas J. and McInerney, James O. and Waldron, John (2002) Distributed computing for DNA analysis. In: PPPJ '02/IRE '02 Proceedings of the inaugural conference on the Principles and Practice of programming, 2002 and Proceedings of the second workshop on Intermediate representation engineering for virtual machines, 2002. National University of Ireland Maynooth, pp. 65-70. ISBN 0901519871
Enright, Michael R. and Finnegan, Michelle and McInerney, James O. and O'Laighleis, Matthew and Griffin, Christine (2001) Specific Adherence of Sporangia of a Paenibacillus Sp. Bacterium to Heterorhabditis Spp. Nematodes. Hitching a Ride to Lunch? In: Developments in entomopathogenic nematode/bacterial research: Proceedings of the workshop held at the National University of Ireland Maynooth 13 to 15 April 2000. Office for Official Publications of the European Communities, pp. 301-306. ISBN 9289404671
