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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
Pisani, Davide and Mohun, Samantha and Harris, Simon and McInerney, James and Wilkinson, Mark (2006) Molecular evidence for dim-light vision in the last common ancestor of the vertebrates. Current Biology, 16 (9). pp. 318-319.
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.
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.
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
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
