Publications
132. Bapteste, E., van Iersel, L. Janke, A., Kelchner, S., Kelk, S., McInerney, J.O., Morrison, D.A., Nakhleh, L., Steel, M., Stougie, L. and Whitfield, J. (2013). Networks: Expanding evolutionary thinking. Trends in Genetics (in Press).
131. Alvarez-Ponce, D., Lopez, P., Bapteste, E. and McInerney, J.O. (2013). Gene similarity networks provide new tools for understanding eukaryote origins and evolution. Proceedings of the National Academy of Sciences USA doi: 10.1073/pnas.1211371110. [pdf]
130. Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Burglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Soon Heng Tan C, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus B. (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biology 14(2):R11
129. Hill, MS, Hill, AL, Lopez, J., Peterson, KJ, Pomponi, S., Diaz, MC, Thacker, RM, Adamska, M, Boury-Esnault, N, Cordenas, P, Chaves-Fonnegra, A, Danka, E, De Laine, B-E, Formica, D, Hajdu, E, Lobo-Hajdu, G, Klontz, S, Morrow, CC, Patel, J, Picton, B, Pisani, D, Pohlmann, D, Redmond, NE, Reed, J, Richie, S, Riesgo, A, Rubin, E, Russell, Z, Koetzler, Sperling, EA, di Stefano, M, Tarver, JD, Collins, AG (2013) Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes. PLoS ONE 8(1): e50437. doi:10.1371/journal.pone.0050437
128. Svinti, V., Cotton, J.A. and McInerney, J.O. (2013) New approaches for unravelling reassortment pathways. BMC Evolutionary Biology 13:1. doi:10.1186/1471-2148-13-1
127. Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J. O., Deppenmeier, U., and Martin, W.F. (2012) Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proceedings of the National Academy of Sciences USA. 109 (50) 20537-20542, doi: 10.1073/pnas.1209119109.[pdf]
126. Feuda, R., Hamilton, S.C., McInerney, J.O. and Pisani, D. (2012) Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences, USA 109:(46) 18868-18872, doi: 10.1073/pnas.1204609109 [pdf]
125. Bapteste, E., Bouchard F., Baquero F., McInerney J.O., Lopez P. and Burian R.M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proceedings of the National Academy of Sciences, USA 109:(45) 18266-18272 doi: 10.1073/pnas.1206541109 [pdf]
124. Fitzpatrick DA, O’Halloran DM. Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network. Int J Evol Biol. 2012;2012:548081. doi: 10.1155/2012/548081.PubMed PMID: 23056995; PubMed Central PMCID: PMC3465961. [pdf]
123. Rota Stabelli, O., Lartillot, N., Philippe, H. and Pisani, D. (2012) Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study. Systematic Biology. doi: 10.1093/sysbio/sys077.
122. O’Hanlon KA, Margison GP, Hatch A, Fitzpatrick DA, Owens RA, Doyle S, Jones GW. Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus. Nucleic Acids Res. 2012 Sep;40(16):7806-20. doi: 10.1093/nar/gks522. PubMed PMID: 22669901; PubMed Central PMCID: PMC3439912.[pdf]
121. Doherty, A., Alvarez-Ponce, D. and McInerney, J.O. (2012) Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein–protein interaction network. Molecular Biology and Evolution 29 (11): 3563-3573 [pdf].
120. McInerney, J.O., Cummins, C.A. and Haggerty, L.S. (2012) Goods-thinking versus tree-thinking: finding a place for mobile genetic elements. Mobile Genetic Elements 1, (4), 304-308. [pdf].
2011
119. Fitzpatrick DA. Horizontal gene transfer in fungi. FEMS Microbiol Lett. 2011 Nov 23. PMID:22112233 [advance access]
118. Fitzpatrick DA, O’Brien J, Moran C, Hasin N, Kenny E, et al. (2011) Assessment of Inactivating Stop Codon Mutations in Forty Saccharomyces cerevisiae Strains: Implications for [PSI+] Prion- Mediated Phenotypes. PLoS ONE 6 (12): e28684. doi:10.1371/journal.pone.0028684
117. Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals. Science Vol. 334 (6059) pp. 1091-1097. DOI: 10.1126/science.1206375 [link]
116. Medina E.M and Fitzpatrick D.A. (2011) Fungal Genomics. In: Biology and Applications 2nd Edition. Ed Kevin Kavanagh. Wiley Press. [pdf]
115. Medina E.M., Jones G.W. and Fitzpatrick D.A. (2011) Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom. Journal of Molecular Evolution. DOI 10.1007/s00239-011-9461-4. [link]
114. Pisani, D., Feuda, R., Peterson, K.J., and Smith, A.B. (2011) Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships. Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2011.08.028
113. Campbell, L.I., Rota-Stabelli, O., Edgecombe, G.D., Marchioro, T., Longhorn, S.J., Telford, M.J., Philippe, H., Rebecchi, L., Peterson, K.J., and Pisani D. (2011) MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proceedings of the National Academy of Science, USA. doi: 10.1073/pnas.1105499108 [link]
112. Ding C., Yin J., Tovar E.M., Fitzpatrick D.A., Higgins D.G., and Thiele D.J. (2011) The copper regulon of the human fungal pathogen Cryptococcus neoformans H99. Mol Microbiol. 2011 Aug 8. doi: 10.1111/j.1365-2958.2011.07794.x. [link]
111. Creevey C.J., Doerks T., Fitzpatrick D.A., Raes J., and Bork P. (2011) Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One. 6 (8): e22099. [link]
110. Alvarez-Ponce, D. and McInerney, J.O. (2011) The Human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biology and Evolution vol. 3, pp. 782-790 [pdf]
109. McInerney, J.O., Martin, W.F., Koonin, E.V., Allen, J.F., Galperin, M.Y., Lane, N., Archibald, J.M., and Embley, T.M. (2011) Planctomycetes and eukaryotes: a case of analogy not homology. BioEssays 33:(11) 810-817. doi: 10.1002/bies.201100045. [link] [pdf]
108. McInerney, J.O., Pisani, D., Bapteste, E., and O’Connell, M.J. The Public Goods Hypothesis for the Evolution of Life on Earth. Biology Direct doi:10.1186/1745-6150-6-41. [link]
107. Anderson, B.M., Pisani, D., Miller, A.I. and Peterson, K.J. (2011) The environmental affinities of marine higher taxa and possible biases in their first appearances in the fossil record. Geology doi:10.1130/G32413.1. [link]
106. McInerney, J.O., Martin, W., Koonin, E.V., Allen, J.F., Galperin, M.Y., Lane, N., Archibald, J.M. and Embley, T.M. (2011) On Planctomycetes, Eukaryotes and Analogy. Science 25 May 2011http://www.sciencemag.org/content/330/6008/1187/reply#sci_el_13985.
105. Cummins, C.A. and McInerney, J.O. (2011) A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Systematic Biology 60 (6) 833-844. doi: 10.1093/sysbio/syr064. [link] [pdf]
104. Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) Molecular paleobiological insights into the origin of the Brachiopoda. Evolution and Development, 13:3 290-303. DOI: 10.1111/j.1525-142X.2011.00480.x
103. Rota-Stabelli, O., Campbell, L., Brinkmann, H., Edgecombe, G.D., Longhorn, S.J., Peterson, K.J., Pisani, D., Philippe, H., and Telford, M.J. (2011) A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proceedings of the Royal Society: B series, 278:1703 298-306. doi: 10.1098/rspb.2010.0590. See also the Nature article linked to this paper.
2010
102. Fitzpatrick, D.A. and Butler, G (2010) Comparative Genomic Analysis of Pathogenic Yeasts and the Evolution of Virulence. InThe Yeast Handbook, 2010:Pathogenic Yeasts 1-18. [link]
101. Mohun, S.M., Davies, W.L., Bowmaker, J.K., Pisani, D., Himstedt, W., Gower, D.J., Hunt, D.M., and Wilkinson, M. (2010) Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes. J. Exp. Biol. 213:3586-3592. [link]
100. Cotton, J.A., and McInerney, J.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, USA 107:40 17252-17255. [link]. See also, Logsdon, J.M. (2010) Eukaryotic Evolution: The Importance of Being Archaebacterial. Current Biology, 20:24, R1078-R1079.pdf
99. Fitzpatrick, D.A., O’Gaora, P., Byrne, K.P., Butler, G. (2010) Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics 11:290. [pdf]
98. Rota-Stabelli, O., Kayal, E., Gleeson, D., Daub, J., Boore, J., Telford, M., Pisani, D., Blaxter, M., and Lavrov, D., (2010) Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biology and Evolution doi:10.1093/gbe/evq030.
97. Holton, T.H. and Pisani, D. (2010) Deep genomic-scale analyses of the Metazoa reject Coelomata: evidence from single and multi gene families analysed under a supertree and supermatrix paradigm. Genome Biology and Evolution 2:310-324 [pdf].
96. Sperling, E.A., Robinson, J.M., Pisani, D. and Peterson, K.J. (2010) Where’s the Glass? Biomarkers, Molecular Clocks and microRNAs suggest a 200 Million Year Missing Precambrian Fossil Record of Siliceous Sponge Spicules. Geobiology 8:1 24-36. [pdf]
2009
95. Sperling, E.A., Peterson, K.J. and Pisani, D. (2009) Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Molecular Biology and Evolution 26(10):2261-2274. [pdf]
94. Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459(7247):657-662. Link
93. Reardon, W., Fitzpatrick, D.A., Fares, M.A., and Nugent, J.M. (2009) Evolution of flower shape in Plantago lanceolata. Plant Molecular Biology 71(3): 241-250. [pdf]
92. Ragan, M.A., McInerney, J.O. and Lake, J.A. (2009) The network of life: genome beginnings and evolution. Philosophical Transactions of the Royal Society of London: B Series. 364, 2169-2175. [pdf]
91. Haggerty, L.S., Martin, F.J., Fitzpatrick, D.A. and McInerney, J.O. (2009) Gene and Genome Trees Conflict at Many Levels. Philosophical Transactions of the Royal Society of London: B Series. 364, 2209-2219. [pdf]
90. Hatadani, L.M., McInerney, J.O., de Medeiros, H.F., Martins Junqueira, A.C., de Azerdo-Espin, A.M. and Klaczko, L.B. (2008) Molecular Phylogeny of the Drosophila tripunctata and Closely Related Species Groups (Diptera: Drosophilidae). Molecular Phylogenetics and Evolution. 51(3):595-600. [pdf] PMID: 19285146
89. Creevey, C.J. and McInerney, J.O. (2009) Trees from Trees: Constructing Phylogenetic Supertrees Using CLANN. In: DNA sequence analysis, Ed. David Posada. Humana Press. 537:139-161.[pdf]
88. Pisani D. (2009) Arthropoda. In: The Timetree of Life (S.B. Hedges and S. Kumar eds). Oxford University Press. ISBN13:9780199535033 572 pages.
87. Regeai, S.O., Dolan, K.M., Fitzpatrick, D.A., Browne, J.A., Jones, J.T. and Burnell, A.M. (2009). Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross-amplification in seven other Heterorhabditis species. Molecular Ecology Resources9(1) 421-424. [pdf]
86. Martin, F.J. and McInerney, J.O. (2009) Recurring cluster and operon assembly for Phenylacetate degradation genes. BMC Evolutionary Biology 9:36 doi:10.1186/1471-2148-9-36. [pdf]
85. Fitzpatrick, D.A. (2009). Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species. Journal of Molecular Evolution 68(2):171-85. [pdf]
2008
84. McCann, A., Cotton, J.A. and McInerney, J.O. (2008) The Tree of Genomes: An Empirical Comparison of Genome Phylogeny Reconstruction Methods. BMC Evolutionary Biology 8:312. [pdf]
83. Lloyd, G.T., Davis, K.E., Pisani, D., Tarver, J.E., Ruta, M., Sakamoto, M., Hone, D.W.E., Jennings, R. Benton, M.J. (2008) Dinosaurs and the Cretaceous Terrestrial Revolution. Philosophical Transactions of the Royal Society of London: Biological Sciences. 275 (1650) 2483-2490.[pdf]
82. Peterson, K., Cotton, J.A., Gehling, J.G. and Pisani, D. (2008) The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society of London: Biological Sciences. 363 (1496) 1435-1443. [pdf]
81. McInerney, J.O., Cotton, J.A. and Pisani, D. (2008) The Prokaryotic Tree of Life: Past, Present…and Future? Trends in Ecology and Evolution 23 (5) 276-281 [pdf]
80. Fitzpatrick DA, Logue ME, Butler G. (2008). Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evolutionary Biology. 8:181. [pdf]
2007
79. Johnston CR, O’dushlaine C, Fitzpatrick D.A., Edwards RJ, Shields DC. (2007). Evaluation Of Whether Accelerated Protein Evolution In Chordates Has Occurred Before, After Or Simultaneously With Gene Duplication. Molecular Biology and Evolution. Jan;24(1):315-23. [pdf]
78. McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391. [pdf]
77. Pisani, D., Cotton, J.A. and McInerney, J.O. (2007). Supertrees Disentangle The Chimeric Origin of Eukaryotic genomes. Molecular Biology and Evolution24(8):1752-1760. [pdf]
76. Sperling, E.A., Pisani D. and Peterson, K.J. (2007) Poriferan paraphyly and its implications for Precambrian palaeobiology. In: The Rise and Fall of the Ediacaran Biota. (Vickers-Rich P. and Komarower P. eds) Geological Society of London Special Publications 286:355-367. [pdf]
75. Pisani, D., Benton, M.J. and Wilkinson, M. (2007) Congruence of morphological and molecular phylogenies. Acta Biotheoretica 55:269-281. [pdf]
74. Loader S., Pisani D., Cotton, J.A., Gower D., Day. J. and Wilkinson, M. (2007) Relative timescales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biology Letters 3(5):505-508. [pdf]
73. Ruta M., Pisani D., Lloyd G.T., and Benton M.J. (2007) A supertree of Temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods. Proceedings of the Royal Society B. 274:3087-3095. [pdf]
72. Keane, T.M., Naughton, T.J. and McInerney, J.O. (2007). MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids research doi:10.1093/nar/gkm359 [pdf]
71. Puigbo, P., Garcia-Vallve, S. and McInerney, J.O. (2007). TOPD/FMTS: a new software program to compare phylogenetic trees. Bioinformatics 23(12):1556-1558. [pdf]
70. Wilkinson, M, McInerney, J.O., Hirt, R.P., Foster, P.G. and Embley, T.M. (2007). Of Clades and Clans: Terms for Phylogenetic Relationships in Unrooted Trees.Trends in Ecology and Evolution, 22(3) 114-115. [pdf]
69. O’Connell, M.J. and McInerney, J.O. (2007). Reconstructing the ancestral eukaryote: Lessons from the past. In Ancestral Sequence Reconstruction. Ed: David Liberles. Oxford University Press. pp103-113. [pdf]
68. McInerney J.O., Pisani D., O’Connell M.J., Fitzpatrick D.A. and Creevey C.J. (2007). Evolutionary history of the prokaryotes: Tree or No Tree? In Towards the tree of life: taxonomy and systematics of large and species rich clades (T. Hodkinson, J. Parnell, and S. Waldren, eds.). CRC Press, UK. [pdf]
67. Harris, S.R., Pisani D., Gower, D., and Wilkinson, M. (2007) Investigating stagnation in morphological phylogenetics: An approach using consensus data.Systematic Biology 56:125-129. [pdf]
66. Wilkinson, M., Cotton, J.A., Lapointe, F.J. and Pisani, D. (2007) On some consensus properties of some supertree methods. Systematic Biology 56:330-337.[pdf]
2006
65. McInerney, J.O. (2006). The Causes of Protein Evolutionary Rate Variation.Trends in Ecology and Evolution, 21(5), 230-232. [pdf]
64. O’Halloran, D.M., Fitzpatrick, D.A., McCormack, G.P., McInerney, J.O. and Burnell, A.M. (2006). The Molecular Phylogeny and Functional Significance of a Nematode Specific Clade of Heterotrimeric G-protein -Subunit Genes. Journal of Molecular Evolution 63: 87-94.[pdf]
63. Fitzpatrick D.A, Logue ME, Stajich JE, Butler G. (2006). A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 6(1):99. [pdf]
62. McInerney J.O., Finnerty C.S., Commins J.M., Philip G.K. (2006) Gene evolution and drug discovery. Methods in Molecular Biology, 316:87-109.
61. Keane T.M., Creevey, C.J., Pentony, M.M., Naughton, T.J. and McInerney, J.O. (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 [pdf]
60. McInerney, J.O. (2006). On the Desirability of Models for Inference of Genome Phylogenies. Trends in Microbiology 14(1) [pdf]
59.Fitzpatrick, D.A., O’Halloran, D.M. and Burnell, A.M. Multiple Lineage Specific Expansions in the Guanylyl Cyclase Gene Family. BMC Evolutionary Biology 2006, 6:26. [pdf]
58. Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2006). Genome Phylogenies Indicate a Meaningful -Proteobacterial Phylogeny and Support A Grouping of the Mitochondria With the Rickettsiales. Molecular Biology and Evolution 23: 74-85.[pdf]
57. Keane, T.M., Page, A.J., Naughton, T.J, Travers, S.A.A, McInerney, J.O. (2006). Building large phylogenetic trees on coarse-grained parallel machines.Algorithmica. 45(3), 285-300. [pdf]
56. Pisani, D., Samantha, M. Mohun, Simon, R. Harris, James, O. McInerney and Mark Wilkinson (2006). Molecular evidence for dim-light vision in the last common ancestor of the vertebrates. Current Biology 16(9):R318. [pdf] [Supplementary Information]
55. Smith, A.B., Pisani, D., MacKenzie Dodds, J.A., Stockley, B., Webster, B., and Littlewood, D.T.L. (2006). Testing the molecular clock: molecular and paleontological estimates of rates and patterns of evolution in the Echinoidea (Echinodermata).Molecular Biology and Evolution 23(10):1832-1851. [pdf]
2005
54. Shannon, A. Browne, JA. Boyd, J. Fitzpatrick, DA and Burnell, AM (2005). The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus. Journal of Experimental Biology 208:2433-2445. [pdf]
53. O’Connell, M.J. and McInerney, J.O. (2005). Adaptive Evolution of the Human Fatty Acid Synthase Gene: Support for the Cancer Selection and Fat Utilisation Hypotheses? Gene 360, 151-159.[pdf]
52. O’Connell, M.J. and McInerney, J.O. (2005). Gamma Chain Receptor Interleukins: Evidence for Positive Selection Driving the Evolution of Cell-to-Cell Communicators in the Mammalian Immune System. Journal of Molecular Evolution Nov; 61(5): 608-619. [pdf]
51. Wilkinson, M., Cotton, J., Creevey, C.J., Eulenstein O., Harris, S.R., Lapointe, F-J. McInerney, J.O., Pisani, D and J. Thorley (2005). The Shape of Supertrees to Come: Input Tree Shape Biases and Some Axiomatic Properties of Fourteen Supertree Methods. Systematic Biology 54(3): 419-431. [pdf]
50. Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2005) Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens. Journal of Molecular Evolution 60 (1), 90-98. [pdf]
49. Philip, G.K., Creevey, C.J. and McInerney, J.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, 1175-1184. [pdf]
48. Keane, T.M., Naughton, T.J., Travers, S.A.A, McInerney, J.O. and McCormack, G.P. (2005). DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood.Bioinformatics 21: 969-974. [pdf]
47. McInerney, J.O. and Wilkinson, M. (2005). New Methods Ring Changes for The Tree of Life. Trends in Ecology and Evolution 20 (3) 105-107. [pdf]
46. Fitzpatrick, D.A. and McInerney, J.O. (2005). Evidence of Positive Darwinian Selection in Omp85, a Highly Conserved Bacterial Outer Membrane Protein Essential for Cell Viability. Journal of Molecular Evolution 60(2) 268-273. [pdf]
45. Creevey, C.J. and McInerney, J.O. (2005). CLANN: Investigating Phylogenetic Information Through Supertree Analysis. Bioinformatics 21 (3) 390-392. [pdf]
44. Travers, S.A.A., O’Connell, M.J., McCormack, G.P. and McInerney, J.O. (2005). Evidence for heterogeneous selective pressures in the evolution of the env gene in different HIV-1 subtypes. Journal of Virology 79 (3) 1836-1841. [pdf]
43. Hone, D., Keesey, T.M., Pisani, D. & Purvis, A. (2005). Macroevolutionay Trends within Dinosauria: Cope’s Rule. Journal of Evolutionary Biology 18:587-595. [pdf]
42. Wilkinson, M., Cotton, J.A., Creevey, C., Eulenstein, O., Harris, S.R., Lapointe, F.-J., Levasseur, C., McInerney, J.O., Pisani, D., Thorley, J.L. (2005). The shape of supertrees to come: tree shape related properties of fourteen supertree methods.Systematic Biology 54:419-31. [pdf]
41. Wilkinson, M., Pisani, D., Cotton, J. & Corfe, I. (2005). Measuring Support and Finding Unsupported Relationships in Supertrees. Systematic Biology 54:823-831.[pdf]
2004
40. Creevey, C.J., Fitzpatrick, D.A., Philip, G.K., Kinsella, R.J., O’Connell, M.J., Pentony, M.M., Travers, S.A.A., Wilkinson, M., and McInerney, J.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):2551-8. [pdf]
39. Travers, S.A.A., Clewley, J.P., Glynn, J.R., Fine, P.E.M., Crampin, A.C., Sibande, F., Mulawa, D., McInerney, J.O., and McCormack, G.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), 10501-10506. [pdf]
38. Casey, O.M., Fitzpatrick, R., McInerney, J. O., Morris, D., Powell, R., and Sreenan, J.M. (2004). Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs. Biochim Biophys Acta.1679(1):10-17. [pdf]
37. Wilkinson, M., Thorley, J.L., Pisani, D.E., Lapointe, F-J and McInerney, J.O. (2004) Some Desiderata for Meta-Analytical Supertrees. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic Publishers, Dordrecht. ISBN 1-4020-2329-4. 564 pp.
36. Mahony, S., McInerney, J.O, Smith, T. and Golden, A (2004) Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics 5(1): 23. [pdf]
35. Wilkinson, M., Thorley, J.L, Pisani, D., Lapointe F.-J. & McInerney, J.O. (2004). Some Desiderata of Liberal Supertrees. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (O.R.P. Bininda-Emonds, Ed). Kluwer series in Computational Biology, Volume 4. Kluwer Academic Publishers, Dordrecht. [pdf]
34. Pisani, D., Poling, L. & Hedges, S.B. (2004). A Molecular Clock Analysis of Arthropod Evolution and the Colonization of Land by Animals. BMC Biology 2:1. [pdf]
33. Pisani D. (2004) Removing Fast Evolving Sites Using Compatibility Methods: An Example from the Arthropoda. Systematic Biology 53(6):983-994. [pdf]
2003
32. Kinsella, R.J. and McInerney J.O. (2003). Eukaryotic genes in Mycobacterium tuberculosis? Possible alternative explanations. Trends in Genetics, 19, issue 12 687-689. [pdf]
31. McInerney, J.O., Littlewood, D.T.J. and Creevey, C.J. (2003). Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist. Advances in Parasitology 54, 360-379. [pdf]
30. Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J. and McInerney J.O. (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution and gene duplication. Proceedings of the National Academy of Sciences USA, 100, 10320-10325. [pdf]
29. Creevey, C.J. and McInerney J.O. (2003). CRANN: A Program for Detecting Adaptive Evolution in Protein-Coding DNA Sequences. Bioinformatics. 19, issue 13, 1726. [pdf]
28. Enright M.R., McInerney J.O. and Griffin CT. (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. 53 435-441. [pdf]
2002
27. Pisani, D., Yates, A.M., Langer, M.C. & Benton, M. J. (2002). A Phylogenetic Supertree of the Dinosauria. Proceedings of the Royal Soiety of London, B 269:915-921. [pdf]
26. Creevey, C.J. and McInerney, J.O. (2002) An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene: 300 (1-2) 43-51. [pdf]
25. Keane, T., Allen, R., Naughton, T.J., McInerney, J.O. and J. Waldron (2002). Distributed computing for DNA analysis. in Principles and Practice of Programming in Java. James F. Power and John T. Waldron, Eds., pp. 65-70.
24. McInerney, J.O., Wernecke, M., Mullarkey, M. and Powell, R. (2002) Bacteria and Archaea: Molecular techniques reveal astonishing novel diversity. Biodiversity 3:3-10. [pdf]
23. McInerney, J. O. (2002) Bioinformatics in a Post-Genomic Era – The need for an Integrative Approach. The Pharmacogenomics Journal. 2:207-208. [pdf]
22. Pisani, D. & Wilkinson, M. (2002). MRP, Total Evidence, and Taxonomic Congruence. Systematic Biology 51:151-155. [pdf]
1995-2002
21. Enright, M.R., Finnegan, M.M., McInerney, J.O., O’Laighleis, M., and Griffin, C.T. (2001) Specific adherence of psorangia of a Paenibacillus sp. Bacterium to Heterohabditis spp. Nematodes: Hitching a ride to lunch? In Developments in Entomopathogenic Nematode/Bacterial Research, pp 301-306.
20. McInerney JO, Mullarkey M, Wernecke ME and Powell R. (2001) The impact of taxonomic gene libraries on our knowledge of bacterial diversity: an example using the marine Archaea. In Biological Collections and Biodiversity. Eds. B.S. Rushton, P. Hacknet and C.R. Tyrie, Ch. 17, pp 155-163, Linnean Society Occasional Papers 3.
19. Murphy, M., Harte, T., McInerney, J.O., and Smith, T. (2000). Molecular Cloning Of Atlantic Salmon Nucleoside Diphosphate Kinase And Its Pattern Of Expression During Embryogenesis. Gene 257(1) 139-148. [pdf]
18. McCormack, G.P., Keegan, B.F., McInerney, J.O. and Powell, R (2000). Spectral Analysis of Echinoderm 18S Ribosomal DNA data. Molecular Phylogenetics and Evolution. 15(2) 327-329. [pdf]
17. McInerney, J.O. and Wolfe, K.H. (1999). Genomic Analysis Methods.Microbiology Today, Vol. 26 p157-159.[ pdf]
16. McInerney, J.O., Adams, C.L., Borges, K., and Kelly-Borges, M. (1999). Phylogenetic Resolution Potential Of 18S And 28S rRNA Genes Within The Lithistid Astrophorida. Memoirs of the Queensland Museum: 44 343-352
15. Adams, C.L., McInerney, J.O. and Kelly-Borges, M. (1999). Indications Of Relationships Between Poriferan Classes Using Full-Length 18S rRNA Gene Sequences. Memoirs of the Queensland Museum: 44 33-45.
14. McInerney, J.O. (1998). Replicational and Transcriptional Selection on Codon Usage in Borrelia burgdorferi. Proceedings of the National Academy of Sciences USA: 95 10698-10703. [pdf]
13. Pisani, D. & Bulla S. (1998). Andamento dell’attivita’ diurna in funzione della strategia predatoria in Podarcis sicula (Reptilia, Squamata, Lacertidae). Rivista di Idrobiologia 38:409-415. [In Italian with English Summary].
12. Goldman, G.H., Pellizzon, C.H., Marins, M., McInerney, J.O., and de S. Goldman, M.H., (1998). Trichoderma spp. genome and gene structure. In: Trichoderma and Gliocladium. Ed.s P. Kubicek and G.E. Harman. Taylor and Francis, London, UK. pp. 209-224. [pdf]
11. McInerney, J.O. (1998). GCUA (General Codon Usage Analysis). Bioinformatics: 14 (4) 372-373. [pdf]
10. McInerney, J.O., Mullarkey, M., Wernecke, M. and Powell, R. (1997). Phylogenetic Analysis of Marine Archaeal rRNA Sequences Emphasizes The Hidden Diversity Within The Archaea. Proceedings of the Royal Society of London (Biology series): 264 1-7. [pdf]
9. McInerney, J.O. (1997). Prokaryotic Genome Evolution As Assessed By Multivariate Analysis of Codon Usage Patterns. Microbial and Comparative Genomics: 2 (1), 1-10. [pdf]
8. McInerney, J.O. (1997). Codon Usage in Trichomonas vaginalis. European Journal of Protistology: 33(3), 266-273. [pdf]
7. McInerney, J.O. (1996). Codon Usage in The Atlantic salmon (Salmo salar L.). (1996) Molecular Marine Biology and Biotechnology: 5 (3), 344-351.
6. McCormack, G., Mooney, J., McInerney, J.O., Powell, R. and Keegan, B. (1995) Comparison of DNA extraction techniques from amphuirid species (Ophiuroidea: Echinodermata) suitable for polymerase chain reaction. In: Echinoderm Research1995. Ed.s R.H. Emson, A.B. Smith and A.C. Campbell. A.A. Balkema, Rotterdam. pp. 43-50.
5. McInerney, J.O., Wilkinson, M., Patching, J.W., Embley, T.M. and Powell, R. (1995). Recovery and Phylogenetic Analysis of Archaeal SSU rRNA Sequences From a Deep-Sea Deposit Feeder. Applied and Environmental Microbiology: 61 (4), 1646-1648. [pdf]
4. McInerney, J.O., Paskins, L., Eardly, D., Patching, J.W., and Powell, R. (1995). Extraction of Prokaryotic genomic DNA from Marine Microbial Communities, Suitable For Use In The Polymerase Chain Reaction. International Revue der Gesamten Hydrobiologie: 80 (2), 351-360.
3. Powell, R., Mullarkey, M., O’Brien, D.J. and McInerney, J.O. (1995). Detection of Microorganisms In The Environment. Biochemical Society Transactions: 23, 435-437. [pdf]
2. Doyle, L., McInerney, J.O., Mooney, J., Powell, R., Haikara, A. and Moran, A.T. (1995). Sequence of the Gene Encoding The 16S rRNA Of The Beer-Spoilage Organism Megasphaera cerevisiae. J. Industrial Microbiology: 15, 67-70. [pdf]
1. Hanley, S. McInerney, J.O., and Powell R. (1995). Sequence Analysis and Evolutionary Aspects of Piscine alpha-1-Microglobulin/Bikunin mRNA Transcripts.Molecular Marine Biology and Biotechnology: 4 (2), 105-109.
