123. Beavan, A., Domingo-Sananes, MR, and McInerney, JO. (2023) Contingency, Repeatability and Predictability in the Evolution of a Prokaryotic Pangenome. bioRxiv, 2023.03. 20.533463

122. McInerney, J.O. (2023) Prokaryotic Pangenomes Act as Evolving Ecosystems. Molecular Biology and Evolution 40 (1), msac232 https://doi.org/10.1093/molbev/msac232


121. Ou, Y. and McInerney, JO. (2022) High Frequency of Dynamic Rearrangements in CRISPR Loci. bioRxiv doi: https://doi.org/10.1101/2022.05.19.492656

120. Cummins, E., Hall, R.J., Connor, C., McInerney, J.O., and McNally, A. (2022) Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microbial Genomics 8:000903. https://doi.org/10.1099/mgen.0.000903

119. Beavan, A.J.S., and McInerney, J.O. (2022) Gene essentiality evolves across a pangenome. Nature Microbiology https://doi.org/10.1038/s41564-022-01231-8.

118. Cummins, E.A., Hall, R.J., McInerney, J.O. and McNally, A. (2022) Prokaryote pangenomes are dynamic entities. Current Opinion in Microbiology, 66, 73-78. https://doi.org/10.1016/j.mib.2022.01.005.


117. Hall, R.J., Whelan, F.J., Cummins, E.A., Connor, C., McNally, A., and McInerney, J.O., (2021) Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility.  Microbial Genomics 7: 000650 https://doi.org/10.1099/mgen.0.000650.

116. Whelan, F.J., Hall, R.J. and McInerney, J.O. (2021) Evidence for selection in the abundant accessory gene content of a prokaryote pangenome. Molecular Biology and Evolution 38 (9) 3697–3708. https://doi.org/10.1093/molbev/msab139

115. Domingo-Sananes, M.R. and McInerney, J.O. (2021) Mechanisms That Shape Microbial Pangenomes. Trends in Microbiology 29(6) 493-503 https://doi.org/10.1016/j.tim.2020.12.004


114. Hall, R.J., Whelan, F.J., McInerney, J.O., Ou, Y., Domingo Sananes, M.R. (2020) Horizontal gene transfer as a source of conflict and cooperation in prokaryotes. Frontiers in Microbiology 11, 1569. https://doi.org/10.3389/fmicb.2020.01569

113. Whelan, F.J. Rusilowicz, M. and McInerney J.O. (2020) Coinfinder: detecting significant associations and dissociations in pangenomes. Microbial Genomics. DOI 10.1099/mgen.0.000338

112. McInerney, J.O., Whelan, F.J., Domingo-Sananes, M.R., McNally, A., and O’Connell, M.J. (2020) Pangenomes and Selection: The Public Goods Hypothesis. In: The Pangenome (eds. Hervé Tettelin and Duccio Medini). Springer. https://doi.org/10.1007/978-3-030-38281-0_7.

111. McInerney, J.O. (2020) Traits and Homology. In: The Theory of Evolution: Principles, Concepts, and Assumptions by Samuel Scheiner, David Mindell (ISBN: 9780226671024) https://www.press.uchicago.edu/ucp/books/book/chicago/T/bo45713136.html).


110. Ou, Y., and McInerney, J.O. (2019) Eukaryote genes are more likely than prokaryote genes to be composites. Genes 10(9), 648. https://www.mdpi.com/2073-4425/10/9/648

109. McCartney A.M., Hyland, E.M., Cormican, P., Moran, R.J., Webb, A.E., Lee, K.D., Hernandez, J., Prado-Martinez, J., Creevey, C.J., Aspden, J.L., McInerney, J.O., Marques-Bonet, T., O’Connell M.J. (2019) Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human. Genome Biology and Evolution 11(9):2678-2690. https://doi.org/10.1093/gbe/evz163

108. Newman, D., Whelan, F., Moore, M., Rusilowicz, M. and McInerney. J.O. (2019) Reconstructing and Analysing The Genome of The Last Eukaryote Common Ancestor to Better Understand the Transition from FECA to LECA. bioRxiv 538264; doi: https://doi.org/10.1101/538264


107. Meheust, R., Bhattacharya, D. Pathmanathan, J. S. McInerney, J. O. Lopez, P. and Bapteste, E. (2018). Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biology 16(1): 30. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-018-0500-0

106. Corel, E., Méheust, R., Watson, A.K., McInerney, J.O., Lopez, P., and Bapteste, E., (2018) Bipartite network analysis of gene sharings in the microbial world. Molecular Biology and Evolution DOI: 10.1093/molbev/msy001 [LINK]


105. McInerney, J.O., McNally, A., and O’Connell, M.J. (2017) Reply to ‘The population genetics of pangenomes’. Nature Microbiology 2 1575. [PDF]

104. McInerney, J.O. and Erwin, D.H. (2017) The Role of Public Goods in Planetary Evolution. Proceedings of the Royal Society of London, A Series. 375 20160359; DOI: 10.1098/rsta.2016.0359. [PDF]

103. Bruns, H., Crüsemann, M., Letzel, A., Alanjary, M., McInerney, JO., Jensen, P., Schulz, S. and Moore B. and Ziemert, N. (2017). Function-related Pathway Replacement of Bacterial Siderophore ISME Journal doi: 10.1038/ismej.2017.137 .

102. McInerney, J.O., McNally, A and O’Connell, M.J. (2017) Why Prokaryotes have Pangenomes. Nature Microbiology 2, 17040. [LINK]

101. McInerney, J.O. (2017) Horizontal Gene Transfer Is Less Frequent in Eukaryotes Than Prokaryotes But Can Be Important (retrospective on DOI 10.1002/bies.201300095). BioEssays 10.1002/bies.201700002.

100. McInerney, J.O. and O’Connell, M.J. (2017) Minding the gaps in cellular evolution. Nature 541, 297–299 doi:10.1038/nature21113 Link: https://t.co/I3ZKKyHSXp


99. McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., Vehkala, M., Välimäki, N., Prentice, M.B., Ashour, A., Avram, O., Pupko, T., Dobrindt, U., Literak, I., Guenther, S., Schaufler, K., Wieler, L.H., Zhiyong, Z., Sheppard, S.K., McInerney, J.O. and Corander, J. (2016) Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet 12(9): e1006280. doi: 10.1371/journal.pgen.1006280.

98. McInerney, J.O. (2016) Evolution: A four billion year old metabolism. Nature Microbiology. 1, Art. No. 16139. [PDF]

97. Fondi, M., Karkman, A., Tamminen, M., Bosi, E., Virta, M., Fani, R., Alm, E., and McInerney J.O. (2016) Every gene is everywhere but the environment selects: Global geo-localization of gene sharing in environmental samples through network analysis. Genome Biology and Evolutiondoi:10.1093/gbe/evw077


96. McInerney, J.O., Pisani, D. and O’Connell, M. J. (2015) The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data. Philos Trans R Soc Lond, B, Biol Sci 370, 20140323.

95. Akanni, W.A., Siu-Ting, K., Creevey, C.J., McInerney, J.O., Wilkinson, M., Foster, P.G., and Pisani, D. (2015) Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis. Philos Trans R Soc Lond B. Biol Sci. 370, 20140337. DOI: 10.1098/rstb.2014.0337.

94. Ku, C.,Nelson-Sathi, S., Roettger, M., Sousa, F.L. Lockhart, P.J., Bryant, D., Hazkani-Covo, E., McInerney, J.O., Landan, G. and Martin, W.F. (2015) Endosymbiotic origin and differential loss of eukaryotic genes Nature 524, 427–432. doi:10.1038/nature14963.

93. Coleman, O., Hogan, R., McGoldrick, N., Rudden, N., McInerney, J.O. (2015) Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes. Computation 2015, 3(2), 114-127; doi:10.3390/computation3020114 [pdf].

92. Nelson-Sathi S., Sousa F.L., Roettger M., Lozada-Chávez N., Thiergart T., Janssen A., Bryant D., Landan G., Schönheit P., Siebers B., McInerney J.O., Martin W.F., (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria Nature, doi:10.1038/nature13805. [pdf]


91. McInerney, J.O. and O’Connell, M.J. (2014) Evolutionary developmental biology: Ghost locus appears. Nature 514, 570–571 doi:10.1038/514570a [pdf]

90. McInerney, J.O., O’Connell, M.J., and Pisani, D. (2014) The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology 12(6):449-455. doi:10.1038/nrmicro3271.

89. Liu S., Lorenzen E.D., Fumagalli M., Li B., Harris K., Xiong Z., Zhou L., Korneliussen T.S., Somel M., Babbitt C., Wray G., Li J., He W., Wang Z., Fu W., Xiang X., Morgan C.C., Doherty A., O’Connell M.J., McInerney J.O., Born E.W., Dalén L., Dietz R., Orlando L., Sonne C., Zhang G., Nielsen R., Willerslev E., Wang J. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157 (4):785–794. [pdf]

88. Haggerty, L.S., Jachiet, P.A.,  Hanage, W.P., Fitzpatrick, D., Lopez, P., O’Connell, M.J., Pisani, D., Wilkinson, M., Bapteste, E., and McInerney, J.O., (2014) A pluralistic account of homology: adapting the models to the data. Molecular Biology and Evolution 31 (3): 501-516. [pdf]

87. Bogumil, D., Alvarez-Ponce, D., Landan, G., McInerney, J.O. and Dagan, T. (2014) Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. Molecular Biology and Evolution 31(2) 410-418. [pdf]


86. McInerney, J.O. (2013) More than Tree Dimensions: inter-lineage evolution’s ecological importance. Trends in Ecology and Evolution 28(11) 624-625. [pdf]

85. Doherty, A. and McInerney, J.O. (2013) Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Molecular Biology and Evolution 30(10) 2263-2267. [pdf]

84. Halary, S., McInerney, J.O., Lopez, P., and Bapteste E. (2013) EGN: a wizard for construction of gene and genome similarity networks. BMC Evolutionary Biology 23 (13) 146. [pdf]

83. Morgan, C.C., Foster., P.G., Webb, A.E., Pisani, D., McInerney, J.O. and O’Connell, M.J. (2013) Heterogeneous models place the root of the placental mammal phylogeny. Molecular Biology and Evolution 30(9): 2145-2156.  [pdf]

82. 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 29(8) 439-441. [pdf]

81. 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 110(17): E1594-603. [pdf]

80. 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


79. 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]

78. 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]

77. 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].

76. 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].

75. 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].


74. 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]

73. 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]

72. McInerney, J.O., Pisani, D., Bapteste, E., and O’Connell, M.J. (2011) The Public Goods Hypothesis for the Evolution of Life on Earth. Biology Direct doi:10.1186/1745-6150-6-41. [link]

71. 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.

70. 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]


69. 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


68. 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]

67. 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]

66. Hatadani, L.M., McInerney, J.O., de Medeiros, H.F., Martins Junqueira, A.C., de Azerdo-Espin, A.M. and Klaczko, L.B. (2009) Molecular Phylogeny of the Drosophila tripunctata and Closely Related Species Groups (Diptera: Drosophilidae). Molecular Phylogenetics and Evolution. 51(3):595-600. [pdfPMID: 19285146

65. 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]

64. 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]


63. 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]

62. 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]


61. McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391. [pdf]

60. 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]

59. 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]

58. 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]

57. 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]

56. 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]

55. 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]


54. McInerney, J.O. (2006). The Causes of Protein Evolutionary Rate Variation.Trends in Ecology and Evolution, 21(5), 230-232. [pdf]

53. 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.

52. 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]

51. McInerney, J.O. (2006). On the Desirability of Models for Inference of Genome Phylogenies. Trends in Microbiology 14(1) [pdf]

50. Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.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: 74-85.[pdf]

49. 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]

48. 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]

47. 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 α-Subunit Genes. Journal of Molecular Evolution, 63: 87-94.


46. 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]

45. 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]

44. 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]

43. 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]

42. Keane, T.M, Page, A.J. McInerney, J.O. and Naughton, T.J. (2005). A high-throughput bioinformatics distributed computing platform. Proceedings – IEEE Symposium on Computer-Based Medical Systems. p. 377-382.

41. 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]

40. 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]

39. 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]

38. Creevey, C.J. and McInerney, J.O. (2005). CLANN: Investigating Phylogenetic Information Through Supertree Analysis. Bioinformatics 21 (3) 390-392. [pdf]

37. 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]

36. 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]


35. 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]

34. 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]

33. 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]

32. 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.

31. 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]

30. 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]


29. 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]

28. 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]

27. 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]

26. 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]

25. 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]


24. 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]

23. 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.

22. 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]

21. McInerney, J. O. (2002) Bioinformatics in a Post-Genomic Era – The need for an Integrative Approach. The Pharmacogenomics Journal. 2:207-208. [pdf]


20. 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.

19. 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.

18. 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]

17. 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]

16. McInerney, J.O. and Wolfe, K.H. (1999). Genomic Analysis Methods.Microbiology Today, Vol. 26 p157-159.[ pdf]

15. 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.

14. 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.

13. 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]

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 vaginalisEuropean 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.