Publications


2017
  • Rubino F.; Carberry C.; Waters S.; Kenny D.; McCabe M.; Creevey C.J. (2017) Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. The ISME Journal. doi:10.1038/ismej.2016.172. Link
  • Matthews, D., Diskin, M.G., Kenny, D.A., Creevey, C.J., Keogh, K. and Waters, S.M., 2017. Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology. BMC genomics, 18(1), p.857. Link
  • Dougal, K., Harris, P.A., Girdwood, S.E., Creevey, C.J., Curtis, G.C., Barfoot, C.F., Argo, C.M. and Newbold, C.J., 2017. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks. Frontiers in Microbiology8, p.1502. Link
  • Oyama, L.B., Crochet, J.A., Edwards, J.E., Girdwood, S.E., Cookson, A.R., Fernandez-Fuentes, N., Hilpert, K., Golyshin, P.N., Golyshina, O.V., Privé, F. and Hess, M., 2017. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Frontiers in chemistry5, p.51. Link

2016
  • Moran B.; Cummins S.B.; Creevey C.J.; Butler S.T. (2016) Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. BMC Genomics. 17 (1), 603. Link
  • Velmurugan J.; Mollison E.; Barth S.; Marshall D.; Milne L.; Creevey C.J.; Lynch B.; Meally H.; McCabe M.; Milbourne D.; (2016) An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. Annals of Botany Ann Bot 118(1): 71-87. Link
  • Mollison, E.M.B., Barth, S., Milbourne, D., Milne, L., Halpin, C., McCabe, M., Creevey, C. and Marshall, D.F., 2016. De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. In Breeding in a World of Scarcity (pp. 127-131). Springer International Publishing. Link
  • Huws, S.A; Edwards, J.E; Creevey, C.J; Stevens, P.; Lin, W.; Girdwood, S.E; Pachebat, J.A; Kingston-Smith, A.H; (2016) Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass. FEMS microbiology ecology 92:fiv137. Link
2015
  • McGettigan, PA, Browne, JA, Carrington, SD, Crowe, MA, Fair, T, Forde, N, Loftus, BJ, Lohan, A, Lonergan, P, Pluta, K, Mamo, S, Murphy, A, Roche, J, Walsh, SW, Creevey, CJ, Early, B, Keady, S, Kenny, D A, Matthews, D, McCabe, M, Morris, D, O'Loughlin, A, Waters, S, Diskin, M G & Evans, A C O (2015) Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle. Reproduction, Fertility and Development 28. Link
  • Moran, B.; Butler, S.T; Moore, S.G; MacHugh, D.E; Creevey, C.J; (2015) Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits. Reproduction, Fertility and Development. doi: 10.1071/RD15128. Link
  • Akanni, W.A; Siu-Ting, K.; Creevey, C.J; McInerney, J.O; Wilkinson, M.; Foster, P.G; Pisani, D.; (2015) Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis. Philosophical Transactions of The Royal Society B Biological Sciences 370:2014033. Link
  • Akanni, W.A; Wilkinson, M.; Creevey, C.J; Foster, P.G; Pisani, D.; (2015) Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. Royal Society open science 2:140436. Link
  • Siu-Ting, K., Pisani, D., Creevey, C. J., and Wilkinson, M. (2015). Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction. Systematic biology, 64 (1): 137-143. Link
2014
  • Doran, A. G., Berry, D. P., and Creevey, C. J. (2014). Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle. BMC genomics15(1), 837. Link
  • Snelling, T. J., Genç, B., McKain, N., Watson, M., Waters, S. M., Creevey, C. J., and Wallace, R. J. (2014). Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods. PloS one9(9), e106491. Link
  • Akanni, W. A., Creevey, C. J., Wilkinson, M., and Pisani, D. (2014). LU St: a tool for approximated maximum likelihood supertree reconstruction. BMC bioinformatics15(1), 183. Link
  • Creevey, C.J., Kelly, W.J., Henderson, G. and Leahy, S.C. (2014). Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology, doi: 10.1111/1751-7915.12141. Link
  • Akanni, W. A., Creevey, C. J., Wilkinson, M., and Pisani, D. (2014). LU St: a tool for approximated maximum likelihood supertree reconstruction. BMC bioinformatics, 15(1), 183. Link
  • Ciric, M., Moon, C. D., Leahy, S. C., Creevey, C. J., Altermann, E., Attwood, G. T., Rakonjac, J. and Gagic, D. (2014). Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC genomics, 15(1), 356. Link
  • Rudder, S., Doohan, F., Creevey, C. J., Wendt, T., and Mullins, E. (2014). Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomesBMC genomics15(1), 268. Link
  • Carberry C.A., Waters S.M., Kenny D.A.,  and Creevey C.J. (2014) Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type. Applied and Environmental Microbiology 80:586-594. Link
2013
    • Powell S., Forslund K., Szklarczyk D., Trachana K., Roth A., Huerta-Cepas J., Gabaldón T., Rattei T., Creevey C., Kuhn M. (2014) Eggnog V4. 0: Nested Orthology Inference across 3686 Organisms. Nucleic Acids Research 42:D231-D239. Link
    • van Noort V., Bradatsch B., Arumugam M., Amlacher S., Bange G., Creevey C., Falk S., Mende D.R., Sinning I., Hurt E. (2013) Consistent Mutational Paths Predict Eukaryotic Thermostability. BMC Evolutionary Biology 13:7. Link
    • Mullen M.P., McClure M.C., Kearney J.F., Waters S.M., Weld R., Flynn P., Creevey C.J., Cromie A.R., Berry D.P. (2013) Development of a Custom Snp Chip for Dairy and Beef Cattle Breeding, Parentage and Research. Interbull Bulletin 47:58-66. Link
    • Doran A.G., Creevey C.J. (2013) Snpdat: Easy and Rapid Annotation of Results from De Novo SNP Discovery Projects for Model and Non-Model Organisms. BMC Bioinformatics 14:45. Link
    2012
      • Mullen M.P., Creevey C.J., Berry D.P., McCabe M.S., Magee D.A., Howard D.J., Killeen A.P., Park S.D., McGettigan P.A., Lucy M.C. (2012) Polymorphism Discovery and Allele Frequency Estimation Using High-Throughput DNA Sequencing of Target-Enriched Pooled DNA Samples. BMC Genomics 13:16. Link
      • McCabe M., Waters S., Morris D., Kenny D., Lynn D., Creevey C. (2012) Rna-Seq Analysis of Differential Gene Expression in Liver from Lactating Dairy Cows Divergent in Negative Energy Balance. BMC Genomics 13:193. Link
      • Foley C., Chapwanya A., Creevey C.J., Narciandi F., Morris D., Kenny E.M., Cormican P., Callanan J.J., O’Farrelly C., Meade K.G. (2012) Global Endometrial Transcriptomic Profiling: Transient Immune Activation Precedes Tissue Proliferation and Repair in Healthy Beef Cows. BMC Genomics 13:489. Link
      2011
        • Creevey C.J., Muller J., Doerks T., Thompson J.D., Arendt D., Bork P. (2011) Identifying Single Copy Orthologs in Metazoa. PLoS Computational Biology 7:e1002269. Link
        • Creevey C.J., Doerks T., Fitzpatrick D.A., Raes J., Bork P. (2011) Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer. PloS One 6:e22099. Link
        • Berry D., Meade K., Mullen M., Butler S., Diskin M., Morris D., Creevey C. (2011) The Integration of ‘Omic’disciplines and Systems Biology in Cattle Breeding. Animal 5:493-505. Link
        2010
          • Soyer O., Creevey C. (2010) Duplicate Retention in Signalling Proteins and Constraints from Network Dynamics. Journal of Evolutionary Biology 23:2410-2421. Link
          • Procter J.B., Thompson J., Letunic I., Creevey C., Jossinet F., Barton G.J. (2010) Visualization of Multiple Alignments, Phylogenies and Gene Family Evolution. Nature methods 7:S16-S25. Link
          • Muller J., Creevey C.J., Thompson J.D., Arendt D., Bork P. (2010) Aqua: Automated Quality Improvement for Multiple Sequence Alignments. Bioinformatics 26:263-265. Link
          2009
            • Jensen L.J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M. (2009) String 8—a Global View on Proteins and Their Functional Interactions in 630 Organisms. Nucleic Acids Research 37:D412-D416. Link
            • Creevey C.J., McInerney J.O. (2009) Trees from Trees: Construction of Phylogenetic Supertrees Using Clann. In: Posada D. editor. Bioinformatics for DNA Sequence Analysis. New York, NY: Humana Press. p.139-161. Link
            2008
              • Foerstner K.U., Doerks T., Creevey C.J., Doerks A., Bork P. (2008) A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data. PloS One 3:e3515. Link
              2007
                • Sorek R., Zhu Y., Creevey C.J., Francino M.P., Bork P., Rubin E.M. (2007) Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer. Science 318:1449. Link
                • McInerney J., Pisani D., O'Connell M., Fitzpatrick D., Creevey C. (2007) Evolutionary History of Prokaryotes: Tree or No Tree? In: Hodkinson T.R., Parnell J.A. editors. Reconstructing the Tree of Life. Taxonomy and Systematics of Species Rich Taxa. Boca Raton, FL: CRC Press. p. 49-59. Link
                2006
                  • Keane T., Creevey C., Pentony M., Naughton T., Mclnerney J. (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
                  • Fitzpatrick D.A., Creevey C.J., McInerney J.O. (2006) Genome Phylogenies Indicate a Meaningful Α-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales. Molecular Biology and Evolution 23:74-85. Link
                  • Ciccarelli F.D., Doerks T., Von Mering C., Creevey C.J., Snel B., Bork P. (2006) Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 311:1283. Link
                  2005
                    • 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 54:419-431. Link
                    • Philip G.K., Creevey C.J., 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. Link
                    • Fitzpatrick D.A., Creevey C.J., McInerney J.O. (2005) Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens. Journal of Molecular Evolution 61:90-98. Link
                    • Creevey C.J. (2005) Can You See the Wood for the Trees? Trends in Ecology and Evolution 20:366. Link
                    • Creevey C., McInerney J. (2005) Clann: Investigating Phylogenetic Information through Supertree Analyses. Bioinformatics 21:390-392. Link
                    2004
                      • Creevey C.J., Fitzpatrick D.A., Philip G.K., Kinsella R.J., O'Connell M.J., Pentony M.M., Travers S.A., Wilkinson M., McInerney J.O. (2004) Does a Tree–Like Phylogeny Only Exist at the Tips in the Prokaryotes? Proceedings of the Royal Society of London. Series B: Biological Sciences 271:2551. Link
                      2003
                        • McInerney J., Littlewood T., Creevey C.J. (2003) Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist. Advances in Parasitology 54:359-379. Link
                        • Kinsella R.J., Fitzpatrick D.A., Creevey C.J., 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 100:10320. Link
                        • Creevey C.J., McInerney J.O. (2003) Crann: Detecting Adaptive Evolution in Protein-Coding DNA Sequences. Bioinformatics 19:1726. Link
                        2002
                          • Creevey C.J., McInerney J.O. (2002) An Algorithm for Detecting Directional and Non-Directional Positive Selection, Neutrality and Negative Selection in Protein Coding DNA Sequences. Gene 300:43-51. Link