Dr Chris Creevey M.Sc. Ph.D.

Dr Chris Creevey

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Dr Creevey completed a double honours degree in Computer Science and Biology in 1997 and a research masters in Ecology in 1999. In 2002 he received his PhD from the National University of Ireland for his work in the area of phylogenetics and comparative microbial genomics. Following this he worked as a postdoctoral researcher for the McInerney Lab in NUI Maynooth developing methods of resconstructing phylogenetic supertrees and detecting horizontal gene transfer (HGT) in genomic data. In 2005 he took up a postdoctoral position in the Euorpean Molecular Biology Laboratory (EMBL) in Heidelberg, Germany where the focus of his research involved the reconstruction of the tree of life, and the use of metagenomic and expressed sequence tag (EST) data for the phylogenetic analysis of unculturable organisms or for those we have no genomic information. In 2009 Dr. Creevey was awarded a Science Foundation Ireland Stokes Lecturership, at Teagasc, (The Irish agriculture and food development authority) in Ireland where his group worked on identifying the genomic factors influencing phenotypic changes in organisms from Bacteria to Eukaryotes, and the development of novel approaches to investigating metagenomic data from rumen microbial communities. He started his current position in IBERs in 2013.

Teaching

Research

Dr. Creevey is currently the Theme Director of Research for Animal and Aquatic Sciences in IBERS. He is also part of the Herbivore Gut Ecosystems group where he lab specialises in using computational approaches to understanding the ecology and evolution of microbial ecosystemsMy research interests include:

  • Developing novel computational approaches to understanding the complex interaction of the host-associated microbiomes.
  • Understanding the effect of host-associated microbial community structure on the efficiency and health of the host
  • Metagenomic and metatranscriptomic analysis of microbial communities.
  • Application of graph (phylogenetic and network) techniques to metagenomic and metatranscriptomic samples.
  • Analysis of whole genomes of microbial organisms.
  • Development of novel approaches for phylogenomic and evolutionary analyses.

For more information see the Creevey lab website.

Publications

2017

Dougal, K., Harris, P.A., Girdwood, S., Creevey, C., Curtis, G., Barfoot, C.F., Argo, C.M., Newbold, C. 2017. Changes in the total fecal bacterial population in individual horses maintained on a restricted diet over 6 weeks. Frontiers in Microbiology 1502 10.3389/fmicb.2017.01502

Oyama, L.B., Crochet, J., Edwards, J.E., Girdwood, S., Cookson, A., Fernandez-Fuentes, N., Hilpert, K., Golyshin, P.N., Golyshina, O.V., Privé, F., Hess, M., Mantovani, H.C., Creevey, C., Huws, S. 2017. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Frontiers in Chemistry 5 51 10.3389/fchem.2017.00051 Cadair

Rubino, F., Carberry, C.A., Waters, S.M., Kenny, D.A., McCabe, M., Creevey, C. 2017. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. ISME Journal 11 (4) pp. 932-944. 10.1038/ismej.2016.172 Cadair

2016

Moran, B., Cummins, S., Creevey, C., Butler, S. 2016. Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. BMC Genomics 17 603 10.1186/s12864-016-2938-1 Cadair

Velmurugan, J., Mollison, E., Barth, S., Marshall, D., Milne, L., Creevey, C., 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 118 (1) pp. 71-87. 10.1093/aob/mcw081 Cadair

Mollison, E.M.B., Barth, S., Milbourne, D., Milne, L., Halpin, C., McCabe, M., Creevey, C., Marshall, D.F. 2016. De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. In I. Roldán-Ruiz., J. Baert., D. Reheul. (eds) Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia. Springer Nature pp. 127-131. 10.1007/978-3-319-28932-8_19 Cadair

Huws, S., Edwards, J.E., Creevey, C., Rees Stevens, P., Lin, W., Girdwood, S., Pachebat, J., Kingston-Smith, A. 2016. Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass. FEMS Microbiology Ecology 92 (1) fiv 137 10.1093/femsec/fiv137 Cadair

Clamp, R., Creevey, C., Natoli, M., Barnea, E.R., Nash, D., Rose, M. 2016. Interaction of preimplantation factor with the bovine global endometrial transcriptome. British Society of Animal Science Annual conference. Cadair

2015

McGettigan, P.A., Browne, J.A., Carrington, S., Crowe, M., Fair, T., Forde, N., Loftus, B.J., Lohan, A., Lonergan, P., Pluta, K., Mamo, S., Murphy, A., Roche, J., Walsh, S., Creevey, C., Early, B., Keady, S., Kenny, D., Matthews, D., McCabe, M., Morris, D., O'Loughlin, A., Waters, S., Diskin, M.G., Evans, A. 2015. Fertility and genomics: Comparison of gene expression in contrasting reproductive tissues of female cattle. Reproduction, Fertility and Development 28 (2) pp. 11-24. 10.1071/RD15354 Cadair

Akanni, W.A., Siu-Ting, K., Creevey, C., 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 (1678) 20140337 10.1098/rstb.2014.0337 Cadair

Akanni, W.A., Wilkinson, M., Creevey, C., Foster, P., Pisani, D. 2015. Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics. Royal Society Open Science 2 140436 10.1098/rsos.140436 Other Cadair

Moran, B., Butler, S., Moore, S., McHugh, D., Creevey, C. 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 29 (2) pp. 274-282. 10.1071/RD15128 Cadair

2014

Akanni, W.A., Creevey, C.J., Wilkinson, M., Pisani, D. 2014. L.U.St: a tool for approximated maximum likelihood supertree reconstruction. BMC Bioinformatics 15 (1) 183 10.1186/1471-2105-15-183 Cadair

Carberry, C.A., Waters, S.M., Kenny, D.A., 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 (2) pp. 586-94. 10.1128/AEM.03131-13 Cadair

Morgan, C.C., Creevey, C.J., O'Connell, M.J. 2014. Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mammalian Genome pp. 1-12. 10.1007/s00335-014-9544-9 Other Cadair

Doran, A.G., Berry, D.P., 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 Genomics 15 (1) 837 10.1186/1471-2164-15-837 Cadair

Snelling, T.J., Genç, B., Mckain, N., Watson, M., Waters, S.M., Creevey, C.J., Wallace, R.J.White, B.A. 2014. Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods. PLoS One 9 (9) e106491 10.1371/journal.pone.0106491 Other Cadair

Siu-Ting, K., Pisani, D., Creevey, C.J., Wilkinson, M. 2014. Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction. Systematic Biology 10.1093/sysbio/syu066 Cadair

Creevey, C.J., Kelly, W.J., Henderson, G., Leahy, S.C. 2014. Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology 7 (5) pp. 467-79. 10.1111/1751-7915.12141 Cadair

Ciric, M., Moon, C.D., Leahy, S.C., Creevey, C.J., Altermann, E., Attwood, G.T., Rakonjac, J., Gagic, D. 2014. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 15 (1) 356 10.1186/1471-2164-15-356 Cadair

Rudder, S., Doohan, F., Creevey, C.J., Wendt, T., Mullins, E. 2014. Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. BMC Genomics 15 268 10.1186/1471-2164-15-268 Cadair

Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C., Bork, P. 2014. eggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Research 42 (D1) pp. D231-D239. 10.1093/nar/gkt1253 Cadair

2013

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 10.1186/1471-2105-14-45 Cadair

van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C.J., Falk, S., Mende, D.R., Sinning, I., Hurt, E., Bork, P. 2013. Consistent mutational paths predict eukaryotic thermostability. BMC Evolutionary Biology 13 13 10.1186/1471-2148-13-7 Cadair

2012

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 10.1186/1471-2164-13-489 Cadair

McCabe, M., Waters, S., Morris, D., Kenny, D., Lynn, D., Creevey, C.J. 2012. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 13 193 10.1186/1471-2164-13-193 Cadair

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., Machugh, D.E., Waters, S.M. 2012. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. BMC Genomics 13 16 10.1186/1471-2164-13-16 Cadair

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 (12) e1002269 10.1371/journal.pcbi.1002269 Cadair

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 (8) e22099 10.1371/journal.pone.0022099 Cadair

Berry, D.P., Meade, K.G., Mullen, M.P., Butler, S., Diskin, M.G., Morris, D., Creevey, C.J. 2011. The integration of 'omic' disciplines and systems biology in cattle breeding. Animal 5 (4) pp. 493-505. 10.1017/S1751731110002120 Cadair

2010

Soyer, O.S., Creevey, C.J. 2010. Duplicate retention in signalling proteins and constraints from network dynamics. BMC Evolutionary Biology 23 (11) pp. 2410-2421. 10.1111/j.1420-9101.2010.02101.x Cadair

Procter, J.B., Thompson, J., Letunic, I., Creevey, C.J., Jossinet, F., Barton, G.J. 2010. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods 7 (3 Suppl) pp. S16-25. 10.1038/nmeth.1434 Cadair

Muller, J., Creevey, C.J., Thompson, J.D., Arendt, D., Bork, P. 2010. AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics 26 (2) pp. 263-265. 10.1093/bioinformatics/btp651 Cadair

2009

Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C.J., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., von Mering, C. 2009. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research 37 (Supp 1) D412-416 10.1093/nar/gkn760 Cadair

Creevey, C.J., McInerney, J.O. 2009. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann. Methods in Molecular Biology. Springer Nature pp. 139-61. 10.1007/978-1-59745-251-9_7 Cadair

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 (10) e3515 10.1371/journal.pone.0003515 Cadair

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 (5855) pp. 1449-1452. 10.1126/science.1147112 Cadair

2006

Keane, T.M., Creevey, C.J., Pentony, M.M., Naughton, T.J., Mclnerney, 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 10.1186/1471-2148-6-29

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 (5765) pp. 1283-1287. 10.1126/science.1123061 Cadair

Fitzpatrick, D.A., Creevey, C.J., McInerney, J.O. 2006. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Molecular Biology and Evolution 23 (1) pp. 74-85. 10.1093/molbev/msj009 Cadair

2005

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 (1) pp. 90-98. 10.1007/s00239-004-0290-6 Cadair

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 (5) pp. 1175-1184. 10.1093/molbev/msi102 Cadair

Creevey, C.J., McInerney, J.O. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3) pp. 390-392. 10.1093/bioinformatics/bti020 Cadair

Wilkinson, M., Cotton, J.A., Creevey, C.J., Eulenstein, O., Harris, S.R., Lapointe, F., 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 (3) pp. 419-431. 10.1080/10635150590949832 Cadair

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 B: Biological Sciences 271 (1557) pp. 2551-2558. 10.1098/rspb.2004.2864 Cadair

2003

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 of the United States of America 100 (18) pp. 10320-10325. 10.1073/pnas.1737230100 Cadair

Creevey, C.J., McInerney, J.O. 2003. CRANN: detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics 19 (13) 1726 10.1093/bioinformatics/btg225 Cadair

McInerney, J.O., Littlewood, D.T.J., Creevey, C.J. 2003. Detecting adaptive molecular evolution: additional tools for the parasitologist. Advances in Parasitology 54 pp. 359-379. 10.1016/S0065-308X(03)54009-X Cadair

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 (1-2) pp. 43-51. 10.1016/S0378-1119(02)01039-9 Cadair