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

Spherical: an iterative workflow for assembling metagenomic datasetsHitch, T. C. A. & Creevey, C. J. 2018 In : BMC Bioinformatics.19, 1, 20
Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genesHitch, T., Thomas, B. J., Friedersdorff, J. C. A., Ougham, H. & Creevey, C. 2018 In : Environmental Pollution.235, p. 571-5755 p.
The rumen microbiome: an underexplored resource for novel antimicrobial discoveryOyama, L. B., Girdwood, S. E., Cookson, A. R., Fernandez-fuentes, N., Privé, F., Vallin, H. E., Wilkinson, T. J., Golyshin, P. N., Golyshina, O. V., Mikut, R., Hilpert, K., Richards, J., Wootton, M., Edwards, J. E., Maresca, M., Perrier, J., Lundy, F. T., Luo, Y., Zhou, M., Hess, M., Mantovani, H. C., Creevey, C. J. & Huws, S. A. 2017 In : npj Biofilms and Microbiomes.3, 1, 33
Changes in the total fecal bacterial population in individual horses maintained on a restricted diet over 6 weeksDougal, K., Harris, P. A., Girdwood, S., Creevey, C., Curtis, G., Barfoot, C. F., Argo, C. M. & Newbold, C. 2017 In : Frontiers in Microbiology.8, 1502
Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalisOyama, L. B., Crochet, J-A., 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 In : Frontiers in Chemistry.5, 51
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiomeRubino, F., Carberry, C. A., Waters, S. M., Kenny, D. A., McCabe, M. & Creevey, C. 2017 In : ISME Journal.11, 4, p. 932-944
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes.Moran, B., Cummins, S., Creevey, C. & Butler, S. 2016 In : BMC Genomics.17, 603
An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assemblyVelmurugan, J., Mollison, E., Barth, S., Marshall, D., Milne, L., Creevey, C., Lynch, B., Meally, H., McCabe, M. & Milbourne, D. 2016 In : Annals of Botany.118, 1, p. 71-87
De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial RyegrassMollison, E. M. B., Barth, S., Milbourne, D., Milne, L., Halpin, C., McCabe, M., Creevey, C. & Marshall, D. F. 2016 Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia. Roldán-Ruiz , I., Baert, J. & Reheul , D. (eds.). Springer Nature, p. 127-131
Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrassHuws, S., Edwards, J. E., Creevey, C., Rees Stevens, P., Lin, W., Girdwood, S., Pachebat, J. & Kingston-Smith, A. 2016 In : FEMS Microbiology Ecology.92, 1, fiv 137
Interaction of preimplantation factor with the bovine global endometrial transcriptome.Clamp, R., Creevey, C., Natoli, M., Barnea, E. R., Nash, D. & Rose, M. 2016
Fertility and genomics: Comparison of gene expression in contrasting reproductive tissues of female cattleMcGettigan, P. A., Browne, J. A., Carrington, S. D., Crowe, M. A., Fair, T., Forde, N., Loftus, B. J., Lohan, A., Lonergan, P., Pluta, K., Mamo, S., Murphy, A., Roche, J., Walsh, S. W., Creevey, C., 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 In : Reproduction, Fertility and Development.28, 2, p. 11-24
Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of EukaryogenesisAkanni, W. A., Siu-Ting, K., Creevey, C., McInerney, J. O., Wilkinson, M., Foster, P. G. & Pisani, D. 2015 In : Philosophical Transactions of the Royal Society B: Biological Sciences.370, 1678, 20140337
Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogeneticsAkanni, W. A., Wilkinson, M., Creevey, C., Foster, P. & Pisani, D. 2015 In : Royal Society Open Science.2, 9 p., 140436
Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traitsMoran, B., Butler, S., Moore, S., McHugh, D. & Creevey, C. 2015 In : Reproduction, Fertility and Development.29, 2, p. 274-282
Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial communityCiric, M., Moon, C. D., Leahy, S. C., Creevey, C. J., Altermann, E., Attwood, G. T., Rakonjac, J. & Gagic, D. 2014 In : BMC Genomics.15, 1, 356
Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomesRudder, S., Doohan, F., Creevey, C. J., Wendt, T. & Mullins, E. 2014 In : BMC Genomics.15, 268
eggNOG v4.0: Nested orthology inference across 3686 organismsPowell, 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 In : Nucleic Acids Research.42, D1, p. D231-D2399 p.
L.U.St: a tool for approximated maximum likelihood supertree reconstructionAkanni, W. A., Creevey, C. J., Wilkinson, M. & Pisani, D. 2014 In : BMC Bioinformatics.15, 1, 183
Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet typeCarberry, C. A., Waters, S. M., Kenny, D. A. & Creevey, C. J. 2014 In : Applied and Environmental Microbiology.80, 2, p. 586-949 p.
Mitochondrial data are not suitable for resolving placental mammal phylogenyMorgan, C. C., Creevey, C. J. & O'Connell, M. J. 2014 In : Mammalian Genome.p. 1-12
Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattleDoran, A. G., Berry, D. P. & Creevey, C. J. 2014 In : BMC Genomics.15, 1, 837
Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different MethodsSnelling, T. J., Genç, B., Mckain, N., Watson, M., Waters, S. M., Creevey, C. J., Wallace, R. J. & White, B. A. (ed.) 2014 In : PLoS One.9, 9, e106491
Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic ReductionSiu-Ting, K., Pisani, D., Creevey, C. J. & Wilkinson, M. 2014 In : Systematic Biology.
Determining the culturability of the rumen bacterial microbiomeCreevey, C. J., Kelly, W. J., Henderson, G. & Leahy, S. C. 2014 In : Microbial Biotechnology.7, 5, p. 467-7913 p.
Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organismsDoran, A. G. & Creevey, C. J. 2013 In : BMC Bioinformatics.14, 45
Consistent mutational paths predict eukaryotic thermostabilityvan 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 In : BMC Evolutionary Biology.13, 13
Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cowsFoley, 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 In : BMC Genomics.13, 489
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balanceMcCabe, M., Waters, S., Morris, D., Kenny, D., Lynn, D. & Creevey, C. J. 2012 In : BMC Genomics.13, 193
Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samplesMullen, 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 In : BMC Genomics.13, 16
Identifying single copy orthologs in MetazoaCreevey, C. J., Muller, J., Doerks, T., Thompson, J. D., Arendt, D. & Bork, P. 2011 In : PLoS Computational Biology.7, 12, e1002269
Universally distributed single-copy genes indicate a constant rate of horizontal transferCreevey, C. J., Doerks, T., Fitzpatrick, D. A., Raes, J. & Bork, P. 2011 In : PLoS One.6, 8, e22099
The integration of 'omic' disciplines and systems biology in cattle breedingBerry, D. P., Meade, K. G., Mullen, M. P., Butler, S., Diskin, M. G., Morris, D. & Creevey, C. J. 2011 In : Animal.5, 4, p. 493-50513 p.
Duplicate retention in signalling proteins and constraints from network dynamicsSoyer, O. S. & Creevey, C. J. 2010 In : BMC Evolutionary Biology.23, 11, p. 2410-242112 p.
Visualization of multiple alignments, phylogenies and gene family evolutionProcter, J. B., Thompson, J., Letunic, I., Creevey, C. J., Jossinet, F. & Barton, G. J. 2010 In : Nature Methods.7, 3 Suppl, p. S16-25
AQUA: automated quality improvement for multiple sequence alignmentsMuller, J., Creevey, C. J., Thompson, J. D., Arendt, D. & Bork, P. 2010 In : Bioinformatics.26, 2, p. 263-2653 p.
STRING 8--a global view on proteins and their functional interactions in 630 organismsJensen, 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 In : Nucleic Acids Research.37, Supp 1, D412-416
Trees from Trees: Construction of Phylogenetic Supertrees Using ClannCreevey, C. J. & McInerney, J. O. 2009 Methods in Molecular Biology.Springer Nature, Vol. 537, p. 139-6123 p.
A computational screen for type I polyketide synthases in metagenomics shotgun dataFoerstner, K. U., Doerks, T., Creevey, C. J., Doerks, A. & Bork, P. 2008 In : PLoS One.3, 10, e3515
Genome-wide experimental determination of barriers to horizontal gene transferSorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Bork, P. & Rubin, E. M. 2007 In : Science.318, 5855, p. 1449-14524 p.
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 justifiedKeane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & Mclnerney, J. O. 2006 In : BMC Evolutionary Biology.6, 29
Toward automatic reconstruction of a highly resolved tree of lifeCiccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. 2006 In : Science.311, 5765, p. 1283-12875 p.
Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the RickettsialesFitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. 2006 In : Molecular Biology and Evolution.23, 1, p. 74-8512 p.
Evidence of positive Darwinian selection in putative meningococcal vaccine antigensFitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. 2005 In : Journal of Molecular Evolution.61, 1, p. 90-989 p.
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 EcdysozoaPhilip, G. K., Creevey, C. J. & McInerney, J. O. 2005 In : Molecular Biology and Evolution.22, 5, p. 1175-118410 p.
Clann: investigating phylogenetic information through supertree analysesCreevey, C. J. & McInerney, J. O. 2005 In : Bioinformatics.21, 3, p. 390-3923 p.
The shape of supertrees to come: tree shape related properties of fourteen supertree methodsWilkinson, M., Cotton, J. A., Creevey, C. J., Eulenstein, O., Harris, S. R., Lapointe, F-J., Levasseur, C., McInerney, J. O., Pisani, D. & Thorley, J. L. 2005 In : Systematic Biology.54, 3, p. 419-43113 p.
Does a tree-like phylogeny only exist at the tips in the prokaryotes?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 In : Proceedings of the Royal Society B: Biological Sciences.271, 1557, p. 2551-25588 p.
Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplicationKinsella, R. J., Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. 2003 In : Proceedings of the National Academy of Sciences of the United States of America.100, 18, p. 10320-103256 p.
CRANN: detecting adaptive evolution in protein-coding DNA sequencesCreevey, C. J. & McInerney, J. O. 2003 In : Bioinformatics.19, 13, 1726
Detecting adaptive molecular evolution: additional tools for the parasitologistMcInerney, J. O., Littlewood, D. T. J. & Creevey, C. J. 2003 In : Advances in Parasitology.54, p. 359-37921 p.
An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequencesCreevey, C. J. & McInerney, J. O. 2002 In : Gene.300, 1-2, p. 43-519 p.