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

Powell, S, Forslund, K, Szklarczyk, D, Trachana, K, Roth, A, Huerta-Cepas, J, Gabaldón, T, Rattei, T, Creevey, C, Kuhn, M, Jensen, LJ, von Mering, C & Bork, P 2014, 'eggNOG v4.0: Nested orthology inference across 3686 organisms' Nucleic Acids Research, vol 42, no. D1, pp. D231-D239. DOI: 10.1093/nar/gkt1253
Akanni, WA, Creevey, CJ, Wilkinson, M & Pisani, D 2014, 'L.U.St: a tool for approximated maximum likelihood supertree reconstruction' BMC Bioinformatics, vol 15, no. 1, 183. DOI: 10.1186/1471-2105-15-183
Carberry, CA, Waters, SM, Kenny, DA & Creevey, CJ 2014, 'Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type' Applied and Environmental Microbiology, vol 80, no. 2, pp. 586-94. DOI: 10.1128/AEM.03131-13
Doran, AG & Creevey, CJ 2013, 'Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms' BMC Bioinformatics, vol 14, 45. DOI: 10.1186/1471-2105-14-45
van Noort, V, Bradatsch, B, Arumugam, M, Amlacher, S, Bange, G, Creevey, CJ, Falk, S, Mende, DR, Sinning, I, Hurt, E & Bork, P 2013, 'Consistent mutational paths predict eukaryotic thermostability' BMC Evolutionary Biology, vol 13, 13. DOI: 10.1186/1471-2148-13-7
Foley, C, Chapwanya, A, Creevey, CJ, Narciandi, F, Morris, D, Kenny, EM, Cormican, P, Callanan, JJ, O'Farrelly, C & Meade, KG 2012, 'Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows' BMC Genomics, vol 13, 489. DOI: 10.1186/1471-2164-13-489
McCabe, M, Waters, S, Morris, D, Kenny, D, Lynn, D & Creevey, CJ 2012, 'RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance' BMC Genomics, vol 13, 193. DOI: 10.1186/1471-2164-13-193
Mullen, MP, Creevey, CJ, Berry, DP, McCabe, MS, Magee, DA, Howard, DJ, Killeen, AP, Park, SD, McGettigan, PA, Lucy, MC, Machugh, DE & Waters, SM 2012, 'Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples' BMC Genomics, vol 13, 16. DOI: 10.1186/1471-2164-13-16
Creevey, CJ, Muller, J, Doerks, T, Thompson, JD, Arendt, D & Bork, P 2011, 'Identifying single copy orthologs in Metazoa' PLoS Computational Biology, vol 7, no. 12, e1002269. DOI: 10.1371/journal.pcbi.1002269
Creevey, CJ, Doerks, T, Fitzpatrick, DA, Raes, J & Bork, P 2011, 'Universally distributed single-copy genes indicate a constant rate of horizontal transfer' PLoS One, vol 6, no. 8, e22099. DOI: 10.1371/journal.pone.0022099
Berry, DP, Meade, KG, Mullen, MP, Butler, S, Diskin, MG, Morris, D & Creevey, CJ 2011, 'The integration of 'omic' disciplines and systems biology in cattle breeding' Animal, vol 5, no. 4, pp. 493-505. DOI: 10.1017/S1751731110002120
Soyer, OS & Creevey, CJ 2010, 'Duplicate retention in signalling proteins and constraints from network dynamics' BMC Evolutionary Biology, vol 23, no. 11, pp. 2410-2421. DOI: 10.1111/j.1420-9101.2010.02101.x
Procter, JB, Thompson, J, Letunic, I, Creevey, CJ, Jossinet, F & Barton, GJ 2010, 'Visualization of multiple alignments, phylogenies and gene family evolution' Nature Methods, vol 7, no. 3 Suppl, pp. S16-25. DOI: 10.1038/nmeth.1434
Muller, J, Creevey, CJ, Thompson, JD, Arendt, D & Bork, P 2010, 'AQUA: automated quality improvement for multiple sequence alignments' Bioinformatics, vol 26, no. 2, pp. 263-265. DOI: 10.1093/bioinformatics/btp651
Jensen, LJ, Kuhn, M, Stark, M, Chaffron, S, Creevey, CJ, 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, vol 37, no. Supp 1, D412-416. DOI: 10.1093/nar/gkn760
Creevey, CJ & McInerney, JO 2009, Trees from Trees: Construction of Phylogenetic Supertrees Using Clann. in Methods in Molecular Biology. vol. 537, Springer Nature, pp. 139-61. DOI: 10.1007/978-1-59745-251-9_7
Foerstner, KU, Doerks, T, Creevey, CJ, Doerks, A & Bork, P 2008, 'A computational screen for type I polyketide synthases in metagenomics shotgun data' PLoS One, vol 3, no. 10, e3515. DOI: 10.1371/journal.pone.0003515
Sorek, R, Zhu, Y, Creevey, CJ, Francino, MP, Bork, P & Rubin, EM 2007, 'Genome-wide experimental determination of barriers to horizontal gene transfer' Science, vol 318, no. 5855, pp. 1449-1452. DOI: 10.1126/science.1147112
Keane, TM, Creevey, CJ, Pentony, MM, Naughton, TJ & Mclnerney, JO 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, vol 6, 29. DOI: 10.1186/1471-2148-6-29
Ciccarelli, FD, Doerks, T, von Mering, C, Creevey, CJ, Snel, B & Bork, P 2006, 'Toward automatic reconstruction of a highly resolved tree of life' Science, vol 311, no. 5765, pp. 1283-1287. DOI: 10.1126/science.1123061
Oyama, LB, Girdwood, SE, Cookson, AR, Fernandez-fuentes, N, Privé, F, Vallin, HE, Wilkinson, TJ, Golyshin, PN, Golyshina, OV, Mikut, R, Hilpert, K, Richards, J, Wootton, M, Edwards, JE, Maresca, M, Perrier, J, Lundy, FT, Luo, Y, Zhou, M, Hess, M, Mantovani, HC, Creevey, CJ & Huws, SA 2017, 'The rumen microbiome: an underexplored resource for novel antimicrobial discovery' npj Biofilms and Microbiomes, vol 3, no. 1, 33. DOI: 10.1038/s41522-017-0042-1
Dougal, K, Harris, PA, Girdwood, S, Creevey, C, Curtis, G, Barfoot, CF, Argo, CM & Newbold, C 2017, 'Changes in the total fecal bacterial population in individual horses maintained on a restricted diet over 6 weeks' Frontiers in Microbiology, vol 8, 1502. DOI: 10.3389/fmicb.2017.01502
Oyama, LB, Crochet, J-A, Edwards, JE, Girdwood, S, Cookson, A, Fernandez-Fuentes, N, Hilpert, K, Golyshin, PN, Golyshina, OV, Privé, F, Hess, M, Mantovani, HC, Creevey, C & Huws, S 2017, 'Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis' Frontiers in Chemistry, vol 5, 51. DOI: 10.3389/fchem.2017.00051
Rubino, F, Carberry, CA, Waters, SM, Kenny, DA, McCabe, M & Creevey, C 2017, 'Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome' ISME Journal, vol 11, no. 4, pp. 932-944. DOI: 10.1038/ismej.2016.172
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, vol 17, 603. DOI: 10.1186/s12864-016-2938-1
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, vol 118, no. 1, pp. 71-87. DOI: 10.1093/aob/mcw081
Mollison, EMB, Barth, S, Milbourne, D, Milne, L, Halpin, C, McCabe, M, Creevey, C & Marshall, DF 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. DOI: 10.1007/978-3-319-28932-8_19
Huws, S, Edwards, JE, 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, vol 92, no. 1, fiv 137. DOI: 10.1093/femsec/fiv137
Clamp, R, Creevey, C, Natoli, M, Barnea, ER, Nash, D & Rose, M 2016, 'Interaction of preimplantation factor with the bovine global endometrial transcriptome.' Paper presented at British Society of Animal Science Annual conference, Chester, United Kingdom of Great Britain and Northern Ireland, 2016 - 2016, .
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, C, Early, B, Keady, S, Kenny, DA, Matthews, D, McCabe, M, Morris, D, O'Loughlin, A, Waters, S, Diskin, MG & Evans, ACO 2015, 'Fertility and genomics: Comparison of gene expression in contrasting reproductive tissues of female cattle' Reproduction, Fertility and Development, vol 28, no. 2, pp. 11-24. DOI: 10.1071/RD15354
Akanni, WA, Siu-Ting, K, Creevey, C, McInerney, JO, Wilkinson, M, Foster, PG & 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, vol 370, no. 1678, 20140337. DOI: 10.1098/rstb.2014.0337
Akanni, WA, Wilkinson, M, Creevey, C, Foster, P & Pisani, D 2015, 'Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics' Royal Society Open Science, vol 2, 140436. DOI: 10.1098/rsos.140436
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, vol 29, no. 2, pp. 274-282. DOI: 10.1071/RD15128
Morgan, CC, Creevey, CJ & O'Connell, MJ 2014, 'Mitochondrial data are not suitable for resolving placental mammal phylogeny' Mammalian Genome, pp. 1-12. DOI: 10.1007/s00335-014-9544-9
Doran, AG, Berry, DP & Creevey, CJ 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, vol 15, no. 1, 837. DOI: 10.1186/1471-2164-15-837
Snelling, TJ, Genç, B, Mckain, N, Watson, M, Waters, SM, Creevey, CJ, Wallace, RJ & White, BA (ed.) 2014, 'Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods' PLoS One, vol 9, no. 9, e106491. DOI: 10.1371/journal.pone.0106491
Siu-Ting, K, Pisani, D, Creevey, CJ & Wilkinson, M 2014, 'Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction' Systematic Biology. DOI: 10.1093/sysbio/syu066
Creevey, CJ, Kelly, WJ, Henderson, G & Leahy, SC 2014, 'Determining the culturability of the rumen bacterial microbiome' Microbial Biotechnology, vol 7, no. 5, pp. 467-79. DOI: 10.1111/1751-7915.12141
Ciric, M, Moon, CD, Leahy, SC, Creevey, CJ, Altermann, E, Attwood, GT, Rakonjac, J & Gagic, D 2014, 'Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community' BMC Genomics, vol 15, no. 1, 356. DOI: 10.1186/1471-2164-15-356
Rudder, S, Doohan, F, Creevey, CJ, 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, vol 15, 268. DOI: 10.1186/1471-2164-15-268
Fitzpatrick, DA, Creevey, CJ & McInerney, JO 2006, 'Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales' Molecular Biology and Evolution, vol 23, no. 1, pp. 74-85. DOI: 10.1093/molbev/msj009
Fitzpatrick, DA, Creevey, CJ & McInerney, JO 2005, 'Evidence of positive Darwinian selection in putative meningococcal vaccine antigens' Journal of Molecular Evolution, vol 61, no. 1, pp. 90-98. DOI: 10.1007/s00239-004-0290-6
Philip, GK, Creevey, CJ & McInerney, JO 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, vol 22, no. 5, pp. 1175-1184. DOI: 10.1093/molbev/msi102
Creevey, CJ & McInerney, JO 2005, 'Clann: investigating phylogenetic information through supertree analyses' Bioinformatics, vol 21, no. 3, pp. 390-392. DOI: 10.1093/bioinformatics/bti020
Wilkinson, M, Cotton, JA, Creevey, CJ, Eulenstein, O, Harris, SR, Lapointe, F-J, Levasseur, C, McInerney, JO, Pisani, D & Thorley, JL 2005, 'The shape of supertrees to come: tree shape related properties of fourteen supertree methods' Systematic Biology, vol 54, no. 3, pp. 419-431. DOI: 10.1080/10635150590949832
Creevey, CJ, Fitzpatrick, DA, Philip, GK, Kinsella, RJ, O'Connell, MJ, Pentony, MM, Travers, SA, Wilkinson, M & McInerney, JO 2004, 'Does a tree-like phylogeny only exist at the tips in the prokaryotes?' Proceedings of the Royal Society B: Biological Sciences, vol 271, no. 1557, pp. 2551-2558. DOI: 10.1098/rspb.2004.2864
Kinsella, RJ, Fitzpatrick, DA, Creevey, CJ & McInerney, JO 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, vol 100, no. 18, pp. 10320-10325. DOI: 10.1073/pnas.1737230100
Creevey, CJ & McInerney, JO 2003, 'CRANN: detecting adaptive evolution in protein-coding DNA sequences' Bioinformatics, vol 19, no. 13, 1726. DOI: 10.1093/bioinformatics/btg225
McInerney, JO, Littlewood, DTJ & Creevey, CJ 2003, 'Detecting adaptive molecular evolution: additional tools for the parasitologist' Advances in Parasitology, vol 54, pp. 359-379. DOI: 10.1016/S0065-308X(03)54009-X
Creevey, CJ & McInerney, JO 2002, 'An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences' Gene, vol 300, no. 1-2, pp. 43-51. DOI: 10.1016/S0378-1119(02)01039-9