Dr Chris Creevey M.Sc. Ph.D.
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.
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.
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. ISME Journal 11 (4) pp. 932-944. Cadair2017.
De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. In (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. 127-131.2016.
Interaction of preimplantation factor with the bovine global endometrial transcriptome. British Society of Animal Science Annual conference, Chester, United Kingdom of Great Britain and Northern Ireland, 06/04/2016 - 07/04/2016.2016.
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. BMC Genomics 17 603 Cadair2016.
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. Cadair2015.
Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle. Reproduction, Fertility and Development 28 (2) pp. 11-24. Cadair2015.
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 Cadair2015.
Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics. Royal Society Open Science 2 140436 Cadair2015.
Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology 7 (5) pp. 467-79. Cadair2014.
Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods. PLoS One 9 (9) e106491 Cadair2014.
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 Cadair2014.
L.U.St: a tool for approximated maximum likelihood supertree reconstruction. BMC Bioinformatics 15 (1) 183 Cadair2014.
Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 15 (1) 356 Cadair2014.
Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mammalian Genome pp. 1-12. Other2014.
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. Cadair2014.
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 Cadair2014.
eggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Research 42 (D1) pp. D231-D239. Cadair2014.
Consistent mutational paths predict eukaryotic thermostability. BMC Evolutionary Biology 13 13 Cadair2013.
Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. BMC Bioinformatics 14 45 Cadair2013.
Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows. BMC Genomics 13 489 Cadair2012.
Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. BMC Genomics 13 16 Cadair2012.
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 13 193 Cadair2012.
Identifying single copy orthologs in Metazoa. PLoS Computational Biology 7 (12) e1002269 Cadair2011.
The integration of 'omic' disciplines and systems biology in cattle breeding. Animal 5 (4) pp. 493-505. Cadair2011.
Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One 6 (8) e22099 Cadair2011.
Duplicate retention in signalling proteins and constraints from network dynamics. BMC Evolutionary Biology 23 (11) pp. 2410-2421. Cadair2010.
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research 37 (Supp 1) D412-416 Cadair2009.
Trees from Trees: Construction of Phylogenetic Supertrees Using Clann. Methods in Molecular Biology. Springer Nature pp. 139-61. Cadair2009.
A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS One 3 (10) e3515 Cadair2008.
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 Cadair2006.
Toward automatic reconstruction of a highly resolved tree of life. Science 311 (5765) pp. 1283-1287. Cadair2006.
Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3) pp. 390-392. Cadair2005.
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. 1175-1184.2005.
Detecting adaptive molecular evolution: additional tools for the parasitologist. Advances in Parasitology 54 pp. 359-379. Cadair2003.
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. 10320-10325.2003.