Dr Christopher Creevey
Reader in Rumen Systems Biology
Office: Room F.15, Carwn James Building, Penglais Campus, Aberystwyth, Ceredigion, Wales
Phone: +44(0)1970 621612
Work Package Leader, Rumen Systems Biology ISPG.
My research interests include:
- Developing novel computational approaches to understanding the complex interaction of the rumen microbiome.
- Understanding the effect of microbial community structure on the efficiency and health of ruminants
- Metagenomic and metatranscriptomic analysis of microbial communities.
- Investigation of the host influence on the rumen microbiome.
- Application of graph (phylogenetic and network) techniques to metagenomic and metatranscriptomic samples.
- Analysis of whole genomes of rumen microbial organisms.
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.
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/mcw0812016.
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 pp. 127-131. 10.1007/978-3-319-28932-8_192016.
Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass. FEMS Microbiology Ecology 92 (1) fiv 137 10.1093/femsec/fiv1372016.
Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits. Reproduction, Fertility and Development 10.1071/RD151282015.
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/RD153542015.
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 Philosophical Transactions B: Biological Sciences 370 (1678) 20140337 10.1098/rstb.2014.0337 Other2015.
Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction. Systematic Biology 10.1093/sysbio/syu0662014.
Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology 7 (5) pp. 467-79. 10.1111/1751-7915.121412014.
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 10.1186/1471-2164-15-2682014.
L.U.St: a tool for approximated maximum likelihood supertree reconstruction. BMC Bioinformatics 15 (1) 183 10.1186/1471-2105-15-1832014.
Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 15 (1) 356 10.1186/1471-2164-15-3562014.
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.03131-132014.
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 10.1186/1471-2164-15-8372014.
eggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Research 42 (D1) pp. D231-D239. 10.1093/nar/gkt12532014.
Consistent mutational paths predict eukaryotic thermostability. BMC Evolutionary Biology 13 13 10.1186/1471-2148-13-72013.
Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. BMC Bioinformatics 14 45 10.1186/1471-2105-14-452013.
Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows. BMC Genomics 13 489 10.1186/1471-2164-13-4892012.
Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. BMC Genomics 13 16 10.1186/1471-2164-13-162012.
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 13 193 10.1186/1471-2164-13-1932012.
Identifying single copy orthologs in Metazoa. PLoS Computational Biology 7 (12) e1002269 10.1371/journal.pcbi.10022692011.
The integration of 'omic' disciplines and systems biology in cattle breeding. Animal 5 (4) pp. 493-505. 10.1017/S17517311100021202011.
Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One 6 (8) e22099 10.1371/journal.pone.00220992011.
AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics 26 (2) pp. 263-265. 10.1093/bioinformatics/btp6512010.
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.x2010.
Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods 7 (3 Suppl) pp. S16-25. 10.1038/nmeth.14342010.
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/gkn7602009.
Trees from Trees: Construction of Phylogenetic Supertrees Using Clann. Methods in Molecular Biology. Humana Press pp. 139-61. 10.1007/978-1-59745-251-9_72009.
A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS One 3 (10) e3515 10.1371/journal.pone.00035152008.
Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318 (5855) pp. 1449-1452. 10.1126/science.11471122007.
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 10.1186/1471-2148-6-292006.
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/msj0092006.
Toward automatic reconstruction of a highly resolved tree of life. Science 311 (5765) pp. 1283-1287. 10.1126/science.11230612006.
Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3) pp. 390-392. 10.1093/bioinformatics/bti0202005.
Evidence of positive Darwinian selection in putative meningococcal vaccine antigens. Journal of Molecular Evolution 61 (1) pp. 90-98. 10.1007/s00239-004-0290-62005.
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/msi1022005.
The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Systematic Biology 54 (3) pp. 419-431. 10.1080/106351505909498322005.
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.2004.28642004.
CRANN: detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics 19 (13) 1726 10.1093/bioinformatics/btg2252003.
Detecting adaptive molecular evolution: additional tools for the parasitologist. Advances in Parasitology 54 pp. 359-379. 10.1016/S0065-308X(03)54009-X2003.
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 Proceedings of the National Academy of Sciences 100 (18) pp. 10320-10325. 10.1073/pnas.17372301002003.
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)01039-92002.