Robert Davey

Post-doctoral Researcher - Computational Biology

Curriculum vitae

Projects

CURRENT PROJECT:

Ribosomal DNA (rDNA) plays a key role in the biogenesis of the ribosome. The genes that encode the subunits of this cellular organelle are vital for efficient cellular protein manufacture and hence are highly conserved and normally present in high copy numbers. In Saccharomyces cerevisiae there are ~100 tandem rDNA repeats housed at a single locus on chromosome XII. Stability and sequence homogeneity of the rDNA array is essential for function, and this is achieved primarily by the mechanism of gene conversion. To try and validate the true stability and sequence homogeneity of the rDNA array, we attempt to detect fine-scale variation that was previously thought not to be preset within individual genomes. We have analysed approx. 50 Mbp of rDNA sequence obtained from the Sanger Genome Resequencing Project (SGRP), comprising 34 strains of S. cerevisiae and have found, contrary to expectation, significant rDNA sequence variation within each singular tandem array.

Many of the detected polymorphisms are not fully resolved. For this type of sequence variation we introduce the term `partial single nucleotide polymorphism', or `pSNP'. pSNP dynamics may provide a reliable new measure of genome origin and stability.

See Genome Research Abstract, Nature Abstract, and the IFR Press Release.

PREVIOUS PROJECTS:

Integrating genomic data across species boundaries is critical to the successful exploitation of previous investment in this area. Systematic attempts to do this have thus far carried a single species focus e.g. annotating the genome of one species using functional data from a second. Due to the multiple potential views that could be applied to the combined data set, a generaliseda `warehousing' approach will not succeed.

We are developing Fluxion, a new GRID-based system to capture the details of relationships between genomic data either within or across species in a way that will enable complex ad-hoc queries to be run and demonstrate that the underlying raw data can be combined to draw maximum benefit from those data for all genomic communities.

PhD PROJECT:

MPP is a new Java application that may be used to predict whole genome gene content from CGH datasets. MPP encompasses a fast novel algorithm that determines the probability of the presence or absence of each gene in a genome. MPP uses this information to provide an estimate of whole genome gene content. These results may be compared to existing gene content information produced from sequencing experiments and can also be used to make a phylogenetic inference.

Recent Software

• The Fluxion Data Integration Framework SVN access on Sourceforge
• R. P. Davey, J. Dicks and I.N. Roberts (2005-) MPP - Microarray-To-Phylogeny Pipeline. Link to MPP software

Publications

• Davey RP, Roberts IN, Dicks JL and Rayward-Smith VJ (2004) MPP: A microarray-to-phylogeny pipeline for gene content analysis. ISMB/ECCB 2004, July 31 - August 4, 2004, Glasgow, UK
• Davey R, Lacey G, MacKenzie DA, Defernez M, Mellon F, Huber K, Moulton V and Roberts IN (2005) Comparative metabolomics of Saccharomyces yeasts. First FEBS Advanced Course on Systems Biology: From Molecules & Modeling To Cells March 12- 18, 2005, Gosau, Austria, EU
• Flavell AJ, Jing R, Bolshakov VN, Knox MR, Lee JM, Vershinin AV, Dicks J, Davey R, Ambrose M and Ellis THN (2006) Genotyping a germplasm collection – The genetic diversity of Pisum. Plant and Animal Genome XIV, San Diego
• Davey R, Savva G, Jing R, Lott M, Ellis THN, Ambrose M, Moulton V, Flavell A, Roberts I and Dicks J (2006) Germplasm collections: Gaining new knowledge from old datasets. Proceedings of the 2nd UK KDD Conference pp 32-38.
• Davey RP, Savva G, Dicks J and Roberts IN (2007) MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets. Bioinformatics 23 (8): 1023-1025 Link to copy in PDF format
• Davey RP, Savva G, Dicks J and Roberts IN Refinement and Validation of Algorithms for deduction of gene content from CGH microarrays. (In preparation) (Supplemental Data)
• Davey RP, Roberts IN and Dicks J Deduction of marker content and network structure of a Pisum germplasm collection from TAM microarrays. (In preparation)
• Burdett AJ, Davey RP, Pocock M, Dicks J, Roberts IN and Wipat N (2009) Runcible: Integrating ontologies using a rule-based mapping engine. ISMB, Stockholm, Sweden
• Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ (2009) Population genomics of domestic and wild yeasts. Nature 458, 337-341 doi:10.1038/nature07743
• James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research 19: 626-635 doi:10.1101/gr.084517.108

Designed by Virginia Barnard
LAST UPDATED: 29th Oct 2009