John Innes Centre, Norwich Research Park,
Colney Lane, Norwich, NR4 7UH, UK.

Telephone: +44(0) 1603 450833 (direct)
+44(0) 1603 450000 (switchboard)
+44(0) 1603 450595 (fax)

Curriculum vitae

1998 - 2001: BSc (2i Hons) Biological Sciences, University of East Anglia
2001 - 2005: PhD (Bioinformatics) John Innes Centre/Institute of Food Research/University of East Anglia
2005 - Pres: Post-doctoral Researcher, John Innes Centre/Institute of Food Research

Projects

CURRENT PROJECT:

Fine-scale phylogeny using a mathematical model of the dynamics of rDNA repeat sequence evolution

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:

ComparaGRID - ComparaGRID website
Fluxion - Fluxion project page on Sourceforge

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:

Refinement and Validation of Algorithms for Deduction of Gene Content from CGH Microarrays.

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

Publications

Designed by Virginia Barnard
LAST UPDATED: 29th Oct 2009