[BiO BB] PhD available in comparative genomics, Oxford, UK

Dawn Field dfield at ceh.ac.uk
Sun Apr 13 18:18:38 EDT 2003

A NERC funded PhD position is available entitled:

"Comparative Genomics, Phylogeny, Ecology and the study of Collections
of Genomes"

Supervisors: Dr Dawn Field, Prof Mark Bailey, Ed Feil (University
Advisor, University of Bath)
Primary Location: CEH Oxford, Oxford UK
Approaches:  Molecular Evolution and Bioinformatics, Large-scale
comparative genomics
Application Deadline: May 2 (Eligibility extends to UK residents. EU
residents can apply but only for fee-based support).

For more information please contact Dawn Field (dfield at ceh.ac.uk) or Ed
Feil (e.feil at bath.ac.uk).  To apply, please send a CV, brief statement
of past research experience and future research goals, and the names of
two academic referees to Angela Morrison (asmor at ceh.ac.uk, 0865-281630).


Whole genome sequencing is fuelling an information revolution that is
changing the face of biology. The ability to determine the complete
complement of DNA of a wide range of organisms is allowing us to ask in
unprecedented detail fundamental questions about the molecular basis of
life. There are now more than 1900 genomes from bacteria (Eubacteria and
Archaea), plasmids, phage, viruses and organelles in public databases. 
These genomes are so numerous that they constitute 'collections' of
genomes instead of small sets.  These collections are rapidly growing
and their evolutionary and ecological richness provides an unparalleled
opportunity to investigate the molecular basis of ecological adaptation
using computational approaches.  We are in the process of establishing a
database that combines complete genomes with evolutionary and ecological
meta-data.  Specific tasks to be carried out in this PhD include 1)
writing programming code to detect and characterise core genomic
features, 2) collecting a wider range of descriptive meta-data, and most
importantly, 3) using this resource to test a range of hypotheses about
the evolution and biological significance of shared and unshared genomic

Key areas of research to be addressed using data primarily from
bacterial genome sequences include, but are not limited to 1) testing
for relationships between ecological features and genomic features, 2)
examining the rate of evolution of features like G+C content and genome
size by mapping traits onto 16S RNA phylogenies and trees based on whole
proteome comparisons, 3) extracting 16S RNA operons from all bacterial
genomes to study the evolution of 16S RNA operons and their flanking
sequences, 4) detecting and studying the numbers and distributions of
orphan genes (putative proteins with no known homologues), and 5)
detecting and quantifying the number of conserved hypothetical

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