PhD Studentship: Simulation of Protein-DNA Interactions
Department of Chemistry
Vacancy Reference No: MA06719
Limit of tenure applies*

A PhD studentship is available from October 2010 to model protein-DNA
interactions and gene regulation. The 'second code in DNA' - how genes
are regulated - is poorly understood. Site-specific transcription factors
are proteins that bind to DNA and regulate gene expression. The base-pair
sequence in DNA combined with the structural information of a protein (as
determined by its amino acid sequence) results in specific interactions
that predispose a particular protein-DNA interaction to be favourable.
There is a combinatorial aspect to this, as there is thought to be an
interdependence of favourable amino acid-DNA interactions over the DNA
sequence which results in a hierarchy of favourable DNA regions in the
genome, and hence different affinities. With better tools to reliably
predict binding sites, novel regulatory elements can be discovered,
which is an important step to make sense of the huge volume of genome
sequences that have become available. In collaboration with experimental
studies in the Adryan lab 
(http://www.sysbiol.cam.ac.uk/index.php?page=dr-boris-adryan) we will
develop novel methods to predict gene regulation computationally. 


Applicants should have obtained, or expect to obtain, at least the
equivalent of a II.1 UK honours degree in chemistry, biology or a
related scientific discipline, and must have a good background knowledge
in both the life sciences and computer science. 


Applications should include a CV, contact details for two professional
referees, and should be sent to Professor Robert Glen, Department of
Chemistry, Lensfield Road, Cambridge CB2 1EW (email: smb28=cam.ac.uk).
The studentship is funded for EU applicants only.


* Limit of tenure: 3 years.


Closing date: 30 June 2010.

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