Andrew Dalby
Dr Andrew Dalby
Research interests:
Systems Biology, Metabolic Network Analysis, Stochastic Modelling of Metabolic Network Regulation, Protein Misfolding, SNPs and Protein Repeats.
Since joining the statistics department I have focused increasingly on systems biology research and in particular the analysis of metabolic networks. We are currently building a organism independent metabolic database that can be used for network reconstruction and statistical analysis. One the network has been successfully modelled the next step is to model network dynamics and regulation. This can be done using parameter free computational models such as Petri-nets or it can use probabilistic models based on known kinetic parameters where these are available. The intention is to create a combined approach using agent based approaches which will hopefully add a spatio-temporal description to network analysis.
I am also continuing my work on protein misfolding diseases such as nvCJD. One interesting result from an analysis of the malarial genome is the large number of potentially prion forming domains found in malarial proteins. The reason for the evolution of these domains and their effects on protein structure and stability remain unexplained.
Selected publications:
β-sheet containment by flanking prolines: Molecular Dynamic Simulations of the inhibition of β-sheet elongation by proline residues in human prion protein. Biophysical Journal (2007) (with M. S. Shamsir)
One gene, two diseases and three conformations: Molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures. Proteins: Structure, Function and Genetics (2005) 59, 275-290 (with M. S. Shamsir)
COPASAAR - A database for proteomic analysis of single amino acid repeats. BMC Bioinformatics (2005) 6 (with D. P. Depledge)
Evaluation of mutual information and genetic programming for feature selection in QSAR. Journal of Chemical Information and Computer Sciences (2004) 44, 1686-1692 (with V. Venkatraman & Z. R. Yang)
Constructing an enzyme-centric view of metabolism. Bioinformatics (2004) 20, 2050-2055 (with A. B. Horne, T. C. Hodgman & H. D. Spence)
Biographical Sketch:
I did my undergraduate degree in chemistry and law at the University of Exeter where I also did my PhD in protein crystallography and molecule modelling. My post-doctoral research was in protein crystallography and protein sequence analysis, which led to me being appointed as lecturer in bioinformatics when Exeter established an MSc programme in bioinformatics.
I came to Oxford in 2005 as a Departmental Lecturer. My main responsibilities are in the teaching and administration of the Oxford Bioinformatics Programme which is run by the Departments of Statistics and Continuing Education.
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