Research Interests

Keywords: Bioinformatics, cophylogeny, combinatorics

I have just been thinking of some open questions I'm interested in.

Bioinformatics is a growing field that crosses many disciplines, from mathematics and statistics through molecular biology and evolution, to computer science and optimization. If you ask 20 people 'what is bioinformatics' you'll get at least 20 different answers, but one thing they tend to have in common is the idea that bioinformatics deals with huge amounts of biological data. I see bioinformatics as

The [development of][the computational, mathematical and statistical] tools that we need to get knowledge from lots of biological data.
That makes bioinformatics a big subject: it includes
• molecular evolution,
• phylogenetic reconstruction (finding out what are the evolutionary relationshps among species),
• analysis of micro-array data
• predicting protein structure and function
• determination of markers to efficiently identify cancers
• mapping quantitative traits to gene expression
• ... and more.

My main area of interest is in cophylogeny, that is, the study of how groups of ecologically linked species evolve with each other. Parasites (of which there are many more types than there are non-parasites) evolve with their hosts, and pathogens (disease agents) evolve in a constant arms race with their "victims". As many as three quarters of emergent diseases in humans have come from other species. Genes can be considered to 'parasitise' their 'hosts', because they undergo the same kinds of processes as do parasites and pathogens. Even languages can, in a sense, parasitise people.

The problem is computationally very tough, as well as being statistically hard, and there have been several different approaches. One is by cophylogeny mapping, which is easily the most intuitive method, and happens to have other nice properties as well. In this method the dependent phylogeny (another term for evolutionary tree) P is mapped into the independent phylogeny, in order to show how the two phylogenies have been associated with each other in the past. I developed the "jungle" which is a graph containing a set of feasible maps from P into H, and is implemented in the program TREEMAP.

I have been interested in biological modelling for many years and lately have begun working with Steve Simpson and Fiona Clissold. on Modelling Unbalanced Nutrient Climate with Heterogeneity (MUNCH).

I am also far too interested in combinatorial optimization, parallel search heuristics, phylogeny reconstruction, and molecular evolution. I have begun to be interested in the analysis of microarray data (though I make no claims of expertise in this). Life is far too short not to be interested in most of it...