Me enjoying a traditional Japanese kaiseki meal in a ryokan somewhere outside Kyoto

I am currently nearing the end of my PhD and planning to submit by the end of the year.

My work has involved aspects of the prediction and utilisation of protein domains. I did some work on using profile-profile methods of remote homology detection to detect CATH domains and solved some of the problems associated with benchmarking such methods which have remarkable abilities in predicting very remote homologues (Reid et al, 2007). The paper describes which methods are best for different uses and at varying degrees of sequence identity.

Subsequently I have been involved in an international collaboration, set up through the ENFIN network to predict protein function (Kahlem & Birney, 2007). This has allowed members of our group and two other bioinformatics groups to attempt to predict proteins in human which might be involved in the mitotic spindle. These predictions were tested experimentally and the bioinformatic methods were shown to drastically increase the success rate in finding relevant proteins. Our prediction method is called BioMiner. BioMiner is a protein function predictor which integrates several different approaches. As part of BioMiner I wrote a program called CODA which is an update of the gene fusion approach to protein function prediction originally introduced simultaneously by Edward Marcotte & David Eisenberg and Anton Enright & Christos Ouzounis in 1999. CODA is geared towards predicting functions in eukaryotes where gene fusion has traditionally been less reliable. I used a new way of scoring the results to get the round the problems associated with large eukaryotic genomes and the method performs very well against others. This work is in submission.

My most recent work has involved looking at protein complexes in yeast and E. coli. I'm interested in how these complexes form in evolution and how they encapsulate function. Some very interesting papers on this subject include one from Martijn Huynen's lab (Gabaldon et al, 2005) where they trace the evolution of a large protein complex (NADH:Ubiquinone Oxidoreductase) through the eukaryotes, Gavin et al (2006) which describes an exhaustive TAP assay showing that complexes are probably composed of constant cores and variable modules and a recent paper from Sarah Teichmann's lab (Levy et al, 2008) looking at whether assembly of protein complexes reflects their evolution.

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Outside of science I spend my time cooking, playing bass in my band Party in Hiroshima and reading. Current favourites are Midnight's Children by Salman Rushdie and Guns, Germs & Steel by Jared Diamond.