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cathteam:reid [2008/07/25 08:34]
cathteam:reid [2008/07/25 08:38] (current)
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 +====== Adam Reid ======
 +{{:cathteam:kaiseki.jpg|Me enjoying a traditional Japanese kaiseki meal in a ryokan somewhere outside Kyoto}}
 +Me enjoying a traditional Japanese kaiseki meal in a ryokan somewhere outside Kyoto
 +===== PhD student =====
 +I am currently nearing the end of my PhD and planning to submit by the
 +end of the year.
 +===== Research Interests =====
 +==== Prediction and utilisation of protein domains for function prediction ====
 +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.
 +==== Evolution of protein complexes ====
 +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.
 +===== Selected Publications =====
 +===== Other Interests =====
 +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.
 +===== Other CATH Team Members =====
 +~~DIR?cols=page;description&hdrs=Person; Description~~