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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.
+Refs
+{{pubmed>short:15843018}}
+{{pubmed>short:16429126}}
+{{pubmed>short:18563089}}
+{{pubmed>short:17934049}}
+{{pubmed>short:10427000}}
+{{pubmed>short:10573422}}
+===== Selected Publications =====
+{{pubmed>long:17709341}}
+{{pubmed>long:18032434}}
+{{pubmed>long:17135200}}
+===== Other Interests =====
+Outside of science I spend my time cooking, playing bass in my band [[http://www.myspace.com/partyinhiroshima|Party in Hiroshima]] and reading. Current favourites are [[http://en.wikipedia.org/wiki/Midnight%27s_Children|Midnight's Children]] by Salman Rushdie and [[http://en.wikipedia.org/wiki/Guns_germs_and_steel|Guns, Germs & Steel]] by Jared Diamond.
+===== Other CATH Team Members =====
+~~DIR?cols=page;description&hdrs=Person; Description~~

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