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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~~ | ||
+ | |||