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Adam Reid

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.


Gabaldón Tet al.J Mol Biol348p857-70(2005 May 13)
Gavin ACet al.Nature440p631-6(2006 Mar 30)
Levy EDet al.Nature453p1262-5(2008 Jun 26)
Kahlem Pet al.Ann N Y Acad Sci1115p23-31(2007 Dec)
Marcotte EMet al.Science285p751-3(1999 Jul 30)
Enright AJet al.Nature402p86-90(1999 Nov 4)

Selected Publications

Gene3D: comprehensive structural and functional annotation of genomes.
Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C
Nucleic Acids Res36pD414-8(2008 Jan)
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA
Nucleic Acids Res35pD291-7(2007 Jan)

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

Person Description
benoit Former Member In September 2011 I moved to Osaka, Japan, to work as a Post-Doctoral Fellow in Dr Mizuguchi's group at the National Institute of Biomedical Innovation. Research Interests My main research interests include the study of interactions between proteins and other molecules, both at the structural and network levels.
clegg [Andrew with a half-metre sausage, found (and eaten) on holiday in Germany recently] Senior Research Associate, CATH Development A member of the Orengo group since June 2008, I am the technical lead on the FuncNet platform, which brings together an ensemble of protein function analysis tools from various groups around Europe. This work is supported by the EU-funded EMBRACE and ENFIN research networks.
cuff [ Me and my Cat] CATH Manager I am responsible for the general management and manual curation of CATH. Academic Background As a undergraduate, I read for a BSc(Hons) degree in Biomedical Sciences at the University of Durham and then, after deciding I wanted to pursue Bioinformatics research, I took a MSc degree in Information Technology at the University of Teesside (this was all back in the days before MSc courses in Bioinformatics became available!).
lee [ ] Post Doctoral Research Fellow I work for the Midwest Center for Structural Genomics (MCSG). My responsibilities include selecting protein targets for structure determination, monitoring the success of target selection strategies, and providing homology models of relatives of MCSG structures.
lees Gene3D Since arriving in October 06 I've been doing development of the Gene3D database in collaboration with Corin Yeats. I also maintain the current Gene3D website. I am involved in several collaborations with experimentalists. Recently (June 2009) I have started a new post employed by ENFIN coordinating a chromosome condensation prediction project, with Juan Ranea (Malaga) and the Ellenberg group (EMBL) (amongst others). We are using novel high throughput phenotype data (Ellenberg Group) a…
lewis [Me in Malaysia] Senior Programmer I was heavily involved in the complete rewrite of the CATH update procedure that culminated in CATH v3.0.0. I am still involved in maintaining and developing CATH in an ongoing consultancy capacity. Academic Background MSc Intelligent Systems, UCL (2002-2003)
orengo See departmental staff page
perkins [Me] London Pain Consortium PhD Student I am a member of the London Pain Consortium, an initiative formed in 2002 by a grant from the Wellcome Trust. I am currently moving into the first year proper of my PhD, supervised by Christine and based in the CATH lab, having completed a year of 3 rotations, working on projects with different labs.
phil [Me] Role in CATH I am post doctoral research associate. One of my responsibilities is the target selection database for the Center for Structural Genomics of Infectious Diseases's structural genomics project. Research Interests CSGID applies state-of-the-art high-throughput structural biology technologies to experimentally characterise the three dimensional atomic structure of targeted proteins from pathogens in the NIAID Category A-C priority lists and organisms causing emerging and re-eme…
redfern [Posing on the southbank of the Thames] Post-Doctoral Research fellow I work as part of the Midwest Consortium for Structural Genomics, aiding target selection and analysis of the novelty of the protein structures they produce. In parallel, I also develop methods for homology recognition and function prediction from protein structure and sequence.
rentzsch [Me] Former PhD student I did my PhD in the lab between 2007 and 2012, funded by a EU grant (ENFIN). The ENFIN Network of Excellence aims at close collaboration between experimental and computational groups throughout Europe. I've also worked as a research assistant here.
sillitoe [Me with one of the Sillitoe clan (I'm the one on the right)] CATH Technical Manager I am responsible for the technical aspect of CATH. This generally involves maintaining and developing both the front-end interfaces (internal and external web pages and webservices) and back-end code library and databases.
studer {{ :cathteam:picture.jpg|Me}} {Role in CATH} Description of role in CATH Academic Background Current Research Interests Your research interests go here. Put some pretty pictures in with something like the following: {{ :cathteam:consensus_contact_map_example.png?300 |Example of a consensus structural alignment and contact map }}
yeats Gene3D and BioMiner Gene3D: Design and development, HMM library construction and prediction verification, and web services. Academic Background PhD at the Sanger Institute (2004), supervised by Alex Bateman (Pfam). Thesis: Biological Investigations Through Sequence Analysis.