CATH Team

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.

My PhD work focused on protein functional annotation using sequence, sequence profile, and clustering-based methods. This is to enrich functional annotation data for the CATH and Gene3D resources and will form the basis of domain-centric comparative (meta)genomic studies.

In a large-scale sequence comparison study I revisited sequence identity thresholds for safe function transfer between known and uncharacterised protein sequences. The use of CATH domain superfamily-specific thresholds, comparing sequences at the domain level, proved to yield higher transfer rates than comparisons on the whole protein level. Following that I wrote a review on protein function annotation.

Finally, I developed a pipeline that enables the subclustering of large Gene3D domain superfamilies (see GeMMA). Due to the high computational demands of this project it was implemented on the UCL high-performance compute cluster Legion and other, smaller HPC resources.

For my M.Sc. thesis at CUBIC in Cologne, Germany (now relocated to TU Braunschweig, headed by Dietmar Schomburg and home of the BRENDA enzyme database) I established a novel protocol for the annotation of prokaryotic genomes and in particular the genome of C. glutamicum. This 'reverse' protocol omits the gene prediction step (the conventional approach being gene prediction followed by similarity searches, i.e. spatial followed by functional annotation): all annotation is done by integrating the results of exhaustive similarity searches against the given genome.

Prior to this I had studied Biology at the Westfalian Wilhelms University in Muenster, Germany, including work on site-dependent evolutionary constraints in bHLH transcription factor proteins in the group of Erich Bornberg-Bauer. Believe it or not, I also did some very enjoyable wet lab biochemistry on human Grx2 in Arne Holmgren's lab at the Karolinska Institute in Stockholm, Sweden.

I quite enjoy listening to and making music (git, drums, voc). The same goes for the lyrics that often come along with it. Poetry, films and philosophy are good too. And running.

Here you can find my attempts with scientific writing, the outcome of an internship at Nature's Munich office:

Rentzsch R Nature News, doi:10.1038/news060220-18 (2006 Feb 24)
Giles J & Rentzsch R Nature News, doi:10.1038/news060220-4 (2006 Feb 20)

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.
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.
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.