James Perkins
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.
Academic Background
I took my undergraduate degree in biology at Leeds, with an erasmus year at UAM in Madrid, followed by a year long MSc in Imperial. After this I worked in Computer Science for a year before starting my PhD program.
In my masters degree in bioinformatics I helped in the development of a web based server aimed at prediction of miRNA binding sites in Arabidopsis at Malaga University, and produced a web based application for pathway database searching using OpenLaszlo software.
Current Research Interests
In my 3 rotations I have been dealing with expression data from microarray experiments from the pain group, normally of pain models. I have produced a database for expression profiles, which implements some analysis attempting to find novel genes involved in pain. I am also interested in gene set enrichment in microarray experiments, and am using these to try to find more information about pathways involved in pain.
For future work I intend to combine more publically available datasets with the current data in the LPC, and compare this with proteomics data to try and find the correlation between expression and protein level. I also intend to use comparative genomic techniques to help elucidate the evolution of signalling pathways involved in pain, and identify novel targets for pain management
Other Interests
I am a keen drummer and guitar player, and I attend the Bloomsbury gym regularly, which I find is a great way of dealing with programming related stress.
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 |
| 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. |
| 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. |