Research

Rebecca Hamer
Bacterial Chemotaxis

I am researching into chemosensory pathways of bacteria using bioinformatics methods, with the aim of identifying the constituents of different pathways and how they interact to alter swimming direction in motile bacteria. The chemosensory pathway of E. coli has been studied extensively and is well understood. However, other bacteria have much more complicated systems with multiple pathways involving different homologues of each Che protein. Starting with the pathways in the bacterium Rhodobacter sphaeroides we plan to work out what determines which proteins interact with each other and use this information to create a model which can be used to predict chemotaxis pathways in other organisms.

Schematic diagram of the chemosensory system of E. coli.
George Wadhams and Judith Armitage,
Nature Reviews Molecular Cell Biology, Vol 5, pp1024-1037, Dec 2004

Rhodri Saunders
Protein Structure Prediction

I am interested in protein structure and work on the protein folding problem using simplified models. My research is focused on vectorial protein folding and more specifically co-translational protein folding. This work means that I explore all aspects of proteins from mRNA via the ribosome to solved structures. My long term goal is to be able to computationally model protein folding with a view to structure prediction.

Protein structure on a 3D lattice

Waqar Ali
Protein Interaction Networks

My research interests lie in large scale analysis of protein interaction networks. Currently my primary focus is on investigating the use of network alignment techniques across multiple species for identification of conserved modules which can be used for functional and structural prediction.

A schematic representation of a hypothetical protein-protein interaction network. Within an interaction network, smaller local interaction networks or 'clusters' may form (A-E)
Giorgini and Muchowski, Genome Biology 2005 6:210 doi:10.1186/gb-2005-6-3-210

Sebastian Kelm
Structural Modelling of Transmembrane Domains

My ultimate aim is to predict the structure of membrane proteins better than any existing method. Current methods are designed for soluble proteins, which exist in a very different chemical environment. This results in low accuracy structural predictions of membrane proteins. Nevertheless, there are now sufficient amounts of membrane proteins with known structure to create an appropriate, specialised method.

Membrane insertion of the protein 1YEW (particulate methane monooxygenase of Methylococcus capsulatus).
Red: inner membrane layer;
yellow: outer membrane layer;
blue: outside the membrane

Yoonjoo Choi
Protein Loop Structure Prediction

I am interested in protein loop structure prediction. Despite the recent success in homology modeling, loop structure prediction still remains a notoriously difficult problem in protein structure prediction. My research is also aimed at selection of correct loop conformation using MQAPs (Model Quality Assessment Programmes).

Predicted protein loops

Sumeet Agarwal
Protein Interaction Networks

I am interested in the functional organisation of protein interaction networks, and their dynamics as regulated by gene expression levels. I am looking at the use of network analysis and community detection methods for problems like protein clustering and protein function prediction.

Communities in the protein interaction network of Baker's Yeast (Saccharomyces cerevisiae)

Anna Lewis
Protein Interaction Networks

I am currently researching community structure of protein interaction networks, looking at the relationship between topological and functional properties. I am co-supervised by Nick Jones (physics) and Mason Porter (maths).