Dr David Robertson

Funding: Funding available for eligible UK/EU applicants.

Subject Area

• Bioinformatics
• Biomolecular Sciences
• Evolutionary Biology
• Genetics
• Microbiology
• Molecular Biology

Description

Next generation sequencing technologies such as 454 GS-FLX have massively parallelized the determination of nucleotide order within genetic material resulting in the ability to produce extremely large data sets at relatively low cost. However, the sequence reads produced are significantly shorter than Sanger sequencing and error rates can be high and non-uniform. As a consequence we are currently in a situation where experiments are generating data sets of such magnitude and complexity that we do not have appropriate methodologies for efficiently processing them let alone for effective analysis. As a result there is a need for new computational tools for efficient and appropriate analysis of this data. In this project we will focus on the analysis of variation in next generation population data sets available in public databases or from collaborators. The study of high-depth (or ultra-deep) data sets is of particular importance in the identification of low frequency mutations or variants in the context of viral infections, bacterial populations and metagenomic projects. The specific aims of the project will be to investigate polymorphism frequencies versus error rates, phylogenetic inference and visualisation of evolutionary history, co-evolution, recombination detection and other appropriate properties of high-depth data sets. This will complement existing projects in the group, for example, www.bioinf.manchester.ac.uk/segminator (Archer et al. 2009; AIDS 23:1209-18). The candidate should ideally have experience in computational biology, bioinformatics, molecular evolution, computer science or related subject area.

Other projects are available within our Faculty. See our Postgraduate section, where you can also find out other useful information relating to postgraduate study including information on How to apply.

Funding: Project available for individuals with self arranged funding.

Subject Area

• Bioinformatics
• Evolutionary Biology
• Genetics

Description

Research in my group is focussed on bioinformatics and molecular evolution. We study evolution at the molecular level from genes to genomes to systems biology, and use computers to address analytical and theoretical questions/hypotheses. Specific PhD projects available include:

1. Duplication, “rewiring” and redundancy in protein-protein interaction networks.
2. Co-evolution of binding specificity in protein interaction networks.
3. Co-evolution of viruses with their hosts.
4. Quantification of constraints on viral diversity and evolution.

    

Fee Band

This project has a Band 1 fee.

Details of different fee bands are available for UK/EU or International applicants.

Other projects are available within our Faculty. See our Postgraduate section, where you can also find out other useful information relating to postgraduate study including information on How to apply.

Funding: Project available for individuals with self arranged funding.

Subject Area

• Bioinformatics
• Cell Matrix Research
• Evolutionary Biology
• Molecular Biology

Description

A collagen-based extracellular matrix (ECM) is one defining feature of all metazoa. We are interested in determining the mechanisms by which and principles governing how the collagen-based ECM found in different phyla and species has evolved. One model system we are investigating is the cnidarian hydra. We use combinations of gene cloning and bioinformatics to study the matrix present in hydra and compare and contrast this matrix with that of vertebrates. Projects involving bench work and/or in silico studies are available to suitably qualified applicants. This project will be supervised by Prof Ray Boot-Handford and Dr David Robertson.

Related Publications

• Huxley-Jones, J., Robertson, D.L. & Boot-Handford, R.P. (2007) On the origins of the extracellular matrix in vertebrates. Matrix Biol. 26, 2-11 Epub 2006 Sep 19.
• Zhang, X., Boot-Handford, R.P¹., Huxley-Jones, J., Forse, L.N., Mould, A.P., Robertson, D.L., Li, L., Athiyal, M. and Sarras, M.P. Jr (2007) The collagens of hydra provide insight into the evolution of metazoan extracellular matrices J. Biol. Chem. 282, 6792-6802. (¹Jt 1^st and corresponding author)

Fee Band

This project has a Band 2 fee.

Details of different fee bands are available for UK/EU or International applicants.

Other projects are available within our Faculty. See our Postgraduate section, where you can also find out other useful information relating to postgraduate study including information on How to apply.