These are some examples of projects we have currently involved in.
LVB, High-performance computing in the search for the Tree of Life
LVB seeks parsimonious trees from an aligned nucleotide data matrix. It uses heuristic searches consisting of simulated annealing followed by hill-climbing. In contrast to the more usual heuristic searches used to find parsimonious trees, simulated annealing can ‘jump out’ of local optima.
With the aim of allowing reconstruction of extremely large phylogenies, accurately and in feasible time, we are improving the algorithm, designing and implementing code parallelisation to run on a variety of high performance computer (HPC) platforms.
We are working closely with STFC Scientific Computing Department staff (Dr Martyn Winn’s Computational Biology Group), who bring expertise in software engineering and code parallelisation, as well as access to a variety of HPC platforms.
PI: Daniel Barker
Plasmodium knowlesi is a malaria parasite of the long- and pig-tailed macaques of Southeast Asia. Recently a group working in Sarawak Malaysian Borneo discovered a large entry of P. knowlesi into the human population. P.knowlesi was masquerading as a more benign type of malaria and required molecular methods for accurate identification. The goal of the malaria pathophysiology study at University St Andrews is to identify P. knowlesi genetic loci that contribute to virulence in human infections. To achieve this aim we sequence 15 different isolates of P.knowlesi in HiSeq 2000, and we expect to unveil mechanisms that are responsible for the different level of virulence in human infections.
PI: Janet Cox Singh
Handedness shows some correlation with cerebral asymmetries where being right-handed implies left-hemisphere dominance for language. It has been proposed that handedness emerged as a consequence of language evolution and a link between hand preference and psychiatric disorders have been extensively investigated. This is supported by some evidence from imaging studies showing atypical cerebral asymmetries in patients including individuals with dyslexia and specific language impairment (SLI).
In this study several Illumina microarrays are ran in a big set of cohorts and we expect to identify several variations responsible for these conditions.
PI: Silvia Paracchini
Common Variants in Left/Right Asymmetry Genes and Pathways Are Associated with Relative Hand Skill
Brandler, W., Morris, A., Evans, D., Scerri, T., Kemp, J., Timpson, N., St Pourcain, B., Davey Smith, G., Ring, S., Stein, J., Monaco, A., Talcott, J., Fisher, S., Webber, C. & Paracchini, S. 12 Sep 2013 In : PLoS Genetics.
We have several projects running in transcriptomics, most of them related with Eukariotics genomes without reference. We are developing a new tool, which performs several analyses, keeping all of them in a database accessible through a web site, to make them searchable. With this tool the researches can keep focus on their researcher and leave the computational problems to the bioinformatics expert.
PI: Ian Alistair Johnston