People......

Research Fellows Dr Andrew Pocklington Research Associates Dr Mike Dewar James Heward Tim Lukins Jo Young	Research Students John Davey Lena Hansson Seymour Knowles-Barley Mark Longair Bilal Malik Lysimachos Zografos
Moved on...
Adriano Werhli Dr Paul Crook Jane Ewins Dr Dean Baker Ming Tso Chiang	Stephen Henderson Dr Kit Longden Mark Cumiskey Jigna Patel

Research Programmes....

Brainwave-Discovery [BWD] is a new company spinning out from the Universities of Edinburgh and Glasgow that provides new solutions and services to the CNS drug discovery industry. Psychiatric and neurological disorders constitute 15% of the medical burden in developed countries yet there is a shortage of new drugs for these devastating, often long-term illnesses. Genome wide association studies (human genetics) are identifying hundreds of new candidate drug targets per indication per year. Prioritising these is a significant problem for the industry especially since current method of choice (transgenic mouse models) is slow, expensive and is coming under increasing ethical pressure from the market. BWD technology combines BrainWave in vivo brain physiology (patent granted) with synthetic biology and automated behaviour assessment. This enables human target prioritisation within the fruit-fly Drosophila and the use of Drosophila assays in chemical screening. Brainwave offers custom services for target prioritisation followed up by in-licensing agreements for in vivo in-house compound screening. Genes2Cognition. Molecules in the brain form large and dense complexes that process electrical and chemical signals. Mutations affecting key members of these complexes are often linked to psychiatric disorders and in turn the complexes are often the targets of drug therapies aimed at treating such conditions. We are building simulations of these complexes and modelling the information flow through them. The results are being used to predict new molecules involved in psychiatric disorders and potential new drug targets. Funded by the Wellcome Trust, the Genes2Cognition programme brings together research groups from across the University of Edinburgh and the Wellcome Trust Sanger Institute. Together with the Jarman group we are looking to extend these models into the developing nervous system. Automatic analysis of Behaviour Modern molecular science can study entire genomes in a single experiment (10s of thousands of genes) yet behavioural research is still largely rooted in a human observer watching the animals behave, especially within social or interactive environments. We have been developing a range of tools that automate behavioural analysis and data capture. These tools are essential to bridge the gap between the level of analysis we can perform in large protein complexes to their phenotypes in integrated studies. Further, the use of computer vision and tracking algorithms can capture information that is extremely hard to obtain using any other method. These techniques are also providing new insights into behaviour. Drosophila behaviour. We have on-going research interests in various aspects of complex behaviour. We use these behaviours as a functional readout of of the fly nervous system and are in the process of linking these studies to the Systems Biology of the Synapse programme described above. Specifically we are investigating fly orthologues (or transgenic chimeras) of genes linked to human cognitive disorders. Our recent work focusses on courtship (see above) and Gravity. The latter is perceived by all animals but how is this information sensed and used by the nervous system remains laregly unknown. Funded by the BBSRC we are using a variety of transgenic technologies to dissect the neuronal structures and molecular pathways involved in the behavioural response in Drosophila melanogaster. See also Dean Baker's homepage. In addition to our studies at Edinburgh, we are working towards a flight study onboard the International Space Station as part of a NASA funded study with our collaborators in Kate Beckingham's group at Rice and Sharmila Bhattacharya's group at NASA Ames. Neuroanatomy and Gene expression. fly-trap was the first freely available database for enhancer-trap expression patterns in the insect brain. 300 P{GawB} strains from the collection are still available for researchers. We have an on-going interests in tools for visualising brain structure and in database tools for sharing and querying neuroscience data. We are currently working on characterising the effect of mutations in a range of developmentally regulated genes in the adult brain. For example, see our interactive java models of the icebox phenotype. We also have a series of tools under development for rapidly comparing expression patterns across brains. Bioinformatics: Linking all of the projects above is a research programme in bioinformatics that starts with the analysis of genome structure, in particular the analysis of gene RIDGEs (with Peter Ghazal), gene structure and their relationship to gene expression (with Andrew Jarman). We are also interested in the analysis of microarray and proteomic datasets in particular those from time series experiments and from identified cell types (with Stuart Aitken and Dirk Husmeier). In all our studies we need to rapidly curate information from the literature and build databases of prior knowledge to integrate with newly acquired data from synthetic models with our own wet lab results and data from the laboratories of our collaborators. The research interests briefly summarised above do not occur in isolation, we have a network of collaborative links throughout Edinburgh, the UK and beyond. In particular, our laboratory is closely linked with that of Prof Andrew Jarman in the Centre for Integrative Physiology, our Bioinformatics activities are located in the Institute for Adaptive and Neural Computation and in the Edinburgh Centre for Bioinformatics and our interests in mammalian systems biology are in collaboration with several groups including those of Prof Seth Grant, Prof Peter Ghazal and Prof David Porteous. PhD positions: We have PhD positions available for both theoretical and wet-lab based projects. If you are interested then please email me with a CV and brief outline of interests. You should also review the information about the Informatics Graduate School. You may also be interested in the Doctoral Training Centre in Neuroinformatics

Teaching......

M.Sc in Informatics with specialism in Bioinformatics
Bioinformatics II: Algorithms and Data Analysis.
Previous Courses:
Applied Databases

Copyright J. D. Armstrong, University of Edinburgh 2005-2007 all rights reserved