skip to primary navigationskip to content
 

Dr Richard Coulson

Departments

Cambridge Institute for Medical Research:
Senior bioinformatician

Research Interests

My research used to focus on analysing eukaryotic gene regulation experimentally; with the availibilty of complete genome sequences, I moved to the European Bioinformatics Institute to facilitate the understanding of this biological process in organisms where there is insufficient experimental information about it. I demonstrated that bioinformatic methodologies provide an alternative and complementary approach of studying transcription in protozoan and fungal pathogens, and proteins controlling gene activation exhibit considerable sequence diversity across the eukaryotic domain reflecting major differences in mechanisms altering transcript levels.

I now employ my computational biology expertise on the genomics of auto immune diseases such as type I diabetes, and most recently vasculitis and inflammatory bowel disease. This encompasses the analysis of high-throughput genomic / genetic, transcriptomics and epigenetic data. Furthermore, I develop tools and infrastructure to facilitate the housing and querying of large datasets; examples are microarray reannotation pipelines linking probes to a range of gene attributes and functional annotations, and an automated graphics tool displaying the results of sequence searches as pie charts.

Keywords

genomics ; computational biology ; microbial pathogenesis ; bioinformatics ; control of gene expression

Key Publications

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. Lawler, K., Hammond-Kosack, K., Brazma, A. & Coulson, R.M.R. (2013) BMC Systems Biology 7, 52.

An automated graphics tool for comparative genomics: The Coulson plot generator. Field, H.I., Coulson, R.M.R. & Field, M.C. (2013) BMC Bioinformatics 14, 141.

Post-thymic expansion in human CD4 naive T cells defined by expression of functional high affinity IL-2 receptors. Pekalski, M.L., Ferreira, R.C., Coulson, R.M.R. et al. (2013) Journal of Immunology 190, 2554-2566.

T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. Burren, O.S., Adlem, E.C., Achuthan, P., Christensen, M., Coulson, R.M.R. & Todd, J.A. (2011) Nucleic Acids Res. 39, D997-1001.

The genome of the kinetoplastid parasite, Leishmania major. Ivens A.C., Peacock, C.S., Worthey, E.A. et al. (2005) Science 309, 436-442.

Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Coulson, R.M.R., Hall, N. & Ouzounis, C.A. (2004) Genome Res. 14, 1548-1554.

A Coulson plot generated by the Coulson Plot Generator Java application. A collection of data corresponding to complexes or functional systems within the eukaryotic trafficking pathway have been used to illustrate the principle aspects of the plot format. On the left, supergroup designations and taxa (species) are colored by supergroup; at the top is a key that displays the complex name and a smaller gray pie where the sectors are labelled with its members. Below this, in rows, are the individual pies representing gene distributions for each species, with colors matching the taxon supergroup colors. This grid arrangement allows easy detection of patterns in the data.