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Education 1980-1987: Seaford Head School - 'A' levels in Biology (A), Chemistry (A), Maths (B), Physics (A). 'S' levels in Biology (1) and Chemistry (1). 1987-1991: University of Oxford - B.A. (Hons) in Biochemistry (Class IIi). 1991-1992: University of Sussex - P.G.C.E. in Secondary Science. 1996-1997: University of Exeter - M.Sc. in Biological Research Methods (Distinction). 1997-2000: University of Exeter - Ph.D. supervised by Professor N.J.Talbot - "Regulation of the pathogenicity gene MPG1 in the rice blast fungus Magnaporthe grisea." Work Experience 1992-1996: Hampden Park School, Eastbourne - Teacher of secondary science. 2000-now: University of Exeter - Research Fellow in School of Biosciences. Research Interests For more than five years I have been responsible for the design, implementation and delivery of the Phytopathogenic Fungi and Oomycete EST Database that was formed as part of the COGEME (Consortium for the Genomics of Microbial Eukaryotes) project. This resource now contains 61,534 annotated unisequences from eighteen species of fungi and oomycetes and is considered an invaluable resource by the phytopathogen research community. Statistics on the use of this database can be viewed by clicking here. As well as providing a resource for the research community, I have also been analysing the sequence data we have to provide insights into the nature of pathogenicity. One example of this is an analysis of transcript abundance in the rice-blast fungus Magnaporthe grisea. Since September 2004, I have been involved in the e-Fungi project in collaboration with the University of Manchester. The aim of this project is to develop an object-oriented data-warehouse that integrates sequence and functional data from a number of fungal species that will enable the study of less well understood species with reference to model organisms. A library of bioinformatic queries will be developed that will support comparative functional genomics and the study of cellular processes, pathogenicity and evolution. The data-warehouse and analysis libraries will be made available within a service-oriented Grid to support computationally intensive tasks and to integrate these tasks with other web and grid services. The current release of this database contains genomic and functional data from 36 species of fungi and oomycetes. As part of this project I have been looking at the differences in gene inventories of phytopathogenic and non-pathogenic species of fungi. I am especially interested in looking at the potential expansion of certain gene families during the evolution of phytopathogens. I have developed a number of tools to aid this work, for example, a comparison of the occurrence of Pfam domains in the predicted protein sets from a number of fungal species. I am also part of the BluGen consortium responsible for the sequencing of the genome of the powdery mildew fungus Blumeria graminis, which will be especially interesting since this species is an obligate biotroph. As well as this, I have been involved in aiding curation of PHI-base (Plant-Host Interactions Database). I work as part of the Molecular Genetics Group at the University of Exeter, run by Professor Nick Talbot, that works primarily on the rice blast fungus Magnaporthe grisea. I work closely with experimental scientists in this group identifying novel targets for them to work on. As part of this work I have annotated a number of metabolic pathways using the recently published genome of M. grisea. Computer Experience I have extensive experience of designing and implementing databases using both MySQL and Microsoft Access. In addition, I have practical experience of constructing web-based interfaces to databases. The COGEME phytopathogen EST database is implemented using MySQL on a Solaris workstation. The same workstation also acts as a web-server using Apache. Queries are run using HTML forms and CGI-Perl scripts to interact with the database. I have practical experience in programming using Perl, Java and Visual Basic. I have used these languages to parse data and populate the database. I passed a distance learning course on Java programming run by the University of Exeter in 2000. Teaching Experience For the past six years I have been teaching on the MSc in Bioinformatics course at the University of Exeter, contributing to modules on databases and sequence analysis, as well as supervising project students. I am at present co-ordinating modules BIOM504 (Sequence Analysis and Structural Bioinformatics) and BIOM506 (Genomics, Transcriptomics and Proteomics). Publications: Research papers Soanes, D.M., and Talbot, N.J. (2008) Moving targets: rapid evolution of oomycete effectors. Trends in Microbiology 16: 507-510. [pdf] Soanes, D.M., Alam, I., Cornell, M.J., Wong, H.M., Hedeler, C., Paton, N.W., Rattray, M., Hubbard, S.J., Oliver, S.G., and Talbot, N.J. (2008) Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS ONE 3: e2300. [pdf] Soanes, D.M., Richards, T.A., Talbot, N.J. (2007) Insights from sequencing fungal and oomycete genomes: What can we learn about plant disease and the evolution of pathogenicity? Plant Cell 19: 3318-3326. [pdf] Soanes, D.M., Talbot, N.J. (2006) Comparative genomic analysis of phytopathogenic fungi using expressed sequence tag (EST) collections. Molecular Plant Pathology 7: 61-70. [pdf] Soanes, D.M., Talbot, N.J. (2005) A bioinformatics tool for analysis of EST abundance during infection-related development by Magnaporthe grisea. Molecular Plant Pathology 6: 503-512. [pdf] Soanes, D.M., Kershaw, M.J., Cooley, R.N., Talbot, N.J (2002) Regulation of the MPG1 hydrophobin gene from Magnaporthe grisea. Molecular Plant-Microbe Interactions 15: 1253-1267. [pdf] Soanes, D.M., Skinner, W., Keon, J., Hargreaves, J., Talbot, N.J. (2002) Genomics of phytopathogenic fungi and the development of bioinformatic resources. Molecular Plant-Microbe Interactions 15: 421-427. [pdf] Hedeler, C., Wong, H.M., Cornell, M.J., Alam, I., Soanes, D.M., Rattray, M., Hubbard, S.J., Talbot, N.J., Oliver, S.G., Paton, N.W. (2007) e-Fungi: a data resource for comparative analysis of fungal genomes. BMC Genomics 8: 426. [pdf] Cornell, M.J., Alam, I., Soanes, D.M., Wong, H.M., Hedeler, C., Paton, N.W., Rattray, M., Hubbard, S.J., Talbot, N.J., and Oliver, S.G. (2007) Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi. Genome Res. 17: 1809-22. [pdf] Alam, I., Cornell, M.J., Soanes, D.M., Hedeler, C., Wong, H.M., Rattray, M., Hubbard, S.J., Talbot, N.J., Oliver, S.G., Paton, N.W. (2007) A Methodology for Comparative Functional Genomics. Journal of Integrative Bioinformatics 4: 69. [pdf] Wang, Z-Y, Soanes, D. M., Kershaw, M.J., Talbot, N.J. (2007) Functional analysis of lipid metabolism in Magnaporthe grisea reveals a requirement for peroxisomal fatty acid ß-Oxidation during appressorium-mediated plant infection. Molecular Plant-Microbe Interactions 20: 475–491. [pdf] Bhambra, G.K., Wang, Z.Y., Soanes, D.M., Wakley, G.E., Talbot, N.J. (2006) Peroxisomal carnitine acetyl transferase is required for elaboration of penetration hyphae during plant infection by Magnaporthe grisea. Mol Microbiol. 61: 46-60. [pdf] Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Kulkarni, R., Xu, J.R., Pan, H., Read, N.D., Lee, Y.H., Carbone, I., Brown, D., Oh, Y.Y., Donofrio, N., Jeong, J.S., Soanes, D.M. et al (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986. [pdf] Wang, Z.Y., Jenkinson, J.M., Holcombe, L.J., Soanes, D.M, Veneault-Fourrey, C., Bhambra, G.K. (2005) The molecular biology of appressorium turgor generation by Magnaporthe grisea. Biochem. Soc. Trans. 33: 384-388. [pdf] Giles, P.F., Soanes, D.M., Talbot N.J. (2003) A relational database for the discovery of genes encoding amino acid biosynthetic enzymes in pathogenic fungi. Comp. Funct. Genom. 4: 4-15. Publications: Book Chapters Soanes, D.M., Talbot, N.J. (2004) Gene diversity and conservation in phytopathogenic fungi revealed by EST sequencing initiatives and comparative genomics. In Plant Genome Biodiversity and Evolution Volume 2 Part A.(Sharma, A.K. and Sharma, A. eds). Enfield, USA: Science Publishers, pp 129-166 Ahmad, S.A., Soanes, D.M., Barooah, M.J., Talbot, N.J. (2005) Investigating the evolution of fungal virulence by functional genomics. In the Mycota Vol XII. Fungal Genomics (Brown, A.J.P ed). Berlin: Springer-Verlag., pp 35-49. Gilbert M.J., Soanes D.M, Talbot N.J. (2004) Functional genomic analysis of the rice blast fungus Magnaporthe grisea. In Applied Mycology and Biotechnology Volume 4 (Arora, D.K. and Khachatourians, G.G eds). Amsterdam: Elsevier B.V., pp 331-352. Contact details Dr. Darren Soanes School of Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom. Email: d.m.soanes@exeter.ac.uk Tel: +44 (0)1392 263497 |