martin urban

Science

Dr Martin Urban

Wheat Pathogenomics - Data Scientist

Protecting Crops and the Environment

PUBLICATIONS
Location
Rothamsted Research, Harpenden, AL5 2JQ
Tel
+44 (0) 1582 938 149
Email
Martin.Urban@rothamsted.ac.uk
Professional Platforms
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Research ID
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Associated Websites

Biography

Martin is microbiologist and data scientist. His research is focused on the discovery of strategies for controlling plant pathogenic microbes that cause considerable losses in crop yield and contaminate food products with toxins. Specifically, he investigates Fusarium graminearum, a phytopathogenic fungus that causes globally important diseases on cereal crops, primarily wheat, barley and maize. Using targeted gene deletions in Fusarium, candidate virulence genes and fungicide resistance genes are investigated. Genome editing and whole-genome sequencing approaches are used to identify novel fungal intervention targets. To survey microbial pathogen genes important for animal and plant virulence, Martin launched, in 2005, the multispecies database, PHI-base. The Pathogen-Host Interaction database is freely accessible at http://www.PHI-base.org and contains gold standard, manually curated information extracted from the scientific literature for 264 pathogen species infecting 176 plant, animal or other hosts. Martin uses computational approaches (Linux, R, Python) to manage the database, increase its usability and mine the curated phenotypic and genotypic information for broad- and narrow-spectrum antimicrobial intervention targets. Since 2011, PHI-base has a strong link with the European Bioinformatics Institute (http://www.phytopathdb.org) as a data provider. Since 2016, PHI-base is part of the European infrastructure for life science information via its ELIXIR UK node (http://www.elixir-uk.org).

Strategic Programme

  • Designing Future Wheat (DFW)

Science Projects

  • Phytopath an infrastructure for hundreds of plant pathogen genomes
  • Bilateral BBSRC-Embrapa: Using disease risk forecasting, NGS and HIGS to explore and control Fusarium Head Blight disease in wheat fields

PhD Projects

  • Suppression of wheat defences by Fusarium graminearum effectors
  • An exploration of the function of specific components of the predicted secretome of Fusarium graminearum during wheat infection
  • Network approaches for exploring predicted proteins of unknown function in the sequenced genomes of plant pathogenic fungi
  • Phyto-gene therapy: development of RNAi mediated gene silencing in crops for disease control without GM?
  • Exploring how fungal pathogens communicate with plant cells and cause disease
  • Characterisation of the role of effectors in the Fusarium graminearum-wheat floral interaction

Awards

  • PhD in Biological Sciences, Free University of Berlin, Germany

Measures of Esteem

  • PhD supervision
  • Data provider for Ensembl Genomes and ELIXIR UK
  • Microbiological containment category 2/3 laboratory manager