PhD Studentship in Computational Biology at UCL in partnership with Bayer CropScience (UK residents eligible only)

Fully-funded 4 year position, starting Oct 2015.
Supervisors: Dr. Christophe Dessimoz and Dr. Henning Redestig

PROJECT DESCRIPTION

Biological interpretation of omics data for crop species is hampered by the highly redundant nature of plant genomes originating from their complex history of duplication and hybridisation events. With almost all genes being available in several copies on multiple sub-genomes, the use of comparative genomics is essential in order to distil biological information from scattered data on single genes. Genes that have common ancestors, similar expression patterns, or are physically close to each other may share biological function.

In this project, we will develop a statistical framework to infer novel and propagate existing functional annotations within and orthologous groups, and rigorously test it using multiple benchmarking strategies. The project builds upon a comprehensive set of hierarchical orthologous groups computed for >20 public plant genomes and experience developed with an ongoing collaboration between the host laboratory and the industrial partner. This rich set of data will be augmented with primary gene expression, genome position and QTL data as well as existing high-quality functional data from the Gene Ontology annotations.

The project is part of a larger collaboration between the Dessimoz Lab at UCL and Bayer CropScience NV (Ghent, Belgium), leading agronomical company, for the development of new methods and resources to better characterise evolutionary and functional relationships between model plant genomes and agronomically-relevant crop genomes. This project will enable more effective crop biotechnology, which is key to ensure food security and sustainable agriculture.

The successful applicant will be provided with strong mentorship and be given ample scientific training opportunities. She or he will based at UCL, with opportunities for short-term visits to Belgium and Switzerland. In particular, the project includes a 6-month placement at Bayer CropScience in Ghent, Belgium.

More info on the host lab at http://lab.dessimoz.org

ESSENTIAL REQUIREMENTS

• Strong (first or upper second class) undergraduate or postgraduate degree, preferably with a strong quantitative component (bioinformatics, genetics, computer science, statistics, mathematics, or related subject).

DESIRABLE REQUIREMENTS

• High degree of self-motivation
• Good ability to work independently and as part of a team
• Effective written and oral communication skills
• Demonstrated programming skills
• Ideally, prior experience in computational biology research


HOW TO APPLY

To apply, please send the following documents as single PDF by email to Dr Christophe Dessimoz (c.dessimoz at ucl.ac.uk):
• a covering letter highlighting your reasons for applying and your suitability for this studentship
• a copy of your CV
• the names and contact details of 2-3 references
• if available, links to your Bachelor or Master thesis, publications, code projects (e.g. GitHub repo) are appreciated
The position will remain open until filled.

For informal enquiries, please contact Dr Dessimoz to this above address.

ABOUT US

At the interface between biology and computer science, the Dessimoz Laboratory seeks to better understand evolutionary and functional relationships between genes, genomes, and species. The lab is part of both the UCL Department of Genetics, Evolution and Environment and the UCL Department of Computer Science. More information on the lab is available at http://lab.dessimoz.org.