Bioinformatics PhD Studentship (near London): Text mining, data mining and 
database development in Bioinformatics

Supervisors
Dr Jacob Koehler, Biomathematics and Bioinformatics Division, Rothamsted 
Research, Harpenden, UK
Dr Kim Hammond-Kosack, Plant-Pathogen Interaction Division, Rothamsted 
Research, Harpenden, UK

Sophia Ananiadou, University Supervisor, School of Computer Science, 
University of Manchester, National Centre for Text Mining


Project Description: 
The successful candidate will do research on developing text- and data 
mining methods using ONDEX http://ondex.sf.net/ which is written in Java. 
The methods to be developed are generic and generally applicable. However, 
they will be tested and applied to support the curation and analysis of 
data in the Pathogen-Host Interaction database: http://www.phi-base.org/. 
Other important aspects of the project include the extension of the 
database, the development of data curation interfaces and the development 
of data analysis methods.

We anticipate that the successful candidate will have a good degree in 
computer science or bioinformatics. the focus of the project will be on 
developing the software and analysis methods, which will require well-
developed programming skills.

Location: You will be based at Rothamsted Research (in Harpenden near 
London) where you will be part of a growing and vibrant bioinformatics 
research group http://www.rothamsted.bbsrc.ac.uk/bab/index.php?
folder=bioinformatics and in close contact with the expanding molecular 
genetics group identifying fungal genes required to cause disease on cereal 
plants, http://www.rothamsted.bbsrc.ac.uk/ppi/wptop.html. You will be a 
registered at the University of Manchester, where you will work in close 
collaboration with the National Centre of Text Mining (NaCTeM) 
http://www.nactem.ac.uk/.

Training: This project will offer training in two key areas – data mining 
and database development. You will also get the opportunity to experience 
research training in both a research institute and university setting. 
Furthermore, you will develop excellent software development skills using a 
range of methods (algorithm development, requirement analysis, Unit testing 
etc), programming languages (Java, PHP, SQL, shell scripting etc) and tools 
(Eclipse, software versioning systems and release management, UML). You 
will also learn to work on high performance computers, including a medium 
sized computer cluster. As a result, you will develop a high level of 
expertise in all aspects of software development.

Funding and eligibility: The studentship will cover tuition fees as well as 
provide an initial annual maintenance stipend of £12,600. It is anticipated 
that the project will commence in October 2007. The studentship is 
restricted to UK nationals and European students who have been resident in 
the UK for three years. Full eligibility criteria can be found on the BBSRC 
web site.

Enquiries and Applications: Please send your CV (tabular format, include 
grades or expected grades), cover letter and the names of 3 references to:
Jacob Koehler, Principal Investigator, Bioinformatics, BAB
Rothamsted Research
Harpenden, Hertfordshire, AL5 2JQ
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Phone: +44-(0)1582763133-2851
Fax: +44 (0)1582 763010