The Bloomsbury Colleges | PhD Studentships | Studentships 2011 | Integrated Informatic and Statistical Tools to Assist the Translation of Pathogen Sequencing Data Derived from New Sequencing Technologies
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Integrated Informatic And Statistical Tools To Assist The Translation Of Pathogen Whole Genome Data Derived From New Sequencing Technologies    

Lead Supervisor: Dr Taane Clark (LSHTM)

Co-Supervisor: Dr Nigel Martin (Bbk)

This project provides a unique opportunity to work on whole genome (WG) data of pathogens, potentially leading to insights of public health benefit. The application of new or second generation sequencing technologies (e.g. Illumina HiSeq2000) are generating WG data on organisms, such as pathogens, thereby revolutionising genomic epidemiology and biomedical research. An understanding of the genomic diversity of pathogens, such as malaria parasites and hospital-acquired infections (e.g. Clostridium difficile virulent stomach bug and MRSA ‘superbug’), could ultimately lead to new diagnostics, treatments and reduce disease burden. The WG sequencing of many pathogen isolates (domestically or worldwide) will facilitate the development of genomic variation maps that include point mutations and larger structural genomic variants, which may be used to detect new forms of drug resistance and barcode infections. One roadblock is that the new technologies generate extremely high volumes of raw data that can be difficult to manage and complex to analyse. Therefore to take full advantage of the large datasets and their potential for understanding outbreaks of infectious disease requires the development of methods and software in bioinformatics and statistics – the focus of this studentship. In particular, we seek a candidate with an interest in bioinformatics, computer science, mathematics or statistics to develop new approaches for identifying genomic variants associated with geography, drug resistance or other pathogen-specific outcomes. It is expected that the methods developed will be implemented in a high-level programming language, and the resulting software shared with the research community and public health policymakers. WG sequence data are immediately available from malaria and tuberculosis studies.   

This studentship would suit a candidate with a strong quantitative and computing background, possibly with graduate qualifications in biology,  bioinformatics, computer science, mathematics/statistics or some other relevant subject. This is a unique opportunity to train in fields such as bioinformatics and genomic epidemiology,  through participation on courses and conferences, and interactions within the colleges. The candidate will be exposed to the world-class research in the genetic epidemiology of infectious disease conducted at the LSHTM. Clinical, laboratory and statistical teams support this epidemiological research, and there will be many opportunities for the PhD candidate to develop or advance their skills in the epidemiological field. Birkbeck Computer Science is a leading centre of expertise in information and knowledge management, intelligent systems and computational intelligence and their application to the life sciences. Exposure to the research at Birkbeck College will lead to advanced skills in the technologies of these fields. Upon completion of the PhD it is anticipated that the candidate will have good depth of skills across multiple disciplines, including genetics, epidemiology, statistics, bioinformatics and computer science, making them an attractive prospect for post-doctoral research funding.   

Further details about the project may be obtained from:

Lead Supervisor: Dr Taane Clark,,

Co-Supervisor: Dr Nigel Martin,,

Further information about PhDs at London School of Hygiene and Tropical Medicine is available from:

How to apply:

Applications must be in writing and must clearly state which studentship you are applying for.

Applications should consist of:

  1. Research Application Form (
  2. Research Applicant Reference Form (
  3. Equal Opportunities Monitoring Form (
  4. A full, original, transcript of the applicant's academic record
  5. Two-page CV, including names of two academic referees
  6. Please note: candidates must supply a 1,500 word research proposal stating how they would approach their chosen project.
  7. Your current postal, e-mail address and telephone number

Please send applications to:

London School of Hygiene & Tropical Medicine
Keppel Street
London WC1E 7HT
United Kingdom.

Tel: +44 (0)20 7299 4646
Fax: +44 (0)20 7299 4656

When applying, please indicate where you found out about this studentship (please state the publication title/ web address).

Closing date for applications: This studentship is now closed.