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.
Requirements
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, taane.clark@lshtm.ac.uk,
http://www.lshtm.ac.uk/people/clark.taane
Co-Supervisor: Dr Nigel Martin, nigel@dcs.bbk.ac.uk, http://www.dcs.bbk.ac.uk/~nigel
Further information about PhDs at London School of
Hygiene and Tropical Medicine is available from:
http://www.lshtm.ac.uk/prospectus/howto/applforstudy.html
How to apply:
Applications must be in writing and must clearly state which
studentship you are applying for.
Applications should consist of:
- Research Application Form (http://www.lshtm.ac.uk/prospectus/howto/lshtm_app_form_research_2011_12.pdf)
- Research Applicant Reference Form (http://www.lshtm.ac.uk/prospectus/howto/research_application_reference_form.pdf)
- Equal Opportunities Monitoring Form (http://www.lshtm.ac.uk/prospectus/howto/equal_opportunities_form.pdf)
- A full, original, transcript of the applicant's academic
record
- Two-page CV, including names of two academic referees
- Please note: candidates must supply a 1,500 word
research proposal stating how they would approach
their chosen project.
- Your current postal, e-mail address and telephone number
Please send applications to:
Registry
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
Email: registry@lshtm.ac.uk
When applying, please indicate where you found out
about this studentship (please state the publication title/
web address).
Closing date for applications: 15 April
2011