Professor David R Westhead

Profile

Post doctoral work at Zeneca plc, Proteus Molecular Design Ltd. and European Bioinformatics Institute with Professor Janet Thornton FRS. Appointed Lecturer in Bioinformatics 1998,  Senior Lecturer 2003 and  Professor 2006. Head of the School of Molecular and Cellular Biology, 2011-2018.

Research interests

The group is interested in prediction methods for biological problems based on machine learning and statistical methods. Presently our main application areas are genetic regulation and cancer, and we work with genome scale data sets derived from a number of different technologies, including high-throughput sequencing. Our motivation is to solve biological problems using data and computational methods, for instance understanding the molecular networks that underlie cancer and how they relate to prognosis and useful therapy.

We collaborate extensively with groups who generate data, locally with St. James University Hospital and Nationally through large networks, for instance in the area of haematological oncology. We are part of Leeds Institute of Data Analytics (LIDA) and the Leeds Omics group.

• Targeting transfer RNA-derived fragments during KSHV infection
• Virus manipulation of host non-coding RNA regulatory networks

Qualifications

• MA, Cambridge, 1992; DPhil, Oxford, 1992

Student education

I teach on School of Molecular and Cellular Biology degree programmes in Biochemistry, Biological Sciences and Microbiology, and also contribute to teaching in other Schools in the Faculty. I teach in general areas, for example first year tutorials, as well as providing specialist teaching in bioinformatics and haematological oncology. I also provide training in statistics to research students in the Faculty and on our Research Council and Wellcome Trust PhD programmes, where I have an interest in the effective use of statistical methods and their contribution to reproducibility.

Studentship information

We do research in the area of bioinformatics where our focus is on the analysis and integration of genome scale data sets. Current projects include integration of gene expression data (from RNA sequencing) with transcription factor binding, chromatin modification and accessibility data to understand genetic regulatory networks. The main focus of this project is regulation of the development of healthy blood cells. When blood cell development goes wrong, cancers (leukaemia and lymphoma) can result. Another aspect of our research is classification of these cancers into subsets with different molecular mechanisms, prognosis and treatment. The ultimate aim of these projects is stratified medicine: in this case identifying the key cancer driving processes in individual patients and targeting these with specific therapies.

We offer two types of practical project. The first type is data analysis, and should be accessible to anyone on the biological undergraduate programmes. These projects typically involve analysing specific proteins or specific protein families using standard bioinformatics methods (BLAST searches, multiple sequence alignments, structural analysis and displays etc.).  In each case we would chose protein or family of interest to the group, for instance a transcription factor or signalling molecular known to be involved in blood development or blood cancer.

Recent projects have involved detailed analysis of the somatic mutations that occur in these molecules in cancer patients. The second type of project would involve some aspect of computer programming: for instance designing and implementing a program or WWW site to accomplish a specific task.  These projects require at the very least a student who is keen to develop computer programming as a new skill, and in the past have usually been done by students who already have some experience in this area. Projects will be different depending on the skills, interests and experience of the student, and students interested in this area are advised to contact us for early discussions of what might constitute a suitable project.

Literature projects are available in a variety of areas, for example:

1. A critical review of the progress of stratified medicine for a particular cancer or group of cancers (e.g. diffuse large B cell lymphoma or chronic lymphocytic leukaemia).
2. A review of polyclonal nature of cancer cells as revealed by new single cell data generation methods: what we are learning and how it might affect treatment?
3. An analysis of the opportunities for using analysis of circulating free DNA (in blood) in the diagnosis and treatment of cancer.
4. Progress in mechanistic understanding of genetic regulation in eukaryotes: have large scale data sets (e.g. ENCODE) taught us anything?
5. What is the scope for ‘epigenetic’ drugs in precision medicine for aggressive lymphoma?
6. What are new experimental methods telling us about 3D genome structure and its relevance to genetic regulation in eukaryotes.

PhD projects

PhD projects are available in the above areas, and specific details change according to current research progress and available funding. Specific projects are advertised on FindaPhD.com but prospective students are encouraged to contact us at any time to discuss possiblities.

See also:

• Faculty Graduate School
• FindaPhD Project details:
  • Project 41266