Research Summary


Our research focuses on the following topics:

  • Using Next Generation Sequencing to analyse immune system repertoires (notably "antibodyomes"): application to vaccine design for HIV and influenza
  • Tracking antigenic escape using "epitope clustering": application to surveillance of rapidly mutating viruses and vaccine design
  • Predicting human T cell responses: application to the stratification of patient responses to viral pathogens, therapeutic proteins and tumour antigens.
Currently we focus on several viral pathogens — influenza A, HIV-1, hepatitis B virus and herpes simplex virus — and specific diseases — haemophilia A and hepatocellular carcinoma (HCC). We are also developing tools to aid the analysis and visualization of high-throughput data, including Phylogenetic Analysis Tools that assist the ancestral reconstruction and analysis of B-cell clonal lineages.


External Collaborators

  • Prof Michael Cho (Co-Director of Center for Advanced Host Defense Immunobiotics and Translational Comparative Medicine, Iowa State University, US)
  • Dr Shilpa Chokshi (Head of Viral Hepatitis/Alcohol Group and Institute Scientific Manager, Institute of Hepatology)
  • Prof Oliver Garden (Professor of Comparative Medicine and Immunology, Royal Veterinary College)
  • Dr Keith Gomez (Consultant in Haemostasis, Royal Free/UCL Medical School)
  • Dr Dan Hart (Consultant in Haemostasis, Barts/Queen Mary)
  • Dr John McCauley (Director of the Worldwide Influenza Centre, Francis Crick Institute)
  • Dr Nigel Temperton (Medway School of Pharmacy).

Joining the Group


Current internship vacancies. We are currently interested in recruiting interns to work on Next Generation Sequencing (NGS) applied to immune system repertoires and related topics. These positions would suit graduates with good programming skills wishing to gain a track record in NGS research. Projects are also available for people with immunological expertise.

General recruitment. We are keen to recruit highly motivated and talented people to work in our group, ranging from undergraduate to post-doctoral level. All interested individuals are encouraged to email Dr Shepherd (, but please bear in mind the following points:

Funding. The group has no earmarked funding available unless it is clearly advertised on this page. PhD studentships are available at specific times of the year through the ISMB PhD Programmes. Applications must be made via that website, but feel free to get in touch informally if you wish to discuss possible projects. The same advice applies to internships, for which support is available through the ISMB Summer Internship Programme. For those who are unable to get funding, it is worth noting that Birkbeck specializes in part-time education for people in work, including at PhD level.

Skills. All our work is computational. We welcome applications from from people with good programming skills (in any language) and/or specialist knowledge about the human immune system. We are also happy to consider applications from those with other bioinformatics skills and interests, such as homology modelling.


Supported By


We would like to thank the following organisations for supporting our research: