Antibody repertoire analytics: the development of a visualization toolkit and its application to high-throughput Ig-seq data

Dr Adrian Shepherd. Department of Biological Sciences, Birkbeck University of London
Mr James Snowden, UCB

Project Description

Next Generation Sequencing (NGS) of antibodies (Abs) – known as Ig-seq or Rep-seq – is increasingly used to address fundamental immunological questions, such as: How do immune responses to pathogens, vaccines and therapeutic Abs differ? And what are the differences between healthy Ab repertoires and those associated with immune dysfunction? A typical Ig-seq dataset consists of millions of partial mRNA Ab sequences.

The aim of this project is to develop a toolkit for visually analysing Ig-seq, enabling biologists to rapidly explore their data, generate novel hypotheses and make new discoveries. The priority will be to support whole Ab repertoire analytics and to characterize fundamental properties (repertoire diversity, Ab convergence within and between repertoires, and the dynamics of repertoire evolution) relevant to vaccine design and therapeutic Ab discovery.



The student on this project will engage in two complementary activities: tool development and immunology research. S/he will benefit from the preliminary work undertaken within the group to evaluate open-source network visualization platforms such as Cytoscape and Gephi, and interactive visualization of Ig-seq data using a Data-Driven Documents (D3) framework. Both activities will be undertaken in close collaboration with our collaborators at UCB, the leading UK company focusing on therapeutic Ab discovery.

Application

This project would suit a student with good programming skills who is interested in apply these skills to an area of biology that is of immediate therapeutic relevance.

Applicants must hold, or be expected to achieve, a first or high upper second-class undergraduate honours degree or equivalent (for example BA, BSc, MSci) or a Masters degree in a relevant subject. Interested applicants are encouraged to contact Adrian Shepherd (a.shepherd@mail.cryst.bbk.ac.uk) in advance of the deadline, Monday 15th May 2017 at 5pm.


To apply you will need to send the following documents in a single email to: LIDo.Admissions@ucl.ac.uk. All documents must be submitted in unprotected PDF format.


  • Completed Application Form (Sections A and B) including details of two Academic References
  • The disability and ethnic origin monitoring form
  • Official Final Transcripts from Completed Programmes of Study
  • Official Interim Transcripts from On-going Programmes of Study
  • English Language Qualification (if required, please see below)
  • Academic CV
  • Copy of Passport

Please click the relevant links below to download a zipped folder of application documents in your preferred format.
Application Pack (Word).zip
Application Pack (PDF).zip