Novel tools for analysis of high-dimensional cytometry data - implications for cancer immunology and immunotherapy

The Systems Immunity Research Institute at Cardiff University is delighted to offer a full-time PhD studentship in Bioinformatics / Computational Biology funded by the Cardiff Cancer Research Hub for 3 years, starting on 1 April, 1 July or 1 October 2023 depending on the candidate's preference and availability.

Cytometry - the method of identifying and counting cells – has become a cornerstone of biomedical research. This is particularly true for many cancers where our understanding of the role of cancer stem cells and the fine balance between anti-tumour and pro-tumour functions of immune and non-immune cells in the microenvironment remains limited.

However, multicolour flow and mass cytometry generates massive datasets currently too unwieldy to manage efficiently, and existing algorithms for cytometry analysis typically only handle a fraction of the available dataset and are limited to few options, thereby biasing outputs, compromising reliability and ultimately slowing scientific progress.

Your project aims to visualise and interpret cytometry datasets at a quality, speed, resolution and reproducibility not seen before, by developing new mathematical tools embedded in a uniquely versatile bespoke software (‘CytoPy’) and applying them to publicly available immune profiles of cancer patients.

Your work will help demonstrate the utility of immune phenotyping approaches to suggest optimal treatment combinations for patient subgroups and identify novel correlates of disease progression and successful response to treatment, in order to make therapies more effective, more specific and safer.

You will develop novel technologies for dimension reduction and visualisation without loss of information. You will also implement innovative consensus methods that scale to large datasets and benchmark this work against existing datasets and clustering solutions. You will validate these algorithms using real-world datasets with a view to confirming known and identifying new cell signatures related to the immunopathology, protection and/or response to treatment in different types of cancers.

You will be able to take advantage of the combined expertise of your supervisory team at the forefront of cancer research, immunology and data science, which guarantees a vibrant and interdisciplinary training environment for your studies. All three supervisors have a strong track record in research, teaching, mentoring and disseminating science. They will help you to receive extensive training in research, communication, scientific writing, multitasking and problem-solving skills.

You will be expected to become computationally fluent in programming, multivariate statistics and machine learning methods, with knowledge of cancer immunology to succeed in the process. You will also be encouraged to develop an ability to question and refine current concepts and think outside the box. Together, this will provide a unique skill set appropriate for a future career in academia, industry, education and the third sector.

All previous PhD students in the Eberl Lab published at least one first-author research paper from their studies, and most co-authored further papers, reviews or editorials. The high standard of research in the team is also illustrated by the fact that presentations by PhD students are regularly awarded prizes and/or competitive travel bursaries at national and international conferences. 

In his role as Academic Lead for Public Involvement and Engagement at the School of Medicine in Cardiff and as Engagement Secretary of the British Society for Immunology, Prof Eberl is also in a prime position to offer ample opportunity for training and activities related to science communication and public engagement and involvement.

Entry Requirements  

Applicants should possess a minimum of an upper second class Honours degree, master's degree, or equivalent in a relevant subject. 

Applicants whose first language is not English are normally expected to meet the minimum University requirements (e.g. 6.5 IELTS). 

How to Apply  

This studentship has a start date of 1st April, 1st July or 1st October 2023 (please specify start date in your application).. In order to be considered you must submit a formal application via Cardiff University’s online application service.

There is a box at the top right of the page labelled ‘Apply’, please ensure you select the correct ‘Qualification’ (Doctor of Philosophy), the correct ‘Mode of Study’ (Full Time) and the correct ‘Start Date’. This will take you to the application portal. 

In order to be considered candidates must submit the following information: 

 • Supporting statement 

• CV 

• Qualification certificates 

• References x 2 

• Proof of English language (if applicable) 

International applicants are welcomed if the difference in fees can be covered.