The computational analysis of chromatin structure in normal and malignant immune cells

Faculty: Cancer Sciences Unit, Medicine

Main Supervisor: Jonathan Strefford

Other members of the supervisory team: Mark Cragg, Stephen Thirdborough, Stephen Beers, Dean Bryant

Duration of the award: October 2018 – September 2022

Full time or part time: Full time

Project description: Antibody immunotherapy is becoming commonplace in cancer treatment. Although impressive effects are seen, responses are variable and resistance/relapse is common. To make further progress a better understanding of the modes of action and resistance of antibody drugs are required. A guiding principle derived from our studies is that Fc gamma Receptors (FcgR) in the local tumour microenvironment are central to the therapeutic effects of antibody therapeutics. One of the main objectives of our Cancer Research UK funded programme is to gain a comprehensive understanding of FcgR regulation and use this to promote more effective antibody treatments. We are now seeking a bright and motivated graduate student to investigate the gene expression and epigenetic modifications controlling this system. The successful candidate will focus on the analysis and integration of next generation sequencing (NGS)-based expression and epigenetics data, including ATAC-seq, with subsequent downstream modelling and molecular studies. The ultimate aim will be to identify and functionally characterize expression/regulation patterns determining resistance to current treatments; highlighting potential therapeutic targets.

The successful candidate will develop experience of the molecular and cellular analysis of multiple omics datasets in the context of cancer immunotherapy within a dynamic, productive and friendly team of geneticists, bioinformaticians and molecular / cellular biologists based at Southampton General Hospital. This project offers the opportunity to develop a wide range of NGS, bioinformatics and molecular biology skills, and provides the prospect of collaborative work with national and international opinion-leaders.

The successful candidate will enter our 4 year Integrated PhD programme (link https://www.southampton.ac.uk/medicine/postgraduate/research_degrees/degrees/phd_biomed_cancer_pathway.page), developing powerful computational skills in the area of cancer epigenetics, next generation sequencing, immunotherapy and bioinformatics. Following 3 lab rotations with the programme team in year 1, the applicant will develop a main theme for the remainder of the PhD.

Please contact: Professor Jonathan Strefford: [Email Address Removed] or Mark Cragg [Email Address Removed]


Person Specification: See person doctoral specification link below
https://jobs.soton.ac.uk/Upload/vacancies/files/17408/03%20Doctoral%20Researcher%20Person%20Specification_UoS_FoM_PhD.docx

We seek a candidate with the following qualities:
• A genuine enthusiasm for the computational/ bioinformatics analysis of gene expression/regulation in the context of immunotherapy
• A confident independent attitude enabling them to work collaboratively across the bioinformatics interface, between biologists and computational scientists in Southampton and across Europe.
• A computer scientist with a keen interest in biology/immunology, or a biologist/immunologist with an interest in bioinformatics.
• A good team worker and communicator.
• An organised thinker, able to drive diverse project aspects and manage time efficiently.
The successful candidate is likely to have the following qualifications:
• A 1stor 2:1 degree in computer or biological sciences and/or second degree with a related Masters

Administrative contact and how to apply:
Please complete the University’s online application form, which you can find at
https://studentrecords.soton.ac.uk/BNNRPROD/bzsksrch.P_Login?pos=7205&majr=7205&term=201819

You should enter Jonathan Strefford as your proposed supervisor. To support your application provide an academic CV (including contact details of two referees), official academic transcripts and a personal statement (outlining your suitability for the studentship, what you hope to achieve from the PhD and your research experience to date).

Informal enquiries relating to the project or candidate suitability should be directed to Jonathan Strefford ([Email Address Removed]) or Mark Cragg ([Email Address Removed]).

Interview date: 21st February 2018