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Computational multi-omics for understanding the functional impact of alternative splicing in human cancer

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  • Full or part time
    Prof Conrad Bessant
    Dr P Rajan
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

We are seeking an outstanding individual with a passion for devising novel computational solutions to data-rich bioscience problems, to help us make a transformational change in our understanding of the functional impact of alternative pre-mRNA splicing in human cancer.

About the project:
Cancer represents a significant public health problem worldwide, with high mortality rates despite early detection programmes and recent therapeutic advances, including game-changing developments in immuno-oncology. Large scale consortia-led “omics” studies from several hundred patients have generated terabytes of data and facilitated a better understanding of pan-cancer genomes, transcriptomes, and proteomes. However, studies integrating pan-cancer omics datasets have been lacking, and this has limited how, for example, misregulation of transcriptomes impacts on proteomic diversity and influences human cancer phenotypes. Alternative pre-mRNA splicing (AS) is a ubiquitous genetic process that results in the “shuffling” of coding and non-coding information in the genome, creating proteomic diversity. Recently, global misregulation of AS has been associated with cancer phenotypes due to changes both within tumour cells and the microenvironment, but little is known of the global impact on pan-cancer proteomes.

The aim of this project is to devise, implement and apply computational methods to integrate transcriptomics and proteomics data from existing large scale cancer studies, to study qualitative and quantitative changes in human pan-cancer proteomes. The project will be supervised by Conrad Bessant (Professor of Bioinformatics, School of Biological and Chemical Sciences) and Dr Prabhakar Rajan (Clinical Senior Lecturer in Urology, Barts Cancer Institute and Consultant Urologist, Barts Health NHS Trust).
We will take an interdisciplinary approach, based on the proteomics informed by transcriptomics (PIT) methodology developed by the Bessant lab. Using this methodology, we will seek new findings in the context of novel cancer cell and microenvironment transcriptomic and proteomic datasets generated by the Rajan lab. The project aims to produce findings that are likely to yield novel insights into cancer cell biology, potential cancer biomarkers and possible therapeutic targets. This will provide the student with a unique opportunity to gain valuable multidisciplinary training of direct clinical relevance. As well as developing a deep understand of integrated omics, there will also be an opportunity to implement analysis tools as stand-alone software and for inclusion in the popular Galaxy platform.

About you:
You must have a first degree (BA or BSc Honours or equivalent, at upper second class or above) in a relevant subject (e.g. biomedicine, biochemistry, computer science, physics, mathematics) with a strong interest in developing computational solutions to biological research problems. A Masters qualification (at Merit or above with evidence of some Distinction level work) in a discipline related to the studentship (e.g. bioinformatics) would be a distinct advantage, as would the ability to code in Python. Specialist knowledge of cancer biology is not essential, but you should have an interest in applying computational solutions to answer biological questions using data from this field. All applicants will be judged according to the same criteria, namely: record of academic and/or professional achievement; and compatibility with the theme of the studentship.

The closing date for applications is 9th May 2018. Interviews are expected to be held 23rd May 2018.

About the Life Science Institute:
This project is supported by QMUL’s Life Sciences Initiative (LSI). The LSI aims to be a truly cross-faculty endeavour; the overall purpose of the initiative is to establish a unique life sciences cluster stretching across our east London campuses, which will act as a beacon attracting partners from higher education, NHS and industry. Working with these partners, QMUL will make significant contributions to the translational health agenda in London and beyond, benefiting patients in the local population and acting as a major catalyst for the regeneration of Whitechapel.

Funding Notes

The studentship is open to UK and EU nationals. It will cover tuition fees and provide an annual tax-free maintenance allowance for 3 years at Research Councils UK rates (£16,777 in 2018/19).


Relevant PubMed IDs: 18978789, 27197215, 23142869, 23629695, 26269333.

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FTE Category A staff submitted: 23.39

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