York Centre for Cross-disciplinary Systems Analysis & Departments of Mathematics and Biology, University of York
Post-Doctoral Research Associate in Computational Biophysics & Bioinformatics in Virology
During our interdisciplinary Wellcome Trust-funded programme New perspectives for anti-viral therapy: The regulatory roles of genomic RNA in virus assembly, infection and evolution we have discovered a second code other than the genetic code of human viruses – see, e.g., work on Hepatitis B virus (Patel et al., Nat. Microbiol. 2:17098, 2017) and Parechovirus (Shakeel et al, Nat. Commun. 8:5, 2017) – that acts as an instruction manual for virion assembly. This code is written in the form of multiple dispersed RNA sequence/structure motifs in the viral genome each with affinity for the cognate coat proteins that form the viral capsids, i.e., the protein containers encapsulating and thus protecting the genetic message between rounds of infection.
We seek a post-doctoral fellow with programming experience to refine, further develop and apply computational strategies developed by the York team to identify this code in a wide range of RNA viruses (including HIV, picornaviruses, such as the common cold virus, as well as multipartite and newly emerging viral infections such as Chikungunya) based on state-of-the-art experimental data provided by our experimental collaborators based in Leeds. In particular, you will develop, refine and apply computational strategies to analyse X-ray synchrotron footprinting data of packaged viral RNAs, an experimental technique that the Leeds team are pioneering for viruses, in order to characterise the RNA sequence/structure motifs of the assembly code. You will also contribute to the exploitation of the assembly code in drug/gene delivery, therapy and vaccination. This includes the development of computational strategies to optimize the assembly code for the design of virus like particles in close collaboration with the experimental team (Patel et al, PNAS 114:12255, 2017), and the identification of its evolutionarily conserved features in order to identify potential drug targets. You will also further develop a novel network approach for the identification of RNA-RNA interactions in multipartite viruses (AlShaikhahmed et al., Nucleic Acids Research 46:12087, 2018) and apply it to Bluetongue and influenza viruses.
We are looking for applicants with a PhD in Computational Biophysics, Bioinformatics or Theoretical Biology, a proven track record in programming, and a keen interest in working in close collaboration with experimental scientists. Ability and creativity in developing, and not just implementing, computational approaches to analyse and interrogate biological systems, and a passion for the exciting biological questions and therapeutic applications are essential for this post.
You will join the interdisciplinary team of Professor Reidun Twarock (York/theory, where this post will be based) and Professor Peter Stockley (Leeds/experiment), and contribute to the production of high quality research papers, as well as assist with the dissemination of the research.
We offer excellent career prospects and mentoring, which makes this an ideal springboard for an ambitious scientist with career aspirations in academia or industry.
For enquiries please contact: Prof Reidun Twarock (Reidun.Twarock@york.ac.uk)
This post is available on a fixed term basis for 3 years.
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