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Genomics, bioinformatics and evolution of inherited chromosomal integrated human herpesvirus 6.


Project Description

We are inviting applications for a 3-4 year PhD student in the area of bioinformatics and evolutionary genomics of endogenous Human Herpesvirus 6 (HHV-6).

This project uses bioinformatics and evolutionary genomics to unravel the biology of integrated Human Herpesvirus 6. In humans, ~1% carry a heritable HHV-6 genome, which sits in the telomeres of various chromosomes. HHV-6 and the inherited form are involved in various diseases including graft rejection and heart disease. We want to understand the basics of how the genome integrates, why is it maintained through generations and what the consequences of its presence are.

The successful candidate will learn and apply bioinformatics techniques to analyse human genome data containing the viral sequence, in order to understand the evolutionary history and ongoing biology of HHV-6 integration. The project will be supervised by Dr. Amr Aswad and Professor Kaufer in the institute of virology at the Freie University of Berlin. The Kaufer lab consists of range of students and postdocs from international backgrounds and a wide range of interests and skills.

The successful candidate should have a keen interest in genomics and evolutionary biology, as well as an enthusiasm for large scale data analysis. As part of a wider team of virologists, the candidate will have the opportunity to collaborate with wet bench colleagues to generate new data and address questions beyond the scope of computational analyses.

The successful candidate must:

- hold a degree in biology or similar. Candidates from a computer science or similar background will also be considered
- Have at least a basic understanding of computer programming (or a willingness to learn!)
- Must have strong command of written and spoken English
- Demonstrate sincere interest in the project (research the subject before applying!)

The ideal candidate will:

- Have some experience in the area of computational biology or similar
- Have an understanding of evolutionary biology and phylogenetics techniques and theory
- have a proven record of independent research skills
- have an active interest in the area of next generation sequencing, genomics, bioinformatics, virology

How to Apply :

Please send an email to with your CV (1-2 pages) and a short paragraph explaining your interest in this project and why you would make a good candidate.

Funding Notes

Various funding opportunities depending on country of origin.
While there are no tuition fees, self-funded students must be able to maintain living expenses in Berlin.

References

1. Kaufer B, Flamand L. Chromosomally integrated HHV-6: impact on virus, cell and organismal biology. Curr Opin Virol. 2014;
2. Wallaschek N, Sanyal A, Pirzer F, Gravel A, Mori Y, Flamand L, et al. The Telomeric Repeats of Human Herpesvirus 6A (HHV-6A) Are Required for Efficient Virus Integration. Ling PD, editor. PLOS Pathog. Public Library of Science; 2016;12: e1005666. doi:10.1371/journal.ppat.1005666
3. Aswad A, Katzourakis A. The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses. PLoS Genet. 2014;10. doi:10.1371/journal.pgen.1004332
4. Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet. 2010;6. doi:10.1371/journal.pgen.1001191
5. Aswad, Amr, Katzourakis A. Paleovirology: The Study of Endogenous Viral Elements. In: Weaver SC, Denison M, Roossinck M, Vignuzzi M, editors. Virus Evolution: Current Research and Future Directions. 1st ed. Poole: Caister Academic Press; 2016. pp. 273–292. doi:10.21775/9781910190234
6. Lassner D, Kuhl U, Escher F, Wallaschek N, Gross U, Seeberg B, et al. Prevalence and treatment of chromosomally integrated human herpesvirus 6 in patients with symptomatic heart failure. Eur Heart J. GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS; 2014;35: 1095.

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