We seek a talented and dedicated scientist with a background in computational biology, statistics, phylogenetics and bioinformatics, to analyse experimental and field data for virus infections in chickens, and to help develop phylodynamic inference and models for the effects of vaccination on virus transmission and evolution. This is one of two 3 year positions at Roslin Institute, University of Edinburgh, UK, and is part of the international collaborative project: “Combined influence of imperfect vaccines, host genetics, and non-genetic drivers on virus transmission and virulence evolution” funded by the international Ecology and Evolution of Infectious Diseases (EEID) Programme.

Project overview:
To maintain human and animal health, it is extremely important to understand how pathogens like viruses are transmitted and evolve to higher virulence. In this project, an international, interdisciplinary team investigates the impact of vaccination and selective breeding on the spread and evolution of two avian pathogenic viruses - Marek’s disease virus (MDV) and infectious bronchitis virus (IBV) – both of which are primarily controlled by imperfect vaccines. It has been argued that imperfect vaccines like those to MDV and IBV, or host genetic resistance may alter the balance of selection between pathogen transmission and virulence by allowing a few more divergent but still virulent strains to be transmitted. However, these hypotheses have not been proven, and predictive frameworks are lacking for determining the combined influence of host and viral genetics, as well as vaccination on viral transmission and evolution to increased virulence.
This project will generate informative, high-resolution empirical data to monitor virus transmission and establish the role of genome variability on virulence evolution. The main tasks of the successful candidate will be to analyse chicken transmission experiment data, including infection data and viral sequence data; and to help develop the statistical and phylodynamic models to describe how transmission and viral evolution changes with hosts of different immune status or genetic background, in transmission experiments and in the field. This will help to develop strategies to control the ecology, evolution and economic burden of viral diseases in poultry and other species.

Eligibility, qualifications and skills:
We welcome applications from all over the world that meet the following qualifications: as well as having a PhD (or MSc with compensatory experience) in a quantitative discipline with substantial statistical and computational components, applicants should have a track record and abilities in :
·Deploying computational and statistical bioinformatics techniques.
·Phylogenetics, ideally viruses or other fast evolving organism.
·Bayesian and frequentist statistical methods applied to temporal / genomic data.
·Ability to code or script in at least one language.
·Ability and interest in learning and applying new quantitative methods
·Publishing in high impact scientific journals
·Ability to work effectively in a multi-disciplinary project team and presenting technical methods and results to non-quantitative audiences
·Ability and willingness to actively contribute to regular international project meetings and conferences (physical and virtual).
In addition, experience with phylodynamic inference (e.g. BEAST software), experience in machine learning methods, R and Java, and experience with deep sequence or within-host variation viral data is highly desirable.

Research environment and how to apply:
The successful candidate will be based at the Roslin Institute under the joint supervision of Dr. Samantha Lycett and Prof. Andrea Doeschl-Wilson. The candidate will work closely together with the project partners in Roslin, the US and Ghana. The candidate will join a welcoming, vibrant, multi-disciplinary research environment consisting of bio-mathematicians, livestock geneticists, epidemiologists, statisticians, bioinformaticians, and molecular biologists to improve livestock and human health and to train the next generation of world-class scientists.
The post is available immediately and until 31.12.2023.
Interviews will be held in February 2021 (via Zoom / MSTeams or Skype).
If invited for interview you will be required to evidence your right to work in the UK. Further information is available on our right to work webpages.
Further information on the above post, including how to apply, is available on the Roslin website. Closing date 31 Jan 2021; Potential applicants may contact Dr Samantha Lycett (samantha.lycett@ed.ac.uk) or Professor Andrea Doeschl-Wilson (andrea.wilson@roslin.ed.ac.uk) to discuss the position.