Postdoctoral Researchers to support the work of Prof. Rambaut
University of Edinburgh, Institute of Evolutionary Biology
United Kingdom

Postdoctoral Research Associate


Vacancy Ref: : 042022

Closing Date : 03-Jan-2018


Contact Person : Prof Andrew Rambaut

Contact Number :


Contact Email : a.rambaut@ed.ac.uk


In recent viral outbreaks of Ebola, MERS-CoV and Zika, viral genome sequencing revealed critical insights into the evolution and transmission of the virus, offering tantalizing examples of the potential value of this for future outbreak control efforts. To maximize the utility of this information, it needs to be achieved in real-time, providing virus genome data and actionable analysis and interpretation within hours of patients being sampled. The ARTIC project, funded by The Wellcome Trust, will achieve this by producing a mobile virus sequencing system, including statistically rigorous analysis frameworks, to prepare for the next outbreak and ensure that viral genome sequencing is positioned to have full impact on the public health response.

 

The Institute of Evolutionary Biology at the University of Edinburgh seeks to appoint two Postdoctoral Researchers to support the work of Prof. Rambaut, developing computational and statistical approaches to viral genome sequence analysis in real time during an outbreak or epidemic.

 

Candidates will have a PhD in a relevant field (computational biology, computer science, mathematical biology or statistics), experience of developing statistical models of molecular epidemiology, phylodynamics and phylogography, and/or demonstrable knowledge and experience of software development, High Performance Computing, and GPGPU development. The candidates will have a track-record of publishing in peer-reviewed, academic journals, excellent communication skills, and the ability to deal with a variety of tasks to set deadlines. The project will involve working with project team members including virologists, bioinformaticians and epidemiologists to create an integrated, practical system for public health emergencies.

 

The posts are full-time for 5 years.

 

Please include a CV and supporting statement with details of how you meet the knowledge, skills and experience required.

 

Informal enquiries to Prof. Andrew Rambaut (a.rambaut@ed.ac.uk).

 

1. Job Details

Job title: Postdoctoral Research Associate (PDRA)
School/Support Department: School of Biological Sciences
Unit (if applicable): Institute of Evolutionary Biology (IEB)
Line manager: Professor Andrew Rambaut

 

2. Job Purpose

The aim of the project is to create a sample-to-response molecular epidemiology system for acute RNA virus outbreaks in resource-limited locations. Based on the Oxford Nanopore Technology’s MinION portable sequencing platform, the system will include a ‘lab-in-a-suitcase’ for virus isolation and sequencing, in-country bioinformatics of MinION data, real-time phylodynamic analysis, integration of epidemiological data, and interpretation and visualization of the results to inform public health responses. The position advertised here will focus on the computational and statistical aspects of the project including the development of phylodynamic analyses of outbreaks capable of updating in real-time as new data becomes available.

 

3. Main Responsibilities

Research – To develop methods and software for the real-time analysis of virus genome sequence data from emerging outbreaks and epidemics. To undertake research on phylodynamic models of acute viral outbreaks to inform public health response. (60%).
Preparing presentations and manuscripts for publication in the peer-reviewed scientific literature based on the research work described above. Preparing material for presentation at scientific conferences. (20%).
Liaison with project partners. Attending workshops and meetings related to the project and presenting research findings. (10%).
Support for research group activities, including helping to demonstrate and supervise undergraduate and postgraduate students. (10%).


4. Planning and Organising

Carry out the activities listed to time and quality standards. Prioritise own tasks and allocate time to own tasks.

5. Problem Solving

Consult with colleagues, project partners and/or line manager as required. Seek advice for academic/technical contacts. Make intelligent use of on-line support services.

6. Decision Making

Selecting approaches to allotted task. Contributing to project planning meeting, suggest solutions to technical problems.

7. Key Contacts/Relationships

Prof Andrew Rambaut (Line Manager; Edinburgh PI); Group research staff.

8. Knowledge, Skills and Experience Needed for the Job

 

Qualifications/Training

Essential


A PhD (or A PhD to be obtained soon) in computational biology, computer science or related discipline.

 

Experience

 

Essential


Software development.
Record of publication in international journals.

 

Desirable


Experience of developing large, complex, software packages.
The molecular epidemiology of infectious diseases.
Bayesian phylogenetics or related statistical fields.

 

Knowledge, Skills and Competencies

 

Essential


Software development in Java, Python or C++.
UNIX/Linux based environments.

 

Desirable


High-performance computing including OpenCL, CUDA or MPI.
Data visualization using JavaScript.
Database development.
Modern collaborative development environments such as GitHub.
Administration of LINUX systems.

 

Personal Attributes

 

Essential


Commitment to collaborative research.
Effective project and time management skills.
Excellent communication skills.

 

9. Dimensions

 

This post is full time (35 hrs/ week) and funded for 5 years from the start date.

 

10. Job Context and any other relevant information

 

This post is part of a wider collaboration (ARTIC Network, funded as a collaborative award by The Wellcome Trust) of about 15 researchers at the universities of Birmingham, Cambridge, Oxford, Leuven, University of California Los Angeles and the Fred Hutchinson Cancer Research Center, Seattle. The post-holder will focus on particular work-packages of the project and will need to liaise and collaborate with the other PIs and PDRAs to ensure a fully integrated project is delivered.

 

Application Procedure

 

All applicants should apply online by clicking the apply link at the bottom of this page. The application process is quick and easy to follow, and you will receive email confirmation of safe receipt of your application. The online system allows you to submit a CV and other attachments.

 

You will be notified by email whether you have been shortlisted for interview or not.

 

The closing date is 5pm GMT on 03 January 2018.

 

Eligibility to Work

 

In accordance with the Immigration, Asylum and Nationality Act 2006 the University of Edinburgh, as an employer, has a legal responsibility to prevent illegal working and therefore must check that all employees are entitled to work in the United Kingdom (UK).

 

To do so, the University of Edinburgh requires to see original documents evidencing right to work in the UK before commencement of employment and this is normally carried out at interview. Details will be provided in any letter of invitation to interview.

 

For further information on eligibility to work please visit our eligibility to work website

 

If you are not currently eligible to work in the UK, the University has the authority to issue a Certificate of Sponsorship (CoS) to successful candidates who meet the eligibility criteria. The CoS enables candidates to apply for a Tier 2 (general visa) in accordance with current UK Visas and Immigration rules.

 

For applicants interested in sponsorship information is available on our Working in the UK website

 

However, if you have previously been sponsored by an employer within the UK but your leave has expired or lapsed and you are no longer in the UK, according to Home Office Visa Immigration rules you cannot apply for sponsorship under any category of Tier 2 for a period of 12 months after the date your visa expired and/or you left the UK.

 

If you are an academic in the field of sciences; humanities; engineering; medicine; digital technology; or the arts and come from outside the EEA, it may be possible for you to apply for a Tier 1 (Exceptional Talent) visa.

 

The Tier 1 (Exceptional Talent) visa route offers a greater flexibility in your employment compared to other UK immigration routes, meaning you can, for example, move organisation, location and/or job role. By contrast with, a Tier 2 visa where you are ‘tied to a UK sponsor’. Tier 1 provides greater flexibility in undertaking additional engagements, such as collaborations and is intended as a route to settlement. Allowed absences from the UK are up to 180 days per year without losing the eligibility to qualify for settlement, with no restriction on the reason for absence (unlike Tier 2, where any absences from the UK must be for a purpose consistent with the person’s employment or economic activity, including paid annual leave, or for serious or compelling personal reasons).

 

You would initially need to apply to be endorsed as an internationally recognised leader or emerging leader in your particular field by a designated competent body (Arts Council England, British Academy, Royal Academy of Engineering, Royal Society, Tech City UK).

 

Tier 1 (Exceptional Talent)

 

Once successfully endorsed, you are able to apply for a Tier 1 (Exceptional Talent) visa. More information on this entry route is available at UKVI Website.

 

Conditions of Employment

 

Pension Scheme

 

This role is grade UE07 and therefore the post holder is automatically included in membership of the Universities Superannuation Scheme (USS), subject to the USS membership criteria, unless they indicate that they choose not to join the Scheme.

 

For further information please visit our Pensions website.

 

Salary

 

The role is grade UE07 and attracts an annual salary of £32,548 to £38,833 for 35 hours each week. Salary is paid monthly by direct transfer to your Bank or Building Society account, normally on the 28th of the month. Salaries for part-time staff are calculated on the full-time scales, pro-rata to the Standard Working Week.

 

The University reserves the right to vary the candidate information or make no appointment at all. Neither in part, nor in whole does this information form part of any contract between the University and any individual.

 

The Institute of Evolutionary Biology (IEB)


At the Institute of Evolutionary Biology we study evolution in the broadest possible sense, from virtually every angle and using a great range of organisms and techniques.

 

Our research falls under three broad themes:

 

Evolutionary and Quantitative Genetics


We study fundamental and applied aspects of genetics, from theoretical population genetics to the genetics of complex traits.

 

Evolutionary Ecology and Behaviour


We explore the evolutionary causes and consequences of ecological interactions and behaviour, using theoretical and empirical approaches.

 

Biodiversity and Ecology


We examine biodiversity and ecological complexity, from genomes to ecosystems.

 

Our interdisciplinary research and teaching benefits from strong links with members of the Institute of Immunology and Infection Research (IIIR), the Edinburgh Infectious Diseases network (EID (http://www.eid.ed.ac.uk)), the Centre for Immunity, Infection and Evolution (http://ciie.bio.ed.ac.uk), the Institute of Genetics and Molecular Medicine (http://www.igmm.ed.ac.uk), the Life Physics Group, the Roslin Institute (http://www.roslin.ed.ac.uk), and the Royal Botanic Garden Edinburgh (http://www.rbge.org.uk). Our funders include BBSRC, NERC, charities and government bodies.



School of Biological Sciences


As the modern inheritors of our 400-year-old reputation for excellence, our staff and students contribute to a vibrant academic community whose visions are shaping tomorrow’s world.

 

The School of Biological Sciences is at the leading edge in teaching, research and innovation. Independent rankings such as the Times Higher Education consistently place us amongst the top 25 universities in the world for biological sciences.

 

Teaching and learning: Our undergraduate students rate us highly for the quality of our education, recording 92% overall satisfaction with their biology course at Edinburgh and an even higher rating for the quality of our teaching (2014 National Student Survey). Today’s students can study a wide range of topics, providing a strong grounding in fundamental biology with the flexibility to gain experience of the most recent research developments in biological and biomedical science in the later years of their degree programme. More than 300 students per year are admitted to our taught programmes, which are managed and supported by the Biology Teaching Organisation.

 

Undergraduate programmes

 

Masters programmes

 

Research: Our students are taught by some of the world’s leading scientists. We are one of the top biology departments in the UK for the quality and impact of our research. More than half of our research activity was rated as ‘world-leading’ in quality and scope in the 2014 UK national research assessment, placing us second in the UK amongst university teaching departments. The success of our research is testament to the excellence of our people: some 130 academic teaching staff and independently-funded research fellows, and the 400 research assistants and technicians and more than 200 PhD students who work with these Principal Investigators. The Graduate School of Biological Sciences provides overarching training and support for our PhD students.

 

Our research is wide-ranging in scope and is structured around themes which build links from fundamental science to research that addresses global problems. We are investing in growth and expanding our facilities to accommodate new research directions. Our aim is to create innovation and impact from our research by integrating expertise across our research themes to generate transformational new knowledge.

 

Research Themes, Institutes and cross-disciplinary Centres

 

The School is a member of SULSA, the Scottish Universities Life Science Alliance.

 

Professional services: The School’s academic success is supported by a large professional services team who deliver administrative, IT and technical services.

 

Working in the School: We aim to ensure that our culture and systems support flexible and family-friendly working and to recognise and value diversity across all our staff and students. The School has an active programme offering support and professional development opportunities for all staff. We place a particular focus on development for early-career researchers (postgraduate and postdoctoral research staff and personal fellowship holders), offering mentoring and an active ‘BioDocSoc’ organisation that brings together researchers for networking, events and training opportunities.

 

The School of Biological Sciences holds a Silver Athena SWAN award in recognition of our commitment to advance the representation of women in science, mathematics, engineering and technology.

 

Our website contains more information about the School.



College of Science and Engineering (http://www.ed.ac.uk/science-engineering)


The College of Science and Engineering (CSE) is one of the largest and highest-ranked science and engineering groupings in the UK. Headed by Professor Dave Robertson, CSE comprises seven Schools (Biological Sciences, Chemistry, Engineering, GeoSciences, Informatics, Mathematics, and Physics and Astronomy). Informatics is located in the University’s Central Area near George Square, with the other six 2 miles further south at the King’s Buildings. The College has over 3,000 academic and support staff, and educates some 6,000 undergraduates, over 1000 taught postgraduates and more than 2,000 research students. It is in the front rank of UK university science and engineering groupings for research quality and income, and is a key player in many European and international research collaborations.

 

Research Excellence Framework (REF) 2014

 

In the 2014 REF over 95% of our staff were submitted. Of our seven submissions, four of which were as a joint research school in combination with a strategic research university partner through pooling, 3 were ranked top in the UK and all 7 were in the top 5 in their discipline in the Times Higher Power rankings.


The University of Edinburgh


For more than four centuries, our people and their achievements have rewritten history time and again. They’ve explored space, revolutionised surgery, published era-defining books, paved the way for life-saving medical breakthroughs and introduced to the world many inventions, discoveries and ideas from penicillin to Dolly the sheep. We have believed that anything is possible, we still do.


The latest Research Excellence Framework highlighted our place at the forefront of international research. This adds to our international reputation for the quality of our teaching and our student experience excellence. The University is proud of its success with online teaching initiatives, with 2550 students currently studying its online distance learning postgraduate programmes, and a total to date of more than 2 million enrolments for Edinburgh MOOCs.

 

As a member of staff, you will be part of one of the world's leading universities, with 20 Schools spread over 3 Colleges that offer more than 1600 undergraduate and 600 postgraduate programmes to over 35,000 students each year. Professional services are critical to this success as well as our world-class teaching, research and student facilities. In fact, we are one of the top employers in Edinburgh, with over 13,000 people spread across a wide range of academic and supporting roles.

 

As a world-changing, world-leading university, we offer an exciting, positive, creative, challenging and rewarding place to work. We give you support, nurture your talent, develop and reward success and integrate academic, professional and personal career goals, as well as give your career the benefit of a great and distinguished reputation. In addition, our employees benefit from a competitive reward package and a wide range of staff benefits, which include generous holiday entitlement, a defined benefits pension scheme, staff discounts and much more. Access our staff benefits page for further information and use our reward calculator to find out the total value of pay and benefits provided.

 

The University of Edinburgh holds a Silver Athena SWAN award in recognition of our commitment to advance gender equality in higher education. We are members of the Race Equality Charter and we are also Stonewall Scotland Diversity Champions, actively promoting LGBT equality. The University has a range of initiatives to support a family friendly working environment, including flexible working and childcare vouchers. See our University Initiatives website for further information.

 

University Family Friendly Initiatives


The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.


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