Research Scientist (Bioinformatics/Genomic Epidemiology)
Post Details
Job Title
Research Scientist (Bioinformatics/Genomic Epidemiology)
Post Number
1003595
Closing Date
27 Feb 2019
Grade
SC6
Starting Salary
£31,250 - £38,100
Hours per week
37
Project Title
Genomic approach to transmission and compartmentalisation of extended-spectrum cephalosporin resistance in Enterobacteriaceae from animals and humans
Expected/Ideal Start Date
25 Feb 2019
Months Duration
20

Job Description

Main Purpose of the Job

Applications are invited for a Research Scientist to join the Laboratory of Dr Alison Mather in the Microbes in the Food Chain Programme at the Quadram Institute Bioscience (QIB), based in Norwich, UK.

Join a project focusing on the resistance to extended-spectrum cephalosporin (ESC) drugs, which are used to treat serious bacterial infections such as those caused by Enterobacteriaceae, a large family of Gram-negative bacteria which includes pathogens such as Salmonella and Escherichia coli. Resistance to ESCs in Enterobacteriaceae, including through extended-spectrum beta-lactamases (ESBLs), is a worldwide public health challenge. The international presence of ESC resistance in almost every ecological niche and biological compartment, including humans and other animals, makes it an ideal target to study the spread of antimicrobial resistance (AMR). This project involves a combination of approaches, including whole genome sequencing (WGS), bioinformatics analyses of large datasets and statistical modelling to identify major transmission pathways of ESC resistance between bacteria, between host species, and between countries.

This project involves working with collaborators in Canada, Germany, France and the UK, both in academic institutions and at national surveillance/reference laboratories. Bacteria from their collections have already been sequenced to contribute to a dataset of >2,500 genomes ready for analysis by the post holder. These genomic data, along with the associated epidemiological metadata, provides an incredible opportunity to address key questions in this field, including the relative importance of animals to the burden of AMR in humans.

Key Relationships

Internal: Line manager, group members and, as necessary, other researchers, research support staff and students across research groups.
External: Collaborators in Canada, Germany, France and the UK.

Main Activities & Responsibilities

Bioinformatics analysis of whole-genome sequences of bacteria from animals, food, the environment and humans using high performance computing in a Linux environment
Integrate the genome and epidemiological data to assess transmission and evolution of bacteria and AMR
Contribution to the preparation of written reports and research publications
Present research findings at project meetings, scientific conferences and outreach/translation events
Ensure research and record keeping is carried out in accordance with good practice, scientific integrity and in compliance with local policies and any legal requirements
Contribute to the smooth running of the group, including the effective use of resources, supervision of visitors to the laboratory and assisting with training others, encouraging scientific excellence
Work with collaborators in experimental design and strategic planning of the other work packages of the grant
As agreed with the line manager, any other duties commensurate with the nature of the post

Person Profile

Education & Qualifications

Requirement
Importance
MSc in a relevant subject (e.g. Bioinformatics, Computational Biology, Molecular Genetics or related quantitative discipline)
Essential
PhD in a relevant subject
Desirable

Specialist Knowledge & Skills

Requirement
Importance
Understanding of high-throughput sequencing and genomics (preferably microbial)
Essential
Proficiency in at least one programming language (e.g. python, Perl, R)
Essential
Proficiency in working in the Linux environment
Essential

Relevant Experience

Requirement
Importance
Hands-on experience of working with large next generation sequencing data
Essential
Experience with command-line and cloud-computing environment
Essential
Experience of oral research presentations
Desirable
A good publication record in peer reviewed journals commensurate with experience level
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Excellent communication skills, both written and oral, including the ability to present complex information with clarity
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skills
Essential
Good interpersonal skills, work well as part of a team
Essential
Ability to rapidly attain new technical skills and understanding of new technical concepts
Essential

Additional Requirements

Requirement
Importance
Promotes equality and values diversity
Essential
Ability to undertake occasional travel (national/international) related to collaborations and/or seminars
Essential
Attention to detail
Essential
Ability to maintain confidentiality and security of information where appropriate
Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Willingness to work outside standard working hours when required
Essential

Who We Are

Quadram Institute Bioscience

The Quadram Institute is at the forefront of a new interface between food science, gut biology and health, developing solutions to worldwide challenges in food-related disease and human health.

We are engaged in fundamental and translational food and health research, alongside clinical studies, endoscopy and industry, working together to become a leading international hub for food and health research, combining scientific excellence and clinical expertise, delivering impacts on patient care and accelerating innovation.

Department

Microbes in the Food Chain

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Research Scientist (Bioinformatics/Genomic Epidemiology)

Applications are invited for a Research Scientist to join the Laboratory of Dr Alison Mather in the Microbes in the Food Chain Programme at the Quadram Institute Bioscience (QIB), based in Norwich, UK.

Quadram Institute Bioscience:

QIB provides a vibrant and exciting setting composed of multiple research teams working on microbial genomics, molecular epidemiology, microbial communities and food science. We offer the chance to work with world leading, cutting edge technologies both in IT and computational biology and give you the opportunity to broaden your skills using open source technologies within a bioinformatics context. You will gain experience of working with Big Data, cloud computing, and have the opportunity to publish excellent science in leading peer-reviewed journals.

Background:

The post holder will join a project funded by the Medical Research Council through a Joint Programming Initiative on Antimicrobial Resistance international consortium project aiming to understand the transmission of antimicrobial resistance (AMR) at the genome, bacterium, national and international levels. This research is highly topical and relevant to both human and animal health. The work will be conducted within a One Health framework, consistent with research recommended by several international policy reviews, including the Food and Agriculture Organization, the World Organisation for Animal Health, and the World Health Organization.

The focus of the research is on extended-spectrum cephalosporin (ESC) resistance in Enterobacteriaceae, including extended-spectrum beta-lactamases (ESBLs), comparing bacteria, host populations (humans and domestic animals) and countries. Collaborators on this project are from Canada, France, Germany and the UK.

The role:

The post holder will analyse a dataset of >2,500 sequenced bacterial genomes. These genomic data, along with the associated epidemiological metadata, provides an incredible opportunity to address key questions in this field, including the relative importance of animals to the burden of AMR in humans.

The post holder will also contribute to the preparation of written reports and research publications and present research findings at project meetings, scientific conferences and outreach/translation events. They will contribute to the smooth running of the group, including the effective use of resources, supervision of visitors to the laboratory and assisting with training others, encouraging scientific excellence.

The ideal candidate:

Applicants will have an MSc or PhD in bioinformatics, computational biology or a related quantitative discipline, and experience working with large collections of next generation sequencing data. The candidate must value teamwork and collaboration, be able to work independently, and have excellent communication and interpersonal skills.

Additional information:

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a full time post until 30th September 2020.

We are committed to equal opportunities and welcome applications from all sectors of society. The Institute supports equality of opportunity within the workplace and expects all employees to share and display these values. To support our commitment, we have a range of family, faith and diversity friendly working arrangements to help all staff achieve excellence in their area of work.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.