Postdoctoral Research Scientist (Genomics)
Post Details
Job Title
Postdoctoral Research Scientist (Genomics)
Post Number
1004309
Closing Date
23 Aug 2022
Grade
SC6
Starting Salary
£33,050 - £40,750
Hours per week
37
Project Title
Analysis of wheat fungal pathogen genomes
Expected/Ideal Start Date
01 Oct 2022
Months Duration
36
Interview Date
02 Sep 2022

Job Description

Main Purpose of the Job

The Postdoctoral Research Scientist will join Designing Future Wheat; a cross-institutional BBSRC programme aiming to ensure the delivery of robust wheat crops to support a growing population. Under the supervision of Anthony Hall and Mark McMullan, the candidate will use large genomics-based data sets to address fundamental questions in the evolution of plant pathogens to advance crop science. The project is a collaboration between The Earlham Institute and Rothamsted Research on the Take-all evolution, resistance, and biocontrol with Kim Hammond Kosack. The project will use state-of-the-art approaches for pan- and whole genome comparisons of 20 fungal genomes along with population genetics techniques to investigate genetic variation across hundreds of re-sequenced genomes. The analysis of these genomes is initially to address fundamental questions on the evolution of wheat pathogens and questions on their evolution using wild and agricultural representatives with an aim to develop analysis pipelines for the community for species agnostic analyses.

Key Relationships

Mechanism of management: Day-to-day workload management Mark McMullan. Research planning and monitoring will be achieved via monthly meetings including Anthony Hall and Kim Hammond Kosack (RRes)

Main Activities & Responsibilities

Percentage
Development of pan-genomics and population genetics pipelines as such that they can be rolled out to the wider DSW community
40
Comparative genomics analysis of Take-all and related pathogens to address questions on introgression and adaptation to wheat and treatments
20
Population genomics analysis of global Take-all diversity addressing questions on genetic diversity and gene flow between virulence populations
20
As agreed with the line manager, any other duties commensurate with the nature of the post. Including CPD
10
To facilitate communication with and data integration to international public repositories
5
Write and edit reports for both internal use and publication
5

Person Profile

Education & Qualifications

Requirement
Importance
PhD in a relevant subject or possess equivalent experience of working in molecular or computational biology
Essential

Specialist Knowledge & Skills

Requirement
Importance
Demonstrable understanding of bioinformatics tools
Essential
Good knowledge of molecular biology and computational methods for sequence analysis
Essential
Interest in pan-and/or population genomics
Essential
Knowledge of good practice principles of pipeline development
Desirable
Genome Function
Desirable
Fungal Genomics
Desirable

Relevant Experience

Requirement
Importance
Proven track record in the use of scripting programming languages (e.g. Python, R, Bash)
Essential
Experience in bioinformatics related to sequence analyses
Essential
Experience of working with large datasets
Essential
Experience working in HPC environment
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Excellent communication skills, both written and oral, including the ability to present complex information with clarity
Essential
Good interpersonal skills, with the ability to work as part of a team
Essential
To be able to communicate clearly with EI staff at all levels
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skill
Essential
Excellent time management and organisational skills
Essential
Promotes and strives for continuous improvement
Essential

Additional Requirements

Requirement
Importance
Attention to detail
Essential
Promotes equality and values diversity
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
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
Essential
Willingness to work outside standard working hours when required
Essential

Who We Are

Earlham Institute

Earlham Institute is a vibrant, contemporary research institute and registered charity, working in an area of rapid technological development and innovation.

Earlham Institute is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience. The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The research park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which Earlham Institute contributes strengths in genomics and bioinformatics. Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

Earlham Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. This has been boosted recently by an e-Infrastructure grant to expand the data storage capacity to a multi-petabyte unit, deploying a high performance cluster and large-memory server enabling the allocation of processes requiring several terabytes of computing memory.

Earlham Institute’s state of the art DNA sequencing facility operates multiple complementary technologies for data generation that provide the foundation for analyses furthering our fundamental understanding of genomes and how they function. We aim to be at the forefront of technological advances and are developing and implementing technologies to generate and analyse new types of data. We also develop novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational bioscience. Earlham Institute has one fully owned subsidiary, Genome Enterprise Ltd (GEL) via which it offers genomic and bioinformatics services on a trading basis and works with commercial providers on a partnership basis. Earlham Institute also receives specific funding to enable knowledge exchange programmes which are supported across the institute teams.

Department

Organisms and Ecosystems

Group Details

Mark McMullan’s group is based within Neil Hall’s lab, where members use comparative and evolutionary genomics in pathogens to understand the molecular basis of important phenotypes such as virulence and host specificity. Mark’s team focus on host and pathogen genetic diversity across wild-agricultural boundaries with the aim of determining genes important for pathogen success on crops and the wild host response. The broader implication of this work is in understanding the processes that underpin invasion and rapid pathogen adaptation to new crop varieties/environments.

The Anthony Hall lab strives to develop next-generation genetic approaches to bridge the gap between model (Arabidopsis) and crop species (primarily wheat) with the aim of understanding the genes/networks and genetic variance that underpin key agricultural traits.

To meet this goal we currently have a number of projects investigating the genes and networks underpinning yield robustness under drought and heat stress (India and UK) and enhancing photosynthesis (Mexico, Australia and the UK). We also have projects on the wheat epigenome characterising the epigenome in bread wheat, the variation of the epigenome across a global diversity panel and the role of the epigenome during genome shock (Germany, USA and UK).

Living in Norfolk

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Postdoctoral Research Scientist (Genomics)

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Prof Anthony Hall in the Organism and Ecosystems Programme at the Earlham Institute, based in Norwich, UK.

Background:

The Postdoctoral Research Scientist will join Designing Future Wheat; a cross-institutional BBSRC programme aiming to ensure the delivery of robust wheat crops to support a growing population. Under the supervision of Anthony Hall and Mark McMullan, the candidate will use large genomics-based data sets to address fundamental questions in the evolution of plant pathogens to advance crop science.

The project is a collaboration between the Earlham Institute and Rothamsted Research on Take-all fungus evolution, resistance, and biocontrol with Kim Hammond Kosack. The project will use state-of-the-art approaches for pan- and whole genome comparisons of 20 fungal genomes along with population genetics techniques to investigate genetic variation across hundreds of re-sequenced genomes. The analysis of these genomes is initially to address fundamental questions on the evolution of wheat pathogens and questions on their evolution using wild and agricultural representatives with an aim to develop analysis pipelines for the community for species agnostic analyses.

The role:

The Postdoctoral Research Scientist will join an exciting project in conjunction with the Hall group to analyse fungal wheat pathogen genomes. We are looking for a driven candidate to make a change in providing solutions to agricultural problems through coding and implementation of new software.

This role will be responsible for the design, implementation, and deployment of software pipelines for the integration of the fungal genomic and genetic data available for wheat and related species to build a toolbox for population analyses for fungal and wheat genomes.

The candidate will work independently, with other group members and national and international collaborators to develop computational tools and pipelines to analyse these large datasets. They will play an active part in EI’s collaborative wheat genomics efforts aimed at advancing wheat research through data integration and enhancing communication between bioinformaticians, scientists and breeders. The candidate will work closely with the Grassroots Genomics, 10 plus wheat genome project, Ensembl Plants and other collaborative wheat projects.

The ideal candidate:

The successful candidate will be educated to PhD level or possess equivalent experience of working in molecular or computational biology, with an interest in pan-and/or population genomics. Candidates will need to communicate a deep understanding of bioinformatics tools and molecular biology/computational methods. They will need to show knowledge of good practice principles for software engineering and have a proven track record in the use of programming languages (e.g., Python, R, Bash). Good communication skills are essential as is the ability to work well as part of a team. 

Additional information:

Salary on appointment will be within the range £33,050 to £40,750 per annum depending on qualifications and experience.  This is a full-time post for a contract of 36 months.

Interviews will be held on 2nd September 2022.

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

The closing date for applications will be 23rd August 2022.