- Job Title
- Postdoctoral Scientist (Bioinformatics)
- Post Number
- Closing Date
- 29 Jul 2019
- Starting Salary
- £31,250 - £38,100
- Hours per week
- Project Title
- A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES
- Expected/Ideal Start Date
- 31 Aug 2019
- Months Duration
Main Purpose of the Job
Join a break-through technology project entitled “A Pathway to the Exploitation of Epigenetic Variation in UK, US And International Breeding Programmes”. The project is a collaboration between Anthony Hall at the Earlham Institute and Eduard Akhunov at Kansas State University and is funded by the BBSRC and NSF. The project also includes close collaboration with US, UK and CIMMYT wheat breeders, IBM and LGC. While the initial contract is for 2 years we would hope to extend this, subject to further funding.
Epigenetic modification represents a potential source of variation that can be used in breeding programmes, contributing to trait variation. In wheat, we have evidence for widespread and stable epigenetic variation across global landraces. However, this represents a source of variation that has not to date impacted breeding programmes. In this project we aim to accelerate the translation of this basic knowledge, investigating variation in DNA methylation over a set of agronomically important genes across a panel of UK, US and CIMMYT derived wheat germplasm. This will uncover important information about epigenetic inheritance, stability and its role in adaptation. We will develop an enabling technology for breeders to track epi-alleles. We will use this technology to track epi-alleles that we identify in genes controlling agriculturally important traits and associate them with phenotypic changes.
Day to day workload management with Anthony Hall. Research planning and monitoring will be achieved via monthly meeting including Anthony Hall and Ryan Joynson
Main Activities & Responsibilities
- Bioinformatic analysis of DNA methylation across the UK, US and CIMMYT wheat lines
- Correlation with methylation changes and pedigree information
- Write reports, present data and write publications. Assist in obtaining follow on funding.
- Collaboration with wheat breeders and LGC
- Extract DNA from samples and monitor data production and QC
- As agreed with line manager, any other duties commensurate with the nature of the role
Education & Qualifications
- Educated to Masters level or possess equivalent experience in molecular or computational biology
- PhD in a relevant subject
Specialist Knowledge & Skills
- Demonstrate working knowledge of bioinformatic tools and pipelines
- Good working knowledge of the molecular biology and computational analysis of genome wide DNA methylation data
- Wheat or plant genomics
- Proven track record in scripting in a programming language
- Using an HPC and the command line
- Visualising genomic data
- Bioinformatics related to sequence analysis
Interpersonal & Communication Skills
- Excellent communication skills, both written and oral, including the ability to present complex information with clarity
- Good interpersonal skills, with the ability to work as part of a team
- Demonstrated ability to work independently, using initiative and applying problem solving skills
- Excellent time management and organisational skills
- Promotes and strives for continuous improvement
- Promotes equality and values diversity
- Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
- Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
- Willingness to work outside standard working hours when required
- Attention to detail
Who We Are
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.
Organisms and Ecosystems
The Hall Laboratory 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). Our current research project areas:
• Combining field phenotyping and next generation genetics to uncover markers, genes and biology underlying drought tolerance in wheat
• Using next generation genetic approaches to exploit phenotypic variation in photosynthetic efficiency to increase wheat yield
• INvestigating TRiticeae EPIgenomes for Domestication (INTREPID)
• Sequencing the genic portion of seeds of discovery advance pre- breeding germplasm to uncover the genetic variation
• Is circadian function an important agronomic trait?
• A computational cloud framework for the study of gene families
Postdoctoral Scientist (Bioinformatics)
Applications are invited for a Postdoctoral Scientist with genomics expertise to join the Laboratory of Professor Anthony Hall at the Earlham Institute, Norwich, UK.
The successful applicant will join a break-through technology project entitled “A Pathway to the Exploitation of Epigenetic Variation in UK, US and International Wheat Breeding Programmes”. The project is a collaboration between Anthony Hall at the Earlham Institute and Eduard Akhunov at Kansas State University and is funded by the BBSRC, USDA and NSF. The project also includes close collaboration with US, UK and CIMMYT wheat breeders, IBM and LGC.
In this project we aim to enhance our knowledge of methylation variation in wheat landraces (Gardiner et al. Genome Research 2018) by investigating variation in DNA methylation over a set of agronomically important genes across a panel of UK, US and CIMMYT derived wheat germplasm. This will uncover important information about epigenetic inheritance, stability and its role in adaptation. We will develop an enabling technology for breeders to track epi-alleles. We will use this technology to track epi-alleles that we identify in genes controlling agriculturally important traits and associate them with phenotypic changes.
Working in an international team of researchers, the post holder will conduct bioinformatic analysis of genome wide DNA methylation across multiple wheat lines. They will correlate methylation state variation with pedigree, geophraphic and phenotypic information. In addition, they will extract DNA from samples and work with the Earlham Institute’s Genomic Pipelines team to optimise lab based DNA methylation sequencing protocols.
The post holder will write reports, present data and prepare results for publication. They will collaborate with wheat breeders and also assist in obtaining follow on funding.
The ideal candidate:
To be considered for this position, candidates need to be educated to MSc level or possess equivalent experience of working in computational or molecular biology. A PhD is desirable but not essential. Candidates will need to communicate a deep understanding of bioinformatics tools, utilizing high performance computing resources and basic molecular biology. They will need to show knowledge of running, producing and improving bioinformatics pipelines and have a proven track record in the use of programming languages (e.g. Perl, Python, R). Good communication skills are essential as is the ability to work well as part of a team.
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 for a period of 2 years, with potential for extension subject to further funding.
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 29 July 2019.