Postdoctoral Scientist (Genomics)
Post Details
Job Title
Postdoctoral Scientist (Genomics)
Post Number
1003599
Closing Date
31 Jan 2019
Grade
SC6
Starting Salary
£31,250 - £38,100
Hours per week
37
Project Title
Analysis of the wheat pangenome and pantranscriptome
Months Duration
36
Interview Date
11 Feb 2019

Job Description

Main Purpose of the Job

Join a cross institutional BBSRC programme Designing Future Wheat (DFW) aiming to ensure a robust wheat crop for the future to support a growing population. The candidate will have the opportunity to work on projects across Designing Future Wheat. Using large data sets to address fundamental crop science questions. They will also collaborate with the international 10 Plus Wheat Genomes Project. The focus will be on UK elite wheat cultivars but will also utilise the unique set of international wheat genomes assembled and annotated within the 10 Plus Wheat Genome Project. Under the supervision of Anthony Hall and David Swarbreck, the candidate will be involved in using these huge unique datasets generated in DFW and the 10 Plus Wheat Genome Project to uncover how modern wheat breeding approaches have shaped the genomes of elite cultivars, cultivars design for different global mega-environments. They will analyse transcriptome dataset from across developmental stages for each of the cultivars allowing construction of complex regulatory networks and how these networks vary in structure across these cultivars. This will allow for the first time a systems approach to understand how network components have been selected and the effect of this selection on whole regulatory systems.

In addition to this large collaborative project, the candidate will have the opportunity to work with the assembly group, assisting Mark McMullan and Neil Hall with the assembly of fungal genomes using established methods developed at the Earlham Institute. These genomes would be used to ask fundamental questions around the evolution of wheat pathogens.

We are looking for a bioinformatician or computational biologist. The candidate will work independently and with other group members and national and international collaborators to develop computational tools and pipelines to analyse these large datasets.

Key Relationships

Mechanism of management: Day to day workload management with Anthony Hall. Research planning and monitoring will be achieved via monthly meeting including Mark McMullan, Ryan Joynson, Neil Hall, David Swarbreck and Anthony Hall.

Main Activities & Responsibilities

Percentage
Develop computational tools and pipelines to analyse wheat genome assemblies and transcriptomic data within and between elite cultivars, tools essential for future pangenome analysis projects
30
Evaluate methods and approaches for analysis regulatory network and identify components within networks under selection and implications on whole systems
30
Use existing tools and pipelines to assemble wheat fungal genomes. Use these to identify whether introgression or gene flow is involved in adaptation of Take-all
30
Write and edit reports for both internal use and publication
5
As agreed with line manager, any other duties commensurate with the nature of the post
5

Person Profile

Education & Qualifications

Requirement
Importance
Educated to Masters level or possess equivalent experience in molecular or computational biology
Essential
PhD in a relevant subject
Desirable

Specialist Knowledge & Skills

Requirement
Importance
Demonstrable understanding of bioinformatics tools
Essential
Good knowledge of molecular biology and computational methods for sequence and transcriptome analysis
Essential
Knowledge of good practice principles of pipeline development
Desirable
Genome Function
Desirable
Wheat genomics
Desirable

Relevant Experience

Requirement
Importance
Proven track record in the use of scripting programming languages (e.g. Perl, Python)
Essential
Experience in bioinformatics related to sequence analyses
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
Ability to communicate clearly with EI staff at all levels
Essential

Additional Requirements

Requirement
Importance
Attention to detail
Essential
Promotes equality and values diversity
Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Ability to maintain confidentiality and security of information where appropriate
Essential
Willingness to work outside standard working hours when required
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

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

DFW post will be joint between David Swarbreck, Anthony Hall and Neil Hall. Primary line management will come from Anthony Hall.

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

David Swarbreck’s group also played a leading role in annotation of the wheat genome and the 10+ wheat genomes. David Swarbreck leads the Core Bioinformatics Group, provides high quality computational analyses of a range of sequence data types and develops software and analysis pipelines that support the Institute’s Core Strategic Programmes and National Capability in Genomics and Single Cell Analysis (NCGS). The National Capability provides access to state of the art genomics technologies for research groups throughout t

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Postdoctoral Scientist (Genomics)

Applications are invited for a Postdoctoral Scientist (Genomics) to join the Laboratory of Anthony Hall in the Designing Future Wheat Programme at the Earlham Institute, based in Norwich, UK.

Background:

The post holder will join the Designing Future Wheat Programme, which is a cross institutional BBSRC venture. They will work closely with Anthony Hall, Neil Hall and David Swarbreck Groups.

The Hall Group 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.

The Swarbreck Group explores the complexity of gene expression, mainly in plants (such as Ash, Rubber, Willow, Barley and Wheat), but also in other eukaryotic organisms

The role:

The Earlham Institute (EI) is looking for a highly motivated Bioinformatician or Computational Biologist to join an exciting project in conjunction with the Hall and Swarbreck groups to analyse the wheat pangenome and pantranscriptome. 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.

The successful candidate 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, wheat scientists and breeders. The candidate will work closely with Design Future Wheat, 10 Plus Wheat Genome Project, Ensembl Plants and other collaborative wheat projects.

We are looking for a candidate driven to make a change in providing solutions to agricultural problems through coding and implementation of new software. In particular, this role will be responsible for the design, implementation and deployment of software pipelines for the integration of the genomic and genetic data available for wheat and related species to build a toolbox for functional analyses of wheat genome.

The ideal candidate:

To be considered for this position, candidates need to be educated to MSc level or possess equivalent experience of working in molecular or computational biology. A PhD is desirable but not essential. 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. Perl, Python, R). 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 £31,250 to £38,100 per annum depending on qualifications and experience. This post is for a contract of 36 months.

Interviews will be held in February 2019.

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