Postdoctoral Research Scientist (Bioinformatics - Crop Diversity and Evolution)
Post Details
Job Title
Postdoctoral Research Scientist (Bioinformatics - Crop Diversity and Evolution)
Post Number
1004294
Closing Date
16 Aug 2022
Grade
SC6
Starting Salary
£33,050 - £40,750
Hours per week
37
Project Title
Bioinformatic analysis of the effects of adaptation and selection on the genome and structure of crop populations
Expected/Ideal Start Date
01 Sep 2022
Months Duration
45

Job Description

Main Purpose of the Job

The work will focus on recently-generated NGS datasets, both using Illumina short-reads and Pacbio long-reads, on temperate and tropical forage species. Later work will involve contributing to EI's core research programme on other crop species using similar approaches. The applicant will have direct access to world-class computing and sequencing facilities, and build on the group's track record to deliver new research outputs.
The candidate will work independently, with other group members, and with national and international collaborators to advance the research and deliver impact. The candidate will also support the PI and group in duties appropriate at the appropriate level, such as outreach, student supervision, Institute committees, reporting and writing manuscripts.

Key Relationships

Reporting to Jose De Vega, and working closely with the staff and PhD students (x3) in the group, and MSc/BSc students. As well as with other plant genomics groups at EI, the Head of Plant Genomics, and other groups in the institute. Also interacting with external collaborators in IBERS, RBG Kew, CIAT, etc.

Main Activities & Responsibilities

Percentage
Analysing large NGS datasets of crop populations to explore genetic diversity, population structure, and trait-genotype associations.
40
Developing genome and pangenome references. Developing and testing analysis pipelines that leverage new pangenome references to investigate structural and gene variation, and their functional consequences.
40
Contribute delivering the core research programme of the group and institute. Support the students and visiting researchers in the group. Engage with external collaborators and stakeholders.
10
Disseminate results in conferences, write and lead resaerch papers, report to funders.
10
As agreed with line manager, any other duties commensurate with the nature of the role

Person Profile

Education & Qualifications

Requirement
Importance
PhD (or working towards completing a PhD) in genomics, genetics, bioinformatics or related field
Essential
PhD in plant genetics or genomics
Desirable

Specialist Knowledge & Skills

Requirement
Importance
Bioinformatic analysis of genomes
Essential
Plant or animal genetics and evolution
Essential
Working in an HPC (pipelines, scripting, linux)
Desirable
Basic programming (e.g. python, R)
Desirable
Basic understanding of crop breeding and improvement
Desirable

Relevant Experience

Requirement
Importance
Leading research projects to successful conclusion, track-record of research outputs as driving author
Essential
Evidence of writing and reporting scientific results
Essential
Computational analysis of next-gen sequencing or NGS datasets
Essential
Comparative genomics, association mapping, population analysis
Desirable
Diversity analysis, structural variation at the genome or population level
Desirable
Pangenome analysis, variation graphs
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Ability to communicate and work productively within a multidisciplinary team
Essential
Good organisational skills
Essential
Interacting with collaborators, representing the group and institute externally
Essential
Excellent communication skills, both written and oral
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skill
Essential
Excellent interpersonal skills, with the ability to work alone and as part of a team
Essential
innovative, contribute novel perspectives to projects
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
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
Willingness to travel occasionally to meet with collaborators and attend conferences overseas, representing the PI and institute as requested
Desirable

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

The De Vega's group analyses crop diversity panels and families using bioinformatic methods. Our goal is to understand better adaptation and tolerance in populations to incorporate novel diversity into the genetic background of elite varieties.
Our expertise is in bioinformatics, with a focus on population structure analysis, selection scanning, comparative genomics, association mapping, and transcriptomic gene expression analysis. We collaborate with gene banks, genetic researchers, and pre-breeding institutions from the UK and overseas. We also collaborate with agroindustry partners as part of our impact delivery.
Plants are adapted to a broad range of environmental pressures. This natural diversity provides a reservoir of adaptive and resistance genes that are useful in genetic research and crop improvement, but often unknown or uncharacterised. Cultivated plants are subjected to strong selective forces in agricultural settings, either unconscious selection or systematic breeding. We investigate the effects of this selection on genetic diversity (high LD, perturbed allele frequency patterns, strong population differentiation, etc.) and the functional consequences of these changes (loss of function, gene expression, copy-number variation, etc.).

Management and Leadership

Requirement
Importance
Leading research projects to successful conclusion
Essential

Living in Norfolk

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Postdoctoral Research Scientist (Bioinformatics - Crop Diversity and Evolution)

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Jose De Vega in the Organisms and Ecosystems Programme at the Earlham Institute, based in Norwich, UK.

Background:

The De Vega's group analyses crop diversity panels and families using bioinformatic methods. Our goal is to understand better adaptation and tolerance in populations to incorporate novel diversity into the genetic background of elite varieties. Our expertise is in bioinformatics, with a focus on population structure analysis, selection scanning, comparative genomics, association mapping, and transcriptomic gene expression analysis. We collaborate with gene banks, genetic researchers, and pre-breeding institutions from the UK and overseas. We also collaborate with agroindustry partners as part of our impact delivery.

The role:

To focus on recently-generated NGS datasets, both using Illumina short-reads and Pacbio long-reads, on temperate and tropical forage species.

Later work will involve contributing to Earlham Institute’s core research programme on other crop species using similar approaches. The applicant will have direct access to world-class computing and sequencing facilities, and build on the group's track record to deliver new research outputs. The candidate will work independently, with other group members, and with national and international collaborators to advance the research and deliver impact. The candidate will also support the PI and group in duties appropriate at the appropriate level, such as outreach, student supervision, Institute committees, reporting and writing manuscripts.

The ideal candidate:

The successful candidate will have a PhD (or working towards completion) in genomics, genetics, bioinformatics, or a related field. This post will require a highly motivated and experienced bioinformatician, with strong core scientific skills, demonstrated experience in plant or animal genetics and evolution, and evidence of leading research projects to a successful conclusion.

The position is fully computational and involves analysing crop populations using pan-genome references. Training will be provided in population structure analysis, selection scanning, comparative genomics, association mapping, and transcriptomic gene expression analysis. It is essential that the ideal candidate has initiative and a desire to learn, innovate, contribute, and add novel analysis perspectives to the projects, and to move out of their comfort zone.

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 45 months.

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 16th August 2022.