Main Purpose of the Job

You will be contributing to EI's core research program on non-model crop species by developing computational methods and analyses. Your focus will be on two projects in the group:

1. Chromosomal rearrangements and large structural variations are increasingly being recognized as we transition from single to multiple assembled reference genomes and from short-read to long-read sequencing technology. This genetic diversity is expected to play a crucial role in the development of key adaptive traits in the future. However, identifying these events and their functional impacts is challenging.
You will be working on tuning new tools and methods developed in the Decoding Biodiversity research program to understand the underlying genomic processes and the extent of this variation in two allopolyploid species, banana, and Miscanthus. Your tasks will include developing long-read genome assemblies, annotating their genomes, and using them to build pangenomes. Additionally, you will be exploring pangenome graphs to identify introgressions and CNVs and linking this information to phenotype information using association mapping.

2. We are developing approaches to efficiently identify somatic and epigenetic variation and characterize its functional consequences in clonal sets of crop species, with a focus on banana. This work will enable future crop improvements by developing new ways to remove deleterious variants and incorporate beneficial genetic diversity in clonal lines, which will improve resilience and productivity in clonally propagated crops. You will be using Oxford Nanopore Technologies datasets to characterise DNA methylation and structural variants, as well as reconstructing pangenome graphs for the discovery and functional characterisation of structural variants. We are particularly interested in fruit-related and fungal resistance phenotypes.

The successful candidate will have direct access to world-class computing and sequencing facilities and will 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. Additionally, the candidate will 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 using novel bioinformatic analysis and cutting-edge datasets.

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 research papers, report to funders.

10

As agreed with line manager, any other duties commensurate with the nature of the role

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)

Essential

Basic programming (e.g. python, R)

Essential

Genomic approaches for studying crop evolution

Essential

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

Computaitonal analysis of diversity, structural variation at the genome or population level

Desirable

Pangenome analysis, variation graphs

Desirable

Epigenetic computational analysis

Desirable

Management and Leadership

Requirement

Importance

Leading research projects to successful conclusion, as evidence in publications and repositories

Essential

Interpersonal & Communication Skills

Requirement

Importance

Good organisational skills

Essential

Excellent communication skills, both written and oral

Essential

Ability to communicate and work productively within a multidisciplinary team

Essential

Interacting with collaborators, representing the group and institute externally

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

Earlham Institute

About the Earlham Institute
The Earlham Institute is a hub of life science research, training, and innovation focused on understanding the natural world through the lens of genomics.

We are building a future where the biology of any organism can be understood by analysing its genome. Our mission is to decode the scale and complexity of living systems so we can understand, benefit from, and protect life on Earth.

The Earlham Institute is based on the Norwich Research Park and is one of eight institutes that receive strategic funding from the UKRI Biotechnology and Biological Science Research Council (BBSRC).

Our Science
Earlham Institute scientists specialise in developing and testing the latest tools and approaches needed to decode living systems and make predictions about biology.

We are home to state-of-the-art facilities and technology, creating a unique combination of expertise and infrastructure. We have dedicated laboratories for genome sequencing, single-cell analysis, engineering biology, and large-scale automation; as well as one of the largest supercomputing facilities for life science research in Europe. Our Advanced Training team also provides access to specialised scientific training to upskill the next generation of research and technical staff.

Our Culture
The Earlham Institute champions 'team science'. Our collegiate and innovative research environment comes with significant support, including a commitment to your professional development, research and administrative assistance, and opportunities to build collaborations with scientists and industry on the Norwich Research Park, across the UK, and internationally.

The Institute is also home to talented technical and operational staff, whose invaluable contributions enable our science to have the maximum impact. We aim to recognise, reward, and develop all staff and students so that every individual feels able to achieve their best with us.

We work hard to nurture an engaged and positive workplace, centred on core values that include openness, technical excellence, and collaboration. We attract staff from around the world who contribute to - and benefit from - an environment that enables them to deliver world-class science alongside a supportive and social community.

For more information about working at the Earlham Institute, please click here.

Further Information:

Our Vision and Mission

Our Strategy

Our Culture

Life at Earlham Institute

Department

Research Faculty

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.).

Living in Norfolk

• Visit Norfolk
• Schools in Norfolk
• Childcare in Norfolk

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:

You will contribute to EI's core research program on non-model crop species by developing computational methods and analyses. Your focus will be on two projects in the group:

1. Chromosomal rearrangements and large structural variations are increasingly recognized as we transition from single to multiple assembled reference genomes and from short-read to long-read sequencing technology. This genetic diversity is expected to play a crucial role in developing vital adaptive traits in the future. However, identifying these events and their functional impacts is challenging.
You will be working on tuning new tools and methods developed in the Decoding Biodiversity research program to understand the underlying genomic processes and the extent of this variation in two allopolyploid species, banana and Miscanthus. Your tasks will include developing long-read genome assemblies, annotating their genomes, and using them to build pangenomes. Additionally, you will be exploring pangenome graphs to identify introgressions and CNVs and linking this information to phenotype information using association mapping.

2. We are developing approaches to efficiently identify somatic and epigenetic variation and characterize its functional consequences in clonal sets of crop species, with a focus on bananas. This work will enable future crop improvements by developing new ways to remove deleterious variants and incorporate beneficial genetic diversity in clonal lines, which will improve resilience and productivity in clonally propagated crops.
You will use Oxford Nanopore Technologies datasets to characterise DNA methylation and structural variants and reconstruct pangenome graphs to discover and functionally characterise structural variants. We are particularly interested in fruit-related and fungal resistance phenotypes.

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 genome 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 £36,720 to £39,750 per annum depending on qualifications and experience.  This is a full-time post with an end date of 31 March 2026.

This role meets the criteria for a visa application, and we encourage all qualified candidates to apply.  Please contact the Human Resources Team if you have any questions regarding your application or visa options.

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 24 November 2024.