Postdoctoral Research Scientist (Bioinformatics - Crop Diversity and Evolution)
Job Title: Postdoctoral Research Scientist (Bioinformatics - Crop Diversity and Evolution)
Post Number: 1004778
Closing Date: 24 Nov 2024
Grade: SC6
Starting Salary: £36,720-£39,750
Hours per week: 37
Project Title: Pangenomic and epigenetic analysis to study genome and population evolution in polyploid crops.
Expected/Ideal Start Date: 06 Jan 2025
Months Duration: 36
Job Description
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.
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.
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) - Essential
Basic programming (e.g. python, R) - Essential
Genomic approaches for studying crop evolution - Essential
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
Computational 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
Who We Are
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.
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.
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.
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