Plant Genomics and Variation Team Leader

Plant Genomics and Variation Team Leader

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

Are you ready to shape the future of crop genomics, invertebrate genomics and genetic variation resources at one of the world's leading bioinformatics institutes? We are seeking an internationally minded, community-focused Team Leader with expertise in genomics, particularly crop plants and their associated insect pests and vectors, to provide scientific leadership for Ensembl in the area of plants, invertebrates, and genomic variation, as well as the European Variation Archive (EVA).

Overview

Ensembl is one of the world's leading platforms for the exploration and analysis of genomic data, supporting millions of users across academia, healthcare and industry. The resource is undergoing a major transformation to support the unprecedented expansion in the number of reference genomes and the breadth and complexity of biological data across the tree of life. Our recently released website has been designed to operate at this scale, enabling intuitive exploration, visualisation and dissemination of increasingly rich genomic datasets. Within this portfolio, priority species include major and minor crop plants such as wheat, rice, barley and rye, together with economically important insect pests and vectors including aphids and whiteflies. You will lead the development of data resources, analytical tools and community engagement activities that empower researchers worldwide.

The European Variation Archive

The European Variation Archive is the global archive for genetic variation data from non-human species, serving diverse research communities spanning crop and livestock improvement, biodiversity, evolutionary biology and functional genomics. The EVA is evolving to accommodate the rapidly increasing scale, diversity and complexity of variation data generated through advances in sequencing technologies, pangenomics and population genomics. As part of this scientific area, you will also lead the development of tools and resources for the interpretation of genomic variation in all species, including the widely used Ensembl Variant Effect Predictor (VEP).

The Plant Genomics and Variation Team Leader will be based at EMBL-EBI and is an EMBL Faculty position, offering the opportunity to shape internationally recognised resources, influence scientific strategy, and work closely with a vibrant global research community.

Your role

You will lead a multidisciplinary team consisting of approximately 15 staff members, including bioinformaticians and software developers, to deliver the EVA resource and lead the crop, invertebrate and genetic variation aspects of the Ensembl project. You will work closely with other Team Leaders within Ensembl, and more broadly with leadership across EMBL-EBI and other EMBL sites, to deliver integrated systems and data flows between our EMBL key partners. You will be given the opportunity to collaborate with talented and driven teams working towards a shared vision of delivering the very best scientific resources.

Extensive engagement with external scientific collaborators, both academic and industrial, are a key part of this role. You will also engage with global standards organisations such as AgBioData and GA4GH to both feed into and adopt community standards.

As a member of EMBL Faculty, you will also contribute to developing and delivering EMBL's strategy.

In addition to the above, more specific responsibilities will include:

• Managing the team's budget and staff; communicating with the EMBL's HR and Grants offices;
• Participating in related projects across EMBL-EBI, collaborating closely with other Team Leaders and other staff at EMBL-EBI, in particular with other Team Leaders within the wider Ensembl project;
• Identifying appropriate funding opportunities and applying for external grants;
• Participating in large-scale international scientific consortia as well as more targeted external collaborations with members of the crop community;
• Presenting work in international meetings and preparing scientific publications.

This role reports to the Section Head for Genome Assembly and Annotation, Rob Finn.

You have

• A PhD degree in a relevant field (bioinformatics, life sciences, computing or statistics) or equivalent relevant experience;
• At least 6 years' experience working in the field of bioinformatics or genomics applied to plant science/breeding;
• Experience working and interacting with a genomics research community, ideally crops;
• A demonstrable track record working with genetic variation data;
• Experience working with big data (gigabyte to terabyte scale);
• In-depth knowledge at least two of the following: genome assembly, gene annotation, genetic variant annotation;
• Hands-on experience working with AI tools;
• Project management and staff management experience;
• Experience in budget management and the grant life cycle from pre- to post-award;
• Proven experience of scientific and technical writing including manuscripts and successful grants;
• Excellent communication skills and an ability to engage with stakeholders including domain experts, technical specialists and wider research and industry communities;
• Excellent interpersonal skills, with a collaborative mentality;
• A commitment to continual improvement of systems and processes and to supporting staff development;
• The ambition and drive to develop high-impact data services for the wider research community.

You may also have

• Experience with Ensembl, EVA and other EMBL-EBI resources;
• A track record in leading and delivering scientific projects;
• Experience of some of the following technologies: workflow managers, high-performance computing platforms, databases, and data mining;
• Experience in some of the following domains: software engineering, functional annotation, high throughput sequencing analysis, statistics;
• Experience of some of the following technologies: Python, GraphQL, MongoDB, PostgreSQL, DuckDB;
• Experience of developing and/or applying AI methods for genomic annotation;
• Participation in multi-institute collaborations;
• Participation in public-private scientific partnerships;
• Experience leading work packages for complex multi-partner grants and chairing international steering groups and committees on technical subjects.

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