Bioinformatician - Gene Structure Annotation
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years (renewable to a maximum of 9 years)
Grading: Grade 5 or 6 (starts at £2,738 or £3,063 per month after tax) + other paid benefits
Closing Date: 11 May 2021
Reference Number: EBI01822
Working as part of Ensembl Genebuild, you will join a team Bioinformaticians and Developers who are experts in gene structure annotation.  As a Bioinformatician in this team you will have the opportunity to run our large-scale annotation system producing high quality gene annotation, while collaborating with both internal and external teams to advance the field of genome annotation.

Our team has domain area expertise in software development, large-scale compute, big data, pipeline workflows and automation. We collaborate with consortia and communities from all over the world to annotate new genomes. Current and future projects for the team include: scaling up gene annotation pipelines; containerising these pipelines and deploying them to the cloud; implementing machine learning techniques to improve gene structure annotation; working with long-read (PacBio IsoSeq Nanopore) transcriptomic data with a view to extending existing annotations and identify new splice variants. 

The Ensembl project works at the cutting edge of gene structure annotation, primarily in vertebrate genomes, but increasingly in genomes of more diverse eukaryotic organisms. We design code and pipelines to annotate genomes with genes and other genomic features in diverse species.  One of our primary goals is to create scalable pipelines and processes that can be used to accurately annotate genomes for all 70,000 known species of eukaryotic organisms in Britain and Ireland.

Your role

Reporting to the Genebuild Project Leader, you will play a key role analysing the gene sets generated by the pipeline and collecting feedback from the community in order to improve the quality of the gene sets we create.

More specifically, you will:
  • Produce high-quality, evidence-based gene sets for various species including protein-coding genes, noncoding RNA genes and pseudogenes
  • Collaborate with international partners on genome projects
  • Work in a release-based environment and coordinate with other teams
  • Participate in training users in how to annotate assemblies
  • Work with state-of-the-art primary data to help improve gene annotation
  • Contribute to the Ensembl codebase

You have

You should hold an MSc, PhD or equivalent experience in Computer Science, Bioinformatics, Genetics or a related field.

You will be to write, understand and maintain complex code. You will also have knowledge and experience in the following areas:
  • Genome annotation
  • Methods for DNA/RNA sequencing and sequence alignment
  • The biology of gene expression
  • Proficiency with coding in at least one modern programming language
  • Relational databases
This role will require you to have good communication and interpersonal skills, and be a self-starter who can manage their own time to meet the needs of several projects. The key attributes sought are the ability to work in a team, excellent attention to detail, solid problem-solving skills, and the desire to learn and improve. Furthermore, you should demonstrate your ability to communicate both biological and computational ideas (orally and in writing), time management to deadlines, and a desire to work in an international environment.

You might also have

  • Previous experience of processing large biological data sets in a production environment would be advantageous, including an understanding of compute clusters, pipeline workflows, software design and automation.
  • Evidence of working in a dynamic, team-based environment or contributing to a large, shared code-base is desirable.

Why join us


Do something meaningful

At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.  Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.  Enjoy lots of benefits:
  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible working arrangements
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Generous time off: 30 days annual leave per year, in addition to eight bank holidays
  • Relocation package including installation grant (if required
  • Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
  • Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.
For more details please see our employee benefits page.

What else you need to know

  • Contract duration: This position is a 3 year contract, renewable to a maximum of 9 years. 
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants
  • Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities. 
  • Job location: This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so, if you are currently based abroad. Read more about how we are recruiting during the pandemic
  • How to apply: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date: 11th May 2021.