Ensembl Bioinformatician - Genebuild

Job Location
Wellcome Genome Campus
CB10 1SD
United Kingdom
Monthly salary starting at £2,507 after tax plus mobility and other allowances where applicable

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.
We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.
If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

Job Description

The Vertebrate Annotation team are looking to recruit a highly motivated bioinformatician to join the Ensembl Genebuild project at the European Bioinformatics Institute (EMBL-EBI).

Ensembl Genebuild produces gene annotation for vertebrate species, including the reference gene sets for human and mouse. We are one of the world’s leading groups for identifying the location, structure and tissue-specific expression of genes and their transcripts for large numbers of vertebrate species.

Your main responsibilities will involve running our large-scale annotation system to produce gene annotation. As part of Ensembl Genebuild, you will:

  • Run production pipelines on a large compute cluster to download, process and integrate data from various public sequence archives
  • Produce high-quality, evidence-based gene sets for vertebrate species including protein-coding genes, noncoding RNA genes and pseudogenes
  • Produce tissue-specific RNA-seq alignments and transcript models
  • Collate these data into appropriate databases and files for the Ensembl release cycle
  • Document the data and processes used in gene annotation
  • Contribute to the Ensembl code-base including the design and implementation of new annotation pipelines and software
  • Work collaboratively with other members of Ensembl on data production around the Ensembl release cycles
  • Communicate the team’s work internally and to researchers in the field, including user support

The Ensembl Genebuild project is a component of the Vertebrate Annotation team. As part of Ensembl Genebuild, you will join six bioinformaticians who are experts in gene annotation. We have domain area expertise in public archives, alignment methods, software development, large-scale compute, pipeline workflows and automation. Future projects for the team include: scaling up gene annotation pipelines, improving our annotation of noncoding genes, automating and enhancing our RNA-seq annotation pipeline, and developing methods of analysing new data including full-length transcriptomic reads.

This is a unique opportunity to contribute to Ensembl’s mission to analyse, store and disseminate genomic annotation. For further information about Ensembl, please visit: www.ensembl.org and www.github.com/Ensembl. For further information about Ensembl Genebuild, please visit: www.database.oxfordjournals.org.


Applicants should hold an MSc, PhD or equivalent experience in Computer Science, Bioinformatics, Genetics or related fields including evidence of their ability to write, understand and maintain complex code. The ideal candidate will also have domain experience of genome annotation, the biology of gene expression, current methods for DNA sequencing and sequence alignment.

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.

We are looking for a highly motivated candidate with good communication and interpersonal skills. The ideal candidate will be a self-starter who is team-oriented and 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, candidates should demonstrate their 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.

The post holder must be proficient in object-oriented programming, have experience in compute clusters and in developing software in a primarily Unix-based environment, and be familiar with development tools such as Git. Experience in developing computationally efficient solutions, working on a large but continually-evolving codebase, and familiarity with relational databases would be an advantage.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system  www.embl.org/jobs

About Our Organization

At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

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