Job Location
United Kingdom

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 Ensembl Regulation team seeks an enthusiastic and talented bioinformatician to join the team and contribute to the annotation of regulatory elements across the genome in different cell types and species.

Ensembl is one of the most successful large-scale bioinformatics projects and one of the leading providers of genome annotation. As large-scale sequencing projects are producing genomic data on an unprecedented scale, the Ensembl team aggregates, re-processes and annotates large quantities of data from public archives and develops tools for data access. Ensembl Regulation specialises in epigenomic and cis-regulatory datasets, which are used to define the Ensembl Regulatory Build.

Your main responsibilities include:

  • Maintaining and running our production pipelines on a high performance computing cluster to download, process and integrate new data sets for the functional annotation of new cell types or species;
  • Developing new bioinformatic pipelines to process data sets from different epigenetic assays, such as DNA methylation and Hi-C;
  • Documenting the data and processes used for the annotation of regulatory elements;
  • Extending and maintaining the current MySQL database schemas and the Perl and REST API to handle new data types and results;
  • Collaborating with international and regional consortia (e.g. IHEC, FAANG) to process epigenomic data, provide support and expertise and develop new features or tools to make their research more efficient;
  • Teaching API courses, providing user support for the Ensembl website and APIs and presenting at conferences;
  • Liaising with members of the broader Ensembl team and other groups at EMBL-EBI.

 The Ensembl Regulation project is a component of the Genome Analysis team. You will join a team of four bioinformaticians who 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 regulation annotation pipelines and our data set import pipeline and developing methods of analysing new data including ATAC-seq and DNA methylation.

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: and

For further information about the Ensembl Regulatory Build please visit:


You must have at least two years’ experience developing bioinformatics analysis software, ideally analysing the results of large-scale genomic datasets. Experience in team software development and/or working in large scientific consortia, especially in the field of genomics, will be strongly preferred. Experience in epigenomics or biostatistics will be an advantage.

Competency in working in a UNIX/Linux environment is essential along with experience in programming, preferably using object-oriented Perl, and relational databases. Knowledge of Git or C or high performance cluster computing will be an advantage. Familiarity with the Ensembl code base and/or the eHive pipeline system will also be a plus.

You should be team oriented, ready to contribute to Ensembl's 40+ development team, and will be expected to work in step with the procedures and time constraints of the entire project. You must also be capable of autonomously leading your work in a thorough, timely and detail-oriented fashion, as you will have to keep track of many parallel tasks. Communication and presentation skills will be highly valued.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system which can be foud at

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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