Job Location
Wellcome Trust Genome Campus,
Hinxton near Cambridge
CB10 1SD
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 bioinformatician to join the team and contribute to the annotation of regulatory elements across the genome and across cell types.

Ensembl is one of the most successful large-scale bioinformatics projects and one of the leading providers of genome annotation.  We import massive amounts of data from various archives (genome sequences, variation archives etc.) and use them to create syntheses (gene annotation, whole-genome alignments, gene trees, regulatory elements etc.).  Our services are freely open to all scientists around the world and serve a range of uses, from basic science to biomedical research.  

Ensembl Regulation is specialised in epigenomic and cis-regulatory datasets, which are used to define the Ensembl Regulatory Build. This annotation highlights the regulatory regions of the genome that control when genes are expressed and in which tissues. These elements have been shown to play a significant role in explaining the mechanisms underlying evolution as well as disease. You will work alongside the existing developers and:

  • Incorporate more public databases into our existing database, thus extending our coverage of cell types, tissues and species;
  • Implement new bioinformatics pipelines to process different assay types (e.g. DNA methylation and Hi-C);
  • Perform various downstream analyses (e.g. differential analysis of epigenetic signatures);
  • Support international and regional consortia (e.g. IHEC, FAANG) by processing their data and providing expertise;
  • Help out users of the Ensembl website and APIs and develop new features or tools to make their research more efficient;
  • Extend the current MySQL database schemas and the Perl API to handle new data types/results;

Ensembl Regulation (led by Myrto Kostadima) is a component of the Genome Analysis team (led by Daniel Zerbino), which is itself part of Ensembl (led by Paul Flicek).


Ideally you should hold an MSc or PhD, or have an equivalent qualification/professional experience in:

  • molecular biology;
  • bioinformatics;
  • computer science;
  • statistics or;
  • any related field;


Experience in epigenomics or biostatistics would be a plus.

You must have experience developing scientific software and analysing the results of large-scale experimental datasets. Experience in team software development and/or working in large scientific consortia, especially in the field of genomics, would be strongly preferred. 

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.

Extensive experience with computers and be fluent with the Unix command line and object-oriented Perl is required. Knowledge of MySQL or GIT would be highly advantageous. Experience with the Ensembl code base, the eHive pipeline system or C programming would also be a plus.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system.

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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