Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:3 years
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:4 March 2018
Reference Number:EBI_01139

Job Description

Would you like to work on improving our understanding and representation of human genes? Accurate identification and description of the genes in the human genome provides the foundation for high quality analysis of data informing both genome biology and clinical genomics. There are two widely used methods of annotating protein-coding genes: one led by EMBL-EBI (GENCODE) and the other by NCBI (RefSeq). We are recruiting a bioinformatician to provide bioinformatics support for work on the CREST project, which aims to review the GENCODE and RefSeq annotation at clinically relevant loci in order to build a consensus subset of full length transcripts.
Tasks for this position will include work to:

  • optimise and improve our transcript picking pipeline, developing extensions to the algorithm to reduce the exclusion of functionally important transcripts;
  • identify and reduce differences between RefSeq and GENCODE transcripts to achieve convergence;
  • develop methods to integrate external datasets to facilitate greater automation of annotation of transcript termini;
  • define guidelines and documentation to help interpret the data;
  • create a bulk UTR update script to extend or trim transcripts to the specified position;
  • develop an iterative comparison of GENCODE and RefSeq annotation; identify cases of agreement and disagreement with the aim of resolving these as much as possible; identify and prioritise cases for manual checking and case-by-case discussion with RefSeq;
  • liaise with manual annotators and automated-evidence-based gene annotators, as well as internal and external collaborators.

The bioinformatician will work within a team at the EMBL-EBI and in collaboration with scientists at the National Center for Biotechnology Information (NCBI). The Vertebrate Genomics team at the EMBL-EBI is one of the world’s leading groups for integration, annotation, analysis and presentation of genomic variation data. This environment provides access to an international collection of projects at the cutting edge of human genomic research.

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

Qualifications and Experience

Applicants should have a first degree, or higher qualification, in genetics or biological sciences and several years of relevant work experience. A PhD would be an advantage. An in depth understanding of genomics and annotation is essential. Experience working with Perl, relational databases (SQL) and genomic datasets is highly desirable. The ideal candidate must be comfortable working in a UNIX/Linux environment and have experience with data tracking systems. Experience working with Ensembl would also be an advantage.

We are looking for highly motivated candidates who possess scientific curiosity and initiative. Skill in delivering a high-quality product with excellent attention to detail and within fixed deadlines is essential. Excellent verbal and written communication, and interpersonal skills are a prerequsite.


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.

Application Instructions

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

Additional Information

Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

This position is limited to the project duration specified.

Applications will close at 23:00 GMT on the date listed above.