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:5 August 2018
Reference Number:EBI_01252

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 a project to review the GENCODE and RefSeq annotation at clinically relevant loci in order to build a consensus subset of full length transcripts (Crest Project).

Tasks for this position will include work to:

  • optimise and improve our transcript picking pipeline, developing extensions to the algorithm to increase our ability to identify functionally important transcripts;
  • identify and reduce differences between RefSeq and GENCODE transcripts to achieve convergence;
  • develop an iterative comparison of GENCODE and RefSeq annotation; identify cases of agreement and disagreement with the aim of resolving these computationally; identify and prioritise cases for manual checking and case-by-case discussion with RefSeq;
  • develop methods to integrate external datasets to facilitate greater automation of annotation of transcripts and transcript termini;
  • define guidelines and documentation to help interpret the data;
  • 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.

EMBL-EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry. We have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.

Qualifications and Experience

You should hold an MSc, PhD or equivalent experience in Computer Science, Bioinformatics, Genetics or related fields and be able to write, understand and maintain complex code. You will also have domain experience of eukaryotic genome annotation, the biology of gene expression, and sequence alignment.

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 as are problem solving skills, and the desire to learn and improve.

It is essential that you have proficiency in object-oriented programming and developing software in a primarily Unix-based environment. Familiarity with compute clusters and development tools such as Git would be an advantage.


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.