European Molecular Biology Laboratory (EMBL)

Contract Duration: 3 years

For more information about pay and benefits click here

Job Description
There are two predominant but independent methods of annotating protein-coding genes in the human genome: one set led by EMBL-EBI (GENCODE) and the other by NCBI (RefSeq). We are recruiting a bioinformatician to provide support for work on the CREST project, which aims to review the annotation at clinically relevant loci from both efforts 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. 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 significant relevant experience. A PhD would be an advantage.

An in depth understanding of genomics and annotation is essential. Experience working with Perl 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 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.

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South East England