Bioinformatician – Proteomics data pipelines

We are seeking an enthusiastic Bioinformatician to join the Proteomics Team at the European Bioinformatics Institute (EMBL-EBI)

The team is responsible of the maintenance and further development of the PRIDE (PRoteomics IDEntifications) database and related tools and resources. PRIDE is a world-leading international proteomics database, a founding member of the ProteomeXchange Consortium that is capturing large-scale mass spectrometry (MS)-based proteomics data from the scientific community and currently managing hundreds of TBs of data. In addition, the team aims to re-use and integrate proteomics data in other EMBL-EBI added-value resources such as UniProt, Ensembl and Expression Atlas.

The position is a fantastic opportunity to gain hands-on experience at working on a project with major scientific impact in a world-leading bioinformatics institute.
Your role
The post holder will be working in the context of a BBSRC/NSF grant called “PTMExchange” which aims to:

(i) analyse public proteomics datasets with the objective of disseminating high-quality PTM (post-translational modification) data from PRIDE into UniProt

(ii) develop all the related infrastructure, including further developments in PRIDE, ProteomeXchange and the related data pipelines.

The post holder is also expected to collaborate closely with the other partners in the grant and potentially other external stakeholders. The post holder may also have to contribute to other tasks related to the maintenance and development of the services and tools offered by the team.


Further develop and benchmark open proteomics data analysis pipelines, envisioned for the analysis of PTM data.
Develop infrastructure for the PTMExchange project, including further developments in PRIDE and ProteomeXchange.
Analyse public proteomics datasets.
Collaborate with the EMBL-EBI UniProt team to disseminate and integrate proteomics data from PRIDE into UniProt.
Collaborate with the other partners in the grant and other external collaborators.
Contribute to reports and publications.
Participate in meetings with internal and external collaborators.
You have
You must have a degree in computer science or bioinformatics and be able to demonstrate a minimum of 3 years’ experience in software development and/or bioinformatics data analysis, ideally with some knowledge of cloud technologies.

You must be able to demonstrate at least 3 years’ working experience in a suitable programming language such as Java, C++ or Python. Working experience in bioinformatics and computational proteomics is essential. In addition:
Good understanding of code versioning tools, such as Git.
Good understanding of technologies such as JSON, XML and relational databases.
Applicants will work in a highly international, team-oriented environment and collaborate closely with external partners. Excellent communication skills are essential. The ability to work independently, under time pressure, and the dedication to communicate openly are necessary skills.

You might also have
Experience in analysis of proteomics data using software tools such as Mascot, MSGF+ or MaxQuant.

Why join us
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 over 20 member states and associate member states. 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.

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. For more information about pay and benefits click here.

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.

Many members of the team have families and dependants and we value the importance of a good work-life balance. EMBL-EBI makes progress every year towards building a more diverse workforce, making it an ideal place for smart, curious people across cultures, genders, ethnicities, and lifestyles.

Application Instructions: 

To view a copy of the full job description please visit our website.

To apply please submit a covering letter and CV through our online system.

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website.

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.

Application Closing Date: 
20 January