Bioinformatician - Genomics Core Facility

The European Molecular Biology Laboratory (EMBL) is seeking a full-time bioinformatician as a computational biologist and Laboratory Information Management System (LIMS) administrator to join the Genomics Core Facility (GeneCore) team in its main laboratory in Heidelberg.

In this role, you will participate in next-generation sequencing (NGS) data analysis for projects carried out in collaboration with EMBL users as well as users from EMBL member states. You will work in a highly interdisciplinary environment connecting applications in the field of genomics and you will be responsible for the integrity and reliability of the LIMS operated at GeneCore as well as its interfaces to data management applications used at EMBL.

Your Role

• Monitor the data production and data processing pipelines;
• Analyze, manage and integrate NGS data generated from a wide range of sequencing technologies (Illumina, Pacific Biosciences, Element Biosciences, 10x Genomics, Oxford Nanopore Technologies) and library preparation protocols (DNA-Seq, RNA-Seq, ChIP-seq, (spatial) scRNA-Seq);
• Maintain and evolve GeneCore’s LIMS and data management applications;
• Develop computational workflows to analyze short- and long-read sequencing data sets;
• Implement core pipelines for basecalling, de-multiplexing, data quality control, sequence alignment, variant calling and single-cell analyses;
• Teach and co-organize scientific courses to educate researches at EMBL and elsewhere in critical NGS applications
  
  

Your main task will be the design and maintenance of complete computational workflows required for efficient and timely delivery of NGS data, as well as the development and management of GeneCore's LIMS to process (meta-)data and make it available via interfaces to data management applications at EMBL. Familiarity with high-performance computing environments, application programming interfaces (APIs) and multi-omics data processing is required and a general knowledge of open science data management principles and data infrastructure concepts is considered a plus.

You Have

• Ideally, a PhD in computational biology or a related field with a strong focus on bioinformatics and NGS data analysis
• Strong interest and experience in biological data analysis
• Solid programming skills in Bash, R and Python
• Experience with SQL, APIs, web software development (HTML, CSS, JavaScript) and web frameworks (Django, Flask or equivalent)
• Basic operating system administration knowledge
• Experience in (meta-)data management, data infrastructure and transfer technologies, database technologies, and data integration
• Desire to support and assist biological researchers in their bioinformatics analysis
• Ability to integrate tools into pipelines and workflows and optimize their interoperability, efficiency, usability and portability
• Desire to teach workshops and courses on (multi-) omics data analysis
  
  

As the successful candidate, you will be part of an international interdisciplinary core facility team and needs to be well organized, open-minded, able to work on different projects in parallel, and have a user-orientated spirit with strong problem-solving skills. The ability to create synergies in the assessment of genomics technologies and to support EMBL research groups by contributing to the development of computational methods for the analysis of genomic data is seen as highly positive. You should be able to work independently and also interact well with members of the EMBL Genomics Core facility team and beyond. A working knowledge of English is required. You will be involved in many ongoing cutting-edge research projects and you will collaborate with experts from the scientific community and thus, you have the possibility to acquire new state-of-the-art skills in computational biology.

You might also have

• Experience with cloud infrastructure and technologies (OpenStack, Kubernetes, S3)
• Build efficient, data-driven artificial intelligence systems
• Expertise in machine learning methods and biostatistics
  
  

Why join us

EMBL's Genomics Core Facility is embedded in an excellent ecosystem of outstanding computational and experimental research groups at EMBL, each of which seeks to extend their bioinformatics capabilities and infrastructure; the successful candidate is expected to actively interact and communicate in a highly collaborative manner with international teams. As GeneCore is providing the NGS services also to researchers from EMBL member states, that will include collaborations with them.

EMBL is curiosity-driven, community-oriented and international. As an inclusive, equal opportunity employer, we believe that diversity enables us to collaborate more effectively and be innovative in our approaches.

EMBL offers attractive conditions and benefits appropriate to an international research organisation with a very collegial and family-friendly working environment. Competitive salary and social security benefits, financial support for relocation, a relaxed culture, professional development, an on-site nursery, canteen and other staff facilities make EMBL a great place to work.

What Else You Need To Know

We are Europe’s research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1900 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Please note that appointments on fixed-term contracts can be renewed, depending on circumstances at the time of the review, up to a maximum of 9 years.

• Don’t meet every single requirement? We are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply nevertheless.
  
  

EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.