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Heidelberg, Germany

Staff Category:

Staff Member

Contract Duration:

3 years


6, 7 or 8, depending on experience and qualifications

Closing Date:

21 May 2017

Reference Number:



Job Description

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

EMBL's Genomics Core Facility (GeneCore) is looking for a Senior Bioinformatician to lead its Bioinformatics section. The successful candidate will assist and monitor the production, as well as lead the analysis, management and integration of massively parallel sequencing data generated from a range of sequencing instruments and methodologies (Illumina, Pacific Biosciences, 10x Genomics, Oxford Nanopore, single cell/single DNA strand sequencing [Strand-seq]) and library preparation protocols (DNA-Seq, RNA-Seq, ChIP-seq, Repli-Seq, HiC, and ATAC-Seq). The main task will be the design, implementation and maintenance of complete computational workflows and pipelines required for efficient and timely delivery of large-scale sequencing data including their comprehensive informatics processing and biological analysis.
Developing data analysis strategies for re-sequencing data sets relevant to genomic variation analyses using state-of-the-art concepts from computational biology, algorithmic bioinformatics and biostatistics is expected, and prior experience in one of these areas is thus of particular interest. Familiarity with high-performance computing environments, job scheduling, load balancing and parallel computing is considered as a valuable asset, as is the ability to develop multi-threaded applications that take advantage of modern computing systems. In addition, 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 and the successful candidate is expected to set-up and implement required algorithms and services to support these groups in the use of massively parallel sequencing data relevant to genomics. 
Among other tasks, the successful candidate will have responsibility for:
  • developing computation workflows to monitor the production and perform analyses of DNA-Seq, RNA-Seq, ChIP-Seq and ATAC-Seq data sets
  • implement core pipelines for basecalling, de-multiplexing, data quality control, sequence alignment, variant calling, quantifying gene expression and peak calling
  • design and implement the above applications as software packages that are maintained and disseminated to the research community using widely used code repositories (GitHub, SourceForge, BitBucket), package managers (Bioconda, EasyBuild) and/or Docker application containers
  • analyse massively-parallel sequencing data sets (including applications in the context of genetic variation and genome regulation research) to support other EMBL researchers
  • design web services for common molecular biology tasks and maintain the Genomics Core Facility pipeline management dashboard
  • teach and co-organize scientific courses to educate junior researches at EMBL and elsewhere in crucial applications of massively parallel sequencing data relevant to genomics
Qualifications and Experience

Essential qualifications include:

  • a PhD in computational biology or a related field with a strong focus on methods development and algorithmic bioinformatics
  • advanced programming skills, ideally including R, Python, Unix/Bash, C or C++ and practical experience with HTSlib
  • strong interest and experience in biological data analysis and scientific software development
  • experience in setting up bioinformatics services and computational workflows for large-scale DNA and RNA sequencing data sets using software pipelines in an HPC or cloud environment
  • experience in software development, maintenance and user support
  • the desire to support and assist biological researchers in their bioinformatics analysis
  • the ability to integrate tools into pipelines and workflows and optimize their interoperability, efficiency, usability and portability
  • knowledge of web software development (HTML, css, JavaScript) and web server administration
The successful applicant needs to have strong problem-solving skills, a profound background in scientific software development and analysis workflow management. She/he will be well organized, open-minded, able to work on different projects in parallel, and have a user-orientated spirit. Ability to generate synergies in genomics technology evaluation, supporting EMBL research groups by contributing to development of computational methods for analysis of genomics data will be seen as highly positive. The candidate should be able to work independently and also interact well, and provide supervisory roles to other bioinformaticians within the EMBL Genomics Core facility team environment. A working knowledge of English is required.
Application Instructions
Please apply online through
Additional Information
Interviews are planned to take place at the beginning of June 2017 
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.


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