PhD Position - Development of Methods and Workflows for Robust and Reproducible Mass Spectrometry Analysis and Multi-Omics Integration

Your Job:

• Development of automated workflows (Galaxy, CWL, or Nextflow) for QC (mzQC) and high-throughput analysis (identification, relative & absolute quantification) for lipidomics
  
• Implementation of provenance tracking within the workflow to enable reproducible data analysis, export to mzTab-M format
  
• Integration with EMBL-EBI BioStudies and other relevant repositories, such as MetaboLights (metabolomics) for simplified data storage and submission
  
• Collaboration on tool development for multi-omics data integration (genomics, transcriptomics, proteomics, metabolomics, lipidomics), statistical evaluation and visualization in the Lipidomics Informatics for Life Science network in the de.NBI / ELIXIR-DE network
  
• Participation in working groups of the HUPO-PSI MS standardization initiative, ELIXIR Metabolomics and Proteomics Community, Lipidomics Standards Initiative and participation in corresponding projects
  

Your Profile:

• Master’s degree in computer science, bio/-cheminformatics or natural sciences
  
• Strong programming skills (Python, R, Java, …) and interest to work in polyglot software environments
  
• Practical experience with machine learning and AI methods and an interest to learn, adapt and apply ML methods to challenging problems in mass spectrometry.
  
• Independent and cooperative working in an international, interdisciplinary team across institutes
  
• Excellent communication and organizational skills
  
• Excellent knowledge of the English language
  

Our Offer:

We work on the very latest issues that impact our society and are offering you the chance to actively help in shaping the change! We offer ideal conditions for you to complete your doctoral degree:

• Exciting, interdisciplinary, varied work in a highly topical subject area.
  
• Participation in project meetings and conferences.
  
• Opportunities for limited-time research stays abroad.
  
• Access to state-of-the-art HPC and ML facilities via the de.NBI Cloud and the Jülich Supercomputing Center.
  
• The possibility for participation in the Helmholtz Data Science Initiative and Helmholtz AI.
  
• Strong support and mentoring for building a future career in academia and/or industry.
  
• If the requirements are met, admission to the structured doctoral program within the framework of the Graduate School “Digital Infrastructure for the Life Sciences” at Bielefeld University, Faculty of Technology, will be sought.
  
• Optimal conditions for a good work-life balance and a family-conscious company policy.
  
• The possibility to work flexibly (in terms of location), e.g., in a home office, is generally given after consultation and in accordance with the tasks and (on-site) appointments at hand.
  
• Academic achievements and a company pension scheme.
  
• 30 days holiday plus all bridging days and always off duty between Christmas and New Year.
  

In addition to exciting tasks and a collegial working environment, we offer you much more: https://go.fzj.de/benefits

The position is for a fixed term of 3 years, with possible long-term prospects. Pay in line with 100% of pay group 13 of the Collective Agreement for the Public Service (TVöD-Bund) and additionally 60 % of a monthly salary as special payment („Christmas bonus“). The monthly salaries in euro can be found on the BMI website: https://go.fzj.de/bmi.tvoed.entgelt Further information on doctoral degrees at Forschungszentrum Jülich (including its various branch offices) is available at https://www.fz-juelich.de/en/careers/phd

Place of employment: Bielefeld

We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us.

Further information on diversity and equal opportunities: https://go.fzj.de/equality