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Helm­holtz-Zen­trum Dres­den-Ros­sen­dorf e.V.

Through cutting-edge research in the fields of ENERGY, HEALTH and MATTER, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) solves some of the pressing societal and industrial challenges of our time. Join our 1.500 employees from more than 70 nations at one of our six research sites!

The Center for Advanced Systems Understanding (CASUS) is a German-Polish research center for data-intensive digital systems research. CASUS was founded in 2019 in Görlitz and conducts digital interdisciplinary systems research in various fields such as earth systems research, systems biology and materials research.

CASUS is looking for a

PhD student (f/m/d) on Deep Learning for Virus and Host Genomics.

The Scope of Your Job:

The global SARS-CoV2 Pandemic has demonstrated the urgency to develop new tools for our arsenal against pathogens and human disease. If you are passionate about designing the next generation of genomic algorithms for host-pathogen interactions – we are looking for your talent!

Natural Language Processing has substantially improved deep learning of language and our understanding of linguistics due to unprecedented possibilities for text analysis. In a collaboration between the TU Dresden and CASUS, we use transformer-based deep learning algorithms that treat genomes as text. The project will encompass using deep learning to understand the phylogeny of SARS-CoV-2 and Mpox (monkeypox). Furthermore, the project will involve the analysis of genome-wide siRNA screening data to decipher unknown host-pathogen interactions.

Working field:

  • Design of deep learning tasks to interrogate questions of genome biology
  • Devise novel approaches to incorporate Biology-informed knowledge into the model architecture
  • Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets
  • Collaborate with the research team on other questions of machine learning, functional genomics, genome instability
  • Supervise junior lab members
  • Present results and publish high-impact peer-reviewed research

Requirements:

  • Master or Diploma in a relevant field, such as Molecular Biology, Computational Biology, Bioinformatics, Genetics, Computer Science, Mathematics, Linguistics or equivalent scientific background
  • A solid background in biology, mathematics, software engineering, machine learning or in a related subject
  • Excellent programming skills in languages such as Python
  • Familiarity with modern deep learning frameworks like Tensorflow 2.x.x, PyTorch
  • Previous experience or interest in Bioinformatics, Systems Biology, Natural Language Processing, Deep Learning, Git version control and Slurm cluster environments is a plus
  • Strong motivation to work in a collaborative environment
  • Excellent communication skills in English and in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

What we offer:

  • A vibrant research community in an open, diverse and international work environment
  • Scientific excellence and extensive professional networking opportunities
  • A structured PhD program with a comprehensive range of continuing education and networking opportunities - more information about the PhD program at the HZDR can be found here
  • Salary and social benefits in accordance with the collective agreement for the public sector (TVöD-Bund) including 30 days of paid holiday leave, company pension scheme (VBL)
  • We support a good work-life balance with the possibility of part-time employment, mobile working and flexible working hours
  • Numerous company health management offerings
  • Employee discounts with well-known providers via the platform Corporate Benefits
  • An employer subsidy for the "Deutschland-Ticket Jobticket"

How to apply:

Kindly submit your completed application (including cover letter, CV, diplomas/transcripts, etc.) only via our Online-application-system: https://www.hzdr.de/db/Cms?pNid=490&pLang=en&pOid=70002