For any questions, do not hesitate to ask:
Dr. Michael Bussmann Tel.: +49 3581 37523 11,
Mrs. Weronika Mazur Tel.: +49 3581 37523 23,
+49 171 3635554

Place of work:

Working hours:
39 h/week

31 March 2023

Online application
English / German
Job-Id: 2022/240 (1592)

At HZDR, we promote and value diversity among our employees. We welcome applications from people with diverse backgrounds regardless of gender, ethnic and social origin, belief, disability, age, and sexual orientation. Severely disabled persons are given preference in the event of equal suitability.

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Bautzner Landstraße 400
01328 Dresden

Postdoctoral Researcher (f/m/d) on Deep Learning Language Models for Host-pathogen Interactions

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 50 nations at one of our six research sites and help us moving research to the next level!

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.

The CASUS invites applications as Postdoctoral Researcher (f/m/d) on Deep Learning Language Models for Host-pathogen Interactions. The position will be available from 1 March 2023.

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 on language and our understanding on 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 the training of task-agnostic language models and use these to extract language rules and biological meaning, such as how genome stability is encoded in the genome.

The position will be mainly located in CASUS in Görlitz, Germany, embedded in the team of Artur Yakimovich and in close interaction with the group of Prof. Anna Poetsch at the Biotechnology Center of the TU Dresden, Germany.

Your tasks:

  • Design of deep learning tasks to interrogate questions of genome biology and host-pathogens interactions
  • Devise novel approaches to use human and pathogen genomic data to decipher host-pathogen interactions
  • Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets
  • Collaborate in 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

Your profile:

  • PhD 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 and R
  • 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)

Our offer:

  • A vibrant research community in an open, diverse and international work environment
  • Scientific excellence and extensive professional networking opportunities
  • A wide range of qualification opportunities and individual career counseling provided by the Postdoc Center HZDR-TUD
  • The employment contract is limited to three years with the possibility of longer-term prospects
  • 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 and flexible working hours
  • Numerous company health management offerings

Kindly submit your completed application (including cover letter, CV, diplomas/transcripts, etc.) only via our Online-application-system.