Eye catcher

For any questions, do not hesitate to ask:
Dr. Michael Bussmann Tel.: +49 3581 37523 11,
+49 351 260 2616
,
Dr. Artur Yakimovich

Place of work:
Görlitz

Working hours:
19,5 h/week

Deadline:
31 December 2021

Online application
English / German
Job-Id: 2021/177 (1300)

The HZDR is committed to equal opportunity employment and we strongly encourage applications from qualified female candidates. We also carefully consider all applications from job candidates with severe disabilities.

Helmholtz-Zentrum
Dresden-Rossendorf
Bautzner Landstraße 400
01328 Dresden

PhD (f/m/d) Deep Learning of Virus-Host Interactions from Time-Lapse Microscopy

As a member of the Helmholtz Association of German Research Centers, the HZDR employs about 1,400 people. The Center's focus is on interdisciplinary research in the areas energy, health and matter.

The Center for Advanced Systems Understanding (CASUS) is a German-Polish research center for data-intensive digital systems research. We combine innovative methods from mathematics, theoretical systems research, simulations, data science, and computer science to provide solutions for a range of disciplines – materials science under ambient and extreme conditions, earth system research, systems biology, and autonomous vehicles.

CASUS was jointly founded in August 2019 by the Helmholtz-Zentrum Dresden-Rossendorf, the Helmholtz Centre for Environmental Research, the Max Planck Institute of Molecular Cell Biology and Genetics, the Technical University of Dresden and the University of Wroclaw. The CASUS start-up phase is hosted by the Helmholtz-Zentrum Dresden-Rossendorf and is financed by the Federal Ministry of Education and Research and the Saxon State Ministry of Science and Art.

The Center for Advanced Systems Understanding (CASUS) invites applications as PhD (f/m/d) Deep Learning of Virus-Host Interactions from Time-Lapse Microscopy.

The position will be available from 1 April 2022. The employment contract is limited to three years.

The Scope of Your Job

If YOU are passionate about designing the next generation of algorithms in virology and biomedical imaging – we are looking for YOUR talent!

Viruses require host cells to procreate and spread their progeny. For this, they enter cells, replicate and egress in a stepwise process occurring through interactions between molecules of the host cell and the pathogen molecules. These are known as host-pathogen interactions, they include various host mechanisms exploitations by the pathogen. Synchronized with virus entry, uncoating, and replication through a virus genetic program, virus induce dramatic changes of cell morphology.

Using image data from automated time-lapse microscopy, YOU will design novel Deep Learning algorithms capable to discover mechanistic representations from time-lapse microscopy of Virus-Host interactions.

Tasks:

  • Engage with our international collaborators (London, Zurich, Taipei etc.) to collate time-lapse image-based data

  • Develop novel data-efficient algorithms for representation learning of host-pathogen interactions

  • Design novel deep learning architectures suitable for time-lapse microscopy

  • Publish high-impact peer-reviewed research

Requirements:

  • Master’s degree in computer science, bioinformatics, computational biology, data science, machine learning or relevant discipline
  • A solid background in algorithms, software engineering, machine learning, mathematics, or in a related subject

  • Excellent programming skills in languages such as python and bash

  • Previous experience or interest in Computer Vision, Deep Learning and cluster environments

  • Knowledge of modern deep learning frameworks like Tensorflow 2.x.x, PyTorch

  • Knowledge of C, C++, CUDA, low-level optimization or Biomedical imaging is a plus

  • Strong motivation to work in a collaborative environment

  • Excellent communication skills in English in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

We offer:

  • A vibrant research community in an open, diverse and international work environment
  • Scientific excellence and extensive professional networking opportunities
  • The employment contract is limited to three years
  • Salary and social benefits in conformity with the provisions of the Collective Agreement TVöD-Bund
  • 30 days of paid holiday leave
  • Company pension scheme (VBL)
  • A good work/life balance for which we offer assistance in the form of:
    • Possibility to work part-time

    • Flexible working hours

    • In-house health management

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