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PhD position in Computational and Developmental Biology in Berlin (m/f/d)

Helmholtz Association of German Research Centres
Closing date
22 Oct 2023

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Life Science
Job Type
PhD Studentship
Employment - Hours
Full time
Fixed term

Job Details

Area of research:

PHD Thesis

Starting date:


Job description:The Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association is an international biomedical research center dedicated to understanding the molecular mechanisms of health and disease with the goal to devise new diagnostics and medicines. The MDC is a member of the Helmholtz Association, Germany's largest scientific organization, and offers an engaging research environment with cutting-edge research infrastructure. Currently, ~1250 employees and ~500 guest scientists work at the Berlin-Buch and Berlin-Mitte campuses. Our diverse workforce is a core strength that inspires creativity and innovation at the MDC.

The MDC is committed to improving human health through transformative biomedical research. Our goal is to pioneer discoveries for preventing, treating, and ultimately curing disease.

The Mittnenzweig lab develops new computational approaches for single-cell multiome, genomic and spatial transcriptomics data. We are interested in building quantitative models of the regulatory code and the intercellular signals that drive cell fate decisions in development and disease and how this code has evolved during animal evolution. In collaboration with experimental groups, we are working on vertebrate embryonic development and synthetic organoid models that reconstitute developmental and disease processes.

Our group is looking for a highly motivated PhD student (m/f/d) to develop new machine learning methods for the analysis of spatiotemporal single-cell data in the context of mammalian embryonic development, and to compare it with the embryonic development in other vertebrate model species.

Job Description:
  • You will develop new algorithms to infer cellular differentiation trajectories in the developing embryo from time-resolved single-cell RNA, spatial transcriptomics and lineage tracing data
  • You will use machine learning methods to combine spatial transcriptomics data with other data modalities such as single-cell transcriptome or advanced microscopy data
  • You will compare mouse embryonic development with a variety of other species (e.g. human, fish, bird) and synthetic embryo models
  • You will analyse and compare synthetic organoid development with in vivo embryonic development
  • You will work closely with experimental collaborators
  • You will be an active member in a highly interdisciplinary team, that involves data scientists and computational and experimental biologists

  • MSc degree in the computational or natural sciences
  • Strong computational or quantitative focus (computational biology, bioinformatics, mathematics or a related field)
  • Strong programming skills (Python, R) are essential; experience in building efficient and reusable software would be a plus
  • Excellent communication skills facilitating frequent exchange with group members and scientific collaborators
  • Solid statistical knowledge and experience with state-of-the-art machine learning methods
  • Ability to work independently and to undertake challenging analysis tasks

  • international working environment with communication in English and German
  • interesting career opportunities and a range of opportunities for further qualification and training
  • Compatibility of family and career certified by the workandfamily audit (“berufundfamilie audit”)
  • Support for "New Berliners" through the MDC Welcome & Family Office
  • On-campus health and fitness center

  • Stimulating and international research environment with excellent science
  • Opportunity to work on cutting-edge biomedical data
  • Ability to become an expert in single-cell genomics and machine learning approaches to biomedical data

You also benefit from:
  • A remuneration in accordance with the collective agreement for the federal public service (TVöD-Bund), including additional company pension schemes
  • Flexible working hours and childcare support
  • Subsidy for the job ticket
  • Additional health benefits such as flu vaccination, eye test, ergonomics advice at the workplace
  • The possibility of mobile working

Team: Mittnenzweig Lab
Publication period: 21.09.2023 - 22.10.2023
Desired starting date: 01.02.2024
Job location: MDC Berlin-Mitte
Hannoversche Str. 28
10115 Berlin
Employment period: Fixed Term
Scope of employment: PhD
Salary: Remuneration will be according to the TVöD Bund, depending on the personal requirements, up to the fee group 13
Application: Please use our online portal and submit your application including a cover letter, CV (without photo, age and information about your family status) and other relevant attachments.

If you have a foreign degree, please submit proof of the recognition of your Master's degree in Germany with your application. The proof can be determined via the anabin database ( and can be submitted as a PDF attachment to the application.

For information on fair mobility, click here:

Parity and equal status: All qualified applicants will receive consideration for employment without regard to ethnicity, color, religion, sex, national origin, disability, age, gender identity or sexual orientation. We look forward to receiving applications from open-minded people who enjoy working in diverse teams. Applications from severely disabled persons will be given special consideration.

Further links:

Bei Fragen zur Stelle wenden Sie sich an:
Markus Mittnenzweig
Mittnenzweig Lab

This research center is part of the Helmholtz Association of German Research Centers. With more than 42,000 employees and an annual budget of over € 5 billion, the Helmholtz Association is Germany's largest scientific organisation.


The Helmholtz Association contributes to solving major challenges to assure the future of our society. With more than 39,000 people on staff in 18 national research centres, the Helmholtz Association is Germany’s largest scientific organization. The name Helmholtz stands for concerted research in which networks form the key principle behind inquiring thought and action. Concerted research is efficient and flexible.

The profile of the Helmholtz Association

The Helmholtz Association performs cutting-edge research which contributes substantially to solving the grand challenges of science, society and industry. To succeed in meeting these responsibilities, Helmholtz concentrates its work in six research fields: Energy, Earth and Environment, Health, Key Technologies, Matter, as well as Aeronautics, Space and Transport. Within each of these fields, research programs are developed by our scientists and regularly evaluated by renowned international experts. Their evaluation forms the basis for the programme-oriented funding that is allocated to Helmholtz research. Within the six research fields, Helmholtz scientists cooperate with each other and with external partners – working across disciplinary, organizational and national borders.

Promoting young academics

Helmholtz scientists, a high-performance infrastructure and modern and efficient research management are the ingredients to the Helmholtz Association‘s success and global impact.
Promoting young researchers is a major priority for the Helmholtz Association. Its qualification schemes for young researchers are geared mainly towards PhD students, postdocs and young managers. The Helmholtz Association has set high standards for its talent management. Its strategy begins with targeted recruitment of highly qualified staff at all levels, followed by comprehensive support aimed at further developing their potential. Ensuring equal opportunities is an essential element in all talent management activities undertaken by the Helmholtz Association.

The Helmholtz Graduate Schools and Research Schools at almost all Helmholtz Centres provide doctoral students with the general and specific skills and training they need, as well as ample opportunity to network with other working groups. The period following a doctorate is decisive in determining the direction and success of a scientific career. For this reason, we are about to establish Career Centers for postdoctoral researchers in the Helmholtz centres and a mentoring programme for especially gifted PostDocs in order to foster career orientation. This equips young researchers with the skills they need to go on to head a Helmholtz Young Investigators Group, for example. As a Young Investigator Group leader, junior scientists can independently set up their own group to conduct research in their specialist field.

Within its talent management strategy, the Helmholtz Association pays special attention to the increased recruitment of talented female scientists both from Germany and abroad. To this end, there are currently two funding programs supporting this policy Funding of first-time appointments of excellent women scientists (W2/W3)’ and ‘Funding to recruit top-level international women scientists (W3)’.

The increasing complexity of the content, structures and framework conditions of scientific work today requires researchers to organise their projects, their employees and, of course, themselves in a highly professional and effective way. In response to these demands, we have set up the Helmholtz Management Academy to provide junior leaders in science with professional management training. Furthermore, the Helmholtz network provides a platform for the alumni of the Helmholtz Management Academy and Mentoring programme to come together and share their experiences of leadership, career development and lifelong learning.

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