PhD - Deep Learning and Perturbation Models (f/m/x)


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We are Helmholtz Munich. In a rapidly changing world, we discover breakthrough solutions for better health.

Our research is focused within the areas of metabolic health/diabetes, environmental health, molecular targets and therapies, cell programming and repair, bioengineering, and computational health. We particularly excel in the fields of basic research, bioengineering, artificial intelligence, and technological development.

Through this research, we build the foundations for medical innovation. Together with our partners, we seek to accelerate the transfer of our research, so that laboratory ideas can reach society and improve people’s quality of life at the fastest rate possible.

This is what drives us. Why not join us and make a difference?

The Computational Health Center is a dynamic and innovative institution engaged in the development of artificial intelligence (AI) methods for biomedical applications. In this highly explosive and relevant field of research we are one of the largest and most recognized centers in Germany. On a national and international level we are active and recognized in numerous initiatives and networks.

The Institute of Computational Biology is globally recognised for innovations in data analysis and modelling of biological systems and diseases, anchored at Helmholtz Munich and the Technical University of Munich. At our institute you will find a scientifically stimulating international environment.

The Theis Lab has a long-standing reputation for pioneering machine learning and AI methods in molecular biology, in particular on single-cell genomics.

We are seeking a highly motivated and talented Doctoral Researcher (f/m/x) to join our team for a collaborative research project with Pfizer Inc. The project aims to enable target discovery and precision medicine through the application of scalable and interpretable deep learning and perturbation models. As a PhD candidate, you will play a key role in developing and implementing innovative machine learning algorithms and computational methods to accelerate target discovery, inform precision medicine, and enable preclinical to clinical translation.

Prof. Matthias Tschöp (Dr. Med., Dr. hc.), CEO of Helmholtz Munich:

"We believe that excellent research requires a range of different perspectives. Diverse teams reach better solutions and are more innovative in their research topics.

Establishing our Diversity Management Strategy demonstrates our commitment to ensuring an appreciative company culture based on mutual respect. We are also implementing diversity-sensitive processes throughout our whole organization."

Your tasks

  • Curate, prepare, and analyse immune cell CRISPR data.
  • Integrate large-scale clinical omics data and meta data from public and private clinical studies.
  • Support with the development of deep learning algorithms to compare human diseases and preclinical models.
  • Model both genetic and chemical perturbations in out-of-distribution conditions

Your profile

  • Major in one of the biological sciences, computer science, math, physics, chemistry, etc.
  • Proficiency in programming languages such as Python
  • Experience in analysing and integrating large-scale omics data (e.g., RNA-seq, bulk transcriptomics, single-cell data) and applying machine learning methods
  • Ability to work collaboratively in a multidisciplinary team
  • Interest in obtaining a Ph.D. in Computational Biology with a focus on machine learning, deep learning, or artificial intelligence.

Preferred qualifications:

  • Research experience in developing, applying, and evaluating deep learning algorithms.
  • Experience with deep learning frameworks (e.g., TensorFlow, PyTorch).
  • Familiarity with perturbation models, genetic perturbations, and compound data.
  • Good publication record.


  • Scientific Training: Helmholtz Munich Graduate School
  • Career counseling: Career Center for PhD candidates
  • Recreation: 30 days annual leave, flexi days, plus public holidays
  • Health Promotion: Sports, company doctor, mental health initiatives
  • International Staff Service: Support with the relocation and integration process in Germany

Since 2005, we hold the TOTAL E-QUALITY award for exemplary action in the sense of an equal-opportunity organizational culture.

Helmholtz Munich is actively committed to diversity and inclusion in practice and is sustainably committed to equality.

The Diversity Charter has set itself the goal of promoting diversity in the world of work. By signing the charter, we commit ourselves to create an appreciative working environment for all employees.


This position provides the opportunity for you to build specialist knowledge whilst developing key professional experience, both of which will help you to make strides in your scientific career.

Remuneration and social security benefits are based on the German Collective Wage Agreement for Public-Sector Employees at Federal Level (EG 13 50% TV EntgO Bund). In addition, there is also the possibility of receiving an allowance if the applicable conditions are met. The position has an (initial) fixed term of three years but may be extended under certain circumstances.

We are committed to promoting a culture of diversity and welcome applications from talented people regardless of gender, cultural background, nationality, ethnicity, sexual identity, physical abilities, religion or age. Qualified applicants with physical disabilities will be given preference.
If you have obtained a university degree abroad, we will require further documents from you regarding the comparability of your degree. Please request the Statement of Comparability for Foreign Higher Education Qualifications as early as possible.


Interested in applying?

If you have any questions, feel free to contact Marco Uhrig,, or Emma van Holthe,, who will be happy to help.

Your application should include
    • CV
    • Cover letter
    • Degrees/Diplomas/Certificates
    • Contact details for at least two referees

    We are Helmholtz Munich.


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