Computational Genomics and Systems Genetics

  • Functional and Structural Genomics
Bild Oliver Stegle

Prof. Dr. Oliver Stegle

Division Head

Our research group develops and applies computational approaches to study molecular variations and their phenotypic consequences.

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Our Research

How does our genetic background shape phenotypic traits or cause cancer? How are genetic and environmental factors integrated at different molecular layers, and how variable are molecular states between individual cells?

We use statistical inference and machine learning as our main tools to address these scientific questions. Growing sample sizes and technological advances demand novel analytical strategies and tools that scale to datasets with millions of observations and account for spatial and temporal dependencies. We develop foundational methods in statistics and machine learning, including efficient parameter inference in models to probe genetic associations and methods for dimensionality reduction.

Find out more about our lab at https://steglelab.org/

Research Themes

The diagram consists of two main sections (a and b). Section (a) outlines a model involving gene impairment and phenotype prediction through various modules. Section (b) illustrates the processing of annotated variants, showing how they relate to gene embedding and scoring for gene impairment.

We develop statistical methods to dissect often overlooked dimensions of the genotype-phenotype relationship, including genetic effects of rare variants and indirect genetic effects.

Research Groups

Team

We are an interdisciplinary and international team jointly hosted at the German Cancer Research Center (DKFZ) and the European Molecular Biology Laboratory (EMBL) in Heidelberg. In our team we promote openness and collaboration, and value kindness in everything we do. We take pride in every single member and their achievements and are eager to foster their scientific development.

Entire Team

Open Positions

We are always looking for new talent to strengthen our team!

PhD Applications:
To apply for a PhD position in our group, please refer to the DKFZ International PhD Programme. 

Postdoctoral Applications:
Prospective postdoctoral researchers are encouraged to apply through the DKFZ Postdoctoral Fellowship Programme. Additionally, feel free to send your CV, a letter of motivation and ideally 2 references in a single pdf directly to Oliver Stegle and Brian Clarke.

BSc / MSc thesis or Internships:
Students interested in a BSc or MSc thesis project, or a research internship, are welcome to contact us. Please send a CV and a motivation letter tailored to the research interests of the lab, and include information about your envisioned starting date and duration.

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Selected Publications

2025 - Nature Methods

Aivazidis, A., Memi, F., Kleshchevnikov, V., Er, S., Clarke, B., Stegle, O., & Bayraktar, O. A.

2024 - Nature Genetics

Clarke, B., Holtkamp, E., Öztürk, H., Mück, M., Wahlberg, M., Meyer, K., Munzlinger, F., Brechtmann, F., Hölzlwimmer, F. R., Lindner, J., Chen, Z., Gagneur, J., & Stegle, O.

2024 - Nature Methods

Marconato, L., Palla, G. , Yamauchi, K. A. , Virshup, I., Heidari, E., Treis, T., Toth, M., Shrestha, R. B., Vöhringer, H., Huber, W., Gerstung, M., Moore, J., Theis, F. J. , & Stegle, O.

2022 - Nature Biotechnology

Kleshchevnikov, V., Shmatko, A., Dann, E., Aivazidis, A., King, H. W., Li, T., Elmentaite, R., Lomakin, A., Kedlian, V., Gayoso, A., Jain, M. S., Park, J. S., Ramona, L., Tuck, E., Arutyunyan, A., Vento-Tormo, R., Gerstung, M., James, L., Stegle, O., Bayraktar, O. A.

2022 - Nature Methods

Velten, B., Braunger, J.M., Argelaguet, R., Arnol, D., Wirbel, J., Bredikhin, D., Zeller, G., Stegle, O

2021 - Nature Genetics

Jerber, J., Seaton, D. D., Cuomo, A. S. E., Kumasaka, N., Haldane, J., Steer, J., Patel, M., Pearce, D., Andersson, M., Bonder, M. J., Mountjoy, E., Ghoussaini, M., Lancaster, M. A., Marioni, J. C., Merkle, F. T., Gaffney, D. J., & Stegle, O.

2021 - Nature Genetics

Bonder, M. J., Smail, C., Gloudemans, M. J., Frésard, L., Jakubosky, D., D’Antonio, M., Li, X., Ferraro, N. M., Carcamo-Orive, I., Mirauta, B., Seaton, D. D., Cai, N., Vakili, D., Horta, D., Zhao, C., Zastrow, D. B., Bonner, D. E., Wheeler, M. T., Kilpinen, H., … , Stegle, O.

Get in touch with us

Bild Oliver Stegle

Prof. Dr. Oliver Stegle

Division Head
Employee image

Eva Sabine Blum

Administrative Assistant
Employee image

Dr. Brian Clarke

Group Leader and Deputy Division Head
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