Computational Genomics and Systems Genetics

Functional and Structural Genomics

Prof. Dr. Oliver Stegle

Division Head

Our research group develops and applies computational approaches to study molecular variations and their phenotypic consequences, such as the development of cancer.

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.

Research Themes

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

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.

Prof. Dr. Oliver Stegle

Division Head
Rama Abdulhamid
Alexander Aivazidis
Thibault Bechtler
Eva Sabine Blum
Dr. Brian Clarke
Daniel Dimitrov
Kevin Domanegg
Fritz Donald Hansen
John Andrew Hawkins
Elyas Heidari

PhD Student

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Dr. Florian Heyl
Jan Gunnar Gleixner

Doktorand
Dr. Ilia Kats
Sameesh Kher
Dr. Santiago Lago
Jiawei Luo
Dr. Jusung Lee
Luca Marconato
Katharina Mikulik
Abdul Moeed
Marcel Mück
Dr. Hakime Öztürk
Martin Rohbeck
Manu Saraswat
Felix Schneider
Stefan Schrod
Ezgi Sen
Danai Vagiaki
Florin Walter

Entire Team

Open Positions

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

To apply for a postdoctoral position or PhD position in our group, please refer to the DKFZ Postdoctoral Fellowship and the DKFZ International PhD Programme.
If you do not apply through one of the specific openings mentioned above, feel free to send your CV, a letter of motivation and ideally 2 references in a single pdf directly Oliver Stegle.

We are also pleased to offer opportunities for your BSc or MSc thesis or an internship in our lab. If you are interested, please contact us with a CV and a motivation letter tailored to our lab interests.

Selected Publications

2024 - Nature Genetics

Integration of variant annotations using deep set networks boosts rare variant association testing

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

SpatialData: an open and universal data framework for spatial omics

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

Cell2location maps fine-grained cell types in spatial transcriptomics

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

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

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

2021 - Nature Genetics

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

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

Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics

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

Prof. Dr. Oliver Stegle

Division Head

+49 6221 42 3598

Eva Sabine Blum

Administrative Assistant

+49 6221 42 3601

Kevin Domanegg

Scientific Manager

+49 6221 42 2720