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Bioinformatics Training


Johannes Köster is a computer scientist with a focus on algorithm engineering and data analysis in bioinformatics. Johannes studied computer science at the University of Dortmund (diploma thesis 2010, with Max Planck Institute of Molecular Physiology Dortmund). Then, he did his PhD in the group of Prof. Sven Rahmann (TU Dortmund, 2015). Afterwards, Johannes was a postdoc in the groups of Prof. Shirley Liu and Prof. Myles Brown at Dana Farber Cancer Institute and Harvard University (2015-2016). In 2016, Johannes moved to the lab of Prof. Alexander Schönhuth for a brief second postdoc at Centrum Wiskunde & Informatica Amsterdam, Netherlands (CWI), where he quickly received a VENI grant for an independent position. In 2017, Johannes became the head of the group "Algorithms for reproducible bioinformatics" at the University of Duisburg-Essen in Germany.

Johannes' research is focused on reproducibility in three ways. First, he is the author of the popular workflow management system Snakemake and the founder of the Bioconda project for sustainably distributing bioinformatics software as easily installable packages. Together, these projects form the base for a large fraction of currently performed scalable and reproducible data analysis in bioinformatics.
Second, Johannes is the author of the Rust-Bio library, enabling the use of the Rust programming language for bioinformatics by providing standard bioinformatics algorithms and data structures. Using Rust promotes reproducibilty by guaranteeing thread and memory safety at compile-time.
Third, Johannes is working in the field of Bayesian statistics (e.g., for variant calling and single cell transcriptomics) in order to provide algorithms for analysis of high-throughput data while capturing and quantifying all known sources of uncertainty, thereby providing more reproducible predictions.


Current positions


  • since 2020: DKTK Investigator at the German Consortium of Translational Cancer Research (DKTK) of WTZ and DKFZ.
  • since 2017: Group leader (permanent position), Algorithms for reproducible bioinformatics (, Genome Informatics, Institute of Human Genetics, Faculty of Medicine, University of Duisburg-Essen. Currently eight group members (graduate students).
  • since 2016: Affiliated consulting scientist in Myles Brown’s group (Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School), USA.

Previous positions


  • 2016 – 2017: Researcher (NWO Veni funded, independent) at Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, Netherlands.
  • 2016: Postdoctoral research fellow under the supervision of Alexander Sch¨onhuth, Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, Netherlands.
  • 2016: Consultant (data analysis and workflow management) for Juno therapeutics, 307 Westlake Avenue, Seattle, USA.
  • 2015 – 2016: Postdoctoral research fellow in Xiaole Shirley Liu’s group (Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health) and Myles Brown’s group (Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School), USA.
  • 2011 – 2015: Research fellow at both the Chair of Genome Informatics of Sven Rahmann, University of DuisburgEssen and in the “European Network for Cancer in Children and Adolescents” project under Alexander Schramm, University Hospital Essen, Germany.



  • 2011-2015: Ph.D. in Computer Science (grade “ausgezeichnet”/summa cum laude) at TU Dortmund, Germany. Thesis title: “Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis”. Supervisor: Sven Rahmann, Chair of Genome Informatics, University of Duisburg-Essen. Second assessor: Axel Mosig, Bioinformatics Group, Ruhr University Bochum.
  • 2005 – 2010: Diploma (equiv. to M.Sc.) in Computer Science (grade 1.0/A with honors) at TU Dortmund, Germany. Thesis title: “Propagating Interaction Logic toward Predictive Protein Hypernetworks”. Supervisors: Sven Rahmann, Bioinformatics for High-Throughput-Technologies, Computer Science XI, TU Dortmund and Eli Zamir, Systems Biology of Cell-Matrix Adhesion, Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology Dortmund.


Key publications: 


Ten most important publications

1. Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S.,
Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J (corresponding
author). Sustainable data analysis with Snakemake. F1000Res 10, 33 (2021).

2. Köster, J. (shared first and corresponding author), Dijkstra, L. J., Marschall, T., Schönhuth, A. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome Biology
21, 98 (2020).

3. Lähnemann, D., Köster, J. (shared first and last author), Szczurek, E., McCarthy, D. J., Hicks, S.C.,
Robinson, M.D., Vallejos, C.A., Campbell, K.R., et al. Eleven grand challenges in single-cell data science.
Genome Biology 21, 31 (2020).

4. Köster, J. (corresponding author), Brown, M., Liu, X.S. A Bayesian model for single cell transcript expression
analysis on MERFISH data. Bioinformatics 35, 995–1001 (2019).

5. Grüning, B., Dale, R., Sj¨odin, A., Chapman, B.A., Rowe, J., Tomkins-Tinch, C.H., Valieris, R., the Bioconda
Team, Köster, J. (corresponding author). Bioconda: sustainable and comprehensive software distribution
for the life sciences. Nat Methods 15, 475–476 (2018).

6. Köster, J. Rust-Bio: a fast and safe bioinformatics library. Bioinformatics 32, 444–446 (2016).

7. Li, W., Köster, J. (co-first author), Xu, H., Chen, C.-H., Xiao, T., Liu, J. S., . . . Liu, X. S. Quality control,
modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology, 16(1), 281 (2015).

8. Schramm, A., Köster, J., Assenov, Y., Althoff, K., Peifer, M., Mahlow, E., Odersky, A., Beisser, D., Ernst,
C., Henssen, A. G., Stephan, H., Schröder, C., Heukamp, L., Engesser, A., Kahlert, Y., Theissen, J., Hero, B.,
Roels, F., Altmüller, J., Nürnberg, P., Astrahantseff, K., Gloeckner, C., De Preter, K., Plass, C., Lee, S., Lode,
H. N., Henrich, K., Gartlgruber, M., Speleman, F., Schmezer, P., Westermann, F., Rahmann, S., Fischer, M.,
Eggert, A., Schulte, J. H. Mutational dynamics between primary and relapse neuroblastomas. Nature Genetics,
47(8), 872–877 (2015).

9. Köster, J. (corresponding author), Rahmann, S. Massively parallel read mapping on GPUs with the q-group
index and PEANUT. PeerJ 2, e606 (2014).

10. Köster, J. (corresponding author), Rahmann, S. Snakemake – a scalable bioinformatics workflow engine.
Bioinformatics 28, 2520–2522 (2012).

Teaching and Supervisions




  • Building Computational Pipelines With Snakemake - Training Lead


  • Snakemake Workshop - Training Lead


  • Snakemake Workshop - Training Lead
Johannes Köster

Contact Details

Institute of Human Genetics
University of Duisburg-Essen
Hufelandstr. 55
45147 Essen