Johannes Köster is professor for Bioinformatics and Computational Oncology (Bioinformatische Algorithmen in der Onkologie) at the Institute for AI in Medicine (IKIM), University Medicine Essen, University of Duisburg-Essen. He has a focus on algorithm engineering and data analysis. 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 was appointed full professor at the University of Duisbug-Essen in 2023.

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.

Position Group
Since April 2023 Full professor Bioinformatics and computational oncology (Bioinformatische Algorithmen in der Onkologie), Institute for AI in Medicine (IKIM), University Medicine Essen, University of Duisburg-Essen
August 2017 -
March 2023
Group leader Algorithms for reproducible bioinformatics, Institute of Human Genetics, University of Duisburg-Essen
August 2016 -
July 2017
Researcher Life Sciences, CWI Amsterdam
Since May 2016 Consultant Myles Brown, Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
May 2016 -
July 2016
Postdoc Alexander Schönhuth, Life Sciences, CWI Amsterdam
April 2015 -
April 2016
Postdoc Shirley Liu, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health
Postdoc Myles Brown, Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
January 2011 -
March 2015
PhD student Sven Rahmann, Genome Informatics, University Duisburg-Essen
Guest member Eli Zamir, Systems Biology of Cell Matrix Adhesion, Max-Planck-Institute of Molecular Physiology Dortmund
See here for a full CV.

Research

Publications

Contact

email johannes.koester@uni-due.de
phone +49 (0)201 723 77819
www https://koesterlab.github.io
keybase johanneskoester
office IKIM, Girardetstr. 2, D-45131 Essen, Germany, 4th floor
postal Dr. rer. nat. Johannes Köster
Bioinformatische Algorithmen in der Onkologie
Institute for AI in Medicine (IKIM)
University of Duisburg-Essen
Girardetstr. 8, Girardet Haus 8/2
45131 Essen
Germany