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.
Research
Publications
- Hanssen, F., Gabernet, G., Bäuerle, F., Stöcker, B., Wiegand, F., Smith, N.H., Mertes, C., Neogi, A.G., Brandhoff, L., Ossowski, A., Altmueller, J., Becker, K., Petzold, A., Sturm, M., Stöcker, T., Sivalingam, S., Brand, F., Schmidt, A., Buness, A., Probst, A.J., Motameny, S., Köster, J., 2024. NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling. F1000Research 12:1125.
- Schuler, M., Cuppens, K., Plönes, T., Wiesweg, M., Du Pont, B., Hegedus, B., Köster, J., Mairinger, F., Darwiche, K., Paschen, A., Maes, B., Vanbockrijck, M., Lähnemann, D., Zhao, F., Hautzel, H., Theegarten, D., Hartemink, K., Reis, H., Baas, P., Schramm, A., Aigner, C., 2024. Neoadjuvant nivolumab with or without relatlimab in resectable non-small-cell lung cancer: a randomized phase 2 trial. Nat Med 30, 1602–1611.
- Uzuner, H., Paschen, A., Schadendorf, D., Köster, J., 2024. Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing. BMC Bioinformatics 25, 240.
- Hartmann, T., Schröder, C., Kuthe, E., Lähnemann, D., Köster, J., 2023. Insane in the vembrane: filtering and transforming VCF/BCF files. Bioinformatics 39, btac810.
- Bergkamp, N. D., van Senten, J.R., Brink, H. J., Bebelman, M. P., Bor, J. v. d., Çobanoğlu, T. S., Dinkla, K., Köster, J., Klau, G., Siderius, M., Smit, M. J. A virally encoded GPCR drives glioblastoma through feed-forward activation of the SK1-S1P1 signaling axis. Science Signaling 16 (2023).
- Tüns, A.I., Hartmann, T., Magin, S., González, R.C., Henssen, A.G., Rahmann, S., Schramm, A., Köster, J., 2022. Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing. Frontiers in Genetics 13.
- 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. Sustainable data analysis with Snakemake. F1000Res 10, 33 (2021).
- Köster, J., Dijkstra, L. J., Marschall, T., Schönhuth, A. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome Biology 21, 98 (2020).
- Stöcker, B., Schäfer, T., Mutzel, P., Köster, J., Kriege, N., Rahmann, S. Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. in Similarity Search and Applications 308–322 (Springer International Publishing, 2019).
- Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., Schönhuth, A. Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics
- Johannes Köster, Myles Brown, X. Shirley Liu. A Bayesian Model for Single Cell Transcript Expression Analysis on MERFISH Data. Bioinformatics 2018.
- Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda Team, and Johannes Köster. Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences. Nature Methods 2018.
- Bianca Stöcker, Johannes Köster, Eli Zamir, Sven Rahmann. Modeling and simulating networks of interdependent protein interactions. Integr Biol 2018.
- MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu and Henry W. Long. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics 2018.
- Schulte, M., Köster, J., Rahmann, S. & Schramm, A. Cancer evolution, mutations, and clonal selection in relapse neuroblastoma. Cell Tissue Res 2018.
- Townsend, E. C., Murakami, M. A., Christodoulou, A., Christie, A. L., Köster, J., DeSouza, T. A., … Weinstock, D. M. (2016). The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016
- Li, W., Köster, J., 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 2015.
- Köster, J. Rust-Bio: a fast and safe bioinformatics library. Bioinformatics 2015.
- Schramm, A., Köster, J., Assenov, Y., Althoff, K., Peifer, M., Mahlow, E., ... Schulte, J. H. Mutational dynamics between primary and relapse neuroblastomas. Nature Genetics 2015.
- Köster, J. Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis. PhD-Thesis, TU Dortmund, Germany 2014. ISBN: 978-3737537773.
- Köster, J., Rahmann, S. Massively parallel read mapping on GPUs with the q-group index and PEANUT. PeerJ 2014.
- Köster, Johannes and Sven Rahmann. Snakemake - A scalable bioinformatics workflow engine. Bioinformatics 2012.
- Köster, Johannes, Eli Zamir, and Sven Rahmann. Efficiently Mining Protein Interaction Dependencies from Large Text Corpora. Integrative Biology 2012.
- Köster, Johannes and Sven Rahmann. Building and Documenting Bioinformatics Workflows with Python-based Snakemake. Proceedings of the GCB 2012.
- Schramm A, Köster J, Marschall T, Martin M, Heilmann M, Fielitz K, Büchel G, Barann M, Esser D, Rosenstiel P, Rahmann S, Eggert A, Schulte JH. Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma. Int J Cancer 2012
- Althoff K, Beckers A, Odersky A, Mestdagh P, Köster J, Bray IM, Bryan K, Vandesompele J, Speleman F, Stallings RL, Schramm A, Eggert A, Sprüssel A, Schulte JH. MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A. Int J Cancer. 2013
- Sven Rahmann, Marcel Martin, Johannes H. Schulte, Johannes Köster, Tobias Marschall, Alexander Schramm. Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data. Methods 2012.
- A Schramm, B Schowe, K Fielitz, M Heilmann, M Martin, T Marschall, J Köster, J Vandesompele, J Vermeulen, K de Preter, J Koster, R Versteeg, R Noguera, F Speleman, S Rahmann, A Eggert, K Morik and J H Schulte. Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome. British Journal of Cancer 2012.
- Köster, Johannes. Propagating Interaction Logic towards Predictive Protein Hypernetworks. Diploma Thesis at the Faculty of Computer Science, TU Dortmund 2010. The thesis was honored with the Uhde-Award 2011.
- Engler, S., Köster, J. and Siebert, A. Farmers Food Insecurity Monitoring. Identifying situations of food insecurity and famine. IFHV Working Paper 2014.
Contact
| 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 |