Chair of Bioinformatics and Computational Oncology
Bioinformatische Algorithmen in der Onkologie

We focus on reproducible data analysis, algorithm engineering and Bayesian statistics in Bioinformatics. Our work philosophy is to develop all our approaches into sustainable, well maintained open source products, using state-of-the-art programming languages and libraries. We are responsible for widely used scientific tools and projects like Bioconda, Snakemake, Datavzrd, Rust-Bio, and Varlociraptor.
Member Position
Prof. Dr. Johannes Köster Group leader
Andrea Tonk Office manager
David Lähnemann PhD student
Felix Mölder PhD student
Bianca Stöcker PhD student
Hamdiye Uzuner PhD student
Meijie Li PhD student
Felix Wiegand PhD student
Laura Kühle PhD student

News

Date News
2024-06-06 Our paper "Neoadjuvant nivolumab with or without relatlimab in resectable non-small-cell lung cancer: a randomized phase 2 trial" has been published in Nature Medicine.
2024-01-18 Our paper "NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling" has been published in F1000.
2023-05-25 Johannes has been interviewed for a Nature technology feature about reproducibility of computational environments, which can be found here.
2021-08-23 Registration for the (virtual) Boston Snakemake Days 2021 is now open at this page.
2021-01-18 Our paper "Sustainable data analysis with Snakemake" has been published in F1000. F1000 enables us to treat this as a "rolling paper", which will be updated whenever Snakemake receives a major new feature. Hence, this paper can be seen as an always up-to-date high-level overview of what Snakemake offers for reproducible, adaptable, and transparent data analysis.
2020-04-28 Our paper "Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery" has been published in Genome Biology. This is the first of multiple papers which will describe how Varlociraptor provides a unified statistical model for calling any kind of variant in any kind of scenario (single sample, population, tumors, pedigrees, combinations thereof) and species.
2020-02-07 Our review paper "Eleven grand challenges in single-cell data science" has been published in Genome Biology. This work is the result of an inspiring workshop on single-cell data science with many leaders of the field that we organized at the Lorentz Center in 2018.
2019-11-14 We managed to acquire funding for the Bioconda project by the Chan Zuckerberg Initiative! Bioconda was selected as one of 42 projects out of 293 submissions.
2019-09-24 Johannes has received the Friedmund-Neumann-Prize 2019 for extraordinary fundamental biomedical research from the Schering Foundation. Many thanks goes to Prof. Sven Rahmann (who has nominated Johannes), all colleagues, and the Snakemake, Bioconda, and Rust-Bio communities, without whom this would not have been possible.
2019-03-21 Register here for our Snakemake tutorial in Boston in May 2019
2018-08-23 Our paper "A Bayesian model for single cell transcript expression analysis on MERFISH data" has been published in Bioinformatics!
2018-07-02 The Bioconda paper has been published in Nature Methods!
2017-11-03 The Bioconda project that has been founded by Johannes Köster in 2015 has been acknowledged by Nature. Nature technology editor Jeffrey Perkel has blogged about it here.

Research

Projects

Snakemake

Snakemake is a popular workflow management system. Snakemake reduces the complexity of formalizing and executing data analyses by providing a fast and comfortable execution environment, together with a clean and modern Python-based specification language. Snakemake workflows scale from workstations to compute servers, clusters, the grid and the cloud without the need to adjust the workflow definition.

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Bioconda

A distribution of bioinformatics software realized as a channel for the versatile package manager Conda. Bioconda is a multinational project with hundreds of developers and thousands of software packages.

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Varlociraptor

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control. The project aims to provide a unified theory of variant calling, across all size ranges (small, structural) and calling scenarios (germline, somatic, arbitrary).

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Vembrane

Flexible and fast filtering of VCF/BCF files with a unified pythonic syntax, also supporting advanced features like annotations (ANN/CSQ field) and breakend events.

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Datavzrd

A tool to create visual and interactive HTML reports from collections of CSV/TSV tables. Reports include automatically generated vega-lite histograms per column. Plots can be fully customized by users via a config file. These also allow the user to add linkouts to other websites or link between multiple tables.

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MERFISHtools

A Bayesian model for single-cell transcript (differential) expression analysis on MERFISH data. The model allows to overcome systematic biases occurring with MERFISH and provides measures of uncertainty and control of the false discovery rate in a strictly Bayesian way. MERFISHtools is a corresponding command line client and analysis library written in Rust and Python. MERFISHtools is also available via Bioconda.

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Rust-Bio

A bioinformatics library written in the Rust language. The implementation provides state of the art solutions for common tasks in bioinformatics, focusing on stability by using comprehensive unit tests and continuous integration.

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Protein Hypernetworks

This project aims to model protein networks along with dependencies between interactions like allosteric effects, steric hindrance and competition on binding domains. This allows us to improve the accuracy of protein complex prediction and to simulate the effects of perturbations like knockout or over-expression.

Contact

email johannes.koester@uni-due.de
phone +49 (0)201 723 77819
www https://koesterlab.github.io
office Girardetstr. 2, D-45131 Essen, Germany
4th floor
[Google Maps]
postal Girardetstr. 8, Girardet Haus 8/2, D-45131 Essen, Germany