Johannes Köster
Research Group Leader at University of Duisburg-Essen
Essen, North Rhine-Westphalia, Germany
Summary
🤩
Rockstar🎓
Top School
Top expert inComputational Genomics and Bioinformatics Workflow Development
Johannes Köster is a research group leader and professor in bioinformatics and computational oncology with 13 years of experience bridging academic research and production-grade bioinformatics engineering. He builds robust algorithms and workflows—contributing core sequence algorithms to rust-bio and extensive backend and DevOps work on Snakemake and Bioconda—that power reproducible genomics pipelines. His career spans leading research at the University of Duisburg-Essen, collaboration with CWI, and a postdoc at Harvard, combining rigorous PhD-level computer science with domain expertise in computational biology. Known for improving CI/CD and testing across community projects, he brings an uncommon blend of low-level algorithm implementation and large-scale workflow automation to translational cancer informatics.
13 years of coding experience
Doctor of Philosophy - PhD, Computer Science, A (with honors), Doctor of Philosophy - PhD, Computer Science, A (with honors) at TU Dortmund University
Github Skills (40)
algorithm10
unit-testing10
algorithms10
snakemake10
continuous-integration10
package-management10
python10
cin10
conda10
bash10
circleci10
data-structure10
cicd10
implement10
build-automation10
Programming languages (28)
Github contributions (5)
snakemake/snakemake
Aug 2013 - Jan 2023
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:
Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:73 releases, 1074 reviews, 2679 commits in 9 years 6 months
Contributions summary:Johannes contributed to the Snakemake workflow management system by addressing various issues in the codebase. Their work involved bug fixes related to argument handling, module functionality, and rule inheritance, specifically within the module system. They also implemented features like the ability to add HTML hierarchies to reports and contributed to the automatic containerization with Docker images, indicating involvement in back-end logic. Furthermore, the user has shown expertise in cluster and cloud execution, along with contributions to the setup of the test environment using GitHub actions.
snakemakereproducibilityworkflow-management
rust-bio/rust-bio
Dec 2014 - Sep 2022
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Role in this project:Back-end Developer
Back-end DeveloperContributions:52 releases, 79 reviews, 720 commits in 7 years 10 months
Contributions summary:Johannes's primary contribution involved the development of core bioinformatics algorithms and data structures within the rust-bio library. The commits reveal the implementation of several algorithms, including the Hamming distance, Levenshtein distance, and Myers' bit-parallel algorithm, as well as implementations for generating suffix arrays, LCP arrays, and BWTs. The user also worked on creating the interface for the fasta and fastq readers, and building classes to hold information related to the sequences.
bioinformaticscontinuous-integrationdata-structuredata-structures
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