Building and Documenting Workflows with Python-Based Snakemake. - Johannes Köster; Sven Rahmann (GCB, 2012)

Snakemake - a scalable bioinformatics workflow engine. - Johannes Köster; Sven Rahmann (Bioinform., 2012)

Massively parallel read mapping on GPUs with PEANUT. - Johannes Köster; Sven Rahmann (CoRR, 2014)

Parallelization, scalability, and reproducibility in next generation sequencing analysis - Johannes Köster (2014)

Rust-Bio: a fast and safe bioinformatics library. - Johannes Köster (Bioinform., 2016)

CRISPR-DO for genome-wide CRISPR design and optimization. - Jian Ma; Johannes Köster; Qian Qin; Shengen Hu; Wei Li 035; Chenhao Chen; Qingyi Cao; Jinzeng Wang; Shenglin Mei; Qi Liu; Han Xu; Xiaole Shirley Liu (Bioinform., 2016)

SimLoRD: Simulation of Long Read Data. - Bianca K. Stöcker; Johannes Köster; Sven Rahmann (Bioinform., 2016)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. - MacIntosh Cornwell; Mahesh Vangala; Len Taing; Zachary Herbert; Johannes Köster; Bo Li; Hanfei Sun; Taiwen Li; Jian Zhang; Xintao Qiu; Matthew Pun; Rinath Jeselsohn; et al. (BMC Bioinform., 2018)

Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. - Bianca K. Stöcker; Till Schäfer; Petra Mutzel; Johannes Köster; Nils M. Kriege; Sven Rahmann (SISAP, 2019)

Full-length de novo viral quasispecies assembly through variation graph construction. - Jasmijn A. Baaijens; Bastiaan Van der Roest; Johannes Köster; Leen Stougie; Alexander Schönhuth (Bioinform., 2019)

A Bayesian model for single cell transcript expression analysis on MERFISH data. - Johannes Köster; Myles Brown; Xiaole Shirley Liu (Bioinform., 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. - Yingbo Cui 001; Zihang Wang; Johannes Köster; Xiangke Liao; Shaoliang Peng; Tao Tang 001; Chun Huang; Canqun Yang (BMC Bioinform., 2021)

Sustainable data analysis with Snakemake. - Felix Mölder; Kim Philipp Jablonski; Brice Letcher; Michael B. Hall; Christopher Tomkins-Tinch; Vanessa V. Sochat; Jan Forster; Soohyun Lee; Sven Twardziok; Alexander Kanitz; Andreas Wilm; Manuel Holtgrewe; et al. (F1000Research, 2021)

Cancer Diagnostics and Therapy from Molecular Data. - Sven Rahmann; Alexander Schramm; Johannes Köster (Mach. Learn. under Resour. Constraints Vol. 3 (3), 2022)

Protein Complex Similarity. - Bianca K. Stöcker; Till Schäfer; Petra Mutzel; Johannes Köster; Nils M. Kriege; Sven Rahmann (Mach. Learn. under Resour. Constraints Vol. 3 (3), 2022)

Insane in the vembrane: filtering and transforming VCF/BCF files. - Till Hartmann; Christopher Schröder 002; Elias Kuthe; David Laehnemann; Johannes Köster (Bioinform., 2023)

Applying the FAIR Principles to Computational Workflows. - Sean R. Wilkinson; Meznah Aloqalaa; Khalid Belhajjame; Michael R. Crusoe; Bruno de Paula Kinoshita; Luiz Gadelha; Daniel Garijo; Ove Johan Ragnar Gustafsson; Nick S. Juty; Sehrish Kanwal; Farah Zaib Khan; Johannes Köster; et al. (CoRR, 2024)

Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing. - Hamdiye Uzuner; Annette Paschen; Dirk Schadendorf; Johannes Köster (BMC Bioinform., 2024)

Snakemaker: Seamlessly transforming ad-hoc analyses into sustainable Snakemake workflows with generative AI. - Marco Masera; Alessandro Leone; Johannes Köster; Ivan Molineris (CoRR, 2025)

A terminology for scientific workflow systems. - Frédéric Suter; Tainã Coleman; Ilkay Altintas; Rosa M. Badia; Bartosz Balis; Kyle Chard; Iacopo Colonnelli; Ewa Deelman; Paolo Di Tommaso; Thomas Fahringer; Carole A. Goble; Shantenu Jha; et al. (Future Gener. Comput. Syst., 2026)