Johannes Köster

According to our database, Johannes Köster authored at least 19 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing.

Hamdiye Uzuner, Annette Paschen, Dirk Schadendorf, Johannes Köster

BMC Bioinform., December, 2024

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, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole A. Goble

CoRR, 2024

2023

Insane in the vembrane: filtering and transforming VCF/BCF files.

Till Hartmann, Christopher Schröder, Elias Kuthe, David Laehnemann, Johannes Köster

Bioinform., January, 2023

2022

Protein Complex Similarity.

Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann

Proceedings of the Machine Learning under Resource Constraints - Volume 3: Applications, 2022

Cancer Diagnostics and Therapy from Molecular Data.

Sven Rahmann, Alexander Schramm, Johannes Köster

Proceedings of the Machine Learning under Resource Constraints - Volume 3: Applications, 2022

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, Sven Rahmann, Sven Nahnsen, Johannes Köster

F1000Research, 2021

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments.

Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang

BMC Bioinform., 2021

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, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

PeerJ Prepr., 2019

A Bayesian model for single cell transcript expression analysis on MERFISH data.

Johannes Köster, Myles Brown, Xiaole Shirley Liu

Bioinform., 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

Protein Complex Similarity Based on Weisfeiler-Lehman Labeling.

Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann

Proceedings of the Similarity Search and Applications - 12th International Conference, 2019

2018

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, Myles Brown, Xiaole Shirley Liu, Henry W. Long

BMC Bioinform., 2018

2016

SimLoRD: Simulation of Long Read Data.

Bianca K. Stöcker, Johannes Köster, Sven Rahmann

Bioinform., 2016

CRISPR-DO for genome-wide CRISPR design and optimization.

Jian Ma, Johannes Köster, Qian Qin, Shengen Hu, Wei Li, Chenhao Chen, Qingyi Cao, Jinzeng Wang, Shenglin Mei, Qi Liu, Han Xu, Xiaole Shirley Liu

Bioinform., 2016

Rust-Bio: a fast and safe bioinformatics library.

Johannes Köster

Bioinform., 2016

2014

Parallelization, scalability, and reproducibility in next generation sequencing analysis

Johannes Köster

PhD thesis, 2014

Massively parallel read mapping on GPUs with PEANUT.

Johannes Köster, Sven Rahmann

CoRR, 2014

2012

Snakemake - a scalable bioinformatics workflow engine.

Johannes Köster, Sven Rahmann

Bioinform., 2012

Building and Documenting Workflows with Python-Based Snakemake.

Johannes Köster, Sven Rahmann

Proceedings of the German Conference on Bioinformatics 2012, 2012