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ORCIDJohannes Köster
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2020 – today
- 2024
[j12]Hamdiye Uzuner, Annette Paschen, Dirk Schadendorf
, Johannes Köster:
Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing. BMC Bioinform. 25(1): 240 (2024)- [i5]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:
Applying the FAIR Principles to Computational Workflows. CoRR abs/2410.03490 (2024) - 2023
- [j11]Till Hartmann, Christopher Schröder, Elias Kuthe, David Laehnemann, Johannes Köster:
Insane in the vembrane: filtering and transforming VCF/BCF files. Bioinform. 39(1) (2023) - 2022
- [p2]Sven Rahmann, Alexander Schramm, Johannes Köster:
Cancer Diagnostics and Therapy from Molecular Data. Mach. Learn. under Resour. Constraints Vol. 3 (3) 2022: 43-57 - [p1]Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann:
Protein Complex Similarity. Mach. Learn. under Resour. Constraints Vol. 3 (3) 2022: 85-102 - 2021
- [j10]Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang:
VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. BMC Bioinform. 22(1): 344 (2021) - [i4]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:
Sustainable data analysis with Snakemake. F1000Research 10: 33 (2021)
2010 – 2019
- 2019
- [j9]Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinform. 35(6): 995-1001 (2019) - [j8]Johannes Köster, Myles Brown, Xiaole Shirley Liu:
A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinform. 35(13): 2347 (2019) - [j7]Jasmijn A. Baaijens, Bastiaan Van der Roest, Johannes Köster, Leen Stougie, Alexander Schönhuth:
Full-length de novo viral quasispecies assembly through variation graph construction. Bioinform. 35(24): 5086-5094 (2019) - [c2]Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann:
Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. SISAP 2019: 308-322 - [i3]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:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [j6]Johannes Köster, Sven Rahmann:
Snakemake - a scalable bioinformatics workflow engine. Bioinform. 34(20): 3600 (2018) - [j5]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:
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinform. 19(1): 135:1-135:14 (2018) - 2016
- [j4]Johannes Köster:
Rust-Bio: a fast and safe bioinformatics library. Bioinform. 32(3): 444-446 (2016) - [j3]Bianca K. Stöcker, Johannes Köster, Sven Rahmann:
SimLoRD: Simulation of Long Read Data. Bioinform. 32(17): 2704-2706 (2016) - [j2]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:
CRISPR-DO for genome-wide CRISPR design and optimization. Bioinform. 32(21): 3336-3338 (2016) - 2015
- [i2]Johannes Köster:
Rust-Bio - a fast and safe bioinformatics library. CoRR abs/1509.02796 (2015) - 2014
- [b1]Johannes Köster:
Parallelization, scalability, and reproducibility in next generation sequencing analysis. Dortmund University, Germany, 2014 - [i1]Johannes Köster, Sven Rahmann:
Massively parallel read mapping on GPUs with PEANUT. CoRR abs/1403.1706 (2014) - 2012
- [j1]Johannes Köster, Sven Rahmann:
Snakemake - a scalable bioinformatics workflow engine. Bioinform. 28(19): 2520-2522 (2012) - [c1]Johannes Köster, Sven Rahmann:
Building and Documenting Workflows with Python-Based Snakemake. GCB 2012: 49-56
Coauthor Index
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