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Johannes Köster
Tytuł
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Snakemake—a scalable bioinformatics workflow engine
J Köster, S Rahmann
Bioinformatics 28 (19), 2520-2522, 2012
17802012
Bioconda: sustainable and comprehensive software distribution for the life sciences
B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ...
Nature methods 15 (7), 475-476, 2018
5342018
Eleven grand challenges in single-cell data science
D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ...
Genome biology 21 (1), 1-35, 2020
4372020
Mutational dynamics between primary and relapse neuroblastomas
A Schramm, J Köster, Y Assenov, K Althoff, M Peifer, E Mahlow, ...
Nature genetics 47 (8), 872-877, 2015
2842015
The public repository of xenografts enables discovery and randomized phase II-like trials in mice
EC Townsend, MA Murakami, A Christodoulou, AL Christie, J Köster, ...
Cancer cell 29 (4), 574-586, 2016
2582016
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
W Li, J Köster, H Xu, CH Chen, T Xiao, JS Liu, M Brown, XS Liu
Genome biology 16 (1), 1-13, 2015
2462015
Sustainable data analysis with Snakemake
F Mölder, KP Jablonski, B Letcher, MB Hall, CH Tomkins-Tinch, V Sochat, ...
F1000Research 10, 2021
1902021
MiR‐137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A
K Althoff, A Beckers, A Odersky, P Mestdagh, J Köster, IM Bray, K Bryan, ...
International journal of cancer 133 (5), 1064-1073, 2013
1132013
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
MI Cornwell, M Vangala, L Taing, Z Herbert, J Köster, B Li, H Sun, T Li, ...
BMC bioinformatics 19 (1), 1-14, 2018
1052018
Practical computational reproducibility in the life sciences
B Grüning, J Chilton, J Köster, R Dale, N Soranzo, M van den Beek, ...
Cell systems 6 (6), 631-635, 2018
942018
SimLoRD: simulation of long read data
BK Stöcker, J Köster, S Rahmann
Bioinformatics 32 (17), 2704-2706, 2016
862016
CRISPR-DO for genome-wide CRISPR design and optimization
J Ma, J Köster, Q Qin, S Hu, W Li, C Chen, Q Cao, J Wang, S Mei, Q Liu, ...
Bioinformatics 32 (21), 3336-3338, 2016
522016
Next‐generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN‐amplified neuroblastoma
A Schramm, J Köster, T Marschall, M Martin, M Schwermer, K Fielitz, ...
International journal of cancer 132 (3), E106-E115, 2013
382013
Bioconda: Sustainable and comprehensive software distribution for the life sciences
R Dale, B Grüning, A Sjödin, J Rowe, BA Chapman, CH Tomkins-Tinch, ...
Nature Methods 15 (7), 475-476, 2018
322018
Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome
A Schramm, B Schowe, K Fielitz, M Heilmann, M Martin, T Marschall, ...
British journal of cancer 107 (8), 1409-1417, 2012
282012
Full-length de novo viral quasispecies assembly through variation graph construction
JA Baaijens, B Van der Roest, J Köster, L Stougie, A Schönhuth
Bioinformatics 35 (24), 5086-5094, 2019
262019
Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors
M Schwermer, S Lee, J Köster, T Van Maerken, H Stephan, A Eggert, ...
Oncotarget 6 (17), 15425, 2015
262015
Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy
L Such, F Zhao, D Liu, B Thier, VTK Le-Trilling, A Sucker, C Coch, ...
The Journal of clinical investigation 130 (8), 4266-4281, 2020
242020
Rust-Bio: a fast and safe bioinformatics library
J Köster
Bioinformatics 32 (3), 444-446, 2016
222016
Cancer evolution, mutations, and clonal selection in relapse neuroblastoma
M Schulte, J Köster, S Rahmann, A Schramm
Cell and tissue research 372 (2), 263-268, 2018
212018
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