Benjamin Schubert
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OptiType: precision HLA typing from next-generation sequencing data
A Szolek, B Schubert, C Mohr, M Sturm, M Feldhahn, O Kohlbacher
Bioinformatics 30 (23), 3310-3316, 2014
Best practices for single-cell analysis across modalities
L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ...
Nature Reviews Genetics 24 (8), 550-572, 2023
The EVcouplings Python framework for coevolutionary sequence analysis
TA Hopf, AG Green, B Schubert, S Mersmann, CPI Schärfe, JB Ingraham, ...
Bioinformatics 35 (9), 1582-1584, 2019
scCODA is a Bayesian model for compositional single-cell data analysis
M Buettner, J Ostner, CL Mueller, FJ Theis, B Schubert
Nature communications 12 (1), 6876, 2021
Induction of neoantigen-reactive T cells from healthy donors
M Ali, Z Foldvari, E Giannakopoulou, ML Böschen, E Strønen, W Yang, ...
Nature protocols 14 (6), 1926-1943, 2019
Predicting antigen specificity of single T cells based on TCR CDR 3 regions
DS Fischer, Y Wu, B Schubert, FJ Theis
Molecular systems biology 16 (8), e9416, 2020
Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19
R Kaiser, A Leunig, K Pekayvaz, O Popp, M Joppich, V Polewka, R Escaig, ...
JCI insight 6 (18), 2021
Impaired function and delayed regeneration of dendritic cells in COVID-19
E Winheim, L Rinke, K Lutz, A Reischer, A Leutbecher, L Wolfram, ...
PLoS pathogens 17 (10), e1009742, 2021
Artificial intelligence in early drug discovery enabling precision medicine
F Boniolo, E Dorigatti, AJ Ohnmacht, D Saur, B Schubert, MP Menden
Expert Opinion on Drug Discovery 16 (9), 991-1007, 2021
Designing string-of-beads vaccines with optimal spacers
B Schubert, O Kohlbacher
Genome medicine 8, 1-10, 2016
Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings
B Schubert, R Maddamsetti, J Nyman, MR Farhat, DS Marks
Nature Microbiology 4 (2), 328-338, 2019
EpiToolKit—a web-based workbench for vaccine design
B Schubert, HP Brachvogel, C Jürges, O Kohlbacher
Bioinformatics 31 (13), 2211-2213, 2015
FRED 2: an immunoinformatics framework for Python
B Schubert, M Walzer, HP Brachvogel, A Szolek, C Mohr, O Kohlbacher
Bioinformatics 32 (13), 2044-2046, 2016
Evaluation of peptide selection approaches for epitope‐based vaccine design
B Schubert, O Lund, M Nielsen
Tissue Antigens 82 (4), 243-251, 2013
Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’
DS Fischer, M Ansari, KI Wagner, S Jarosch, Y Huang, CH Mayr, M Strunz, ...
Nature communications 12 (1), 4515, 2021
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
P Domingo-Calap, B Schubert, M Joly, M Solis, M Untrau, R Carapito, ...
PLoS pathogens 14 (10), e1007368, 2018
Population-specific design of de-immunized protein biotherapeutics
B Schubert, C Schärfe, P Dönnes, T Hopf, D Marks, O Kohlbacher
PLoS computational biology 14 (3), e1005983, 2018
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification
L Schneider, T Kehl, K Thedinga, NL Grammes, C Backes, C Mohr, ...
Bioinformatics 35 (24), 5171-5181, 2019
Antigen-specific treg therapy in type 1 diabetes–challenges and opportunities
I Serr, F Drost, B Schubert, C Daniel
Frontiers in immunology 12, 712870, 2021
ImmunoNodes–graphical development of complex immunoinformatics workflows
B Schubert, L de la Garza, C Mohr, M Walzer, O Kohlbacher
BMC bioinformatics 18, 1-7, 2017
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