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- Dynamic systems modeling of gene regulation from single-cell data
- Analysis of high-dimensional omics data, with a focus on mass spectrometry-based proteomics and metabolomics
- Brombacher, E., Schilling, O., & Kreutz, C. (2025). Characterizing the omics landscape based on 10,000+ datasets. Scientific Reports, 15, 3189.
- Dinh, T.-L.J., Rogg, M., Cosenza-Contreras, M., Li, M., Zirngibl, M., Pinter, N., Kurowski, K., Hause, F., Pauli, L., Imberg, F., Huynh, A., Schmid, M., Glavinsky, I., Braun, L., Van Wymersch, C., Bergmann, L., Ungefug, X., Kunz, M., Werner, T., Bernhard, P.,
Espadas, G., Brombacher, E., Schueler, J., Sabido, E., Kreutz, C., Gratzke, C., Werner, M., Grabbert, M., Bronsert, P., Schell, C., & Schilling, O. (2025). Proteomic analysis of non-muscle invasive and muscle invasive bladder cancer highlights distinct
subgroups with metabolic, matrisomal, and immune hallmarks and emphasizes
importance of the stromal compartment. The Journal of Pathology, 265, 41-56.
- Rachel, T. J., Brombacher, E., Woehrle, S., Gross, O., & Kreutz, C. (2024). Dynamic modelling of signalling pathways when ordinary differential equations are not
feasible. Bioinformatics, 40(12), btae683.
- Brombacher, E., & Kreutz, C. (2024). RTF: An R package for modelling time course
data. Bioinformatics, 40(10), btae597.
- Cosenza-Contreras, M., Seredynska, A., Vogele, D., Pinter, N., Brombacher, E., Cueto, R. F. et al (2024). TermineR: Extracting information on endogenous proteolytic
processing from shotgun proteomics data . Proteomics, 2300491.
- Stillger, M. N., Kurowski, K., Bronsert, P., Brombacher, E., Kreutz, C., Werner, M. et al. (2024). Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass. International Journal of Cancer, 154(12), 2162-2175.
- Fröhlich, K., Fahrner, M., Brombacher, E., Seredynska, A., Maldacker, M., Kreutz, C. et al. (2024). Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics. Molecular & Cellular Proteomics, 100800.
- Pfäffle, S. P., Herz, C., Brombacher, E., Proietti, M., Gigl, M., Hofstetter, C. K. et al. (2024). A 14-Day Double-Blind, Randomized, Controlled Crossover Intervention Study with Anti-Bacterial Benzyl Isothiocyanate from Nasturtium (Tropaeolum
majus) on Human Gut Microbiome and Host Defense. Nutrients, 16(3), 373.
- Brombacher, E.*, Hackenberg, M.*, Kreutz, C., Binder, H., & Treppner, M. (2022).
The performance of deep generative models for learning joint embeddings of single-cell multi-omics data. Frontiers in Molecular Biosciences, 9, 962644. (*contributed equally)
- Fröhlich, K.*, Brombacher, E.*, Fahrner, M. et al. (2022). Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale
dataset comprising inter-patient heterogeneity. Nature Communications 13(1), 2622. (*contributed equally)
- Egert, J., Brombacher, E., Warscheid, B., & Kreutz, C. (2021). DIMA: Data-Driven
selection of an imputation algorithm. Journal of Proteome Research, 20(7), 3489-3496.
- Brombacher, E., Schad, A., & Kreutz, C. (2020). Tail-Robust Quantile Normalization. Proteomics, 20(24), 2000068.
- Broek, J. A., Brombacher, E., Stelzhammer, V., Guest, P. C., Rahmoune, H., & Bahn, S. (2014). The need for a comprehensive molecular characterization of autism spectrum disorders. International Journal of Neuropsychopharmacology, 17(4),
651-673.
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| Curriculum Vitae |
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Since 7/2025
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PostDoc in the group of Prof. Dr. Jens Timmer, University of Freiburg |
12/2024 - 6/2025
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PostDoc, Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg |
6/2019 - 12/2024
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Doctoral candidate in the group of Dr. Clemens Kreutz, Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg |
10/2016 - 5/2019
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M.Sc. Computer Science, University of Freiburg |
10/2013 - 9/2016
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B.Sc. Computer Science, University of Freiburg |
10/2008 - 3/2011
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M.Sc. Genome-Based Systems Biology, University of Bielefeld |
10/2005 - 9/2008
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B.Sc. Biological Sciences, University of Konstanz |
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