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M.Sc. Kai Budde

Kai Budde
R: 308

Zur Person

Research assistant in the Infrastructure Support Project of the CRC ELAINE (https://www.elaine.uni-rostock.de/en).

Curriculum Vitae

Since 2022Research assistant in the Signal Theory and Digital Signal Processing Group at the Institute for Communications Engineering, University of Rostock, Germany
2017 - 2022Doctoral researcher in the Modeling and Simulation Group at the Institute for Visual and Analytic Computing, University of Rostock, Germany
2017Substitute Physics teacher, Gymnasium Reutershagen, Rostock, Germany
2013 - 2016M.Sc. Physics, University of Rostock, Germany
2014 - 2015Internship in the Data Analysis Group of Nordex SE, Hamburg, Germany
2010 - 2013B.Sc. Physics, University of Rostock, Germany
2009 - 2010Interdisciplinary Sciences (passed first year examinations), ETH Zurich, Switzerland

Research Interests

  • Research data management
  • Reproducible data analysis
  • Provenance of research data and simulation studies
  • Electrical stimulation of cells and tissue
  • Regenerative Medicine



Wilsdorf, P.; Heller, J.; Budde, K.; Zimmermann, J.; Warnke, T.; Haubelt, C.; Timmermann, D.; van Rienen, U.; Uhrmacher, A. M.:
A Model-Driven Approach for Conducting Simulation Experiments. In: Applied Sciences, Bd. 12, Nr. 16 (8/2022)
ISSN: 2076-3417, doi:10.3390/app12167977
Zimmermann, J.; Budde, K.; Arbeiter, N.; Molina, F.; Storch, A.; Uhrmacher, A. M.; van Rienen, U.:
Using a digital twin of an electrical stimulation device to monitor and control the electrical stimulation of cells in vitro. In: Frontiers in Bioengineering and Biotechnology, Bd. 9 (12/2021)
ISSN: 2296-4185, doi:10.3389/fbioe.2021.765516
Budde, K.; Smith, J.; Wilsdorf, P.; Haack, F.; Uhrmacher, A. M.:
Relating simulation studies by provenance - Developing a family of Wnt signaling models. In: PLoS Computational Biology, Bd. 17, Nr. 8 (8/2021)
Haack, F.; Budde, K.; Uhrmacher, A. M.:
Exploring mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling. In: Journal of Cell Science, Bd. 133, Nr. 15 (8/2020)
ISSN: 0021-9533, doi:10.1242/jcs.243675


Wilsdorf, P.; Haack, F.; Budde, K.; Ruscheinski, A.; Uhrmacher, A. M.:
Conducting Systematic, Partly Automated Simulation Studies - Unde Venis et Quo Vadis. 17th International Conference of Numerical Analysis and Applied Mathematics, S. 020001, Rhodes, Greece, 2020
Budde, K.; Neuhaus, E.; Molina, F.; Zimmermann, J.; Arbeiter, N.; Storch, A.; van Rienen, U.; Uhrmacher, A. M.:
Documenting an Electrical Cell Stimulation Experiment - Guidelines at Work. Conference on Progress in Electrically Active Implants Tissue and Functional Regeneration (ELAINE 2020), S. 21-21, Rostock, Germany, 2020
Budde, K.; Wilsdorf, P.; Smith, J.; Haack, F.; Ruscheinski, A.; Uhrmacher, A. M.:
Reusing provenance information captured in WebProv for automatic generation of experiment specifications. Integrative pathway modeling in systems biology and systems medicine (INCOME 2019), Berlin, Germany, 2019
Budde, K.; Zimmermann, J.; Neuhaus, E.; Schröder, M.; Uhrmacher, A. M.; van Rienen, U.:
Requirements for Documenting Electrical Cell Stimulation Experiments for Replicability and Numerical Modeling. 41st International Engineering in Medicine and Biology Conference (EMBC), S. 1082-108, Berlin, Germany, 2019
Budde, K.; Smith, J.; Ruscheinski, A.; Uhrmacher, A. M.:
WebProv: A web-based tool to access, store, and display provenance information of simulation models. 10th "Computational Modeling in Biology Network" (COMBINE) Meeting, Heidelberg, Germany, 2019
Ruscheinski, A.; Budde, K.; Warnke, T.; Wilsdorf, P.; Hiller, B. C.; Dombrowsky, M.; Uhrmacher, A. M.:
Generating Simulation Experiments Based on Model Documentations and Templates. Winter Simulation Conference (WSC 2018), S. 715-726, Gothenburg, Sweden, 2018
Budde, K.; Helms, T.; Haack, F.; Uhrmacher, A. M.:
Modeling long-range Wnt signaling with the domain-specific language ML-Rules. Workshop on "Multiscale modeling and simulations to bridge molecular and cellular scales" of the Centro di Ricerca Matematica Ennio De Giorgi, Pisa, Italy, 2018
Budde, K.; Krummrich, E.; Ruscheinski, A.; Wilsdorf, P.; Haack, F.; Uhrmacher, A. M.:
The Story Behind Wnt Simulation Models: Interrelating Wnt Models by Provenance Information. European Wnt Meeting 2018, Heidelberg, Germany, 2018
Ruscheinski, A.; Gjorgevikj, D.; Dombrowsky, M.; Budde, K.; Uhrmacher, A. M.:
Towards a PROV Ontology for Simulation Models. 7th International Provenance and Annotation Workshop (IPAW), S. 192-195, London, UK, 2018
Budde, K.; Warnke, T.; Uhrmacher, A. M.; Schätz, E.; Starke, J.; Haack, F.:
Exploiting equation-free analysis for multi-level, agent-based models in cell biology. Winter Simulation Conference (WSC 2017), S. 4564-4565, Las Vegas, NV, USA, 2017
ISSN: 1558-4305, doi:10.1109/WSC.2017.8248206