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# Date: 04/25/2024


@Article{mosi734,
  author = {Wilsdorf, P. and Heller, J. and Budde, K. and Zimmermann, J. and Warnke, T. and Haubelt, C. and Timmermann, D. and van Rienen, U. and Uhrmacher, A. M.},
  title = {{A Model-Driven Approach for Conducting Simulation Experiments}},
  journal = {Applied Sciences},
  year = 2022,
  volume = {12},
  number = {16},
  month = aug,
  issn = {2076-3417},
  doi = {10.3390/app12167977}
}

@Article{mosi732,
  author = {Zimmermann, J. and Budde, K. and Arbeiter, N. and Molina, F. and Storch, A. and Uhrmacher, A. M. and van Rienen, U.},
  title = {{Using a digital twin of an electrical stimulation device to monitor and control the electrical stimulation of cells in vitro}},
  journal = {Frontiers in Bioengineering and Biotechnology},
  year = 2021,
  volume = {9},
  month = dec,
  issn = {2296-4185},
  doi = {10.3389/fbioe.2021.765516}
}

@Article{mosi723,
  author = {Budde, K. and Smith, J. and Wilsdorf, P. and Haack, F. and Uhrmacher, A. M.},
  title = {{Relating simulation studies by provenance - Developing a family of Wnt signaling models}},
  journal = {PLoS Computational Biology},
  year = 2021,
  volume = {17},
  number = {8},
  month = aug,
  publisher = {Public Library of Science},
  doi = {10.1371/journal.pcbi.1009227}
}

@Article{mosi614,
  author = {Haack, F. and Budde, K. and Uhrmacher, A. M.},
  title = {{Exploring mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling}},
  journal = {Journal of Cell Science},
  year = 2020,
  volume = {133},
  number = {15},
  month = aug,
  issn = {0021-9533},
  doi = {10.1242/jcs.243675}
}

@InProceedings{mosi606,
  author = {Wilsdorf, P. and Haack, F. and Budde, K. and Ruscheinski, A. and Uhrmacher, A. M.},
  title = {{Conducting Systematic, Partly Automated Simulation Studies - Unde Venis et Quo Vadis}},
  year = 2020,
  pages = {020001},
  month = nov,
  publisher = {AIP Publishing LCC},
  address = {Rhodes, Greece},
  booktitle = {17th International Conference of Numerical Analysis and Applied Mathematics},
  doi = {10.1063/5.0026939}
}

@InProceedings{mosi623,
  author = {Budde, K. and Neuhaus, E. and Molina, F. and Zimmermann, J. and Arbeiter, N. and Storch, A. and van Rienen, U. and Uhrmacher, A. M.},
  title = {{Documenting an Electrical Cell Stimulation Experiment - Guidelines at Work}},
  year = 2020,
  pages = {21--21},
  month = sep,
  address = {Rostock, Germany},
  booktitle = {Conference on Progress in Electrically Active Implants Tissue and Functional Regeneration (ELAINE 2020)},
  doi = {10.18453/rosdok\_id00002752}
}

@InProceedings{mosi591,
  author = {Budde, K. and Wilsdorf, P. and Smith, J. and Haack, F. and Ruscheinski, A. and Uhrmacher, A. M.},
  title = {{Reusing provenance information captured in WebProv for automatic generation of experiment specifications}},
  year = 2019,
  month = nov,
  address = {Berlin, Germany},
  booktitle = {Integrative pathway modeling in systems biology and systems medicine (INCOME 2019)}
}

@InProceedings{Budde19:EMBC,
  author = {Budde, K. and Zimmermann, J. and Neuhaus, E. and Schr{\"o}der, M. and Uhrmacher, A. M. and van Rienen, U.},
  title = {{Requirements for Documenting Electrical Cell Stimulation Experiments for Replicability and Numerical Modeling}},
  year = 2019,
  pages = {1082--108},
  month = jul,
  address = {Berlin, Germany},
  booktitle = {41st International Engineering in Medicine and Biology Conference (EMBC)},
  doi = {10.1109/embc.2019.8856863}
}

@InProceedings{mosi584,
  author = {Budde, K. and Smith, J. and Ruscheinski, A. and Uhrmacher, A. M.},
  title = {{WebProv: A web-based tool to access, store, and display provenance information of simulation models}},
  year = 2019,
  month = jul,
  url = {http://eprints.mosi.informatik.uni-rostock.de/584/},
  address = {Heidelberg, Germany},
  booktitle = {10th "Computational Modeling in Biology Network" (COMBINE) Meeting}
}

@InProceedings{mosi541,
  author = {Ruscheinski, A. and Budde, K. and Warnke, T. and Wilsdorf, P. and Hiller, B. C. and Dombrowsky, M. and Uhrmacher, A. M.},
  title = {{Generating Simulation Experiments Based on Model Documentations and Templates}},
  year = 2018,
  pages = {715--726},
  month = dec,
  address = {Gothenburg, Sweden},
  booktitle = {Winter Simulation Conference (WSC 2018)},
  doi = {10.1109/WSC.2018.8632515}
}

@InProceedings{mosi554,
  author = {Budde, K. and Helms, T. and Haack, F. and Uhrmacher, A. M.},
  title = {{Modeling long-range Wnt signaling with the domain-specific language ML-Rules}},
  year = 2018,
  month = oct,
  address = {Pisa, Italy},
  booktitle = {Workshop on "Multiscale modeling and simulations to bridge molecular and cellular scales" of the Centro di Ricerca Matematica Ennio De Giorgi}
}

@InProceedings{mosi560,
  author = {Budde, K. and Krummrich, E. and Ruscheinski, A. and Wilsdorf, P. and Haack, F. and Uhrmacher, A. M.},
  title = {{The Story Behind Wnt Simulation Models: Interrelating Wnt Models by Provenance Information}},
  year = 2018,
  month = sep,
  address = {Heidelberg, Germany},
  booktitle = {European Wnt Meeting 2018}
}

@InProceedings{mosi549,
  author = {Ruscheinski, A. and Gjorgevikj, D. and Dombrowsky, M. and Budde, K. and Uhrmacher, A. M.},
  title = {{Towards a PROV Ontology for Simulation Models}},
  year = 2018,
  pages = {192--195},
  month = jul,
  url = {https://eprints.mosi.informatik.uni-rostock.de/549/},
  publisher = {Springer International Publishing},
  address = {London, UK},
  booktitle = {7th International Provenance and Annotation Workshop (IPAW)}
}

@InProceedings{mosi525,
  author = {Budde, K. and Warnke, T. and Uhrmacher, A. M. and Sch{\"a}tz, E. and Starke, J. and Haack, F.},
  title = {{Exploiting equation-free analysis for multi-level, agent-based models in cell biology}},
  year = 2017,
  pages = {4564--4565},
  month = dec,
  publisher = {IEEE},
  address = {Las Vegas, NV, USA},
  booktitle = {Winter Simulation Conference (WSC 2017)},
  issn = {1558-4305},
  doi = {10.1109/WSC.2017.8248206}
}