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Wilsdorf, Pia and Wolpers, Anja and Hilton, Jason D. and Haack, Fiete and Uhrmacher, Adelinde M. (2023) Automatic Reuse, Adaption, and Execution of Simulation Experiments via Provenance Patterns. ACM Transactions on Modeling and Computer Simulation (TOMACS), 33 (1-2), 4:1-4:27. ISSN 1049-3301 (print) 1558-1195 (online).
Ruscheinski, Andreas and Wilsdorf, Pia and Zimmermann, Julius and van Rienen, Ursula and Uhrmacher, Adelinde M. (2022) An Artifact-based Workflow for Finite-Element Simulation Studies. Simulation Modelling Practice and Theory, 116, p. 102464. ISSN 1569-190X.
Haack, Fiete and Köster, Till and Uhrmacher, Adelinde M. (2021) Receptor/raft ratio is a determinant for LRP6 phosphorylation and WNT/β-catenin signaling. Frontiers in Cell and Developmental Biology, 9, p. 2085. ISSN 2296-634X.
Budde, Kai and Smith, Jacob and Wilsdorf, Pia and Haack, Fiete and Uhrmacher, Adelinde M. (2021) Relating simulation studies by provenance—Developing a family of Wnt signaling models. PLoS Computational Biology, 17 (8), pp. 1-21. ISSN 1553-7358 (print) 1553-734X (online).
Johnson, Margaret E. and Chen, Athena and Faeder, James R. and Henning, Philipp and Moraru, Ion I. and Meier-Schellersheim, Martin and Murphy, Robert F. and Prüstel, Thorsten and Theriot, Julie A. and Uhrmacher, Adelinde M. (2021) Quantifying the Roles of Space and Stochasticity in Computer Simulations for Cell Biology and Cellular Biochemistry. Molecular Biology of the Cell, 32 (2), pp. 186-210. ISSN 1059-1524.
Foguelman, Daniel and Henning, Philipp and Uhrmacher, Adelinde M. and Castro, Rodrigo (2021) EB-DEVS: A formal framework for modeling and simulation of emergent behavior in dynamic complex systems. Journal of Computational Science, 53, p. 101387. ISSN 18777503.
Wilsdorf, Pia and Fischer, Nadine and Uhrmacher, Adelinde M. (2021) Exploiting Provenance and Ontologies in Supporting Best Practices for Simulation Experiments: A Case Study on Sensitivity Analysis. In: Winter Simulation Conference (WSC 2021), 13-16 Dec 2021, Phoenix, Arizona, USA. Proceedings, published by IEEE Press, pp. 1-12.
Budde, Kai and Neuhaus, Elisa and Molina, Francia and Zimmermann, Julius and Arbeiter, Nils and Storch, Alexander and van Rienen, Ursula and Uhrmacher, Adelinde M. (2020) Documenting an Electrical Cell Stimulation Experiment–Guidelines at Work. In: Conference on Progress in Electrically Active Implants Tissue and Functional Regeneration (ELAINE 2020), 29-30 Sep 2020, Virtual. Proceedings,, Rostock, Germany, p. 21.
Haack, Fiete and Budde, Kai and Uhrmacher, Adelinde M. (2020) Exploring mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling. Journal of Cell Science, 133 (15), ISSN 0021-9533.
Zwar, Monique and Haack, Fiete and Bansod, Yogesh D. and Spiliotis, Konstantinos and Elhensheri, Mohamed and Molina, Francia and Krüger, Frank, eds. (2020) Proceedings of the Conference on Progress in Electrically Active Implants - Tissue and Functional Regeneration (ELAINE 2020). University of Rostock.
Heller, Jakob and Wilsdorf, Pia and Niemann, Christoph and Plocksties, Franz and Uhrmacher, Adelinde M. and Haubelt, Christian and Timmermann, Dirk (2020) Assisting Early Design Decision For Implantable Neurostimulators Through Virtual Prototyping. In: Conference on Progress in Electrically Active Implants - Tissue and Functional Regeneration (ELAINE 2020), 29-30 Sep 2020, Rostock, Germany. Proceedings,, p. 42. Poster.
Ruscheinski, Andreas and Wolpers, Anja and Henning, Philipp and Warnke, Tom and Haack, Fiete and Uhrmacher, Adelinde M. (2020) Pragmatic Logic-based Spatio-temporal Pattern Checking in Particle-based Models. In: Winter Simulation Conference (WSC 2020), 13-16 Dec 2020, Orlando, Florida, USA. Proceedings, published by IEEE Computer Society, pp. 2245-2256.
Staehlke, Susanne and Haack, Fiete and Waldner, Anna-Christin and Koczan, Dirk and Moerke, Caroline and Mueller, Petra and Uhrmacher, Adelinde M. and Nebe, J. Barbara (2020) ROS Dependent Wnt/β-Catenin Pathway and Its Regulation on Defined Micro-Pillars—A Combined In Vitro and In Silico Study. Cells, 9 (8), p. 1784. ISSN 2073-4409.
Wilsdorf, Pia and Haack, Fiete and Uhrmacher, Adelinde M. (2020) Conceptual Models in Simulation Studies: Making it Explicit. In: Winter Simulation Conference (WSC 2020), 13-16 Dec 2020, Orlando, Florida, USA. Proceedings, published by IEEE Computer Society, pp. 2353-2360.
Köster, Till and Henning, Philipp and Uhrmacher, Adelinde M. (2019) Potential based, spatial simulation of dynamically nested particles. BMC Bioinformatics, 20 (607), ISSN 1471-2105.
Budde, Kai and Smith, Jacob and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) WebProv: A web-based tool to access, store, and display provenance information of simulation models. In: 10th "Computational Modeling in Biology Network" (COMBINE) Meeting, 15-19 Jul 2019, Heidelberg, Germany. Poster.
Budde, Kai and Zimmermann, Julius and Neuhaus, Elisa and Schröder, Max and Uhrmacher, Adelinde M. and van Rienen, Ursula (2019) Requirements for Documenting Electrical Cell Stimulation Experiments for Replicability and Numerical Modeling. In: 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 23-27 July 2019, Berlin, Germany. Proceedings, published by IEEE, pp. 1082-1088.
Budde, Kai and Wilsdorf, Pia and Smith, Jacob and Haack, Fiete and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) Reusing provenance information captured in WebProv for automatic generation of experiment specifications. In: INCOME 2019 (Integrative pathway modeling in systems biology and systems medicine), 25-29 Nov 2019, Berlin, Germany.
Haack, Fiete and Trakooljul, Nares and Gley, Kevin and Murani, Eduard and Hadlich, Frieder and Wimmers, Klaus and Ponsuksili, Siriluck (2019) Deep sequencing of small non-coding RNA highlights brain-specific expression patterns and RNA cleavage. RNA Biology, 16 (12), pp. 1764-1774. ISSN 1547-6286.
Schröder, Max and Raben, Hendrikje and Krüger, Frank and Ruscheinski, Andreas and van Rienen, Ursula and Uhrmacher, Adelinde M. and Spors, Sascha (2019) PROVenance Patterns in Numerical Modelling and Finite Element Simulation Processes of Bio-Electric Systems. In: 41st Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 23-27 Jul 2019, Berlin, Germany. Proceedings, published by IEEE, pp. 3377-3382.
Wilsdorf, Pia (2019) Towards Automatically Generating Simulation Experiments. In: Winter Simulation Conference (WSC 2019), 08-11 Dec 2019, National Harbor, Maryland, USA. Poster.
Wilsdorf, Pia and Haack, Fiete and Budde, Kai and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) Conducting Systematic, Partly Automated Simulation Studies – Unde Venis et Quo Vadis. In: 17th International Conference of Numerical Analysis and Applied Mathematics, 23-28 Sep 2019, Rhodes, Greece. Proceedings, published by AIP Publishing LCC, AIP Conference Proceedings 2293(1), 020001.
Wilsdorf, Pia and Zimmermann, Julius and Dombrowsky, Marcus and van Rienen, Ursula and Uhrmacher, Adelinde M. (2019) Simulation Experiment Schemas - Beyond Tools and Simulation Approaches. In: Winter Simulation Conference (WSC 2019), 08-11 Dec 2019, National Harbor, Maryland, USA. Proceedings, published by IEEE, pp. 2783-2794.
Budde, Kai and Helms, Tobias and Haack, Fiete and Uhrmacher, Adelinde M. (2018) Modeling long-range Wnt signaling with the domain-specific language ML-Rules. In: Workshop on "Multiscale modeling and simulations to bridge molecular and cellular scales" of the Centro di Ricerca Matematica Ennio De Giorgi, 1-5 Oct 2018, Pisa, Italy. Poster.
Budde, Kai and Krummrich, Elisa and Ruscheinski, Andreas and Wilsdorf, Pia and Haack, Fiete and Uhrmacher, Adelinde M. (2018) The Story Behind Wnt Simulation Models: Interrelating Wnt Models by Provenance Information. In: European Wnt Meeting 2018, 12-14 Sep 2018, Heidelberg. Poster.
Ruscheinski, Andreas and Budde, Kai and Warnke, Tom and Wilsdorf, Pia and Hiller, Bjarne Christian and Dombrowsky, Marcus and Uhrmacher, Adelinde M. (2018) Generating Simulation Experiments Based on Model Documentations and Templates. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Proceedings, published by IEEE, pp. 715-726.
Warnke, Tom and Krüger, Frank and Uhrmacher, Adelinde M. (2018) Open Simulation Software - Development and Application. In: ASIM 2018 - 24. Symposium Simulationstechnik, 4-5 Oct 2018, Hamburg, Germany. Proceedings, published by ARGESIM Verlag Wien, pp. 307-312.
Warnke, Tom and Uhrmacher, Adelinde M. (2018) Complex simulation experiments made easy. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Proceedings, published by IEEE, pp. 410-424.
Budde, Kai and Warnke, Tom and Uhrmacher, Adelinde M. and Schätz, Eric and Starke, Jens and Haack, Fiete (2017) Exploiting equation-free analysis for multi-level, agent-based models in cell biology. In: Winter Simulation Conference (WSC 2017), 3-6 Dec 2017, Las Vegas, NV, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 4564-4565. Poster.
