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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).
Henning, Philipp and Köster, Till and Haack, Fiete and Burrage, Kevin and Uhrmacher, Adelinde M. (2023) Implications of different membrane compartmentalization models in particle-based in silico studies. Royal Society Open Science, 10 (7), e221177. ISSN 2054-5703.
Sahm, Franziska and Freiin Grote, Vivica and Zimmermann, Julius and Haack, Fiete and Uhrmacher, Adelinde M. and van Rienen, Ursula and Bader, Rainer and Detsch, Rainer and Jonitz-Heincke, Anika (2022) Long-term stimulation with alternating electric fields modulates the differentiation and mineralization of human pre-osteoblasts. Frontiers in Physiology, 13, ISSN 1664-042X.
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).
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.
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.
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.
Gley, Kevin and Murani, Eduard and Haack, Fiete and Trakooljul, Nares and Zebunke, Manuela and Puppe, Birger and Wimmers, Klaus and Ponsuksili, Siriluck (2019) Haplotypes of coping behavior associated QTL regions reveal distinct transcript profiles in amygdala and hippocampus. Behavioural Brain Research, 372, p. 112038. ISSN 0166-4328.
Peng, Danhua and Warnke, Tom and Haack, Fiete and Uhrmacher, Adelinde M. (2017) Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/β-catenin signaling pathway. Simulation: Transactions of the Society for Modeling and Simulation International, 93 (8), pp. 659-677. ISSN 0037-5497 (online 1741-3133).
Peng, Danhua and Warnke, Tom and Haack, Fiete and Uhrmacher, Adelinde M. (2016) Reusing simulation experiment specifications to support developing models by successive extension. Simulation Modelling Practice and Theory, 68, pp. 33-53. ISSN 1569-190X.
Haack, Fiete and Lemcke, Heiko and Ewald, Roland and Rharass, Tareck and Uhrmacher, Adelinde M. (2015) Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells. PLoS Computational Biology, 11 (3), e104106. ISSN 1553-7358 (print) 1553-734X (online).
Luboschik, Martin and Rybacki, Stefan and Haack, Fiete and Schulz, Hans-Jörg (2014) Supporting the integrated visual analysis of input parameters and simulation trajectories. Computers & Graphics, 39, pp. 37-47. ISSN 00978493.
Haack, Fiete and Fackeldey, Konstantin and Röblitz, Susanna and Scharkoi, Olga and Weber, Marcus and Schmidt, Burkhard (2013) Adaptive spectral clustering with application to tripeptide conformation analysis. The Journal of Chemical Physics, 139 (19), p. 194110. ISSN 0021-9606.
Haack, Fiete and Burrage, Kevin and Redmer, Ronald and Uhrmacher, Adelinde M. (2013) Studying the Role of Lipid Rafts on Protein Receptor Bindings with Cellular Automata. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (3), pp. 760-770. ISSN 1545-5963.
Müller, Felix Johannes and Haack, Fiete and Koester, Till and Uhrmacher, Adelinde M. (2024) Computational model of cell cell interaction in bone remodelling. In: ELAINE 2024, 20-22 Mar 2024, Rostock, Germany. Poster. (In Press)
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.
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.
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.
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.
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.
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.
Rybacki, Stefan and Haack, Fiete and Wolf, Karsten and Uhrmacher, Adelinde M. (2014) Developing simulation models - from conceptual to executable model and back - an artifact-based workflow approach. In: 7th International ICST Conference on Simulation Tools and Techniques (SIMUTools 2014), 17-19 Mar 2014, Lisbon, Portugal. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, pp. 21-30.
Helms, Tobias and Maus, Carsten and Haack, Fiete and Uhrmacher, Adelinde M. (2014) Multi-level modeling and simulation of cell biological systems with ML-rules: a tutorial. In: Winter Simulation Conference (WSC 2014), 7-10 Dec 2014, Savannah, GA, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305 Print ISSN: 0891-7736, pp. 177-191.
Warnke, Tom and Peng, Danhua and Haack, Fiete and Uhrmacher, Adelinde M. (2014) Towards a Language for Specifying Properties of Simulation Trajectories. In: International Conference on Computational Methods in Systems Biology (CMSB 2014), 17-19 Nov 2014, Manchester, UK. Poster.
Bittig, Arne T. and Haack, Fiete and Maus, Carsten and Uhrmacher, Adelinde M. (2011) Adapting rule-based model descriptions for simulating in continuous and hybrid space. In: 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), 21-23 Sep 2011, Paris, France. Proceedings, published by ACM, NewYork, USA, pp. 161-170.
Rybacki, Stefan and Himmelspach, Jan and Haack, Fiete and Uhrmacher, Adelinde M. (2011) WorMS- a framework to support workflows in M&S. In: Winter Simulation Conference (WSC 2011), 11-14 Dec 2011, Phoenix, AZ, USA. Proceedings, published by IEEE, Online ISSN: 0891-7736, pp. 716-727.
Haack, Fiete and Röblitz, Susanna and Scharkoi, Olga and Schmidt, Burkhard and Weber, Marcus (2010) Adaptive Spectral Clustering for Conformation Analysis. In: International Conference of numerical Analysis and Applied Mathematics (ICNAAM 2010), 19-25 Sep 2010, Rhodes, Greece. Proceedings, published by American Institute of Physics, AIP Conference Proceedings, volume 1281, pp. 1585-1588.
Haack, Fiete and Leye, Stefan and Uhrmacher, Adelinde M. (2010) A flexible architecture for modeling and simulation of diffusional association. In: 3rd Workshop From Biology To Concurrency and back, FBTC 2010, 27 Mar 2010, Paphos, Cyprus. Proceedings, published by Electronic Proceedings in Theoretical Computer Science (EPTCS), 19, pp. 70-84.
Haack, Fiete (2016) Exploring the spatio-temporal dynamics of lipid rafts and their role in signal transduction. PhD thesis, Institute of Computer Science, University of Rostock.
