Publikationstyp

Buchbeitrag

• Anne-Cécile Ribou, Tareck Rharass and Jean Vigo (2010): Looking Through the Microscope: What Can We Learn From Fluorescence Lifetime Measurements About Free Radicals in Living Cells?. - In: Handbook of Free Radicals: Formation, Types and Effects, ed. by Dimitri Kozyrev and Vasily Slutsky. Nova Science Publishers, New York, chap. 16, pp. 505-521.
• Adelinde M. Uhrmacher and Mathias Röhl (2007): Agent-Oriented Modeling in Simulation - Agents for Modeling and Modeling for Agents. - In: Handbook on Dynamic System Modeling, ed. by P Fishwick. CRC, Boca Raton, FL, USA, chap. 8, pp. 1-16.

Journalartikel

• Orianne Mazemondet, Mathias John, Stefan Leye, Arndt Rolfs and Adelinde Uhrmacher (accepted): Elucidating the sources of β-catenin dynamics in human neural progenitor cells. - PLOS-One.
• A Jaeger, J Baake, DG Weiss and R Kriehuber (2013): Glycogen synthase kinase-3beta regulates differentiation-induced apoptosis of human neural progenitor cells. - Int J Dev Neurosci, 31(1):61-68.
• Dagmar Waltemath, Richard Adams, Daniel A Beard, Frank T Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T Cooling, Jonathan Cooper, Edmund Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew MIller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert Sauro, Henning Schmidt, Jacky Snoep, Dominic Tolle, Olaf Wolkenhauer and Nicolas Le Novère (2011): Minimum Information About a Simulation Experiment (MIASE). - PLoS Computational Biology, 7(4).
• Yvonne Schmitz, Olaf Wolkenhauer and Katja Rateitschak (2011): Nucleo-cytoplasmic shuttling of APC can maximize beta-catenin/TCF concentration. - Journal of Theoretical Biology, 279:132-142.
• Steffen Hadlak, Hans-Jörg Schulz and Heidrun Schumann (2011): In Situ Exploration of Large Dynamic Networks. - IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2011), 17(12).
• Dagmar Waltemath, Richard Adams, Frank Bergmann, Michael Hucka, Fedor Kolpakov, Andrew Miller, Ion Moraru, David Nickerson, Sven Sahle, Jacky Snoep and Nicolas Le Novere (2011): Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - BMC Systems Biology, 5(198).
• Hans-Jörg Schulz (2011): treevis.net - A Tree Visualization Reference. - IEEE Computer Graphics and Applications, 31(6):6-10.
• Hans-Jörg Schulz, Steffen Hadlak and Heidrun Schumann (2011): The Design Space of Implicit Hierarchy Visualizations: A Survey. - IEEE Transactions on Visualization and Computer Graphics, 17(4):393-411.
• Hans-Jörg Schulz, Steffen Hadlak and Heidrun Schumann (2011): Point-Based Visualization for Large Hierarchies. - IEEE Transactions on Visualization and Computer Graphics, 17(5):598-611.
• Dennis Maciuszek, Sebastian Ladhoff and Alke Martens (2011): Content design patterns for game-based learning. - International Journal of Game-Based Learning.
• Orianne Mazemondet, Rayk Hybner, Jana Frahm, Dirk Koszan, Benjamin M. Bader, Dieter G. Weiss, Adelinde M. Uhrmacher, Moritz J. Frech, Arndt Rolfs and Jiankai Luo (2011): Quantitative und kinetic profile of Wnt/ß-catenin signaling components during human neural progenitor cell differentiation. - Cellular & Molecular Biology Letters, 16(4):515-538.
• Matthias Jeschke, Roland Ewald and Adelinde M. Uhrmacher (2011): Exploring the Performance of Spatial Stochastic Simulation Algorithms. - Journal of Computational Physics, 230(7):2562-2574.
• Anne-Katrin Giese, Jana Frahm, Rayk Hübner, Jiankai Luo, Andreas Wree, Moritz J Frech, Arndt Rolfs and Stefanie Ortinau (2011): Erythropoietin and the effect of oxygen during proliferation and differentiation of human neural progenitor cells. - BMC Cell Biology.
• Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde Uhrmacher and Andrea Unger (2011): Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models. - Formal Aspects of Computing, Online First.
• Marc Streit, Hans-Joerg Schulz, Alexander Lex, Dieter Schmalstieg and Heidrun Schumann (2011): Model-Driven Design for the Visual Analysis of Heterogeneous Data. - IEEE Transactions on Visualization and Computer Graphics.
• Dagmar Waltemath, Ron Henkel, Holger Meyer and Andreas Heuer (2011): Das Sombi-Framework zum Ermitteln geeigneter Suchfunktionen für biologische Modelldatenbasen. - Datenbank-Spektrum.
• Melanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova and colleagues None (2011): Controlled vocabularies and semantics in systems biology. - Nature Molecular Systems Biology, 7(543).
• Alexander Lex, Hans-Jörg Schulz, Marc Streit, Christian Partl and Dieter Schmalstieg (2011): VisBricks: Multiform Visualization of Large, Inhomogeneous Data. - IEEE Transactions on Visualization and Computer Graphics, 17(12).
• Carsten Maus, Stefan Rybacki and Adelinde M. Uhrmacher (2011): Rule-based multi-level modeling of cell biological systems. - BMC Systems Biology, 5(166).
• Alke Martens, Dennis Maciuszek, Géraldine Ruddeck and Martina Weicht (2010 (to appear)): Plug 'n Train -- A Component Based Approach . - Interaction Design and Architecture(s) Journal, Special issue on "Design Centered and Personalized Learning in Liquid and Ubiquitous Learning Places(DULP): Future Visions and Practical Implementations.
• Mathias John, Cédric Lhoussaine, Joachim Niehren and Adelinde Uhrmacher (2010): The Attributed Pi-Calculus with Priorities. - Transactions on Computational Systems Biology XII, 5945/2010:13-76.
• Jan Himmelspach, Mathias Röhl and Adelinde M. Uhrmacher (2010): Component-based models and simulation experiments for supporting valid multi-agent system simulations. - Journal of Applied Artificial Intelligence, 24(5):414-442.
• Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer and Mattias Goksör (2010): A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae. - Molecular BioSystems.
• A.S. Kiselyov, M.N. Semenova, N.B. Chernyshova, A. Leitao, A.V. Samet, K.A. Kislyi, M.M. Raihstat, T. Oprea, H. Lemcke, M Lantow, D.G. Weiss, S.A. Kuznetsov and V.V. Semenov (2010): Novel Derivatives of 1,3,4-Oxadiazoles Are Potent Mitostatic Agents Featuring Strong Microtubule Depolymerizing Activity in the Sea Urchin Embryo and Cell Culture Assays. - European Journal of Medicinal Chemistry, 45(5):1683-1697.
• Jana Frahm, Mats-Olof Mattsson and Myrtill Simkó (2010): Exposure to ELF magnetic fields modulate redox related protein expression in mouse macrophages. - Toxicology Letters, 192(3):330-336.
• Rayk Hübner, Anne-Caroline Schmöle, Andrea Liedmann, Moritz J. Frech, Arndt Rolfs and Jiankai Luo (2010): Differentiation of human neural progenitor cells regulated by Wnt-3a. - Biochem Biophys Res Commun, 400(3):358-362.
• Eik Hoffmann, Sabrina Marion, Bibhuti Mishra, Mathias John, Ramona Kratzke, Syed Ahmad, Daniela Holzer, Paras Anand, Dieter Weiss, Gareth Griffiths and Sergei Kuznetsov (2010): Initial receptor-ligand interactions modulate gene expression and phagosomal properties during both early and late stages of phagocytosis. - European Journal of Cell Biology, 89(9):693-704.
• Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère and Dagmar Waltemath (2010): Ranked retrieval of Computational Biology models. - BMC Bioinformatics, 11(423).
• Christian Lange, Eilhard Mix, Jana Frahm, Änne Glass, Jana Müller, Oliver Schmidt, Anne-Caroline Schmöle, Kristin Klemm, Stefanie ortinau, Rayk Hübner, Moritz J. Frech, Andreas Wree and Arndt Rolfs (2010): Small molecule GSK-3 inhibitors increase neurogenesis in human neural progenitor cells. - Neuroscience Letters.
• Steffen Hadlak, Christian Tominski, Hans-Jörg Schulz and Heidrun Schumann (2010): Visualization of Attributed Hierarchical Structures in a Spatio-Temporal Context. - International Journal of Geographical Information Science, 24(10):1497-1513.
• Anne-Caroline Schmöle, Anne Brennführer, Gnuni Karapetyan, Robert Jaster, Anahit Pews-Davtyan, Rayk Hübner, Stefanie Ortinau, Matthias Beller, Arndt Rolfs and Moritz J. Frech (2010): Novel indolylmaleimide acts as GSK-3beta inhibitor in human neural progenitor cells. - Bioorg Med Chem., 18(18):6785-6795.
• Roland Ewald, Jan Himmelspach, Matthias Jeschke, Stefan Leye and Adelinde M. Uhrmacher (2010): Flexible Experimentation in the Modeling and Simulation Framework JAMES II – Implications for Computational Systems Biology. - Briefings in Bioinformatics, 11(3):290-300.
• Anahit Pews-Davtyan, Annegret Tillack, Anne-Caroline Schmöle, Stefanie Ortinau, Moritz J. Frech, Arndt Rolfs and Matthias Beller (2010): A new facile synthesis of 3-amidoindole derivatives and their evaluation as potential GSK-3beta inhibitors. - Organic & Biomolecular Chemistry, 8(5):1149–1153.
• Peter J Morgan, Stefanie Ortinau, Jana Frahm, Norman Krüger, Arndt Rolfs and Moritz J Frech (2009): Protection of neurons derived from human neural progenitor cells by veratridine. - Neuroreport, 20(13):1225–1229.
• Simone Frey, Thomas Millat, Stefan Hohmann and Olaf Wolkenhauer (2008): How quantitative measures unravel design principles in multi-stage phosphorylation cascades. - Journal of Theoretical Biology, 254(1):27-36.
• O.N. Zefirova, E.V. Nurieva, H. Lemcke, A.A. Ivanov, D.V. Shishov, D.G. Weiss, S.A. Kuznetsov and N.S. Zefirov (2008): Design, synthesis, and bioactivity of putative tubulin ligands with adamantane core. - Bioorganic and Medical Chemistray letters, 18:5091-5094.
• O.N. Zefirova, E.V. Nurieva, H. Lemcke, A.A. Ivanov, N.V. Zyk, D.G. Weiss, S.A. Kuznetsov and N.S. Zefirov (2008): Design, synthesis and bioactivity of simplified taxol analogues on the basis of bicyclo[3.3.1]nonane derivatives. - Mendeleev Communications, 18:183-185.
• Matthias Jeschke, Alfred Park, Roland Ewald, Richard Fujimoto and Adelinde M. Uhrmacher (2008): A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological Simulations. - Performance Evaluation Review, 35(4):22-31.
• Raimund Hoffrogge, Susanne Beyer, Rayk Hübner, Stefan Mikkat, Eilhard Mix, Christian Scharf, Ulf Schmitz, Stefan Pauleweit, Matthias Berth, Igor Z. Zbrzycki, Hilmar Christoph, Jens Pahnke, Olaf Wolkenhauer, Adelinde Uhrmacher, Ulf Völker and Arndt Rolfs (2007): 2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells. - Proteomics, 7(1):33-46.
• Roland Ewald, Carsten Maus, Arndt Rolfs and Adelinde M Uhrmacher (2007): Discrete Event Modelling and Simulation in Systems Biology. - Journal of Simulation, 1(2):81-96.
• Yvonne Schmitz, Martin Baurmann, Bert Engelen and Ulrike Feudel (2007): Pattern Formation of Competing Microorganisms in Sediments. - Mathematical Modelling of Natural Phenomena, 2(4):74-104.
• Adelinde Uhrmacher, Arndt Rolfs and Jana Frahm (2007): DFG Research Training Group 1387/1 dIEM oSiRiS. - information technology, 49(6):388-395.

Konferenzband

• Youwei Zheng and Lars Schwabe (2011): Knowledge representation meets simulation to investigate memory problems after seizures. - In: 2011 International Conference on Brain Informatics, @ Lanzhou ~ China, IEEE, Springer Lecture Notes in Computer Science.
• Steffen Hadlak, Christian Tominski, Hans-Jörg Schulz and Heidrun Schumann (2010 (to appear)): Visualization of Hierarchies in Space and Time. - In: GeoVA(t) - Geospatial Visual Analytics: Focus on Time. Wokshop. Guimaraes, Portugal, 10-11 May. Proceedings.
• H. Lemcke, M. Zefirova,O.N. Lantow, M.N. Semenova, D.G. Weiss and S.A. Kuznetsov (2009): The use of light microscopy techniques and flow cytometric analyses in the search of new synthetic tubulin modulators. - In: 19th Annual Conference of the German Society for Cytometry, talk chosen from abstracts, pp. 30, Leipzig, DGfZ.
• Benjamin M Bader, Ernest Arenas and Dieter G. Weiss (2009): Quantitative image cytometry: nuclear beta-catenin shuttling during differentiation of human and mouse midbrain progenitor cells. - In: Abstract book: "19th Annual Conference of the German Society for Cytometry", pp. 18, Leipzig, DGfZ.
• Benjamin M. Bader and Dieter G. Weiss (2008): Signal protein translocation in differentiating human neural progenitor cells: 3D image quantification for a systems biology approach. - In: Cytometry Part B: Clinical Cytometry, vol. 74B, pp. 383, DGfZ, Wiley InterScience. DGfZ-ESCCA joint abstracts from The 18th Annual Meeting of The German Society of Cytometry (DGfZ) and The 8th Euroconference of Clinical Cell Analysis by The European Society for Clinical Cell Analysis (ESCCA).
• Orianne Mazemondet (2007): Exploration of the canonical Wnt signaling pathway. - In: Dagstuhl "zehn plus eins'' : zehn Informatik-Graduiertenkollegs und ein Informatik-Forschungskolleg stellen sich vor : 4. - 6. Juni 2007 : Kollegbeschreibungen und Kurzfassungen der Forschungsarbeiten von Stipendiaten/Kollegiaten, pp. 167, Dagstuhl. event 07232.
• Rayk Hübner (2007): Influence of Wnt proteins on differentiation of human neural progenitor cells. - In: Dagstuhl "zehn plus eins'" : zehn Informatik-Graduiertenkollegs und ein Informatik-Forschungskolleg stellen sich vor : 4. - 6. Juni 2007 : Kollegbeschreibungen und Kurzfassungen der Forschungsarbeiten von Stipendiaten/Kollegiaten, pp. 159-160, Dagstuhl. event 07232.

Masterthese, Diplomarbeit etc.

• Enrico Seib (2010): Arbeitsabläufe in der Modellierung und Simulation. - Masterthesis, Universität Rostock, Rostock.
• Steffen Hadlak (2009): Visualisierung von hierarchischen Strukturen auf einer Karte mit dem Point-Based Layout. - Diplomarbeit, University of Rostock.
• Alexander Steiniger (2009): Web-basiertes visuelles Monitoring von James II Simulationen. - Diplomarbeit, Universität Rostock, Computergrafik, Rostock.
• Yvonne Oertel (2009): ExML - ein Austauschformat für valide Experimentbeschreibungen zum Austausch zwischen verschiedenen Simulationssystemen. - Diplomarbeit, Universität Rostock, Rostock.
• Ron Henkel (2009): Determining Model Similarities through Ranking Functions using the Example of Biological Computational Models. - Diplomarbeit, Universtity of Rostock.
• Stefan Leye (2008): Grid-Inspired Simulation of Computationally Intensive Models. - Diplomarbeit, University of Rostock.
• Peter Sievert (2008): Parallele Optimierung von Simulationsmodellen. - Diplomarbeit, Universität Rostock.
• Clemens Holzhüter (2006): Visuelle Techniken zur Analyse von Microarraydaten. - Diplomarbeit, University of Rostock.

Online-Dokument

• Dagmar Waltemath, Neil Swainston, Allyson Lister, Frank Bergmann, Ron Henkel, Stefan Hoops, Michael Hucka, Nick Juty, Sarah Keating, Christian Knüpfer, Falko Krause, Camille Laibe, Wolfram Liebermeister, Catherine Lloyd, Goksel Misirli, Marvin Schulz, Morgan Taschuk and Nicolas Le Novère (2011): SBML Level 3 Package Proposal: Annotation. - Webpublished, http://dx.doi.org/10.1038/npre.2011.5610.1.
• Dagmar Waltemath, Frank T Bergmann, Richard Adams and Nicolas Le Novère (2011): Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1. - Webpublished, http://precedings.nature.com/documents/5846/version/1.

PhD These, Doktorarbeit etc.

• Roland Ewald (2010 (to appear)): Automatic Algorithm Selection for Complex Simulation Problems. - PhD thesis, Faculty of Computer Science and Electrical Engineering, University of Rostock.
• Mathias John (2010 (to appear)): Reaction Constraints for the Pi-Calculus - A language for the stochastic and spatial modeling of cell-biological processes. - PhD thesis, Universität Rostock. - PhD thesis, University of Rostock.
• Alexandra Jaeger (2010): Charakterisierung von Apoptoseprozessen während der Differenzierung von humanen neuralen VM197-Progenitorzellen in vitro. - PhD thesis, Universität Rostock, Rostock.
• Andrea Unger (2010): Visual Support for the Modeling and Simulation of Cell Biological Processes. - PhD thesis, Universität Rostock, Rostock.
• Hans-Jörg Schulz (2010): Explorative Graph Visualization. - PhD thesis, Universität Rostock, Rostock.
• Rayk Hübner (2010): Role of Wnt signaling in proliferation and differentiation of human neural progenitor cells (ReNcell VM). - PhD thesis, Universität Rostock.
• Benjamin Bader (2010): Spatio-temporal control of Wnt/β-catenin signaling during fate commitment of human neural progenitor cells. - Doktorarbeit, Universität Rostock, Rostock.
• Mathias Röhl (2008): Definition und Realisierung einer Plattform zur modellbasierten Komposition von Simulationsmodellen. - Doktorarbeit, Universität Rostock.

PosterReference

• Youwei Zheng and Lars Schwabe (2011): Robustness of STDP-induced memory to perturbations of presynaptic activity: a simulation study. - Poster, @ Stockholm ~ Sweden, 20th Annual Computational Neuroscience Meeting.
• Youwei Zheng, Gleb Barmashenko, Timo Kirschstein, Rüdiger Köhling and Lars Schwabe (2011): Robustness of “memory” to paroxysmal activity in simulations of model neurons. - Poster, @ Washington,DC ~ U.S., 41st Annual Meeting of Society for Neuroscience.
• Carsten Maus, Stefan Rybacki and Adelinde M. Uhrmacher (2011): Formal Rule-based Multi-Level Modeling. - Poster, Heidelberg/Mannheim, Germany, 12th International Conference on Systems Biology (ICSB).
• Yvonne Schmitz, Olaf Wolkenhauer and Katja Rateitschak (2010): Mathematical modelling of nucleo-cytoplasmic shuttling of beta-catenin and its antagonist APC. - Poster, Edinburgh, UK, 11th International Conference on Systems Biology.
• Gnuni Karapetyan, Anne-Caroline Schmöle, Anne Brennführer, Robert Jaster, Anahit Pews-Davtyan, Stefanie Ortinau, Arndt Rolfs, Moritz J. Frech and Matthias Beller (2010): The Synthesis of Novel Indolylmaleimides and The Biological Activity as GSK-3β Inhibitors in Human Neural Progenitor Cells. - Poster, .
• Anne-Caroline Schmöle, Lea Maciolek, Anne Brennführer, Robert Jaster, Anahit Pews-Davtyan, Matthias Beller, Arndt Rolfs and Moritz J. Frech (2010): Novel indolylmaleimide acts as GSK-3β inhibitor in human neural progenitor cells. - Poster, .
• Tareck Rharass, Margareta Lantow, Heiko Lemcke, Benjamin M. Bader, Bärbel Redlich, Sergei A. Kuznetsov and Dieter G. Weiss (2010): The Involvement of Reactive Oxygen Species (ROS) in the Regulation of Wnt Signaling Pathways. - Poster, Stockholm, Sweden, WNT Signaling in Physiology and Disease (WNT2010).
• Lars Schwabe, Youwei Zheng, Andre Homeyer and Thomas Kirste (2010): Neural Coding of Natural Vestibular Signals. - Poster, @ Limassol ~ Cyprus, 9th International Neural Coding Workshop.
• Hans-Joerg Schulz and Susanne Jürgensmann (2010): A Visual Survey of Tree Visualization. - Poster, Salt Lake City, Utah, USA, IEEE VisWeek 2010.
• Clemens Holzhüter, Steffen Hadlak and Heidrun Schumann (2010): Multi-Level Visualization for the Exploration of Temporal Trends in Simulation Data. - Poster, Baltimore, Maryland, USA, Winter Simulation Conference 2010.
• Clemens Holzhüter, Hans-Jörg Schulz and Heidrun Schumann (2010): Enriched Heatmaps for Visualizing Uncertainty in Microarray Data. - Poster, Leipzig, Germany, Eurographics Workshop on Visual Computing for Biology and Medicine 2010.
• Ron Henkel, Dagmar Waltemath and Lukas Endler (2010): Searching BioModels Database making use of Information Retrieval. - Poster, , International Conference on Systems Biology (ICSB).
• Carsten Maus, Mathias John, Stefan Rybacki and Adelinde M. Uhrmacher (2010): Towards Rule-Based Multi-Level Modeling. - Poster, Edinburgh, UK, 11th International Conference on Systems Biology (ICSB).
• Nick Juty, Nicolas Le Novère, Dagmar Waltemath and Christian Knüpfer (2010): Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY. - Poster, , International Conference on Systems Biology (ICSB) 2010.
• Rayk Hübner, Anne-Caroline Schmöle, Andrea Liedmann, Moritz J. Frech, Arndt Rolfs and Jiankai Luo (2010): Differentiation of human neural progenitor cells regulated by Wnt-3a. - Poster, .
• R. Garcia-Salcedo, S. Frey, G. Beltran, D. Bosch, K. Elbing, Y. Tian, S. Manchala, K. Rateitschak, O. Wolkenhauer and S. Hohmann (2010): Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae. - Poster, Gothenburg, Sweden, 35th FEBS Congress.
• T. Millat, S. Frey and O. Wolkenhauer (2010): How integrals over dynamic signals can unravel characteristic properties of signal transduction pathway. - Poster, Edinburgh, UK, 11th International Conference on Systems Biology.
• Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer and Mattias Goksör (2010): A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in S. cerevisiae. - Poster, Edinburgh, UK, 11th International Conference on Systems Biology.
• Tareck Rharass, Margareta Lantow, Heiko Lemcke, Fiete Haack, Suchi Smita, Bärbel Redlich, Sergei A. Kuznetsov and Dieter G. Weiss (2010): The Involvement of Reactive Oxygen Species in the Regulation of Wnt Signaling Pathways during Neural Differentiation. - Poster, Leipzig, Germany, DGfZ.
• Margareta Lantow, Tareck Rharass, Jana Markhoff, Carmen Mihoc, Dieter G. Weiss and Eberhard Burkel (2010): Biocompatibility Tests on Quasicrystal-Ultrahigh Molecular Weight Polyethylene (UHMWPE) Composites in Human MG63 Osteoblast-Like Cell Cultures. - Poster, Münster, Germany, Nanobio-Europe.
• Rayk Hübner, Arndt Rolfs and Jiankai Luo (2009): Influence of Wnt Signaling on Proliferation and Neuronal Differentiation of Human Neural Progenitor Cells. - Poster, Odense, Danmark, 6th International Stem Cells School in Regenerative Medicine .
• Michael Fröhlich, Alexandra Jaeger, Dieter G. Weiss and Ralf Kriehuber (2009): Specific inhibition of Bcl-2 leads to diminished neuronal differentiation in VM197 cells. - Poster, Leipzig, 19th Annual Conference of the German Society for Cytometry (DGFZ).
• Alexandra Jaeger, Susanne Klum and Ralf Kriehuber (2009): Apoptosis susceptibility is reduced in differentiated VM197 cells. - Poster, Konstanz, 1st Joint Congress of the Swiss and German Societies for Cell Biology - 32nd Annual Meeting of the German Society for Cell Biology (DGZ).
• Anne-Caroline Schmöle, Anne Brennführer, Anahit Pews-Davtyan, Annegret Tillack, Moritz J. Frech, Matthias Beller, Arndt Rolfs and Stefanie Ortinau (2009): Inhibition of Glycogen Synthase Kinase-3β by novel small molecules activates Wnt signaling in Human Neural Progenitor Cells. - Poster, .
• Anne-Caroline Schmöle, Anne Brennführer, Anahit Pews-Davtyan, Annegret Tillack, Moritz J. Frech, Matthias Beller, Arndt Rolfs and Stefanie Ortinau (2009): New designed small molecules canonical as Wnt modulators in human neural progenitor cells. - Poster, .
• Anne-Cécile Ribou, Tareck Rharass, Jean Vigo and Jean-Marie Salmon (2009): What Can We Learn From Fluorescence Lifetime Measurements About Free Radicals in Living Cells?. - Poster, Leipzig, Germany, DGfZ.
• Bing Wang, Jan Himmelspach, Roland Ewald, Yiping Yao and Adelinde M. Uhrmacher (2009): An Experimental Analysis Environment for Logical Process Simulation Algorithms. - Poster, , Proceedings of the SIMUTools'09: 2nd International Conference on Simulation Tools and Techniques.
• Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde M. Uhrmacher and Andrea Unger (2009): Interactive Poster: Exploring Time-Varying Hyper Graphs. - Poster, Atlantic City, NJ, USA.
• Benjamin M. Bader and Dieter G. Weiss (2009): Nuclear beta-catenin import during differentiation of neural midbrain progenitor cells. - Poster, Arolla, CH, EMBO Workshop: Wnt Signaling in Development and Disease.
• Ron Henkel, Dagmar Köhn, Andre Peters and Carsten Maus (2009): Similarity Measures for Computational Biological Models. - Poster, Manchester, UK, Data Integration in the Life Sciences, 6th International Workshop, DILS 2009.
• Carsten Maus, Matthias Jeschke and Adelinde M. Uhrmacher (2009): Spatial Multi-Level Modelling and Simulation for Systems Biology. - Poster, Bologna, Italy, Computational Methods in Systems Biology (CMSB).
• Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M. Uhrmacher and Arndt Rolfs (2009): Modeling the Cell Cycle Dependency of the Wnt/β-catenin Signaling Pathway in the Imperative π-Calculus. - Poster, Bologna, Italy, Computational Methods in Systems Biology (CMSB).
• Alexandra Jaeger, Michael Fröhlich, Torsten Viergutz, Dieter G. Weiss and Ralf Kriehuber (2009): Activation of apoptosis pathways during the on-set of differentiation of human neural pregenitor cells in vitro. - Poster, Leipzig, 19th Annual Conference of the German Society for Cytometry (DGFZ), Abstract Book, p.62.
• Rayk Hübner, Orianne Mazemondet, Jana Frahm, Dirk Koczan, Dieter G. Weiss, Adelinde M. Uhrmacher, Arndt Rolfs and Jiankai Luo (2009): Spatiotemporal regulation of Wnt signaling components in different differentiation stages of human neural progenitor cells. - Poster, Prague, International Stem Cell School in Regenerative Medicine 2009.
• Dagmar Köhn, Christian Knüpfer and Nicolas Le Novère (2009): Beyond Structure: KiSAO and TEDDY - Two ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology. - Poster, SBML Hackathon, poster presentation.
• Dagmar Köhn, Christian Knüpfer and Nicolas Le Novère (2009): Beyond Structure: Ontologies for Pragmatical and Dynamical Aspects of Computational Models in Systems Biology. - Poster, 12th Annual Bio-Ontologies Meeting, ISMB 2009.
• Dagmar Köhn, Richard Adams, Frank Bergman, Igor Goryanin, Michael Hucka, Fedor Kolpakov, Nicolas Le Novere, Ion Moraru, Sven Sahle and Henning Schmidt (2009): Describing Simulation Experiments using the SED-ML. - Poster, , 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 8th European Conference on Computational Biology (ECCB).
• Géraldine Ruddeck, Jan Himmelspach and Alke Martens (2009): Intelligent Tutoring of Modeling and Simulation Techniques. - Poster, , Winter Simulation Conference.
• Anne-Caroline Schmöle, Anne Brennführer, Anahit Pews-Davtyan, Annegret Tillack, Moritz J. Frech, Matthias Beller, Arndt Rolfs and Stefanie Ortinau (2009): New designed small molecules act as GSK-3 inhibitors in human neural progenitor cells. - Poster, .
• J. Bäder, R. Hübner, M. Menzel, S. Ortinau, A. Rolfs and J. Frahm (2008): TCF activity and neuronal differentiation of immortalized human neural progenitor cell line (ReNcell VM). - Poster, Berlin, 5th International Stem Cell School.
• Benjamin M Bader, Yvonne Schmitz, Bärbel Redlich, Katja Rateitschak, Olaf Wolkenhauer and Dieter G Weiss (2008): Quantitative 3D image analysis to study the beta-catenin translocation during differentiation of human neural progenitor cells. - Poster, Dresden, Proceedings of "2nd International Congress on Stem Cells and Tissue Formation" July 6-9.
• Orianne Mazemondet, Jana Frahm, Arndt Rolfs and Adelinde M. Uhrmacher (2008): Biochemical and computational analyses of Wnt/beta-catenin dependent pathway during differentiation of human neural progenitor cells. - Poster, , Horizons in Molecular Biology-PhD symposium.
• Orianne Mazemondet, Adelinde M. Uhrmacher, Arndt Rolfs and Jana Frahm (2008): Spatio-temporal expression analyses of Wnt/beta-catenin dependent. - Poster, , International Stem Cell School in Regenerative Medicine 2008.
• Arne T. Bittig, David Carling and Olaf Wolkenhauer (2008): A Mathematical Model of the Regulation of AMPK Activation. - Poster, Gothenburg, Sweden, 9th International Conference on Systems Biology.
• Arne T. Bittig and Henning Schmidt (2008): Format Overflow? Handling of Modeling Projects in Systems Biology. - Poster, Gothenburg, Sweden, 9th International Conference on Systems Biology.
• Matthias Jeschke and Adelinde M. Uhrmacher (2008): Multi-Resolution Spatial Simulation. - Poster, , The 6th Conference on Computational Methods in Systems Biology (CMSB'08).
• R. Hübner, E. Mix and Dieter G. Weiss (2008): WNT-8a signaling in HEK293 cells. - Poster, Keystone, CO, USA, Symposium on Wnt/beta-Catenin Signaling in Development and Disease.
• R. Hübner, A. Rolfs and J. Frahm (2008): Wnt target genes in human neural progenitor cells. - Poster, Berlin, 5th International Stem Cell School.
• Benjamin M. Bader, Orianne Mazemondet, Rayk Hübner, Bärbel Redlich, Eilhard Mix, Arndt Rolfs and Dieter G. Weiss (2008): Beta-catenin translocation influences early differentiation of human neural progenitor cells. - Poster, Keystone, CO, USA, Proceedings of Keystone Symposium on Wnt/beta-Catenin Signaling in Development and Disease.
• S. Frey, H. Schmidt, K. Rateitschak, O. Wolkenhauer, G. Beltran, R. Garcia-Salcedo, K. Elbing, D. Bosch, T. Ye and S. Hohmann (2008): Modelling Snf1 regulation in Saccharomyces cerevisiae. - Poster, , ICSB 2008, Gothenburg, Sweden, August 2008 .
• Alexandra Jaeger, Susanne Klum, Dieter G. Weiss and Ralf Kriehuber (2008): The differentiation of human neuronal progenitor cells is accompanied by apoptotic cell death – a protective role of Bcl-2β. - Poster, Luxembourg, Luxembourg, Apoptosis World 2008 - From mechanisms to applications; Jan 23th to 26th, 2008.
• Alexandra Jaeger, Susanne Klum, Benjamin M. Bader, Dieter G. Weiss and Ralf Kriehuber (2008): Expression profile of apoptosis-related genes during differentiation in the human neuronal progenitor cell line VM197. - Poster, Marburg/Lahn, Germany, "German Society for Cell Biology - Annual Meeting 2008", March 12 to March 15, European Journal of Cell Biology, Volume 87S1, Suppl. 58, p 18, ISSN 0171-9335.
• Benjamin M Bader, Bärbel Redlich and Dieter G Weiss (2008): Quantitative 3D analysis and evaluation of confocal images for the study of translocation of Wnt-signalling molecules in human neural progenitor cells . - Poster, Marburg/Lahn, Germany, "German Society for Cell Biology - Annual Meeting 2008", published in European Journal of Cell Biology, Volume 87S1, Suppl. 58, p 18, ISSN 0171-9335..
• Orianne Mazemondet, Jana Frahm, Eilhard Mix and Arndt Rolfs (2008): Kinetic changes of LRP6, Fzd2, CK1, GSK3beta and Axin 2 during differentiation of human neural progenitor cell line. - Poster, Keystone, CO., USA, Wnt/beta-catenin signaling in development and disease.
• Benjamin Bader and Dieter Weiss (2008): A study of protein translocation during differentiation of human neural progenitor cells: Quantitative data generation from confocal 3D images for a systems biology approach. - Poster, Budapest, Hungary, Proceedings of ISAC XXIV International Congress 2008 - Cytometry in the Age of Systems Biology - (International Society for the Advancement of Cytometry).
• Yvonne Schmitz, Benjamin B. Bader, Dieter G. Weiss, Olaf Wolkenhauer and Katja Rateitschak (2008): Elucidating the role of nucleo-cytoplasmic shuttling of β-catenin antagonists by mathematical modelling. - Poster, Tenerife, Spain, 30th September-2nd October, Summer School on Systems Biology for Medical Applications.
• Benjamin Bader, Bärbel Redlich and Dieter Weiss (2008): Neuronal progenitor cell fate: following Wnt-pathway components during glial and neuronal differentiation. - Poster, Berlin, Proceedings of 5th international stem cell school on regenerative medicine.
• Hans-Jörg Schulz, Steffen Hadlak and Heidrun Schumann (2008): Interactive Poster: A Point-Based Layout for Large Hierarchies. - Poster, , Poster Compendium of the IEEE InfoVis.
• Simone Frey, Thomas Millat, S. Hohmann and Olaf Wolkenhauer (2008): How Quantitative Measures unravel Design Principles in multi-stage Phosphorylation Cascades. - Poster, Gothenburg, Sweden, 9th International Conference on Systems Biology.
• Anne-Caroline Schmöle, Anahit Pews-Davtyan, Anne Brennführer, Annegret Tillack, Jana Frahm, Matthias Beller, Arndt Rolfs and Susanne Ortinau (2008): Glycogen Synthase Kinase-3β via the Accumulation of β-catenin in Human Neural Progenitor Cells. - Poster, Berlin, Germany, 5th Stem Cell School for Regenerative Medicine.
• Hans-Jörg Schulz, Mathias John, Andrea Unger and Heidrun Schumann (2008): Interactive Poster: Table-based Visualization and Interaction for Bipartite Graphs. - Poster, Columbus, USA, IEEE Information Visualization.
• C. Lange, E. Mix, J. Müller, A. Glass, K. Klemm, R. Hübner, A. Wree, A.M. Uhrmacher and A. Rolfs (2007): Small molecule GSK-3β inhibitors that mediate Wnt/β-catenin signaling enhance dopaminergic differentiation of human neural progenitor cells. - Poster, University of California, San Diego, Wnt Meeting.
• Benjamin Bader, Orianne Mazemondet, Arndt Rolfs and Dieter G. Weiss (2007): Characterizing the Wnt-pathway components and their subcellular localization in differentiating human neural progenitor cells. - Poster, Hamburg, Molecular pathways in health and disease of the nervous system.
• Stefan Leye, Matthias Jeschke and Mathias John (2007): The SpacePi simulator. - Poster, Edinburgh, Computational Methods in systems Biology.
• Orianne Mazemondet, Benjamin M. Bader, Arndt Rolfs and Dieter G. Weiss (2007): Wnt-pathway in differentiating human neural progenitor cells . - Poster, , Spring School for Regenerative Medicine, Oslo, Norway.
• Hans-Jörg Schulz, Martin Luboschik and Heidrun Schumann (2007): Exploration of the 3D Treemap Design Space. - Poster, Sacramento, USA, Poster Compendium of the IEEE InfoVis Conference.
• James Abello, Hans-Jörg Schulz, Benoit Gaudin and Christian Tominski (2007): Name That Cluster – Text vs. Graphics. - Poster, Sacramento, USA, Poster Compendium of the IEEE InfoVis Conference.
• James Abello, Hans-Jörg Schulz, Heidrun Schumann and Christian Tominski (2007): CGV - Coordinated Graph Visualization. - Poster, Sacramento, USA, Poster Compendium of the IEEE InfoVis Conference.
• Mathias John, Dagmar Köhn and Robert Waltemath (2007): The Pi Markup Language - A First Approach to Make Pi Exchangable. - Poster, Edinburgh, CMSB.
• Carsten Maus, Mathias John and Adelinde M. Uhrmacher (2007): A Multi-Level and Multi-Formalism Approach for Model Composition in Systems Biology. - Poster, Edinburgh (GB), Computational Methods in Systems Biology (CMSB).
• Dagmar Köhn and Mathias John (2007): The Pi Markup Language - Toward Pi-Model Exchange and Reuse. - Poster, Long Beach, California (US), Online Proceedings of the Eighth International Conference on Systems Biology.
• Benjamin M. Bader, Orianne Mazemondet, Arndt Rolfs and Dieter G. Weiss (2007): Wnt-pathway in differentiating human neural progenitor cells (ReNcell VM). - Poster, MDC, Berlin, Germany, Proceedings of "Wnt Signaling in Development and Disease" .
• Benjamin M. Bader and Dieter G. Weiss (2007): Canonical Wnt-Pathway and Cytoskeleton in Human Neural Progenitor Cells (ReNcell VM). - Poster, Hamburg, Germany, Proceedings in "GBM Fall Meeting 2007".
• Alexandra Jaeger, Susanne Klum, Dieter Weiss and Ralf Kriehuber (2007): Expression of apoptosis-related protein during differentiation in the human neuronal progenitor cell line (ReNCell VM 197). - Poster, Hamburg, Germany, Proceedings in "GBM Fall Meeting 2007".
• Benjamin Bader and Dieter Weiss (2007): Lipofection of GFP-fusion-proteins as a tool to investigate the dynamics and plasticity of dendritic spines in primary mouse frontal cortex cultures. - Poster, Hamburg, Molecular pathways in health and disease of the nervous system.
• Andrea Unger, Susanne Biermann, Mathias John, Adelinde Uhrmacher and Heidrun Schumann (2007): Visual Support for Modeling and Simulation of Cell Biological Systems. - Poster, Washington, D.C., USA, Winter Simulation Conference.
• Christian Tominski, Clemens Holzhüter, Andrea Unger and Heidrun Schumann (2007): Interactive Poster: Visualization of Gene Combinations. - Poster, Sacramento, USA, IEEE Information Visualization Conference (InfoVis).
• Stefan Leye, Corrado Priami and Adelinde M. Uhrmacher (2007): POp-BetaSim - A Parallel, Bounded Optimistic Simulator for Beta-binders. - Poster, Edinburgh, Computational Methods in Systems Biology.
• Hans-Jörg Schulz, Heidrun Schumann and Thomas Nocke (2006): Visualizing and Analyzing Large Systems of Differential Equations. - Poster, Monterey, Winter Simulation Conference.
• Dagmar Köhn and Lena Strömbäck (2006): A Schema Matching Architecture for the Bioinformatics Domain. - Poster, Monterey, Winter Simulation Conference.
• Simone Frey, Thomas Millat, Katja Rateitschak and Olaf Wolkenhauer (2006): Quantitative measures to characterize properties of cell signalling cascades. - Poster, Monterey, Winter Simulation Conference.
• Roland Ewald, Enrico Gutzeit, Sebastian Schwanke, Adelinde Uhrmacher, Christian Lange, Susanne Biermann and Carsten Maus (2006): Multi-Level Modeling with DEVS - A Critical Inspection and Steps Towards a Feasible Approach . - Poster, Monterey, Winter Simulation Conference.
• Arne Bittig, Olaf Wolkenhauer and Jan-Hendrik Hofmeyr (2006): A Principal Limitation of Virtual Cell Simulations using Differential Equations . - Poster, Monterey, Winter Simulation Conference.
• Carsten Maus (2006): Simulation of the kinetically controlled riboswitch folding in 5' untranslated mRNA regions. - Poster, Monterey, Winter Simulation Conference.
• Mathias John, Christian Tominski and Heidrun Schumann (2006): Interactive Poster: Two-Tone Pseudo Coloring for Multiple Variables. - Poster, Baltimore, USA, IEEE Symposium on Information Visualization (InfoVis '06).

Sammelbandbeitrag

• Dennis Maciuszek and Alke Martens (2011): A reference architecture for game-based intelligent tutoring. - In: Handbook of Research on Improving Learning and Motivation through Educational Games: Multidisciplinary Approaches, ed. by Patrick Felicia, IGI Global, Hershey, PA.
• Dennis Maciuszek and Alke Martens (2010): Patterns for the design of educational games. - In: Educational Games: Design, Learning and Applications, ed. by Frej Edvardsen and Halsten Kulle, chap. 8, pp. 263-279, Nova, Hauppauge, NY.
• Simone Frey, Olaf Wolkenhauer and Thomas Millat (2009): Quantifying properties of cell signaling cascades. - In: Control Theory and Systems Biology, ed. by Pablo A. Iglesias and Brian Ingalls, chap. 4, pp. 69-84, MIT press.
• Carsten Maus, Mathias John, Mathias Röhl and Adelinde M Uhrmacher (2008): Hierarchical Modeling for Computational Biology. - In: SFM 2008, Formal Methods for Computational Systems Biology, ed. by Marco Bernardo, Pierpaolo Degano and Gianluigi Zavattaro, pp. 81-124, Springer, Berlin Heidelberg.
• Hans-Jörg Schulz and Thomas Nocke (2007): Maschinelle Datenanalyse im Informationszeitalter - Können oder müssen wir ihr vertrauen?. - In: Ordnungen des Denkens - Debatten um Wissenschaftstheorie und Erkenntniskritik, ed. by Ronald Langner, Timo Luks, Anette Schlimm, Gregor Straube, Dirk Thomaschke, LIT-Verlag, Münster.

Sonstiger Literaturtyp

• Ron Henkel and Dagmar Waltemath (2010): Searching the BioModels Database. - Miscellaneous publication, Software Demonstration at the Integrative Bioinformatics 2010 Symposium, Cambridge (UK) .
• Dagmar Köhn, Nicolas Le Novere and Christian Knüpfer (2009): Beyond Structure: KiSAO and TEDDY - Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology. - Miscellaneous publication, 3rd International Biocuration Conference, Available from Nature Precedings .
• Dagmar Köhn and Nicolas Le Novère (2008): The KInetic Simulation Algorithm Ontology (KiSAO) - A Proposal for the Classification of Simulation Algorithms in Systems Biology. - Miscellaneous publication, Invited Talk, Super-Hackathon, Okinawa, Japan.
• Dagmar Köhn and Nicolas Le Novère (2008): Minimum Information About a Simulation Experiment (MIASE) - Toward the Repetition of Simulation Runs. - Miscellaneous publication, Invited Talk, Super-Hackathon, Okinawa, Japan.
• Mathias John (2007): Spatial Modeling of Molecular Biological Systems. - Miscellaneous publication, Dagstuhl.
• Nicolas Le Novère and Dagmar Köhn (2007): Minimum Information About a Simulation Experiment (MIASE) - Toward the Repitition of Simulation Runs. - Miscellaneous publication, The Twelfth Systems Biology Markup Language (SBML) Forum Meeting.
• Alexandra Jaeger (2007): Characterization of apoptosis-pathways in human neuronal progenitor cells. - Miscellaneous publication.

Tagungsband

• Holger Diener, Dennis Maciuszek, Steffen Malo, Alke Martens and Bodo Urban (ed.) (2010): Spielend lernen. Tagungsband der Abschlusskonferenz des Verbundprojektes Alphabit in Zusammenarbeit mit dem 4. Workshop Game-based Learning. - Fraunhofer-Verlag, Stuttgart.
• Matthias Virgin, Andre Peters and Dagmar Köhn (ed.) (2009): 21. Workshop Grundlagen von Datenbanken. - Preprints aus dem Institut für Informatik der Universität Rostock.

Tagungsbeitrag

• Clemens Holzhüter, Alexander Lex, Dieter Schmalstieg, Hans-Jörg Schulz, Heidrun Schumann and Marc Streit (2012 (to appear)): Visualizing Uncertainty in Biological Expression Data. - In: Proceedings of the Visualization and Data Analysis VDA'12.
• Martin Luboschik, Christian Tominski, Arne Bittig, Adelinde M. Uhrmacher and Heidrun Schumann (2012 (accepted)): Towards Interactive Visual Analysis of Microscopic-Level Simulation Data. - In: Proceedings of SIGRAD 2012 – Interactive Visual Analysis of Data, citeulike-article-id = 11450119.
• Hans-Jörg Schulz, Adelinde Uhrmacher and Heidrun Schumann (2011): Visual Analytics for Stochastic Simulation in Cell Biology. - In: Proceedings of the Special Track on Theory and Applications of Visual Analytics (TAVA) of the i-Know'11 Conference, ACM.
• Arne T. Bittig, Fiete Haack, Carsten Maus and Adelinde M. Uhrmacher (2011): Adapting Rule-based Model Descriptions for Simulating in Continuous and Hybrid Space. - In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, pp. 161-170, New York, NY, USA, ACM. CMSB '11.
• Stefan Leye, Orianne Mazemondet and Adelinde M Uhrmacher (2010 (to appear)): Parallel analysis with FAMVal to speed up simulation-based model checking. - In: 4th European Modelling Symposium on Mathematical Modelling and Computer Simulation.
• Sabine Zinn, Jutta Gampe, Jan Himmelspach and Adelinde M. Uhrmacher (2010): A DEVS Model For Demographic Microsimulation. - In: Spring Simulation Multi-Conference - Symposium on Theory of Modeling & Simulation - DEVS Integrative M&S Symposium (DEVS), pp. 146:1--146:8, New York, NY, USA, ACM.
• Dennis Maciuszek, Géraldine Ruddeck and Alke Martens (2010): Component-based development of educational games: The case of the user interface. - In: Proceedings of the 4th European Conference on Games-Based Learning (ECGBL 2010), ed. by Bente Meyer, pp. 208-217, Reading, UK, Academic Publishing.
• Géraldine Ruddeck and Alke Martens (2010): Communication Patterns in Component-Based ITS. - In: ICALT2010.
• Dennis Maciuszek and Alke Martens (2010): Computer-Rollenspiele als didaktikübergreifendes Lernspiel-Genre. - In: Spielend lernen - Tagungsband der Abschlusskonferenz des Verbundprojektes Alphabit in Zusammenarbeit mit dem 4. Workshop Game-based Learning, ed. by Holger Diener, Dennis Maciuszek, Steffen Malo, Alke Martens, Bodo Urban, pp. 43-57, Stuttgart, Fraunhofer-Verlag.
• Stefan Leye, Mathias John and Adelinde M. Uhrmacher (2010): A Flexible Architecture for Performance Experiments with the pi-Calculus and its Extensions. - In: 3rd International ICST Conference on Simulation Tools and Techniques, ICST, Malaga, Spain, ICST/IEEE.
• Fiete Haack, Stefan Leye and Adelinde M. Uhrmacher (2010): A Flexible Architecture for modeling and simulation of diffusional association. - In: EPTCS, vol. 19, pp. 70 - 84.
• Roland Ewald, René Schulz and Adelinde M. Uhrmacher (2010): Selecting Simulation Algorithm Portfolios by Genetic Algorithms. - In: IEEE Workshop on Principles of Advanced and Distributed Simulation (PADS), pp. 48-56, IEEE, Piscataway, NJ, IEEE CPS.
• Arne T Bittig and Adelinde M Uhrmacher (2010): Spatial Modeling in Cell Biology at Multiple Levels. - In: Proceedings of the 2010 Winter Simulation Conference, ed. by B. Johansson, S. Jain, J. Montoya-Torres, J. Hugan, and E. Yücesan, pp. 608-619, IEEE.
• Arne T Bittig, Matthias Jeschke and Adelinde M Uhrmacher (2010): Towards Modelling and Simulation of Crowded Environments in Cell Biology. - In: AIP Conference Proceedings, ed. by Theodore E. Simos, George Psihoyios, Ch. Tsitouras, vol. 1281, pp. 1326-1329.
• Stefan Leye and Adelinde M. Uhrmacher (2010): A Flexible and Extensible Architecture for Experimental Model Validation. - In: 3rd International ICST Conference on Simulation Tools and Techniques, ICST, Malaga, Spain, ICST/IEEE.
• Dennis Maciuszek, Ruddeck Géraldine and Martens Alke (2010): Component-based development of educational games: The case of the user interface. - In: Proceedings of the 4th European Conference on Games-Based Learning.
• Géraldine Ruddeck and Alke Martens (2010): Towards a Tutoring System for Biology Students Learning Modeling and Simulation. - In: Eurosim, chap. 16.
• Jan Himmelspach, Roland Ewald, Stefan Leye and Adelinde M. Uhrmacher (2010): Enhancing the Scalability of Simulations by Embracing Multiple Levels of Parallelization. - In: Proceedings of the 2010 International Workshop on High Performance Computational Systems Biology, pp. 57-66, IEEE CPS.
• Stefan Rybacki, Jan Himmelspach, Enrico Seib and Adelinde M. Uhrmacher (2010): Using workflows in M&S software. - In: Proceedings of the 2010 Winter Simulation Conference, ed. by B. Johansson and S. Jain and J. Montoya-Torres and J. Hugan and E. Yücesan, pp. 535-545, IEEE Computer Science.
• Stefan Leye, Jan Himmelspach and Adelinde M. Uhrmacher (2009): A discussion on experimental model validation. - In: Proceedings of the 11th International Conference on Computer Modeling and Simulation, ed. by David Al-Dabass, Alessandra Orsoni, Adam Brentnall, Ajith Abraham, Richard Zobel, pp. 161-167, IEEE, IEEE Computer Society.
• Hans-Jörg Schulz, Steffen Hadlak and Heidrun Schumann (2009): Point-Based Tree Representation: A new Approach for Large Hierarchies. - In: Proceedings of IEEE PacificVis.
• Dagmar Köhn, Carsten Maus, Ron Henkel and Martin Kolbe (2009): Towards Enhanced Retrieval of Biological Models Through Annotation-based Ranking. - In: Data Integration in the Life Sciences, 6th International Workshop, DILS 2009, Manchester, UK, 20th-22nd July, ed. by Norman W. Paton, Paolo Missier, Cornelia Hedeler, vol. 5647, pp. 204-219, Springer. Lecture Notes in Bioinformatics.
• Dennis Maciuszek, Géraldine Ruddeck, Martina Weicht and Alke Martens (2009): Plug 'n Train für Game-based Learning. - In: Proceedings der Pre-Conference Workshops der DeLFI 2009, Teilband: 3. Workshop Game-based Learning, ed. by Schwill, A. and Apostolopoulos, N., chap. 2, pp. 109-118, Berlin, logos Verlag.
• Roland Ewald, Stefan Leye and Adelinde M. Uhrmacher (2009): An Efficient and Adaptive Mechanism for Parallel Simulation Replication. - In: Proceedings of the 23rd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS 2009), pp. 104-113, IEEE Conference Publishing Services.
• Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M. Uhrmacher and Arndt Rolfs (2009): Integrating Diverse Reaction Types Into Stochastic Models - A Signaling Pathway Case Study in the Imperative Pi-Calculus. - In: Proceedings of the Winter Simulation Conference, Austin, TX, USA, ed. by M. D. Rossetti, R. R. Hill, B. Johansson, A. Dunkin, R. G. Ingalls, pp. 932-943, IEEE Computer Society.
• Olivier Dalle, Judicael Ribault and Jan Himmelspach (2009): Design considerations for m&s software. - In: Proceedings of the Winter Simulation Conference, ed. by M. D. Rossetti and R. R. Hill and B. Johansson and A. Dunkin and R. G. Ingalls, pp. 944-955, IEEE Computer Science.
• Frank van Ham, Hans-Jörg Schulz and Joan DiMicco (2009): HoneyComb: Visual Analysis of Large Scale Social Networks. - In: Proceedings of INTERACT 2009, Springer. LNCS.
• Andreas Schäfer and Mathias John (2009): Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems. - In: APCCM, ed. by Markus Kirchberg and Sebastian Link, vol. 96, pp. 39-48, Australian Computer Society. CPRIT.
• Dagmar Köhn (2009): Enhancing Model Reuse in Systems Biology Using an Integrative Storage and Retrieval System. - In: Proceedings of the 2009 Joint EDBT/ICDT Ph.D. workshop, ACM .
• Christian Knüpfer, Nicolas Le Novère and Dagmar Köhn (2009): Beyond Structure: KiSAO and TEDDY – Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology. - In: First workshop of the GI-working group "Ontologien in Biomedizin und Lebenswissenschaften", pp. 41-42, GI.
• Marc Streit, Hans-Jörg Schulz, Dieter Schmalstieg and Heidrun Schumann (2009): Towards Multi-User Multi-Level Interaction. - In: Workshop on Collaborative Visualization on Interactive Surfaces, Atlantic City, NJ, USA,11 October 2009.
• Bing Wang, Jan Himmelspach, Roland Ewald, Yiping Yao and Adelinde M. Uhrmacher (2009): Experimental Analysis of Logical Process Simulation Algorithms in JAMES II. - In: Proceedings of the Winter Simulation Conference, ed. by M. D. Rossetti and R. R. Hill and B. Johansson and A. Dunkin and R. G. Ingalls, pp. 1167-1179, IEEE Computer Science.
• Andrea Unger and Heidrun Schumann (2009): Visual Support for the Understanding of Simulation Processes. - In: Proceedings of IEEE Pacific Visualization Symposium, Beijing, China, ed. by Peter Eades, Thomas Ertl and Han-Wei Shen, pp. 57-64, IEEE Computer Society.
• Roland Ewald, Adelinde Uhrmacher and Kaustav Saha (2009): Data Mining for Simulation Algorithm Selection. - In: Proceedings of the SIMUTools'09: 2nd International Conference on Simulation Tools and Techniques.
• Andrea Unger, Enrico Gutzeit, Matthias Jeschke and Heidrun Schumann (2009): VioNeS - Visual Support for the Analysis of the Next Sub-volume Method. - In: 13th International Conference on Information Visualisation, IV 2009, Barcelona, Spain, ed. by E. Banissi, L. Stuart, T.G. Wyeld, M. Jern, G. Andrienko, N. Memon, R. Alhajj, R.A. Burkhard, G. Grinstein, D. Groth, A. Ursyn, J. Johansson, C. Forsell, U. Cvek, M. Trutschl, F.T. Marchese, C. Maple, A.J. Cowell and A.V. Moere, pp. 10-17, IEEE Computer Society.
• Jan Himmelspach and Adelinde M. Uhrmacher (2009): What contributes to the quality of simulation results?. - In: Proceedings of the 2009 INFORMS Simulation Society Research Workshop, ed. by L. H. Lee and M. E. Kuhl and J. W. Fowler and S. Robinson, pp. 125-129, INFORMS Simulation Society, University of Warwick, Coventry, U.K..
• Mathias John, Cédric Lhoussaine and Joachim Niehren (2009): Dynamic Compartments in the Imperative Pi-Calculus. - In: CMSB 2009 - Computational Methods in Systems Biology, ed. by Pierpaolo Degano and Roberto Gorrieri, vol. 5688, pp. 235-250, Springer Verlag. LNCS.
• Jan Himmelspach (2009): Toward a Collection of Principles, Techniques, and Elements of Modeling and Simulation Software. - In: Proceedings of the SIMUL 2009, pp. 56-61, IEEE Computer Society.
• Roland Ewald, Jan Himmelspach, Matthias Jeschke, Stefan Leye and Adelinde M. Uhrmacher (2009): Performance Issues in Evaluating Models and Designing Simulation Algorithms. - In: International Workshop on High Performance Computational Systems Biology, 2009. HIBI '09., pp. 71-80, IEEE CPS.
• Jan Himmelspach and Adelinde M. Uhrmacher (2009): The JAMES II framework for modeling and simulation. - In: International Workshop on High Performance Computational Systems Biology, 2009. HIBI '09., pp. 101-102, IEEE CPS.
• Adelinde M. Uhrmacher, Hans-Jörg Schulz, Heidrun Schumann, Lars Schwabe and Dirk Timmermann (2009): Regenerative Systems - Challenges and Opportunities for Modeling, Simulation, and Visualization. - In: Proceedings of VALUETOOLS, pp. 1-10, Create net, ACM, SCS, Mimos, ICST.
• Mathias Röhl and Adelinde M. Uhrmacher (2008): Definition and Analysis of Composition Structure for Discrete-Event Models. - In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose, pp. 942-950.
• Dagmar Köhn and Nicolas Le Novere (2008): SED-ML - An XML Format for the Implementation of the MIASE Guidelines. - In: CMSB 2008, ed. by M. Heiner and A.M. Uhrmacher, Springer-Verlag Berlin Heidelberg. LNBI .
• Nicolas Le Novere and Dagmar Köhn (2008): MIASE - The minimum information about a simulation experiment . - In: Abstract book of The 9th International Conference on Systems Biology (ICSB), pp. 16.
• Andrea Unger, Philipp Muigg, Helmut Doleisch and Heidrun Schumann (2008): Visualizing Statistical Properties of Smoothly Brushed Data Subsets. - In: Proceedings of 12th International Conference Information Visualisation, IV 2008. , ed. by E. Banissi, L. Stuart, M. Jern, G. Andrienko, F.T. Marchese, N. Memon, R. Alhajj, T.G. Wyeld, R.A. Burkhard, G. Grinstein, D. Groth, A, Ursyn, Y. Maple, A. Faiola and B. Craft, pp. 233-239, IEEE Computer Society.
• Mathias John, Cédric Lhoussaine, Joachim Niehren and Adelinde Uhrmacher (2008): The Attributed Pi Calculus. - In: Computational Methods in Systems Biology, International Conference CMSB 2008, ed. by Monika Heiner, Adelinde M. Uhrmacher, vol. 5307, pp. 83-102, Springer Verlag. LNBI.
• A. Jaeger, B.M. Bader, D.G. Weiss and R. Kriehuber (2008): Apoptosis in the human neural progenitor VM197 cell line – a life or death decision during the early differentiation process. - In: Abstract Book.
• Hans-Jörg Schulz, Mathias John, Andrea Unger and Heidrun Schumann (2008): Visual Analysis of Bipartite Biological Networks. - In: Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine 2008, Delft, Netherlands, ed. by Charl Botha, Gordon Kindlmann, Wiro Niessen and Bernhard Preim, pp. 135-142, The Eurographics Association.
• Adelinde M. Uhrmacher, Jan Himmelspach, Matthias Jeschke, Mathias John, Stefan Leye, Carsten Maus, Mathias Röhl and Roland Ewald (2008): One Modeling Formalism & Simulator is not enough! - A Perspective for Computational Biology Based on JAMES II. - In: Proceedings of the 1st FMSB Workshop, ed. by Jasmin Fisher, pp. 123-138, Cambridge, UK, Springer. Lecture Notes of Computer Science, LNBI subseries.
• Jan Himmelspach, Roland Ewald and Adelinde M. Uhrmacher (2008): A flexible and scalable experimentation layer. - In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose, pp. 827-835, IEEE Computer Society.
• Mathias John, Roland Ewald and Adelinde M. Uhrmacher (2008): A Spatial Extension to the Pi Calculus. - In: Electronic Notes in Theoretical Computer Science, vol. 194(3), pp. 133-148.
• Mathias John, Christian Tominski and Heidrun Schumann (2008): Visual and Analytical Extensions for the Table Lens. - In: Visualization and Data Analysis 2008, ed. by Börner, Katy; Gröhn, Matti T.; Park, Jinah; Roberts, Jonathan C., vol. 6809.
• Henry Sonnet, Andrea Unger and Heidrun Schumann (2008): Interactive Images using Illustration Watermarks: Techniques, Studies, and Applications. - In: On-line Proceedings WSCG'2008, The 16-th International Conference in Central Europe on Computer Graphics, Visualization and Interactive Digital Media, Communications Papers, ed. by Vaclav Scala, pp. 245-252, Pilsen, Czech Republic.
• Matthias Jeschke, Roland Ewald, Alfred Park, Richard Fujimoto and Adelinde M. Uhrmacher (2008): Parallel and Distributed Spatial Simulation of Chemical Reactions. - In: Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS 2008), pp. 51 - 59.
• Dagmar Köhn, Andreas Heuer and Carsten Maus (2008): Eine Datenbanklösung für Modellwiederverwendung in der Systembiologie. - In: Tagungsband zum 20. GI-Workshop über Grundlagen von Datenbanken, Apolda, Thüringen, School of Information Technology, International University in Germany.
• Dagmar Köhn and Lena Strömbäck (2008): A Method for Semi-Automatic Integration of Standards in Systems Biology. - In: 19th International Conference on Database and Expert Systems Aplications (DEXA) 2008, vol. 5181(0745), pp. 745-52, Lecture Notes in Computer Science, Springer.
• Heino Hellwig, Matthias Jeschke and Oliver Deussen (2008): A Contact Pressure Model Based on Centroidal Voronoi Diagrams for Surfaces of Revolution. - In: Proceedings of the 5th Annual International Symposium on Voronoi Diagrams in Science and Engineering (ISVD '08).
• Matthias Jeschke and Adelinde M. Uhrmacher (2008): Multi-resolution Spatial Simulation For Molecular Crowding. - In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose.
• Matthias Jeschke and Roland Ewald (2008): Large-Scale Design Space Exploration of SSA. - In: Computational Methods in Systems Biology, vol. Volume 5307/2008, pp. 211-230, Springer Berlin / Heidelberg. Lecture Notes in Computer Science.
• Stefan Leye, Corrado Priami and Adelinde M. Uhrmacher (2008): A bounded-optimistic, parallel Beta-binders Simulator. - In: Proceedings of the 12th IEEE International Symposium on Distributed Simulation and Real-Time Applications, ed. by David Roberts, Abdulmotaleb El Saddik and Alois Ferscha, pp. 139-148, IEEE Computer Society, IEEE Press.
• Stefan Leye, Jan Himmelspach, Matthias Jeschke, Roland Ewald and Adelinde M. Uhrmacher (2008): A grid-inspired mechanism for coarse-grained experiment execution. - In: Proceedings of the 12th IEEE International Symposium on Distributed Simulation and Real-Time Applications, ed. by David Roberts, Abdulmotaleb El Saddik, Alois Ferscha, pp. 7-16, IEEE Computer Society, IEEE Press.
• Mathias John (2008): Die Modellierung von Raum und Struktur in molekularbiologischen Systemen. - In: Modellierung, pp. 221-224.
• Roland Ewald, Johannes Rössel, Jan Himmelspach and Adelinde M. Uhrmacher (2008): A plug-in - based architecture for random number generation in simulation systems. - In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose, pp. 836-844, IEEE Computer Society.
• Carsten Maus (2008): Component-based Modelling of RNA Structure Folding. - In: Computational Methods in Systems Biology, International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings, vol. 5307, pp. 44-62, Berlin / Heidelberg, Springer. Lecture Notes in Computer Science.
• A. Jaeger, S. Klum, D.G. Weiss and R. Kriehuber (2007): Expression of apoptosis-related proteins during differentiation in the human neuronal progenitor cell line VM 197. - In: Abstract Book, Edt. T. Apel; University of Hamburg.
• Yvonne Schmitz (2007): Systems biology of the canonical Wnt pathway. - In: Dagstuhl `Zehn plus eins', pp. 168-169.
• Matthias Jeschke (2007): Flexible and Efficient Simulation of Biological Systems. - In: Dagstuhl ``zehn plus eins'': Kollegbeschreibungen und Kurzfassungen der Forschungsarbeiten von Stipendiaten/Kollegiaten, 4-6 June 2007, Dagstuhl, Germany, pp. 163, Verlagshaus Mainz GmbH Aachen.
• Hans-Jörg Schulz (2007): GRK dIEM oSiRiS: Visual Graph Mining. - In: Dagstuhl ``zehn plus eins'': Kollegbeschreibungen und Kurzfassungen der Forschungsarbeiten von Stipendiaten/Kollegiaten, Dagstuhl ``zehn plus eins'', 4-6 June 2007, Germany, pp. 170, Verlagshaus Mainz GmbH Aachen.
• Andrea Unger (2007): GRK dIEM oSiRiS: Visual support for the development of methods and models for regenerative systems. - In: Dagstuhl zehn plus eins, pp. 171.
• Mathias Röhl and Stefan Morgenstern (2007): Composing Simulation Models Using Interface Definitions Based on Web Service Descriptions. - In: WSC '07, ed. by S. G. Henderson, B. Biller, M.-H. Hsieh, J. Shortle, J. D. Tew, R. R. Barton, pp. 815-822.
• Mathias Röhl, Birgitta König-Ries and Adelinde M. Uhrmacher (2007): An Experimental Frame for Evaluating Service Trading in Mobile ad-hoc Networks. - In: Mobilität und Mobile Informationssysteme (MMS 2007), vol. 104, pp. 37-48. Lect. Notes Inform..
• Adelinde M Uhrmacher, Roland Ewald, Mathias John, Carsten Maus, Matthias Jeschke and Susanne Biermann (2007): Combining Micro and Macro-Modeling in DEVS for Computational Biology. - In: WSC '07: Proceedings of the 39th conference on Winter simulation, pp. 871-880, IEEE Press.
• Dagmar Köhn (2007): Definition, Storage, and Query of XML-based Model Components. - In: Dagstuhl ”zehn plus eins” : zehn Informatik-Graduiertenkollegs und ein Informatik- Forschungskolleg stellen sich vor, pp. 165-166, Verlag Mainz, ISBN: 3-86130-882-7.
• Georg Fuchs, Hans-Jörg Schulz and Heidrun Schumann (2007): Presenting Technical Drawings on Mobile Handhelds. - In: Managing Worldwide Operations and Communications With Information Technology - Proceedings of the 18th IRMA International Conference in Vancouver, Canada, ed. by Mehdi Khosrow-Pour, Information Resources Management Association, IGI Publishing.
• Dagmar Köhn (2007): Working with different pathway standards. - In: biomodels training camp, 2007 Manchester.
• Benjamin M. Bader and Dieter G. Weiss (2007): The role of Wnt-pathway mediated changes in the cytoskeleton-motor-enzyme-system upon differentiation of neural progenitor cells. - In: Dagstuhl "Zehn plus eins".
• Mathias Röhl, Florian Marquardt and Adelinde M. Uhrmacher (2007): Exploiting Web Service Techniques for Composing Simulation Models. - In: WSC '07, ed. by S. G. Henderson and B. Biller and M.-H. Hsieh and J. Shortle and J. D. Tew and R. R. Barton, pp. 833-841.
• Alexandra Jaeger (2007): Characterization of apoptosis-pathways in human neuronal progenitor cells. . - In: Dagstuhl-Band, pp. 161-162.
• Lena Strömbäck and Dagmar Köhn (2006): A Schema Matching Architecture for the Bioinformatics Domain. - In: Proceedings of the Winter Simulation Conference 2006 (PhD Colloquium).
• Adelinde M. Uhrmacher, Jan Himmelspach, Matthias Röhl and Roland Ewald (2006): Introducing Variable Ports and Multi-Couplings for Cell Biological Modeling in DEVS. - In: Proc. of the 2006 Winter Simulation Conference, pp. 832-840.

Technischer Bericht

• Hans-Jörg Schulz (2009): Meine Dissertation - oder Computer-GRAPH-ik in Rostock. - Rostocker Informatik-Berichte, (32):196-197.
• Adelinde M. Uhrmacher, Mathias John, Orianne Mazemondet, Andrea Unger, Tareck Rharass, Benjamin M. Bader and Arndt Rolfs (2009): Computer Science Meets Cell Biology - GRK dIEM oSiRiS. - Universität Rostock, Rostocker Informatik Berichte(32:77-90).
• Stefan Leye, Corrado Priami and Adelinde M. Uhrmacher (2007): A Parallel Beta-binders Simulator. - The Microsoft Research - University of Trento Centre for Computational and Systems Biology.
• Henry Sonnet, Andrea Unger, Lothar Schlesier, Thomas Vogel, Tobias Isenberg and Thomas Strothotte (2006): Interactive Images using Illustration Watermarks: Techniques, Study, and Applications. - Otto-von-Guericke-University Magdeburg, Faculty of Computer Science, Research note.