EPISIM Platform > EPISIM Publications

EPISIM Publications

Peer Reviewed Journal Articles

Safferling K, Sütterlin T, Westphal K, Ernst C, Breuhahn K, James M, Jäger D, Halama N und Grabe N (2013). Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models. Journal of Cell Biology, 203 (4), pp. 691–709.
electronic version

Sütterlin T
, Kolb C, Dickhaus H, Jäger D, Grabe N (2013). Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics. 2013 Jan 15;29(2):223-9. Epub 2012 Nov 18. PubMed
PMID: 23162085.
electronic version  supplements

Sütterlin T, Huber S, Dickhaus H and Grabe N. (2009) Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems, Bioinformatics, 25, 2057-2063.
PMID: 19535533
electronic version  supplements

Book Chapters

Sütterlin T and Grabe N (2014). Graphical Multi-Scale Modeling of Epidermal Homeostasis with EPISIM. In, Querleux,B. (Ed.), Computational Biophysics of the Skin. Pan Stanford Publishing, Singapore, p. 421–460.

Articles in Conference Proceedings

Sütterlin T, Dickhaus H, Grabe N. Automated model-driven generation of software components for the simulation of epithelial tissues. Biomedical Engineering (MECBME)., 2011 1st Middle East Conference on Biomedical Engineering, pp.275-278, 21-24 Feb. 2011, Sharjah, United Arab Emirates (Talk)

electronic version

Sütterlin T, Grabe N. Efficient Modeling of the Spatial Dynamics of Tissues by Automated Transformation of Graphical Cell Behavioral Models into Multi-Agent Based Simulations. Proceedings of the 6th Workshop on Computation of Biochemical Pathways and Genetic Networks, BioQuant Heidelberg, Sept. 2010. Logos Verlag Berlin, ISBN 978-3-8325-2587-3 (Talk)

Abstracts in Conference Proceedings

Sütterlin T, Tsingos E, Bensaci J, Stamatas GN and Grabe N (2015). Multicellular agent-based modeling and simulation of stratum corneum maturation, morphology and turnover. Int. J. Cosmet. Sci., 37, 143–143. (Talk)

Sütterlin T
, Safferling K, Halama N, Jäger D, Grabe N (2014). EPISIM Platform: Graphical multi-
scale modeling and simulation of multicellular systems. 9th European Conference on Mathematical
and Theoretical Biology – ECMTB, Göteborg. (Talk)

Sütterlin T, Safferling K, Halama N, Jäger D, Grabe N (2014). EPISIM: A platform for multiscale
modeling and simulation of multicellular biological systems. 5th Conference on Systems Biology of
Mammalian Cells – SBMC, Berlin. (Talk)

Sütterlin T
, Safferling K, Tsingos E, Grabe N (2014). EPISIM: A user-friendly platform for multiscale,
multicellular modeling and simulation of biological systems. German Conference On
Bioinformatics – GCB, Bielefeld. (Poster)

Safferling K, Sütterlin T, Westphal K, Ernst C, Breuhahn K, James M, Jäger D, Halama N, Grabe
N (2014). Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in
silico models. 5th Conference on Systems Biology of Mammalian Cells – SBMC; Berlin. (Poster)

Sütterlin T
, Dickhaus H, Grabe N (2012). Putting the pieces together: Enhancing Multi-Scale Modeling with Automated Semantic Model Integration. Conference on Systems Biology of Mammalian Cells – SBMC; Leipzig, Germany 2012 (Poster)

Sütterlin T, Dickhaus H, Grabe N (2012). Multi-Scale Tissue Modeling: Semantic Integration of SBML Models in Multi-Cellular Simulations using the EPISIM Platform. Proceedings of the 12th International Conference on Systems Biology; Heidelberg/Mannheim, Germany 2012 (Poster)

Sütterlin T, Dickhaus H, Grabe N (2011). Integration of a flexible polygon cell shape model in the EPISIM multi-agent platform for modelling and simulation of epithelial tissue homeostasis. Goryanin, Igor; Goryachev, Andrew (Eds.). Advances in Systems Biology: Proceedings of the 11th International Conference on Systems Biology. Springer, 1st Edition. ISBN: 978-1-4419-7209-5. (Poster)

Grabe N, Westphal K, Safferling K, Ernst C, Sütterlin T, Halama N (2011). Towards an Automated Platform for Researching the Homeostasis of Epithelial Tissue. Goryanin, Igor; Goryachev, Andrew (Eds.). Advances in Systems Biology: Proceedings of the 11th International Conference on Systems Biology. Springer, 1st Edition. ISBN: 978-1-4419-7209-5. (Poster)

Sütterlin T, Dickhaus H, Grabe N. (2010). Cell based tissue modelling by a polygon shape model in a multi-agent environment for the simulation of epidermal wound healing. Conference on Systems Biology of Mammalian Cells – SBMC; Freiburg, Germany (Poster)

Sütterlin T, Dickhaus H, Grabe N (2009). Modeling and Simulation of Multi-Cellular Behavior in Epidermal Tissue Homeostasis. Startup Conference Medical Informatics. Santiago de Chile (Poster)

Sütterlin T
, Dickhaus H, Grabe N (2008). Graphische Modellierung multizellulärer Systeme. 53. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. , Stuttgart (Talk)
electronic version

Pommerencke T, Sütterlin T, Dickhaus H, Grabe N (2008). Towards an automated platform for researching the homeostasis of epithelial tissue. Abstractband der GCB (Poster).


 
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