Morpheus

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~~NOTOC~~
===== Publications =====


=== Research papers === 

| Meyer, K., Ostrenko, O., Bourantas, G., Morales-Navarrete, H., Porat-Shliom, N., Segovia-Miranda, F., Nonaka, H., Ghaemi, A., Verbavatz, J.M., Brusch, L. and Sbalzarini, I., Kalaidzidis, Y., Weigert, R., Zerial M. \\ [[http://dx.doi.org/10.1016/j.cels.2017.02.008|A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.]] //Cell Systems// 4 (3), 277–290, 2017.|
| K.B. Hoffmann, A. Voss-Böhme, J.C. Rink, L. Brusch. \\ [[http://dx.doi.org/10.1098/rsif.2017.0466|A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns.]] //Journal of the Royal Society Interface// 14 (135), 20170466, 2017. |
| O. Ostrenko, P. Incardona, R. Ramaswamy, L. Brusch, I.F. Sbalzarini. \\ [[http://dx.doi.org/10.1371/journal.pcbi.1005865|pSSAlib: The partial-propensity stochastic chemical network simulator.]] //PLoS Computational Biology// 13(12), e1005865, 2017. |
| O. Parvu and D. Gilbert. \\  [[http://dx.doi.org/10.1371/journal.pone.0154847|A novel method to verify multilevel computational models of biological systems using multiscale spatio-temporal meta model checking]]. \\ //PLoS ONE//, 11(5): e0154847, 2016.|
| M. Herberg, T. Zerjatke, W. de Back, I. Glauche and I. Roeder. \\ [[http://dx.doi.org/10.1002/cyto.a.22598|Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies]]. \\ //Cytometry: Part A//, 2015.|
| O. Parvu and D. Gilbert. \\ [[http://www.biomedcentral.com/1752-0509/8/124/abstract|Automatic validation of computational models using pseudo-3D spatio-temporal model checking.]] \\ //BMC Systems Biology//,  8:124, 2014.|
| A. Köhn-Luque, W. de Back, Y. Yamaguchi, K. Yoshimura, M. A. Herrero and T. Miura. \\  [[http://dx.doi.org/10.1088/1478-3975/10/6/066007|Dynamics of VEGF matrix-retention in vascular network patterning.]] \\ //Physical Biology//, 10:066007, 2013. | 
| W. de Back, R. Zimm, L. Brusch \\ [[http://www.biomedcentral.com/1752-0509/7/77
|Transdifferentiation of pancreatic cells by loss of contact-mediated signaling.]] \\ //BMC Systems Biology//, 7:77, 2013.|
| W. de Back, J. X. Zhou, L. Brusch \\ [[http://dx.doi.org/10.1098/rsif.2012.0766|On the role of lateral stabilization during early patterning in the pancreas]]. \\ //Journal of the Royal Society Interface// 10(79):20120766, 2012. |
| A. Köhn-Luque, W. de Back, J. Starruß, A. Mattiotti, A. Deutsch, J. M. Pérez-Pomares, M. A. Herrero \\ [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024175|Early embryonic vascular patterning by matrix-mediated paracrine signalling]]. \\ //PLoS ONE// 6(9):e24175, 2011. | 
| J. Starruß, T. Bley, L. Søgaard-Andersen, A. Deutsch \\ [[http://dx.doi.org/10.1007/s10955-007-9298-9|A new mechanism for collective migration in Myxococcus xanthus]]. \\ //Journal of Statistical Physics//, 128, 269-286, 2007.|


=== Also cited in ===

| Appleton, E., Madsen, C., Roehner, N. and Densmore, D.,\\ [[http://cshperspectives.cshlp.org/content/early/2017/02/27/cshperspect.a023978.abstract|Design Automation in Synthetic Biology.]] // Cold Spring Harbor Perspectives in Biology//, 2017. |
| Cytowski, M., Szymańska, Z., Umiński, P., Andrejczuk, G. and Raszkowski, K. \\ [[https://www.hindawi.com/journals/sp/2017/8721612/|Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture]]. //Scientific Programming//, 2017. |
| P. Macklin, H. Frieboes, J. Sparks, A. Ghaffarizadeh, S. Friedman, E. Juarez, E. Jonckheere, S. Mumenthaler \\ [[http://link.springer.com/chapter/10.1007/978-3-319-42023-3_12|Progress Towards Computational 3-D Multicellular Systems Biology]] \\ In: // Systems Biology of Tumor Microenvironment // (edited by: K. Rejniak), 2016. |
|J. S. Yu, N. Bagheri. \\ [[http://dx.doi.org/10.1016/j.copbio.2016.04.002|Multi-class and multi-scale models of complex biological phenomena]] \\ // Current Opinion in Biotechnology//, 39:167–173, 2016. |
| O. Chara, E. Tanaka, L. Brusch. \\  [[http://dx.doi.org/10.1016/B978-0-12-391498-9.00011-5|Mathematical Modeling of Regenerative Processes]]. \\ In: // Current Topics in Developmental Biology//: Mechanisms of Regeneration (edited by: B. Galliot) Volume 108, 2014. | 
| S.J. Parker, K. Raedschelders and J. E. Van Eyk. \\ [[http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400448/abstract|Emerging proteomic technologies for elucidating context‐dependent cellular signaling events: A big challenge of tiny proportions]]. \\ //Proteomics//, 2014.|
| L.A. D'Alessandro, S. Hoehme, A. Henney, D. Drasdo and U. Klingmüller. \\ [[http://www.sciencedirect.com/science/article/pii/S0079610714001849|Unraveling liver complexity from molecular to organ level: Challenges and perspectives]]. \\ //Progress in biophysics and molecular biology//, 2014.|
| S. Kang, S. Kahan, J. McDermott, N. Flann and I. Shmulevich. \\ [[http://bioinformatics.oxfordjournals.org/content/30/21/3101.short|Biocellion: accelerating computer simulation of multicellular biological system models]]. \\ // Bioinformatics// 30(2):3101-3108, 2014.|
 
Beyond this selection, 44 sources have so far cited our paper in total (as of Dec. 2017).

=== Conferences === 

Talks and poster presentations at the following conferences and workshops:

| W. de Back, Morpheus 2: Modeling and simulation platform for multicellular systems biology. And MorpheusML: declarative markup language for multicellular systems biology, Workshop "Towards a unified framework for benchmarking multi-cellular models and simulation software" (organized D. Drasdo and S. Hoehme et al., Leipzig, March 2016 (invited talks)|  
| W. de Back, [[http://www.dagstuhl.de/wiki/index.php/14481|Spatial multiscale computational systems biology]], Schloss **Dagstuhl** - Leibniz-Zentrum für Informatik, Germany, November 2014 (talk) |
| L. Brusch, W. de Back, J. Starruß, A. Deutsch, Morpheus: a User-friendly Modeling Environment for Multiscale and Multicellular Systems Biology,  Symposium on "//Executable cell biology for tissue engineering and regenerative medicine//", **[[http://www.termis.org/eu2014/|TERMIS-EU]]**, Genova, Italy, 2014. ({{:documentation:termiseu2014_morpheus.pdf|abstract}}) (talk)|
| W. de Back, Integrative modeling in developmental systems biology, Institute for Medical Informatics and Biometry,  Medical Faculty „Carl Gustav Carus“, Technische Universität Dresden, 2013. (talk)|
| W. de Back, A. Deutsch, Morpheus: Modeling and Simulation in Multicellular System Biology, 1st Sino-German Workshop on Simulation, Changsha, China, 2011. (talk)|