Morpheus

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.
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.
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.
pSSAlib: The partial-propensity stochastic chemical network simulator. PLoS Computational Biology 13(12), e1005865, 2017.

O. Parvu and D. Gilbert.
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.
Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies.
Cytometry: Part A, 2015.

O. Parvu and D. Gilbert.
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.
Dynamics of VEGF matrix-retention in vascular network patterning.
Physical Biology, 10:066007, 2013.

W. de Back, R. Zimm, L. Brusch
Transdifferentiation of pancreatic cells by loss of contact-mediated signaling.
BMC Systems Biology, 7:77, 2013.

W. de Back, J. X. Zhou, L. Brusch
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
Early embryonic vascular patterning by matrix-mediated paracrine signalling.
PLoS ONE 6(9):e24175, 2011.

J. Starruß, T. Bley, L. Søgaard-Andersen, A. Deutsch
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.,
Design Automation in Synthetic Biology. Cold Spring Harbor Perspectives in Biology, 2017.

Cytowski, M., Szymańska, Z., Umiński, P., Andrejczuk, G. and Raszkowski, K.
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
Progress Towards Computational 3-D Multicellular Systems Biology
In: Systems Biology of Tumor Microenvironment (edited by: K. Rejniak), 2016.

J. S. Yu, N. Bagheri.
Multi-class and multi-scale models of complex biological phenomena
Current Opinion in Biotechnology, 39:167–173, 2016.

O. Chara, E. Tanaka, L. Brusch.
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.
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.
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.
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, 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”, TERMIS-EU, Genova, Italy, 2014. (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)