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Center for Computational and Theoretical Biology

Supramolecular and Cellular Simulations

We work on data-driven modelling and simulations of processes at the subcellular, multicellular and multitissue scale. For the data analyses, we develop and apply tools that range from classical statistics to machine learning approaches. To test hypotheses about interactions of structure and function at the different scales, we use mathematical modelling and simulations. In particular, we use on- and off-lattice agent-based modelling in two and three spatial dimensions as well as three-dimensional morphological modelling with Blender. 

We are part of the DFG priority program SPP 2332 "Physics of Parasitism” and associated to the SFB / TRR 225 “Biofabrication”. 

Projects

Beta-Tester for julia programming course

We are looking for people that are interested in learning the programming language julia.

If you want to have a go, feel free to download our course and work on one or more parts of it. We would appreciate it a lot if you would let us know any feedback that you might have. Thank you!

Download:

We offer internships, Bachelor and Master theses as well as Zulassungsarbeiten (Lehramt) from April 2024

In general, we are looking for highly motivated candidates, who are team-oriented, willing to learn and work independently and precisely:

  • Keen interest in one of our projects, quantitative data analysis and/or mathematical modelling, and programming (prior knowledge in any of these is not required)
  • Enthusiasm for communication with experts from other disciplines 

We offer a friendly working environment, excellent computing infrastructure and supportive supervision.

If you are interested, please contact Sabine Fischer for further details.

Publications

2023[ to top ]
  • Tissues as networks of cells: towards generative rules of complex organ development Fischer, Sabine C.; Bassel, George W.; Kollmannsberger, Philip in Journal of The Royal Society Interface (2023). 20(204) 20230115.
  • The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours. Fischer, Sabine; Schardt, Simon; Lilao-Garzon, Joaquin; Munoz-Descalzo, Silvia in bioRxiv (2023). 2023.05.04.539359.
  • Adjusting the range of cell--cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing Schardt, Simon; Fischer, Sabine C. in Journal of Mathematical Biology (2023). 87(4) 54.
2022[ to top ]
  • Recognition and reconstruction of cell differentiation patterns with deep learning Dirk, Robin; Fischer, Jonas L.; Schardt, Simon; Ankenbrand, Markus J.; Fischer, Sabine C. in arXiv (2022). 2212.10058.
  • Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus Schmid, Kerstin; Knote, Andreas; Mück, Alexander; Pfeiffer, Keram; von Mammen, Sebastian; Fischer, Sabine C. in Frontiers in Bioinformatics (2022).
  • Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing Schardt, Simon; Fischer, Sabine C. in arXiv (2022). 2211.07241.
2021[ to top ]
  • On-lattice Vicsek model in confined geometries Kuhn, Andreas; C, Fischer Sabine in arXiv (2021). 2105.08792.
  • NANOG/GATA6 Interactions Revisited: A Statistical Mechanics Approach towards Cell Fate Decisions Schardt, Simon; Fischer, S C in arXiv (2021). 2107.04501.
  • Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus Schmid, Kerstin; Knote, Andreas; Mück, Alexander; Pfeiffer, Keram; von Mammen, Sebastian; Fischer, Sabine C. in bioRxiv (2021). 2021.09.15.460416.
  • Global cell-cell communication enables spatial segregation of cells in organoids of the inner cell mass Schardt, Simon; Fischer, SC in arXiv (2021). 2111.01624.
2020[ to top ]
  • The transition from local to global patterns governs the differentiation of mouse blastocysts Fischer, Sabine C.; Corujo-Simon, Elena; Lilao-Garzon, Joaquin; Stelzer, Ernst H. K.; Muñoz-Descalzo, Silvia in PLOS ONE (2020). 15(5) 1–29.
  • Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach Liebisch, Tim; Drusko, Armin; Mathew, Biena; Stelzer, Ernst H. K.; Fischer, Sabine C.; Matthäus, Franziska in Scientific Reports (2020). 10(1) 22405-.
2019[ to top ]
  • Mouse ICM organoids reveal three-dimensional cell fate clustering Mathew, Biena; Muñoz-Descalzo, Silvia; Corujo Simon, Elena; Schröter, Christian; Stelzer, Ernst H.K; Fischer, Sabine C. in Biophysical Journal (2019). 116 127–141.
  • Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures Knote, Andreas; Fischer, Sabine C.; Cussat-Blanc, Sylvain; Niebling, Florian; Bernard, David; Cogoni, Florian; von Mammen, Sebastian in 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR) (2019). 82–89.
  • An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians Fischer, Sabine C. in Computational Biology, H. Husi (red.) (2019).
  • A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics Steuer Costa, Wagner; Van der Auwera, Petrus; Glock, Caspar; Liewald, Jana F.; Bach, Maximilian; Schüler, Christina; Wabnig, Sebastian; Oranth, Alexandra; Masurat, Florentin; Bringmann, Henrik; Schoofs, Liliane; Stelzer, Ernst H.K.; Fischer, Sabine C.; Gottschalk, Alexander in Nature Communications (2019). 10(4095)
2018[ to top ]
  • The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1 Hofbauer, H F; Gecht, M; Fischer, S C; Seybert, A; Frangakis, A S; Stelzer, E H K; Covino, R; Hummer, G; Ernst, R in J Cell Biol (2018). 217(9) 3109–3126.
  • Electroluminescence imaging and automatic cell classification in mass production of silicon solar cells Alt, M; Fischer, S; Schenk, S; Zimmermann, S; Ramspeck, K; Meixner, M in 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion (WCPEC) (A Joint Conference of 45th IEEE PVSC, 28th PVSEC 34th EU PVSEC) (2018). 3298–3304.
  • E-cadherin, actin, microtubules and {FAK} dominate different spheroid formation phases and important elements of tissue integrity Smyrek, I.; Mathew, B.; Fischer, S. C.; Lissek, S. M.; Becker, S.; Stelzer, E. H. K. in Biology Open (2018). bio.037051.
2017[ to top ]
  • Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids Schmitz, Alexander; Fischer, Sabine C.; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H. K. in Scientific Reports (2017). 7 43693.
2016[ to top ]
  • Identifying the necrotic zone boundary in tumour spheroids with pair-correlation functions Dini, S.; Binder, B. J.; Fischer, S. C.; Mattheyer, C.; Schmitz, A.; Stelzer, E. H. K.; Bean, N. G.; Green, J. E. F. in Journal of The Royal Society Interface (2016). 13 20160649.
2015[ to top ]
  • Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition Mathew, Biena; Schmitz, Alexander; Muñoz-Descalzo, Silvia; Ansari, Nariman; Pampaloni, Francesco; Stelzer, Ernst Hans Karl; Fischer, Sabine Christine in BMC Bioinformatics (2015). 16 187.
  • Lateral assembly of N-cadherin drives tissue integrity by stabilizing adherens junctions Garg, S.; Fischer, S. C.; Schuman, E. M.; Stelzer, E. H. K. in Journal of The Royal Society Interface (2015). 12 20141055.
2014[ to top ]
  • Contractile and Mechanical Properties of Epithelia with Perturbed Actomyosin Dynamics Fischer, Sabine C.; Blanchard, Guy B.; Duque, Julia; Adams, Richard J.; Arias, Alfonso Martinez; Guest, Simon D.; Gorfinkiel, Nicole in PLOS ONE (2014). 9(4) 1–12.
2013[ to top ]
  • Is a Persistent Global Bias Necessary for the Establishment of Planar Cell Polarity? Fischer, Sabine; Houston, Paul; Monk, Nicholas A. M.; Owen, Markus R. in PLOS ONE (2013). 8(4) 1–12.
2011[ to top ]
  • Integrative approaches to morphogenesis: lessons from dorsal closure Gorfinkiel, N; Schamberg, S; Blanchard, G B in Genesis (2011). 49(7) 522–533.
  • Endocytic and recycling endosomes modulate cell shape changes and tissue behaviour during morphogenesis in Drosophila Mateus, A M; Gorfinkiel, N; Schamberg, S; Martinez Arias, A in PLoS One (2011). 6(4)
2010[ to top ]
  • Modelling and Analysis of Planar Cell Polarity Schamberg, S.; Houston, P.; Monk, N. A. M.; Owen, M. R. in Bulletin of Mathematical Biology (2010). 72(3) 645–680.