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Center for Computational and Theoretical Biology

Supramolecular and Cellular Simulations

Our research focuses on image-based mathematical modelling of multicellular systems in biomedical research. The main interest is how cells interact in a tissue, in particular the influence of the local cell neighbourhood on the behaviour of a given cell. We have previously developed discrete reaction-diffusion models to investigate the role of intercellular interactions during Drosophila morphogenesis and a three-dimensional agent-based model to investigate cellular aggregation. A major emphasis is on developing data-informed models. To obtain the necessary data, we have established a multiscale image analysis pipeline for three-dimensional fluorescence microscopy images and implemented three-dimensional cell graphs for studying the cell neighbourhood. Currently, we work on studying cell fate specifications in early mouse embryos.

Projects

Open positions

We have an opening for a PhD position in Mathematical Biology starting on 01/03/2022. The application deadline is 12/12/2021. The official advertisement can be found here.

We offer internships, Bachelor and Master theses, und Zulassungsarbeiten (Lehramt) 

 One of the projects that we currently offer is 

"Agent-based modelling of microtubule dynamics"

 

 

 

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

  • Keen interest in cell-cell interactions, 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

[ 2021 ] [ 2020 ] [ 2019 ] [ 2018 ] [ 2017 ] [ 2016 ] [ 2015 ] [ 2014 ] [ 2013 ] [ 2011 ] [ 2010 ]

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.