Center for Computational and Theoretical Biology

Research summary

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.

Open positions

PhD position in Mathematical biology, starting January 2019

We offer internships, Bachelor and Master theses starting in SS 2019:

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

  • Student in Biology, Mathematics, Physics or a related discipline
  • 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 

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



[ under review ] [ 2018 ] [ 2017 ] [ 2016 ] [ 2015 ] [ 2014 ] [ 2013 ] [ 2011 ] [ 2010 ]

under review[ nach oben ]

  • Actin, microtubules and FAK dominate different spheroid formation phases revealing their importance for tissue integrity.Smyrek, I; Mathew, B; Fischer, SC; Lissek, S; Becker, S; Stelzer, EHK (under review).

2018[ nach oben ]

  • 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.
  • 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 (2018).

2017[ nach oben ]

  • Three-dimensional cell neighbourhood impacts differentiation in the inner mass cells of the mouse blastocyst.Fischer, Sabine C.; Corujo-Simon, Elena; Lilao-Garzon, Joaquin; Stelzer, Ernst H. K.; Munoz-Descalzo, Silvia in bioRxiv (2017).
  • 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[ nach oben ]

  • 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(123)

2015[ nach oben ]

  • 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(104)

2014[ nach oben ]

  • 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[ nach oben ]

  • 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[ nach oben ]

  • 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[ nach oben ]

  • 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.

Center for Computational and Theoretical Biology
Gebäude 32
Campus Hubland Nord
97074 Würzburg

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Hubland Nord, Geb. 32
Hubland Nord, Geb. 32