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

    We offer internships, Bachelor and Master theses:

    We are looking for highly motivated candidates, who are team-oriented, 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 

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

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



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

    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.
    • 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). 116 127-141.
    • 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 ]

    • 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[ 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.

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

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