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 have an open PhD position.

    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
    Klara-Oppenheimer-Weg 32
    Campus Hubland Nord
    97074 Würzburg

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