Center for Computational and Theoretical Biology

Prof. Dr. Sabine Fischer

Professor for Supramolecular and Cellular Simulations

Center for Computational and Theoretical Biology (CCTB)

Campus Hubland Nord 32

Universität Würzburg

97074 Würzburg, Germany

Tel: 0931 - 31 83961

email: sabine.fischer@uni-wuerzburg.de

Google Scholar profile


Previous PhD students

Alexander Schmitz (2017)

Biena Mathew (2018)

Simon Schardt (2023)

Curriculum Vitae

Since 2018


Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany

2017 - 2018

Development engineer

h.a.l.m. Elektronik GmbH, Frankfurt, Germany    

2011 - 2017

Senior postdoc 

Group of Ernst. H. K. Stelzer, Buchmann Institute of Molecular Life Science (BMLS), Goethe University, Frankfurt am Main, Germany

2009 - 2011


Group of Alfonso Martinez Arias, Department of Genetics, University of Cambridge, UK

Project: “Modelling the cooperative behaviour of sheets of cells during embryogenesis”

2006 - 2009

PhD in Mathematics

School of Mathematical Sciences, University of Nottingham, UK

Thesis: “Modelling planar cell polarity”

Supervisors: Markus Owen and Nick Monk

2000 - 2005

Diploma in Mathematics

Faculty of Mathematics and Computer Science, Julius-Maximilians-University, Würzburg, Germany

Thesis: "Filtermethoden für gemischte Komplementaritätsprobleme"

Supervisor: Christian Kanzow


2023[ to top ]
  • 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.
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.