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Center for Computational and Theoretical Biology

Prof. Dr. Sabine Fischer

Prof. Dr. Sabine Fischer

Professor for Supramolecular and Cellular Simulations
Center for Computational and Theoretical Biology (CCTB)
Klara-Oppenheimer-Weg 32
Campus Hubland Nord
97074 Würzburg
Germany
Building: 32
Room: L5
Phone: +49 931 31-83961
ORCID: https://orcid.org/0000-0001-7237-814X

Google Scholar Profile - Sabine C. Fischer

My research focus is on spatial interactions in biological systems at different length scales. For this, I apply and adjust techniques from data analysis and mathematical modelling such as image analysis, spatial statistics, agent-based modelling and machine learning. I enjoy working in an interdisciplinary environment and utilising the different perspectives for solving interesting research questions.
All projects in my group are application- and data-driven and based on close collaborations with experts in the respective field.

Alexander Schmitz (2017)

Biena Mathew (2018)

Simon Schardt (2023)

Kerstin Schmid (2024)

  • since 2018: Professor
    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: Postdoc
    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

2025[ to top ]
  • Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq). Ahmad, Shazeb; Li, Jianhui; Schaust, Joél; Gribling-Burrer, Anne-Sophie; Geiger, Nina; Fischer, Sabine C; Ambi, Uddhav B; Backes, Simone; Ankenbrand, Markus J; Smyth, Redmond P. In Nucleic Acids Research, 53(11). Oxford University Press (OUP), 2025.
2024[ to top ]
  • mTOR controls growth and internal architecture of human breast cancer spheroids. Hötte, Katharina; Fischer, Sabine C.; Schmitz, Alexander; Koch, Michael; Saeifar, Sanam; Stelzer, Ernst H.K.; Pampaloni, Francesco. In bioRxiv, p. 2024.02.24.580871. Cold Spring Harbor Laboratory, 2024.
  • Aggregation of adult parasitic nematodes in sex-mixed groups analysed by transient anomalous diffusion formalism. Leben, Ruth; Rausch, Sebastian; Elomaa, Laura; Hauser, Anja E.; Weinhart, Marie; Fischer, Sabine C.; Stark, Holger; Hartmann, Susanne; Niesner, Raluca. In Journal of The Royal Society Interface, 21(219). The Royal Society, 2024.
  • Inference of alveolar capillary network connectivity from blood flow dynamics. Schmid, Kerstin; Olivares, Andy L.; Camara, Oscar; Kuebler, Wolfgang M.; Ochs, Matthias; Hocke, Andreas C.; Fischer, Sabine C. In American Journal of Physiology-Lung Cellular and Molecular Physiology. American Physiological Society, 2024.
  • Quantification of Trypanosoma Brucei social motility indicates different colony growth phases. Kuhn, Andreas; Krueger, Timothy; Schuettler, Magdalena; Engstler, Markus; Fischer, Sabine C. In bioRxiv. Cold Spring Harbor Laboratory, 2024.
2023[ to top ]
  • Adjusting the range of cell--cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. Schardt, Simon; Fischer, Sabine C. In Journal of Mathematical Biology, 87(4), p. 54. 2023.
  • 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 iScience, p. 108106. Elsevier BV, 2023.
  • Recognition and reconstruction of cell differentiation patterns with deep learning. Dirk, Robin; Fischer, Jonas L.; Schardt, Simon; Ankenbrand, Markus J.; Fischer, Sabine C. In PLOS Computational Biology, 19(10), pp. 1–29. Public Library of Science, 2023.
  • Tissues as networks of cells: towards generative rules of complex organ development. Fischer, Sabine C.; Bassel, George W.; Kollmannsberger, Philip. In Journal of The Royal Society Interface, 20(204), p. 20230115. The Royal Society, 2023.
2022[ to top ]
  • 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, p. 2211.07241. 2022.
  • 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. Frontiers, 2022.
  • 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, p. 2212.10058. 2022.
2021[ to top ]
  • On-lattice Vicsek model in confined geometries. Kuhn, Andreas; C, Fischer Sabine. In arXiv, p. 2105.08792. 2021.
  • 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, p. 2021.09.15.460416. 2021.
  • NANOG/GATA6 Interactions Revisited: A Statistical Mechanics Approach towards Cell Fate Decisions. Schardt, Simon; Fischer, S C. In arXiv, p. 2107.04501. 2021.
  • Global cell-cell communication enables spatial segregation of cells in organoids of the inner cell mass. Schardt, Simon; Fischer, SC. In arXiv, p. 2111.01624. 2021.
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, 15(5), pp. 1–29. Public Library of Science, 2020.
  • 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, 10(1), p. 22405-. 2020.
2019[ to top ]
  • 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, 10(4095). 2019.
  • 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, 116, pp. 127–141. Elsevier, 2019.
  • An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. Fischer, Sabine C. In Computational Biology, H. Husi (ed.). Codon Publications, Brisbane, Australia, 2019.
  • 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), pp. 82–89. 2019.
2018[ to top ]
  • 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), pp. 3298–3304. 2018.
  • 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, 217(9), pp. 3109–3126. 2018.
  • 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, p. bio.037051. The Company of Biologists, 2018.
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, 7, p. 43693. The Author(s), 2017.
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, 13, p. 20160649. The Royal Society, 2016.
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, 16, p. 187. 2015.
  • 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, 12, p. 20141055. The Royal Society, 2015.
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, 9(4), pp. 1–12. Public Library of Science, 2014.
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, 8(4), pp. 1–12. Public Library of Science, 2013.
2011[ to top ]
  • 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, 6(4). 2011.
  • Integrative approaches to morphogenesis: lessons from dorsal closure. Gorfinkiel, N; Schamberg, S; Blanchard, G B. In Genesis, 49(7), pp. 522–533. 2011.
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, 72(3), pp. 645–680. 2010.