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Center for Computational and Theoretical Biology

Prof. Dr. Sabine Fischer

Prof. Dr. Sabine Fischer

Professor for Artificial Intelligence in Computational and Theoretical Biology
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.