Prof. Dr. Sabine Fischer
Prof. Dr. Sabine Fischer
Campus Hubland Nord

Research Interests
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.
Previous PhD students
Alexander Schmitz (2017)
Biena Mathew (2018)
Simon Schardt (2023)
Curriculum Vitae
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 |
Publications
- [ 2023 ]
- [ 2022 ]
- [ 2021 ]
- [ 2020 ]
- [ 2019 ]
- [ 2018 ]
- [ 2017 ]
- [ 2016 ]
- [ 2015 ]
- [ 2014 ]
- [ 2013 ]
- [ 2011 ]
- [ 2010 ]
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Tissues as networks of cells: towards generative rules of complex organ development. . In Journal of The Royal Society Interface, 20(204), bl 20230115. The Royal Society, 2023.
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The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours. . In iScience, bl 108106. Elsevier {BV}, 2023.
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The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours. . In bioRxiv, bl 2023.05.04.539359. Cold Spring Harbor Laboratory, 2023.
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Recognition and reconstruction of cell differentiation patterns with deep learning. . In PLOS Computational Biology, 19(10), bll 1–29. Public Library of Science, 2023.
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Adjusting the range of cell--cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. . In Journal of Mathematical Biology, 87(4), bl 54. 2023.
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Recognition and reconstruction of cell differentiation patterns with deep learning. . In arXiv, bl 2212.10058. 2022.
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Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus. . In Frontiers in Bioinformatics. Frontiers, 2022.
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Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. . In arXiv, bl 2211.07241. 2022.
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On-lattice Vicsek model in confined geometries. . In arXiv, bl 2105.08792. 2021.
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NANOG/GATA6 Interactions Revisited: A Statistical Mechanics Approach towards Cell Fate Decisions. . In arXiv, bl 2107.04501. 2021.
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Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus. . In bioRxiv, bl 2021.09.15.460416. 2021.
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Global cell-cell communication enables spatial segregation of cells in organoids of the inner cell mass. . In arXiv, bl 2111.01624. 2021.
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The transition from local to global patterns governs the differentiation of mouse blastocysts. . In PLOS ONE, 15(5), bll 1–29. Public Library of Science, 2020.
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Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach. . In Scientific Reports, 10(1), bl 22405-. 2020.
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Mouse ICM organoids reveal three-dimensional cell fate clustering. . In Biophysical Journal, 116, bll 127–141. Elsevier, 2019.
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Immersive Analysis of 3D Multi-cellular In-Vitro and In-Silico Cell Cultures. . In 2019 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR), bll 82–89. 2019.
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An Introduction to Image-Based Systems Biology of Multicellular Spheroids for Experimentalists and Theoreticians. . In Computational Biology, H. Husi (red.). Codon Publications, Brisbane, Australia, 2019.
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A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics. . In Nature Communications, 10(4095). 2019.
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The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. . In J Cell Biol, 217(9), bll 3109–3126. 2018.
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Electroluminescence imaging and automatic cell classification in mass production of silicon solar cells. . In 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion (WCPEC) (A Joint Conference of 45th IEEE PVSC, 28th PVSEC 34th EU PVSEC), bll 3298–3304. 2018.
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E-cadherin, actin, microtubules and {FAK} dominate different spheroid formation phases and important elements of tissue integrity. . In Biology Open, bl bio.037051. The Company of Biologists, 2018.
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Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids. . In Scientific Reports, 7, bl 43693. The Author(s), 2017.
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Identifying the necrotic zone boundary in tumour spheroids with pair-correlation functions. . In Journal of The Royal Society Interface, 13, bl 20160649. The Royal Society, 2016.
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Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. . In BMC Bioinformatics, 16, bl 187. 2015.
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Lateral assembly of N-cadherin drives tissue integrity by stabilizing adherens junctions. . In Journal of The Royal Society Interface, 12, bl 20141055. The Royal Society, 2015.
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Contractile and Mechanical Properties of Epithelia with Perturbed Actomyosin Dynamics. . In PLOS ONE, 9(4), bll 1–12. Public Library of Science, 2014.
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Is a Persistent Global Bias Necessary for the Establishment of Planar Cell Polarity?. . In PLOS ONE, 8(4), bll 1–12. Public Library of Science, 2013.
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Integrative approaches to morphogenesis: lessons from dorsal closure. . In Genesis, 49(7), bll 522–533. 2011.
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Endocytic and recycling endosomes modulate cell shape changes and tissue behaviour during morphogenesis in Drosophila. . In PLoS One, 6(4). 2011.
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Modelling and Analysis of Planar Cell Polarity. . In Bulletin of Mathematical Biology, 72(3), bll 645–680. 2010.