Chair for Computational and Theoretical Biology

Spatial Systems Biology

Dr. Patrick Wurzel

Dr. Patrick Wurzel

Chair for Computational and Theoretical Biology (CCTB)
Klara-Oppenheimer-Weg 32
Campus Hubland Nord
97074 Würzburg

 

I lead the Spatial Systems Biology group at the Chair for Computational and Theoretical Biology (CCTB) and I am affiliated with the Mildred Scheel Early Career Center Würzburg (MSNZ). I studied Bioinformatics at the Goethe University Frankfurt, where I completed my PhD with a focus on digital pathology and spatial systems immunology. My research investigates how spatial organization and interaction govern biological function across scales. To address these questions, I develop and apply computational approaches combining spatial omics, especially imaging, graph-based modelling, and machine learning.

Research

Biological systems are highly organized across space and scale. Cells form tissues, tissues establish functional architectures, and interactions between cellular populations shape biological function. Our research focuses on understanding these organizational principles and their functional consequences using computational approaches.

We develop and apply methods for the analysis of spatially resolved biological data, ranging from histopathology and volumetric imaging to spatial omics technologies. A particular focus of our work lies on modelling spatial interactions and biological networks to investigate how tissue architecture, cellular neighbourhoods, and long-range connectivity contribute to biological system behaviour.

To address these questions, we combine approaches from image analysis, graph theory, machine learning, and spatial statistics. We are especially interested in interpretable computational models that bridge biological structure and function and enable the quantitative characterization of complex biological systems. Our work spans multiple application areas including systems immunology, neuroinformatics, and digital pathology.

Group Members

  • Dr. Patrick Wurzel
  • Gungun Saini
  • Muhammad Haseeb

Master students in collaboration with Prof. Dr. Franziska Matthäus, Goethe University Frankfurt:

  • Dennis Ragnar van Reem

Medical doctoral candidates in collaboration with Prof. Dr. Martin-Leo Hansmann, Goethe University Frankfurt:

  • Charlotte Bahlmann
  • Aleksandar Vladisavljevic
  • Diana Elisa Theil
  • Victoria Diederich
  • Christian Gronstedt
  • Marie Tobiasch
  • Leonie Hecker
  • Luisa Hilbert
  • Roxana Langer
  • Nicole Dehnfeld

Thesis Projects

Join our group for an internship, or for your Bachelor or Master thesis. Some projects we currently offer:

  • Imaging-Based Definitions of Immunological Niches in Health and Disease
    How can imaging, spatial omics, and computational modelling be combined to characterize immunological niches and their architectural changes in reactive and neoplastic tissues?
     
  • Graph-Based Modelling of Long-Range Biological Interaction Networks
    How can graph theory be used to characterize long-range interaction structures and connectivity patterns in complex biological systems?
     
  • Systemic Adaptations After Stroke
    How does stroke reshape cellular organization, immune microenvironments, and tissue architecture across the brain and peripheral organs in mice and humans?
     
  • From the Digital Bench to the Bedside
    How can modern computational methods be translated into clinically interpretable biomarkers and diagnostic tools in digital pathology?

If you have your own idea that fits the research interests of the group, we are very happy to discuss it.

Are you interested in spatial biology, computational modelling, machine learning, graph theory, or biomedical image analysis? Then join our team to investigate how biological systems organize, interact, and adapt across scales.

Prior knowledge is helpful, but not required. Motivation, curiosity, and willingness to learn are most important.

Get in touch with Patrick Wurzel to learn more.

Publications

2026

  • Cellular landscape of reactive and neoplastic human lymph nodes in 3D. Diederich, Victoria Julia; Scharf, Sonja; Schäfer, Hendrik; Hartmann, Sylvia; Hansmann, Martin-Leo; Wurzel, Patrick. In Acta Histochemica, 128(1), 152308. 2026.
  • The three-dimensional landscape of tumor-associated macrophages in reactive and neoplastic human lymph nodes. Vladisavljevic, Aleksandar; Scharf, Sonja; Schäfer, Hendrik; Ackermann, Jörg; Hartmann, Sylvia; Koch, Ina; Hansmann, Martin-Leo; Wurzel, Patrick. In PLOS Digital Health, 5(2), e0001227. 2026.

2025

  • Lymphomas in 3D and 4D spaces. Hansmann, Martin-Leo; Scharf, Sonja; Wurzel, Patrick; Hartmann, Sylvia. In Human Pathology, 156, 105699. 2025.
  • 3D examination reveals increased destruction of alpha-actin-positive structures in advanced follicular lymphoma stages. Geib, Katharina; Scharf, Sonja; Schäfer, Hendrik; Hartmann, Sylvia; Hansmann, Martin-Leo; Wurzel, Patrick. In Acta Histochemica, 127(1), 152232. 2025.
  • Behavioral investigation of reactive and neoplastic lymphocytes in human lymph nodes in 4D. Theil, Diana Elisa; Bütow, Cornelius; Scharf, Sonja; Schäfer, Hendrik; Hartmann, Sylvia; Hansmann, Martin-Leo; Wurzel, Patrick. In PLoS One, 20(9), e0331439. 2025.
  • Deletion of ABIN1-LIR motifs impairs hepatic lipid homeostasis and mitophagy via AMPK-TFEB axis in mice. Huber, Lisa Sophie; Merline, Rosetta; Zeng-Brouwers, Jinyang; Vutukuri, Rajkumar; Kraus, Nico; Ortiz, Cristina; Guenther, Stefan; Buhl, Eva Miriam; Hahnefeld, Lisa; Gurke, Robert; et al. In American Journal of Physiology – Cell Physiology. 2025.

2024

  • Computational systems biology of cellular processes in the human lymph node. Scharf, Sonja; Ackermann, Jörg; Wurzel, Patrick; Hansmann, Martin-Leo; Koch, Ina. In Current Opinion in Systems Biology, 38, 100518. 2024.

2023

  • Imaging bridges pathology and radiology. Hansmann, Martin-Leo; Klauschen, Frederick; Samek, Wojciech; Müller, Klaus-Robert; Donnadieu, Emmanuel; Scharf, Sonja; Hartmann, Sylvia; Koch, Ina; Ackermann, Jörg; Pantanowitz, Liron; et al. In Journal of Pathology Informatics, 100298. 2023.
  • Holistic view on the structure of immune response: Petri net model. Scharf, Sonja; Ackermann, Jörg; Bender, Leonie; Wurzel, Patrick; Schäfer, Hendrik; Hansmann, Martin-Leo; Koch, Ina. In Biomedicines, 11(2), 452. 2023.
  • Three-dimensional human germinal centers of different sizes in patients diagnosed with lymphadenitis show comparative constant relative volumes of B cells, T cells, follicular dendritic cells, and macrophages. Schemel, Constantin Maximilian; Wurzel, Patrick; Scharf, Sonja; Schäfer, Hendrik; Hartmann, Sylvia; Koch, Ina; Hansmann, Martin-Leo. In Acta Histochemica, 125(7), 152075. 2023.
  • The E3 ligase TRIM25 impairs apoptotic cell death in colon carcinoma cells via destabilization of Caspase-7 mRNA: a possible role of hnRNPH1. Nasrullah, Usman; Stanke, Kristina; Recknagel, Victoria; Bozkurt, Süleyman; Wurzel, Patrick; Gauer, Stefan; Imre, Gergely; Münch, Christian; Pfeilschifter, Josef; Eberhardt, Wolfgang. In Cells, 12(1), 201. 2023.

2022

  • New definitions of human lymphoid and follicular cell entities in lymphatic tissue by machine learning. Wagner, Patrick; Strodthoff, Nils; Wurzel, Patrick; Marban, Arturo; Scharf, Sonja; Schäfer, Hendrik; Seegerer, Philipp; Loth, Andreas; Hartmann, Sylvia; Klauschen, Frederick; et al. In Scientific Reports, 12(1), 18991. 2022.

2021

  • Detection of follicular regions in actin-stained whole slide images of the human lymph node by shock filter. Wurzel, Patrick; Ackermann, Jörg; Schäfer, Hendrik; Scharf, Sonja; Hansmann, Martin-Leo; Koch, Ina. In Biological Chemistry, 402(8), pp. 991–999. 2021.
  • 3D connectomes of reactive and neoplastic CD30 positive lymphoid cells and surrounding cell types. Lumer, Lukas; Wurzel, Patrick; Scharf, Sonja; Schäfer, Hendrik; Ackermann, Jörg; Koch, Ina; Hansmann, Martin-Leo. In Acta Histochemica, 123(5), 151750. 2021.

2020

  • 3D investigation shows walls and wall-like structures around human germinal centres, probably regulating T- and B-cell entry and exit. Thomos, Miguel; Wurzel, Patrick; Scharf, Sonja; Koch, Ina; Hansmann, Martin-Leo. In PLoS One, 15(11), e0242177. 2020.

2019

  • 3D analysis of morphological alterations of the fibroblastic reticular cells in reactive and neoplastic human lymph nodes. Oswald, Marvin Siegfried; Wurzel, Patrick; Hansmann, Martin-Leo. In Acta Histochemica, 121(7), pp. 769–775. 2019.
  • 3D image analysis reveals differences of CD30 positive cells and network formation in reactive and malignant human lymphoid tissue (classical Hodgkin Lymphoma). Liebers, Julia; Wurzel, Patrick; Reisinger, Kerstin Bianca; Hansmann, Martin-Leo. In PLoS One, 14(10), e0224156. 2019.