Tissue Organisation

Short Introduction

The interdisciplinary group develops, implements and experimentally validates multi-scale computational models of regenerative tissue with a special focus on:

  1. i) 3D cell-based modeling of tissue stem cell organization
  2. ii) genome-based modeling of epigenetic regulation of transcription

Applications: mesenchymal stem cells, hematopoietic stem cells, intestinal stem cells

Running projects:

INDRA : A model of the Intestinal Stem Cell Niche: Development, Regeneration and Ageing 

JRG BMBF Initiative e:Bio

Computational model of epigenetic regulation of myeloid differentiation during homeostasis and malignant transformation.

SPP1463 (DFG): Epigenetic Regulation of normal hematopoiesis and its dysregulation in myeloid neoplasia


Crypt model (Buske 2011, Thalheim 2016): Crypt model


2018 (3)

  • T. Thalheim, M. Quaas, M. Herberg, U. D. Braumann, C. Kerner, M. Loeffler, G. Aust, J. Galle. Linking stem cell function and growth pattern of intestinal organoids. Dev Biol. 2018. 433: 254-261.
  • T. Thalheim, M. Herberg, J. Galle. Linking DNA Damage and Age-Related Promoter DNA Hyper-Methylation in the Intestine. Genes. 2018. 9:
  • Y. A. Miroshnikova, H. Q. Le, D. Schneider, T. Thalheim, M. Rubsam, N. Bremicker, J. Polleux, N. Kamprad, M. Tarantola, I. Wang, M. Balland, C. M. Niessen, J. Galle, S. A. Wickstrom. Adhesion forces and cortical tension couple cell proliferation and differentiation to drive epidermal stratification. Nat Cell Biol. 2018. 20: 69-80.

2017 (4)

  • T. Thalheim, M. Herberg, M. Loeffler, J. Galle. The Regulatory Capacity of Bivalent Genes-A Theoretical Approach. Int J Mol Sci. 2017. 18:
  • J. Przybilla, L. Hopp, M. Lubbert, M. Loeffler, J. Galle. Targeting DNA hypermethylation: Computational modeling of DNA demethylation treatment of acute myeloid leukemia. Epigenetics. 2017. 12: 886-896.
  • K. Keysselt, T. Kreutzmann, K. Rother, C. Kerner, K. Krohn, J. Przybilla, P. Buske, H. Loffler-Wirth, M. Loeffler, J. Galle, G. Aust. Different in vivo and in vitro transformation of intestinal stem cells in mismatch repair deficiency. Oncogene. 2017. 36: 2750-2761.
  • Z. Hamidouche, K. Rother, J. Przybilla, A. Krinner, D. Clay, L. Hopp, C. Fabian, A. Stolzing, H. Binder, P. Charbord, J. Galle. Bistable Epigenetic States Explain Age-Dependent Decline in Mesenchymal Stem Cell Heterogeneity. Stem Cells. 2017. 35: 694-704.

2016 (1)

  • T. Thalheim, P. Buske, J. Przybilla, K. Rother, M. Loeffler, J. Galle. Stem cell competition in the gut: insights from multi-scale computational modelling. J R Soc Interface. 2016. 13:

2015 (1)

  • J. Przybilla, T. Rohlf, J. Galle. Towards a Mechanistic Understanding of Epigenetic Dynamics. In: Computational and Statistical Epigenomics, Springer Netherlands , Dordrecht. 2015. 141--160. Ed: Teschendorff, A.E.

2014 (2)

  • J. Przybilla, T. Rohlf, M. Löffler, J. Galle. Understanding epigenetic changes in aging stem cells--a computational model approach. Aging Cell. 2014. 13: 320-8.
  • P. Buske, J. Przybilla, M. Löffler, J. Galle. The intestinal stem cell niche: a computational tissue approach. Biochem Soc Trans. 2014. 42: 671-7.

2013 (2)

  • H. Binder, L. Steiner, J. Przybilla, T. Rohlf, S. Prohaska, J. Galle. Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation. Phys Biol. 2013. 10: 026006.
  • G. Aust, C. Kerner, S. Gonsior, D. Sittig, H. Schneider, P. Buske, M. Scholz, N. Dietrich, S. Oldenburg, O. N. Karpus, J. Galle, S. Amasheh, J. Hamann. Mice overexpressing CD97 in intestinal epithelial cells provide a unique model for mammalian postnatal intestinal cylindrical growth. Mol Biol Cell. 2013. 24: 2256-68.

2012 (4)

  • L. Steiner, L. Hopp, H. Wirth, J. Galle, H. Binder, S. J. Prohaska, T. Rohlf. A global genome segmentation method for exploration of epigenetic patterns. PLoS One. 2012. 7: e46811.
  • T. Rohlf, L. Steiner, J. Przybilla, S. Prohaska, H. Binder, J. Galle. Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics. 2012. 4: 205-19.
  • J. Przybilla, J. Galle, T. Rohlf. Is adult stem cell aging driven by conflicting modes of chromatin remodeling?. Bioessays. 2012. 34: 841-8.
  • P. Buske, J. Przybilla, M. Loeffler, N. Sachs, T. Sato, H. Clevers, J. Galle. On the biomechanics of stem cell niche formation in the gut--modelling growing organoids. FEBS J. 2012. 279: 3475-87.

2011 (1)

  • M. Hoffmann, J. P. Kuska, M. Zscharnack, M. Löffler, J. Galle. Spatial organization of mesenchymal stem cells in vitro--results from a new individual cell-based model with podia. PLoS One. 2011. 6: e21960.

2010 (3)

  • A. Krinner, M. Hoffmann, M. Löffler, D. Drasdo, J. Galle. Individual fates of mesenchymal stem cells in vitro. BMC Syst Biol. 2010. 4: 73.
  • J. Galle, A. Bader, P. Hepp, W. Grill, B. Fuchs, J. A. Kas, A. Krinner, B. Marquass, K. Müller, J. Schiller, R. M. Schulz, M. von Buttlar, E. von der Burg, M. Zscharnack, M. Löffler. Mesenchymal stem cells in cartilage repair: state of the art and methods to monitor cell growth, differentiation and cartilage regeneration. Curr Med Chem. 2010. 17: 2274-91.
  • H. Binder, H. Wirth, J. Galle. Gene expression density profiles characterize modes of genomic regulation: theory and experiment. J Biotechnol. 2010. 149: 98-114.

2009 (5)

  • M. Zscharnack, C. Poesel, J. Galle, A. Bader. Low oxygen expansion improves subsequent chondrogenesis of ovine bone-marrow-derived mesenchymal stem cells in collagen type I hydrogel. Cells Tissues Organs. 2009. 190: 81-93.
  • A. Krinner, M. Zscharnack, A. Bader, D. Drasdo, J. Galle. Impact of oxygen environment on mesenchymal stem cell expansion and chondrogenic differentiation. Cell Prolif. 2009. 42: 471-84.
  • J. Galle, L. Preziosi, A. Tosin. Contact inhibition of growth described using a multiphase model and an individual cell based model. Applied Mathematics Letters. 2009. 22: 1483-1490.
  • J. Galle, L. Preziosi. Multiphase and Individual Cell-Based Models of Tumour Growth. In: Mathematics, Developmental Biology and Tumour Growth, American Mathematical Society 2009. 492: 103-123. Ed: F. Giraldez and M. A. Herrero.
  • J. Galle, M. Hoffmann, G. Aust. From single cells to tissue architecture-a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems. J Math Biol. 2009. 58: 261-283.

2008 (1)

  • M. Hoffmann, H. H. Chang, S. Huang, D. E. Ingber, M. Löffler, J. Galle. Noise-driven stem cell and progenitor population dynamics. PLoS One. 2008. 3: e2922.

2006 (2)

  • J. Galle, D. Sittig, I. Hanisch, M. Wobus, E. Wandel, M. Loeffler, G. Aust. Individual cell-based models of tumor-environment interactions: Multiple effects of CD97 on tumor invasion. Am J Pathol. 2006. 169: 1802-11.
  • J. Galle, G. Aust, G. Schaller, T. Beyer, D. Drasdo. Individual cell-based models of the spatial-temporal organization of multicellular systems--achievements and limitations. Cytometry A. 2006. 69: 704-10.