Center for Computational and Theoretical Biology


Computational Image Analysis Group: [ Home​​​​ ] [ Research ] [ PI ] [ Group ] [ Publications ] [ Teaching ]


  • Mrestani, A., Kollmannsberger, P., Pauli, M., Repp, F., Kittel, R.J., Eilers, J., Doose, S., Sauer, M., Sirén, A.-L., Heckmann, M., Paul, M.M. (2019) “Active zone compaction for presynaptic strength”, bioRxiv, available: https://www.biorxiv.org/content/early/2019/10/13/802843.
  • Pauli, M., Paul, M.M., Proppert, S., Sharifi, M., Repp, F., Kollmannsberger, P., Sauer, M., Heckmann, M., Sirén, A.-L. (2019) “Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections”, bioRxiv, available: http://biorxiv.org/lookup/doi/10.1101/568279.
  • Mostosi, P., Schindelin, H., Kollmannsberger, P., Thorn, A. (2019) “Automated interpretation of Cryo-EM density maps with convolutional neural networks”, bioRxiv, 644476, available: https://www.biorxiv.org/content/10.1101/644476v1.



  • Spindler, M.-C., Redolfi, J., Helmprobst, F., Kollmannsberger, P., Stigloher, C., Benavente, R. (2019) “Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules”, Communications Biology, 2(1), 376--, available: https://doi.org/10.1038/s42003-019-0621-1.
  • Ehrig, S., Bidan, C.M., West, A., Jacobi, C., Lam, K., Kollmannsberger, P., Petersen, A., Tomancak, P., Kommareddy, K., Fischer, F.D., Fratzl, P., Dunlop, J.W.C. (2019) “Surface tension determines tissue shape and growth kinetics”, Science Advances, 5(9), eaav9394, available: https://advances.sciencemag.org/content/5/9/eaav9394?intcmp=trendmd-adv.
  • Weinkamer, R., Kollmannsberger, P., Fratzl, P. (2019) “Towards a Connectomic Description of the Osteocyte Lacunocanalicular Network in Bone”, Current Osteoporosis Reports, available: https://doi.org/10.1007/s11914-019-00515-z.


  • Kaltdorf, K.V., Theiss, M., Markert, S.M., Zhen, M., Dandekar, T., Stigloher, C., Kollmannsberger, P. (2018) “Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning”, PLoS one, 13(10), e0205348, available: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205348.
  • Kollmannsberger, P., Bidan, C.M., Dunlop, J., Fratzl, P., Vogel, V. (2018) “Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts”, Science Advances, 4(1), eaao4881.


  • Repp, F., Kollmannsberger, P., Roschger, A., Berzlanovich, A., Gruber, G., Roschger, P., Wagermaier, W., Weinkamer, R. (2017) “Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone”, Journal of Stuctural Biology, 199, 177-186.
  • Repp, F., Kollmannsberger, P., Roschger, A., Kerschnitzki, M., Berzlanovich, A., Gruber, G.M., Roschger, P., Wagermaier, W., Weinkamer, R. (2017) “Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons”, Bone Reports, 6, 101-108.
  • Kollmannsberger, P., Kerschnitzki, M., Repp, F., Wagermaier, W., Weinkamer, R., Fratzl, P. (2017) “The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone.”, New Journal of Physics, 19, 073019.
  • Kaltdorf, K.V., Schulze, K., Helmprobst, F., Kollmannsberger, P., Dandekar, T., Stigloher, C. (2017) “FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms”, PLOS Computational Biology, 13(1), 1-21, available: http://dx.doi.org/10.1371%2Fjournal.pcbi.1005317.


  • Yamashita, T., Kollmannsberger, P., Mawatari, K., Kitamori, T., Vogel, V. (2016) “Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces”, Acta Biomaterialia, 45, 85 - 97, available: http://www.sciencedirect.com/science/article/pii/S1742706116304408.
  • Bidan, C.M., Kollmannsberger, P., Gering, V., Ehrig, S., Joly, P., Petersen, A., Vogel, V., Fratzl, P., Dunlop, J.W.C. (2016) “Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth”, Journal of The Royal Society Interface, 13(118), available: http://rsif.royalsocietypublishing.org/content/13/118/20160136.
  • Avalos Vizcarra, I., Hosseini, V., Kollmannsberger, P., Meier, S., Weber, S.S., Arnoldini, M., Ackermann, M., Vogel, V. (2016) “How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics”, Scientific Reports, 6, 18109, available: http://dx.doi.org/10.1038/srep18109.


  • Foolen, J., Yamashita, T., Kollmannsberger, P. (2015) “Shaping tissues by balancing active forces and geometric constraints”, Journal of Physics D: Applied Physics, 49(5), 053001.


  • Hosseini, V., Kollmannsberger, P., Ahadian, S., Ostrovidov, S., Kaji, H., Vogel, V., Khademhosseini, A. (2014) “Fiber-Assisted Molding (FAM) of Surfaces with Tunable Curvature to Guide Cell Alignment and Complex Tissue Architecture”, Small, 10(23), 4851--4857.


  • Möller, J., Emge, P., Vizcarra, I.A., Kollmannsberger, P., Vogel, V. (2013) “Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces”, New Journal of Physics, 15(12), 125016.
  • Yamashita, T., Kollmannsberger, P., Mawatari, K., Vogel, V., Kitamori, T. (2013) “Curvature-induced spontaneous detachment of vascular smooth muscle cell sheets: towards vascular self assembly in microchannels”, Microsystem Technology in Chemistry and Life Science.
  • Lukas, C., Ruffoni, D., Lambers, F.M., Schulte, F.A., Kuhn, G., Kollmannsberger, P., Weinkamer, R., Müller, R. (2013) “Mineralization kinetics in murine trabecular bone quantified by time-lapsed in vivo micro-computed tomography”, Bone, 56(1), 55--60.
  • Bidan, C.M., Kommareddy, K.P., Rumpler, M., Kollmannsberger, P., Fratzl, P., Dunlop, J.W.C. (2013) “Geometry as a factor for tissue growth: towards shape optimization of tissue engineering scaffolds”, Advanced healthcare materials, 2(1), 186--194.
  • Kerschnitzki, M., Kollmannsberger, P., Burghammer, M., Duda, G.N., Weinkamer, R., Wagermaier, W., Fratzl, P. (2013) “Architecture of the osteocyte network correlates with bone material quality”, Journal of Bone and Mineral Research, 28(8), 1837--1845.


  • Bidan, C.M., Kommareddy, K.P., Rumpler, M., Kollmannsberger, P., Bréchet, Y.J.M., Fratzl, P., Dunlop, J.W.C. (2012) “How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue Growth”, PloS one, 7(5), e36336.


  • Kollmannsberger, P., Bidan, C.M., Dunlop, J.W.C., Fratzl, P. (2011) “The physics of tissue patterning and extracellular matrix organisation: how cells join forces”, Soft Matter, 7(20), 9549--9560.
  • Kollmannsberger, P., Mierke, C.T., Fabry, B. (2011) “Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension”, Soft Matter, 7(7), 3127--3132.
  • Lukas, C., Kollmannsberger, P., Ruffoni, D., Roschger, P., Fratzl, P., Weinkamer, R. (2011) “The Heterogeneous Mineral Content of Bone—Using Stochastic Arguments and Simulations to Overcome Experimental Limitations”, Journal of Statistical Physics, 144(2), 316--331.
  • Kollmannsberger, P., Fabry, B. (2011) “Linear and nonlinear rheology of living cells”, Annual Review of Materials Research, 41, 75--97.


  • Mierke, C.T., Kollmannsberger, P., Zitterbart, D.P., Diez, G., Koch, T.M., Marg, S., Ziegler, W.H., Goldmann, W.H., Fabry, B. (2010) “Vinculin facilitates cell invasion into three-dimensional collagen matrices”, Journal of Biological Chemistry, 285(17), 13121--13130.


  • Diez, G., Kollmannsberger, P., Mierke, C.T., Koch, T.M., Vali, H., Fabry, B., Goldmann, W.H. (2009) “Anchorage of vinculin to lipid membranes influences cell mechanical properties”, Biophysical journal, 97(12), 3105--3112.
  • Kollmannsberger, P., Fabry, B. (2009) “Active soft glassy rheology of adherent cells”, Soft Matter, 5(9), 1771--1774.
  • Kasza, K.E., Nakamura, F., Hu, S., Kollmannsberger, P., Bonakdar, N., Fabry, B., Stossel, T.P., Wang, N., Weitz, D.A. (2009) “Filamin A is essential for active cell stiffening but not passive stiffening under external force”, Biophysical journal, 96(10), 4326--4335.
  • Lorenz, C., Brunner, J.G., Kollmannsberger, P., Jaafar, L., Fabry, B., Virtanen, S. (2009) “Effect of surface pre-treatments on biocompatibility of magnesium”, Acta biomaterialia, 5(7), 2783--2789.


  • Mierke, C.T., Zitterbart, D.P., Kollmannsberger, P., Raupach, C., Schlötzer-Schrehardt, U., Goecke, T.W., Behrens, J., Fabry, B. (2008) “Breakdown of the endothelial barrier function in tumor cell transmigration”, Biophysical journal, 94(7), 2832--2846.
  • Rösel, D., Brábek, J., Tolde, O., Mierke, C.T., Zitterbart, D.P., Raupach, C., Bicanová, K.`yna, Kollmannsberger, P., Pavnková, D., Vesel`y, P., others, (2008) “Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces”, Molecular Cancer Research, 6(9), 1410--1420.
  • Mierke, C.T., Kollmannsberger, P., Paranhos Zitterbart, D., Smith, J., Fabry, B., Goldmann, W.H. (2008) “Mechano-coupling and regulation of contractility by the vinculin tail domain”, Biophysical journal, 94(2), 661--670.


  • Kollmannsberger, P., Fabry, B. (2007) “High-force magnetic tweezers with force feedback for biological applications”, Review of Scientific Instruments, 78(11), 114301--114301.