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Center for Computational and Theoretical Biology

Publications


Preprints

  • 1.
    Seifert, R., Markert, S., Britz, S., Perschin, V., Erbacher, C., Stigloher, C., Kollmannsberger, P.: DeepCLEM: automated registration for correlative light and electron microscopy using deep learning [version 1; peer review: awaiting peer review]. F1000Research. 9, (2020).
     
  • 2.
    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.: Active zone compaction for presynaptic strength. bioRxiv. (2019).
     

Publications

2021

  • 1.
    Mrestani, A., Pauli, M., Kollmannsberger, P., Repp, F., Kittel, R.J., Eilers, J., Doose, S., Sauer, M., Sirén, A.-L., Heckmann, M., Paul, M.M.: Active zone compaction correlates with presynaptic homeostatic potentiation. Cell Reports. 37, (2021).
     
  • 2.
    Matikonda, S.S., Helmerich, D.A., Meub, M., Beliu, G., Kollmannsberger, P., Greer, A., Sauer, M., Schnermann, M.J.: Defining the Basis of Cyanine Phototruncation Enables a New Approach to Single-Molecule Localization Microscopy. ACS Central Science. 7, 1144–1155 (2021).
     
  • 3.
    Marquardt, A., Solimando, A.G., Kerscher, A., Bittrich, M., Kalogirou, C., Kübler, H., Rosenwald, A., Bargou, R., Kollmannsberger, P., Schilling, B., Meierjohann, S., Krebs, M.: Subgroup-Independent Mapping of Renal Cell Carcinoma—Machine Learning Reveals Prognostic Mitochondrial Gene Signature Beyond Histopathologic Boundaries. Frontiers in Oncology. 11, (2021).
     
  • 4.
    Pauli, M., Paul, M.M., Proppert, S., Mrestani, A., Sharifi, M., Repp, F., Kürzinger, L., Kollmannsberger, P., Sauer, M., Heckmann, M., Sirén, A.-L.: Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. Communications Biology. 4, 1–13 (2021).
     
  • 5.
    Marquardt, A., Landwehr, L.-S., Ronchi, C.L., di Dalmazi, G., Riester, A., Kollmannsberger, P., Altieri, B., Fassnacht, M., Sbiera, S.: Identifying New Potential Biomarkers in Adrenocortical Tumors Based on mRNA Expression Data Using Machine Learning. Cancers. 13, 4671 (2021).
     

2020

  • 1.
    Mostosi, P., Schindelin, H., Kollmannsberger, P., Thorn, A.: Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo-Electron Microscopy Maps. Angewandte Chemie International Edition. n/a, (2020).
     
  • 2.
    Paul, T.J., Kollmannsberger, P.: Biological network growth in complex environments – a computational framework. PLOS Computational Biology. 16, e1008003 (2020).
     
  • 3.
    Sahlol, A.T., Kollmannsberger, P., Ewees, A.A.: Efficient Classification of White Blood Cell Leukemia with Improved Swarm Optimization of Deep Features. Scientific Reports. 10, 2536 (2020).
     

2019

  • 1.
    Spindler, M.-C., Redolfi, J., Helmprobst, F., Kollmannsberger, P., Stigloher, C., Benavente, R.: Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules. Communications Biology. 2, 376- (2019).
     
  • 2.
    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.: Surface tension determines tissue shape and growth kinetics. Science Advances. 5, eaav9394 (2019).
     
  • 3.
    Weinkamer, R., Kollmannsberger, P., Fratzl, P.: Towards a Connectomic Description of the Osteocyte Lacunocanalicular Network in Bone. Current Osteoporosis Reports. (2019).
     

2018

  • 1.
    Kaltdorf, K.V., Theiss, M., Markert, S.M., Zhen, M., Dandekar, T., Stigloher, C., Kollmannsberger, P.: Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning. PLoS one. 13, e0205348 (2018).
     
  • 2.
    Kollmannsberger, P., Bidan, C.M., Dunlop, J., Fratzl, P., Vogel, V.: Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. Science Advances. 4, eaao4881 (2018).
     

2017

  • 1.
    Repp, F., Kollmannsberger, P., Roschger, A., Kerschnitzki, M., Berzlanovich, A., Gruber, G.M., Roschger, P., Wagermaier, W., Weinkamer, R.: Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons. Bone Reports. 6, 101–108 (2017).
     
  • 2.
    Repp, F., Kollmannsberger, P., Roschger, A., Berzlanovich, A., Gruber, G., Roschger, P., Wagermaier, W., Weinkamer, R.: Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. Journal of Stuctural Biology. 199, 177–186 (2017).
     
  • 3.
    Kollmannsberger, P., Kerschnitzki, M., Repp, F., Wagermaier, W., Weinkamer, R., Fratzl, P.: The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone. New Journal of Physics. 19, 073019 (2017).
     
  • 4.
    Kaltdorf, K.V., Schulze, K., Helmprobst, F., Kollmannsberger, P., Dandekar, T., Stigloher, C.: FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. PLOS Computational Biology. 13, 1–21 (2017).
     

2016

  • 1.
    Bidan, C.M., Kollmannsberger, P., Gering, V., Ehrig, S., Joly, P., Petersen, A., Vogel, V., Fratzl, P., Dunlop, J.W.C.: Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth. Journal of The Royal Society Interface. 13, (2016).
     
  • 2.
    Yamashita, T., Kollmannsberger, P., Mawatari, K., Kitamori, T., Vogel, V.: Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces. Acta Biomaterialia. 45, 85–97 (2016).
     
  • 3.
    Avalos Vizcarra, I., Hosseini, V., Kollmannsberger, P., Meier, S., Weber, S.S., Arnoldini, M., Ackermann, M., Vogel, V.: How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics. Scientific Reports. 6, 18109 (2016).
     

2015

  • 1.
    Foolen, J., Yamashita, T., Kollmannsberger, P.: Shaping tissues by balancing active forces and geometric constraints. Journal of Physics D: Applied Physics. 49, 053001 (2015).
     

2014

  • 1.
    Hosseini, V., Kollmannsberger, P., Ahadian, S., Ostrovidov, S., Kaji, H., Vogel, V., Khademhosseini, A.: Fiber-Assisted Molding (FAM) of Surfaces with Tunable Curvature to Guide Cell Alignment and Complex Tissue Architecture. Small. 10, 4851–4857 (2014).
     

2013

  • 1.
    Möller, J., Emge, P., Vizcarra, I.A., Kollmannsberger, P., Vogel, V.: Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces. New Journal of Physics. 15, 125016 (2013).
     
  • 2.
    Kerschnitzki, M., Kollmannsberger, P., Burghammer, M., Duda, G.N., Weinkamer, R., Wagermaier, W., Fratzl, P.: Architecture of the osteocyte network correlates with bone material quality. Journal of Bone and Mineral Research. 28, 1837–1845 (2013).
     
  • 3.
    Bidan, C.M., Kommareddy, K.P., Rumpler, M., Kollmannsberger, P., Fratzl, P., Dunlop, J.W.: Geometry as a factor for tissue growth: towards shape optimization of tissue engineering scaffolds. Advanced healthcare materials. 2, 186–194 (2013).
     
  • 4.
    Lukas, C., Ruffoni, D., Lambers, F.M., Schulte, F.A., Kuhn, G., Kollmannsberger, P., Weinkamer, R., Müller, R.: Mineralization kinetics in murine trabecular bone quantified by time-lapsed <i>in vivo</i> micro-computed tomography. Bone. 56, 55–60 (2013).
     
  • 5.
    Yamashita, T., Kollmannsberger, P., Mawatari, K., Vogel, V., Kitamori, T.: Curvature-induced spontaneous detachment of vascular smooth muscle cell sheets: towards vascular self assembly in microchannels. Microsystem Technology in Chemistry and Life Science. (2013).
     

2012

  • 1.
    Bidan, C.M., Kommareddy, K.P., Rumpler, M., Kollmannsberger, P., Bréchet, Y.J., Fratzl, P., Dunlop, J.W.: How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue Growth. PloS one. 7, e36336 (2012).
     

2011

  • 1.
    Lukas, C., Kollmannsberger, P., Ruffoni, D., Roschger, P., Fratzl, P., Weinkamer, R.: The Heterogeneous Mineral Content of Bone—Using Stochastic Arguments and Simulations to Overcome Experimental Limitations. Journal of Statistical Physics. 144, 316–331 (2011).
     
  • 2.
    Kollmannsberger, P., Bidan, C., Dunlop, J., Fratzl, P.: The physics of tissue patterning and extracellular matrix organisation: how cells join forces. Soft Matter. 7, 9549–9560 (2011).
     
  • 3.
    Kollmannsberger, P., Fabry, B.: Linear and nonlinear rheology of living cells. Annual Review of Materials Research. 41, 75–97 (2011).
     
  • 4.
    Kollmannsberger, P., Mierke, C.T., Fabry, B.: Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension. Soft Matter. 7, 3127–3132 (2011).
     

2010

  • 1.
    Mierke, C.T., Kollmannsberger, P., Zitterbart, D.P., Diez, G., Koch, T.M., Marg, S., Ziegler, W.H., Goldmann, W.H., Fabry, B.: Vinculin facilitates cell invasion into three-dimensional collagen matrices. Journal of Biological Chemistry. 285, 13121–13130 (2010).
     

2009

  • 1.
    Diez, G., Kollmannsberger, P., Mierke, C.T., Koch, T.M., Vali, H., Fabry, B., Goldmann, W.H.: Anchorage of vinculin to lipid membranes influences cell mechanical properties. Biophysical journal. 97, 3105–3112 (2009).
     
  • 2.
    Kasza, K., Nakamura, F., Hu, S., Kollmannsberger, P., Bonakdar, N., Fabry, B., Stossel, T., Wang, N., Weitz, D.: Filamin A is essential for active cell stiffening but not passive stiffening under external force. Biophysical journal. 96, 4326–4335 (2009).
     
  • 3.
    Lorenz, C., Brunner, J.G., Kollmannsberger, P., Jaafar, L., Fabry, B., Virtanen, S.: Effect of surface pre-treatments on biocompatibility of magnesium. Acta biomaterialia. 5, 2783–2789 (2009).
     
  • 4.
    Kollmannsberger, P., Fabry, B.: Active soft glassy rheology of adherent cells. Soft Matter. 5, 1771–1774 (2009).
     

2008

  • 1.
    Mierke, C.T., Zitterbart, D.P., Kollmannsberger, P., Raupach, C., Schlötzer-Schrehardt, U., Goecke, T.W., Behrens, J., Fabry, B.: Breakdown of the endothelial barrier function in tumor cell transmigration. Biophysical journal. 94, 2832–2846 (2008).
     
  • 2.
    Rösel, D., Brábek, J., Tolde, O., Mierke, C.T., Zitterbart, D.P., Raupach, C., Bicanová, K., Kollmannsberger, P., Paňková, D., Vesel`y, P., others: Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces. Molecular Cancer Research. 6, 1410–1420 (2008).
     
  • 3.
    Mierke, C.T., Kollmannsberger, P., Paranhos Zitterbart, D., Smith, J., Fabry, B., Goldmann, W.H.: Mechano-coupling and regulation of contractility by the vinculin tail domain. Biophysical journal. 94, 661–670 (2008).
     

2007

  • 1.
    Kollmannsberger, P., Fabry, B.: High-force magnetic tweezers with force feedback for biological applications. Review of Scientific Instruments. 78, 114301–114301 (2007).