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Center for Computational and Theoretical Biology

Publications


Preprints

  • 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(1275), Article 1275. https://doi.org/10.12688/f1000research.27158.1
  • Mrestani, A., Kollmannsberger, P., Pauli, M., Repp, F., Kittel, R. J., Eilers, J., Doose, S., Sauer, M., Sir{\’e}n, A.-L., Heckmann, M., & Paul, M. M. Active zone compaction for presynaptic strength. BioRxiv. https://doi.org/10.1101/802843

Publications

2021[ to top ]
  • 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(1), Article 1. https://doi.org/10.1016/j.celrep.2021.109770
  • 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(7), 1144-1155. https://doi.org/10.1021/acscentsci.1c00483
  • 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. https://doi.org/10.3389/fonc.2021.621278
  • 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), 1-13. https://doi.org/10.1038/s42003-021-01939-z
  • 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(18), 4671. https://doi.org/10.3390/cancers13184671
2020[ to top ]
  • 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(n/a), Article n/a. https://doi.org/10.1002/anie.202000421
  • Paul, T. J., & Kollmannsberger, P. Biological network growth in complex environments – a computational framework. PLOS Computational Biology, 16(11), e1008003. https://doi.org/10.1371/journal.pcbi.1008003
  • 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(1), 2536. https://doi.org/10.1038/s41598-020-59215-9
2019[ to top ]
  • 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(1), 376-. 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. Surface tension determines tissue shape and growth kinetics. Science Advances, 5(9), eaav9394. https://doi.org/10.1126/sciadv.aav9394
  • Weinkamer, R., Kollmannsberger, P., & Fratzl, P. Towards a {Connectomic} {Description} of the {Osteocyte} {Lacunocanalicular} {Network} in {Bone}. Current Osteoporosis Reports. https://doi.org/10.1007/s11914-019-00515-z
2018[ to top ]
  • 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(10), e0205348. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205348
  • 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(1), eaao4881. https://doi.org/10.1126/sciadv.aao4881
2017[ to top ]
  • 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.
  • 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. https://doi.org/10.1016/j.jsb.2017.07.004
  • 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.
  • 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), 1-21. https://doi.org/10.1371/journal.pcbi.1005317
2016[ to top ]
  • 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(118), Article 118. https://doi.org/10.1098/rsif.2016.0136
  • 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. https://doi.org/http://dx.doi.org/10.1016/j.actbio.2016.08.044
  • 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. http://dx.doi.org/10.1038/srep18109
2015[ to top ]
  • Foolen, J., Yamashita, T., & Kollmannsberger, P. Shaping tissues by balancing active forces and geometric constraints. Journal of Physics D: Applied Physics, 49(5), 053001.
2014[ to top ]
  • 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(23), 4851-4857.
2013[ to top ]
  • M{\"o}ller, 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(12), 125016.
  • 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(8), 1837-1845.
  • 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(1), 186-194.
  • Lukas, C., Ruffoni, D., Lambers, F. M., Schulte, F. A., Kuhn, G., Kollmannsberger, P., Weinkamer, R., & M{\"u}ller, R. Mineralization kinetics in murine trabecular bone quantified by time-lapsed <i>in vivo</i> micro-computed tomography. Bone, 56(1), 55-60.
  • 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.
2012[ to top ]
  • Bidan, C. M., Kommareddy, K. P., Rumpler, M., Kollmannsberger, P., Br{\’e}chet, Y. J., Fratzl, P., & Dunlop, J. W. How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue Growth. PloS One, 7(5), e36336.
2011[ to top ]
  • 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(2), 316-331.
  • Kollmannsberger, P., Bidan, C., Dunlop, J., & Fratzl, P. The physics of tissue patterning and extracellular matrix organisation: how cells join forces. Soft Matter, 7(20), 9549-9560.
  • Kollmannsberger, P., & Fabry, B. Linear and nonlinear rheology of living cells. Annual Review of Materials Research, 41, 75-97.
  • Kollmannsberger, P., Mierke, C. T., & Fabry, B. Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension. Soft Matter, 7(7), 3127-3132.
2010[ to top ]
  • 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(17), 13121-13130.
2009[ to top ]
  • 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(12), 3105-3112.
  • 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(10), 4326-4335.
  • 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(7), 2783-2789.
  • Kollmannsberger, P., & Fabry, B. Active soft glassy rheology of adherent cells. Soft Matter, 5(9), 1771-1774.
2008[ to top ]
  • Mierke, C. T., Zitterbart, D. P., Kollmannsberger, P., Raupach, C., Schl{\"o}tzer-Schrehardt, U., Goecke, T. W., Behrens, J., & Fabry, B. Breakdown of the endothelial barrier function in tumor cell transmigration. Biophysical Journal, 94(7), 2832-2846.
  • R{\"o}sel, D., Br{\’a}bek, J., Tolde, O., Mierke, C. T., Zitterbart, D. P., Raupach, C., Bicanov{\’a}, K., Kollmannsberger, P., Pa{\v{n}}kov{\’a}, 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(9), 1410-1420.
  • 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(2), 661-670.
2007[ to top ]
  • Kollmannsberger, P., & Fabry, B. High-force magnetic tweezers with force feedback for biological applications. Review of Scientific Instruments, 78(11), 114301-114301.