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Center for Computational and Theoretical Biology

Publications


Preprints

  • DeepCLEM: automated registration for correlative light and electron microscopy using deep learning [version 1; peer review: awaiting peer review]. Seifert, R; Markert, SM; Britz, S; Perschin, V; Erbacher, C; Stigloher, C; Kollmannsberger, P. In F1000Research, 9(1275). 2020.
  • Active zone compaction for presynaptic strength. Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, S{ö}ren; Sauer, Markus; Sir{é}n, Anna-Leena; Heckmann, Manfred; Paul, Mila M. In bioRxiv. Cold Spring Harbor Laboratory, 2019.

Publications

2021[ to top ]
  • Active zone compaction correlates with presynaptic homeostatic potentiation. Mrestani, Achmed; Pauli, Martin; Kollmannsberger, Philip; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, Sören; Sauer, Markus; Sirén, Anna-Leena; Heckmann, Manfred; Paul, Mila M. In Cell Reports, 37(1). 2021.
  • Defining the {Basis} of {Cyanine} {Phototruncation} {Enables} a {New} {Approach} to {Single}-{Molecule} {Localization} {Microscopy}. Matikonda, Siddharth S.; Helmerich, Dominic A.; Meub, Mara; Beliu, Gerti; Kollmannsberger, Philip; Greer, Alexander; Sauer, Markus; Schnermann, Martin J. In ACS Central Science, 7(7), bll 1144–1155. 2021.
  • Subgroup-{Independent} {Mapping} of {Renal} {Cell} {Carcinoma}—{Machine} {Learning} {Reveals} {Prognostic} {Mitochondrial} {Gene} {Signature} {Beyond} {Histopathologic} {Boundaries}. Marquardt, André; Solimando, Antonio Giovanni; Kerscher, Alexander; Bittrich, Max; Kalogirou, Charis; Kübler, Hubert; Rosenwald, Andreas; Bargou, Ralf; Kollmannsberger, Philip; Schilling, Bastian; Meierjohann, Svenja; Krebs, Markus. In Frontiers in Oncology, 11. 2021.
  • Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. Pauli, Martin; Paul, Mila M.; Proppert, Sven; Mrestani, Achmed; Sharifi, Marzieh; Repp, Felix; Kürzinger, Lydia; Kollmannsberger, Philip; Sauer, Markus; Heckmann, Manfred; Sirén, Anna-Leena. In Communications Biology, 4(1), bll 1–13. 2021.
  • Identifying {New} {Potential} {Biomarkers} in {Adrenocortical} {Tumors} {Based} on {mRNA} {Expression} {Data} {Using} {Machine} {Learning}. Marquardt, André; Landwehr, Laura-Sophie; Ronchi, Cristina L.; di Dalmazi, Guido; Riester, Anna; Kollmannsberger, Philip; Altieri, Barbara; Fassnacht, Martin; Sbiera, Silviu. In Cancers, 13(18), bl 4671. 2021.
2020[ to top ]
  • Biological network growth in complex environments – a computational framework. Paul, Torsten Johann; Kollmannsberger, Philip. In PLOS Computational Biology, 16(11), bl e1008003. 2020.
  • Haruspex: {A} {Neural} {Network} for the {Automatic} {Identification} of {Oligonucleotides} and {Protein} {Secondary} {Structure} in {Cryo}-{Electron} {Microscopy} {Maps}. Mostosi, Philipp; Schindelin, Hermann; Kollmannsberger, Philip; Thorn, Andrea. In Angewandte Chemie International Edition, n/a(n/a). 2020.
  • Efficient {Classification} of {White} {Blood} {Cell} {Leukemia} with {Improved} {Swarm} {Optimization} of {Deep} {Features}. Sahlol, Ahmed T.; Kollmannsberger, Philip; Ewees, Ahmed A. In Scientific Reports, 10(1), bl 2536. 2020.
2019[ to top ]
  • Surface tension determines tissue shape and growth kinetics. Ehrig, Sebastian; Bidan, Cécile M.; West, Alan; Jacobi, Cornelius; Lam, Karen; Kollmannsberger, Philip; Petersen, Ansgar; Tomancak, Pavel; Kommareddy, Krishna; Fischer, Franz Dieter; Fratzl, Peter; Dunlop, John W. C. In Science Advances, 5(9), bl eaav9394. 2019.
  • Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules. Spindler, Marie-Christin; Redolfi, Josef; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian; Benavente, Ricardo. In Communications Biology, 2(1), bl 376-. 2019.
  • Towards a {Connectomic} {Description} of the {Osteocyte} {Lacunocanalicular} {Network} in {Bone}. Weinkamer, Richard; Kollmannsberger, Philip; Fratzl, Peter. In Current Osteoporosis Reports. 2019.
2018[ to top ]
  • Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. Kollmannsberger, Philip; Bidan, Cécile M; Dunlop, John; Fratzl, Peter; Vogel, Viola. In Science Advances, 4(1), bl eaao4881. 2018.
  • Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning. Kaltdorf, Kristin V; Theiss, Maria; Markert, Sebastian M; Zhen, Mei; Dandekar, Thomas; Stigloher, Christian; Kollmannsberger, Philip. In PLoS one, 13(10), bl e0205348. Public Library of Science, 2018.
2017[ to top ]
  • The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone. Kollmannsberger, Philip; Kerschnitzki, Michael; Repp, Felix; Wagermaier, Wolfgang; Weinkamer, Richard; Fratzl, Peter. In New Journal of Physics, 19, bl 073019. 2017.
  • Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Kerschnitzki, Michael; Berzlanovich, Andrea; Gruber, Gerlinde M.; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard. In Bone Reports, 6, bll 101–108. 2017.
  • Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Berzlanovich, Andrea; Gruber, Gerlinde; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard. In Journal of Stuctural Biology, 199, bll 177–186. 2017.
  • FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Dandekar, Thomas; Stigloher, Christian. In PLOS Computational Biology, 13(1), bll 1–21. Public Library of Science, 2017.
2016[ to top ]
  • Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth. Bidan, C{é}cile M.; Kollmannsberger, Philip; Gering, Vanessa; Ehrig, Sebastian; Joly, Pascal; Petersen, Ansgar; Vogel, Viola; Fratzl, Peter; Dunlop, John W. C. In Journal of The Royal Society Interface, 13(118). The Royal Society, 2016.
  • Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces. Yamashita, Tadahiro; Kollmannsberger, Philip; Mawatari, Kazuma; Kitamori, Takehiko; Vogel, Viola. In Acta Biomaterialia, 45, bll 85–97. 2016.
  • How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics. Avalos Vizcarra, Ima; Hosseini, Vahid; Kollmannsberger, Philip; Meier, Stefanie; Weber, Stefan S.; Arnoldini, Markus; Ackermann, Martin; Vogel, Viola. In Scientific Reports, 6, bl 18109. The Author(s), 2016.
2015[ to top ]
  • Shaping tissues by balancing active forces and geometric constraints. Foolen, Jasper; Yamashita, Tadahiro; Kollmannsberger, Philip. In Journal of Physics D: Applied Physics, 49(5), bl 053001. IOP Publishing, 2015.
2014[ to top ]
  • Fiber-Assisted Molding (FAM) of Surfaces with Tunable Curvature to Guide Cell Alignment and Complex Tissue Architecture. Hosseini, Vahid; Kollmannsberger, Philip; Ahadian, Samad; Ostrovidov, Serge; Kaji, Hirokazu; Vogel, Viola; Khademhosseini, Ali. In Small, 10(23), bll 4851–4857. 2014.
2013[ to top ]
  • Mineralization kinetics in murine trabecular bone quantified by time-lapsed in vivo micro-computed tomography.. Lukas, Carolin; Ruffoni, Davide; Lambers, Floor M; Schulte, Friederike A; Kuhn, Gisela; Kollmannsberger, Philip; Weinkamer, Richard; M{ü}ller, Ralph. In Bone, 56(1), bll 55–60. Elsevier, 2013.
  • Geometry as a factor for tissue growth: towards shape optimization of tissue engineering scaffolds. Bidan, C{é}cile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Fratzl, Peter; Dunlop, John WC. In Advanced healthcare materials, 2(1), bll 186–194. Wiley Online Library, 2013.
  • Architecture of the osteocyte network correlates with bone material quality. Kerschnitzki, Michael; Kollmannsberger, Philip; Burghammer, Manfred; Duda, Georg N; Weinkamer, Richard; Wagermaier, Wolfgang; Fratzl, Peter. In Journal of Bone and Mineral Research, 28(8), bll 1837–1845. Wiley Online Library, 2013.
  • Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces. M{ö}ller, Jens; Emge, Philippe; Vizcarra, Ima Avalos; Kollmannsberger, Philip; Vogel, Viola. In New Journal of Physics, 15(12), bl 125016. IOP Publishing, 2013.
  • Curvature-induced spontaneous detachment of vascular smooth muscle cell sheets: towards vascular self assembly in microchannels. Yamashita, T; Kollmannsberger, P; Mawatari, K; Vogel, V; Kitamori, T. In Microsystem Technology in Chemistry and Life Science. 2013.
2012[ to top ]
  • How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue Growth. Bidan, C{é}cile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Br{é}chet, Yves JM; Fratzl, Peter; Dunlop, John WC. In PloS one, 7(5), bl e36336. Public Library of Science, 2012.
2011[ to top ]
  • The Heterogeneous Mineral Content of Bone—Using Stochastic Arguments and Simulations to Overcome Experimental Limitations. Lukas, C; Kollmannsberger, P; Ruffoni, D; Roschger, P; Fratzl, P; Weinkamer, R. In Journal of Statistical Physics, 144(2), bll 316–331. Springer, 2011.
  • The physics of tissue patterning and extracellular matrix organisation: how cells join forces. Kollmannsberger, P; Bidan, CM; Dunlop, JWC; Fratzl, P. In Soft Matter, 7(20), bll 9549–9560. Royal Society of Chemistry, 2011.
  • Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension. Kollmannsberger, Philip; Mierke, Claudia Tanja; Fabry, Ben. In Soft Matter, 7(7), bll 3127–3132. Royal Society of Chemistry, 2011.
  • Linear and nonlinear rheology of living cells. Kollmannsberger, Philip; Fabry, Ben. In Annual Review of Materials Research, 41, bll 75–97. Annual Reviews, 2011.
2010[ to top ]
  • Vinculin facilitates cell invasion into three-dimensional collagen matrices. Mierke, Claudia T; Kollmannsberger, Philip; Zitterbart, Daniel Paranhos; Diez, Gerold; Koch, Thorsten M; Marg, Susanna; Ziegler, Wolfgang H; Goldmann, Wolfgang H; Fabry, Ben. In Journal of Biological Chemistry, 285(17), bll 13121–13130. ASBMB, 2010.
2009[ to top ]
  • Anchorage of vinculin to lipid membranes influences cell mechanical properties. Diez, Gerold; Kollmannsberger, Philip; Mierke, Claudia T; Koch, Thorsten M; Vali, Hojatollah; Fabry, Ben; Goldmann, Wolfgang H. In Biophysical journal, 97(12), bll 3105–3112. Elsevier, 2009.
  • Filamin A is essential for active cell stiffening but not passive stiffening under external force. Kasza, KE; Nakamura, F; Hu, S; Kollmannsberger, P; Bonakdar, N; Fabry, B; Stossel, TP; Wang, N; Weitz, DA. In Biophysical journal, 96(10), bll 4326–4335. Elsevier, 2009.
  • Effect of surface pre-treatments on biocompatibility of magnesium. Lorenz, Carla; Brunner, Johannes G; Kollmannsberger, Philip; Jaafar, Leila; Fabry, Ben; Virtanen, Sannakaisa. In Acta biomaterialia, 5(7), bll 2783–2789. Elsevier, 2009.
  • Active soft glassy rheology of adherent cells. Kollmannsberger, Philip; Fabry, Ben. In Soft Matter, 5(9), bll 1771–1774. The Royal Society of Chemistry, 2009.
2008[ to top ]
  • Mechano-coupling and regulation of contractility by the vinculin tail domain. Mierke, Claudia Tanja; Kollmannsberger, Philip; Paranhos Zitterbart, Daniel; Smith, James; Fabry, Ben; Goldmann, Wolfgang Heinrich. In Biophysical journal, 94(2), bll 661–670. Elsevier, 2008.
  • Breakdown of the endothelial barrier function in tumor cell transmigration. Mierke, Claudia Tanja; Zitterbart, Daniel Paranhos; Kollmannsberger, Philip; Raupach, Carina; Schl{ö}tzer-Schrehardt, Ursula; Goecke, Tamme Weyert; Behrens, J{ü}rgen; Fabry, Ben. In Biophysical journal, 94(7), bll 2832–2846. Elsevier, 2008.
  • Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces. R{ö}sel, Daniel; Br{á}bek, Jan; Tolde, Ond{\v{r}}ej; Mierke, Claudia T; Zitterbart, Daniel P; Raupach, Carina; Bicanov{á}, Krist{{\`y}}na; Kollmannsberger, Philip; Paňkov{á}, Daniela; Vesel{{\`y}}, Pavel; others. In Molecular Cancer Research, 6(9), bll 1410–1420. AACR, 2008.
2007[ to top ]
  • High-force magnetic tweezers with force feedback for biological applications. Kollmannsberger, Philip; Fabry, Ben. In Review of Scientific Instruments, 78(11), bll 114301–114301. AIP, 2007.