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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 (2020). 9(1275)
  • Active zone compaction for presynaptic strength Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, S{\"o}ren; Sauer, Markus; Sir{\’e}n, Anna-Leena; Heckmann, Manfred; Paul, Mila M. in bioRxiv (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 (2021). 37(1)
  • 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 (2021). 7(7) 1144–1155.
  • 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 (2021). 11
  • 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 (2021). 4(1) 1–13.
  • 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 (2021). 13(18) 4671.
2020[ to top ]
  • 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 (2020). n/a(n/a)
  • Biological network growth in complex environments – a computational framework Paul, Torsten Johann; Kollmannsberger, Philip in PLOS Computational Biology (2020). 16(11) e1008003.
  • 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 (2020). 10(1) 2536.
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 (2019). 5(9) eaav9394.
  • 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 (2019). 2(1) 376-.
  • 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 ]
  • 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 (2018). 13(10) e0205348.
  • 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 (2018). 4(1) eaao4881.
2017[ to top ]
  • 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 (2017). 199 177–186.
  • 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 (2017). 19 073019.
  • 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 (2017). 13(1) 1–21.
2016[ to top ]
  • Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth Bidan, C{\’e}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 (2016). 13(118)
  • 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 (2016). 45 85–97.
  • 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 (2016). 6 18109.
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 (2015). 49(5) 053001.
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 (2014). 10(23) 4851–4857.
2013[ to top ]
  • Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces M{\"o}ller, Jens; Emge, Philippe; Vizcarra, Ima Avalos; Kollmannsberger, Philip; Vogel, Viola in New Journal of Physics (2013). 15(12) 125016.
  • 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 (2013). 28(8) 1837–1845.
  • Geometry as a factor for tissue growth: towards shape optimization of tissue engineering scaffolds Bidan, C{\’e}cile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Fratzl, Peter; Dunlop, John WC in Advanced healthcare materials (2013). 2(1) 186–194.
  • 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{\"u}ller, Ralph in Bone (2013). 56(1) 55–60.
  • 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{\’e}cile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Br{\’e}chet, Yves JM; Fratzl, Peter; Dunlop, John WC in PloS one (2012). 7(5) e36336.
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 (2011). 144(2) 316–331.
  • Linear and nonlinear rheology of living cells Kollmannsberger, Philip; Fabry, Ben in Annual Review of Materials Research (2011). 41 75–97.
  • The physics of tissue patterning and extracellular matrix organisation: how cells join forces Kollmannsberger, P; Bidan, CM; Dunlop, JWC; Fratzl, P in Soft Matter (2011). 7(20) 9549–9560.
  • Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension Kollmannsberger, Philip; Mierke, Claudia Tanja; Fabry, Ben in Soft Matter (2011). 7(7) 3127–3132.
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 (2010). 285(17) 13121–13130.
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 (2009). 97(12) 3105–3112.
  • 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 (2009). 96(10) 4326–4335.
  • 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 (2009). 5(7) 2783–2789.
  • Active soft glassy rheology of adherent cells Kollmannsberger, Philip; Fabry, Ben in Soft Matter (2009). 5(9) 1771–1774.
2008[ to top ]
  • Breakdown of the endothelial barrier function in tumor cell transmigration Mierke, Claudia Tanja; Zitterbart, Daniel Paranhos; Kollmannsberger, Philip; Raupach, Carina; Schl{\"o}tzer-Schrehardt, Ursula; Goecke, Tamme Weyert; Behrens, J{\"u}rgen; Fabry, Ben in Biophysical journal (2008). 94(7) 2832–2846.
  • Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces R{\"o}sel, Daniel; Br{\’a}bek, Jan; Tolde, Ond{\v{r}}ej; Mierke, Claudia T; Zitterbart, Daniel P; Raupach, Carina; Bicanov{\’a}, Krist{\`y}na; Kollmannsberger, Philip; Pa{\v{n}}kov{\’a}, Daniela; Vesel{\`y}, Pavel; others in Molecular Cancer Research (2008). 6(9) 1410–1420.
  • 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 (2008). 94(2) 661–670.
2007[ to top ]
  • High-force magnetic tweezers with force feedback for biological applications Kollmannsberger, Philip; Fabry, Ben in Review of Scientific Instruments (2007). 78(11) 114301–114301.