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    Center for Computational and Theoretical Biology

    Publications


    Preprints

    • Biological network growth in complex environments – a computational framework. Paul, Torsten Johann; Kollmannsberger, Philip in bioRxiv (2020). 2020.06.01.127407.
       
    • Active zone compaction for presynaptic strength. Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, Sören; Sauer, Markus; Sirén, Anna-Leena; Heckmann, Manfred; Paul, Mila M. in bioRxiv (2019).
       
    • Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. Pauli, Martin; Paul, Mila M.; Proppert, Sven; Sharifi, Marzieh; Repp, Felix; Kollmannsberger, Philip; Sauer, Markus; Heckmann, Manfred; Sirén, Anna-Leena in bioRxiv (2019).
       

    Publications

    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 (2020). n/a(n/a)
       
    • 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

    • 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--.
       
    • 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.
       
    • Towards a Connectomic Description of the Osteocyte Lacunocanalicular Network in Bone. Weinkamer, Richard; Kollmannsberger, Philip; Fratzl, Peter in Current Osteoporosis Reports (2019).
       

    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 (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

    • 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.
       
    • 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.
       
    • 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 (2017). 6 101-108.
       
    • 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

    • Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth. Bidan, Cécile 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

    • 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

    • 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

    • 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, Cécile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Fratzl, Peter; Dunlop, John WC in Advanced healthcare materials (2013). 2(1) 186--194.
       
    • Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces. Möller, Jens; Emge, Philippe; Vizcarra, Ima Avalos; Kollmannsberger, Philip; Vogel, Viola in New Journal of Physics (2013). 15(12) 125016.
       
    • 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; Müller, 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

    • How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue Growth. Bidan, Cécile M; Kommareddy, Krishna P; Rumpler, Monika; Kollmannsberger, Philip; Bréchet, Yves JM; Fratzl, Peter; Dunlop, John WC in PloS one (2012). 7(5) e36336.
       

    2011

    • 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

    • 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

    • 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.
       
    • Active soft glassy rheology of adherent cells. Kollmannsberger, Philip; Fabry, Ben in Soft Matter (2009). 5(9) 1771--1774.
       
    • 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.
       

    2008

    • Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces. Rösel, Daniel; Brábek, Jan; Tolde, Ondvrej; Mierke, Claudia T; Zitterbart, Daniel P; Raupach, Carina; Bicanová, Krist`yna; Kollmannsberger, Philip; Pavnková, 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.
       
    • Breakdown of the endothelial barrier function in tumor cell transmigration. Mierke, Claudia Tanja; Zitterbart, Daniel Paranhos; Kollmannsberger, Philip; Raupach, Carina; Schlötzer-Schrehardt, Ursula; Goecke, Tamme Weyert; Behrens, Jürgen; Fabry, Ben in Biophysical journal (2008). 94(7) 2832--2846.
       

    2007

    • High-force magnetic tweezers with force feedback for biological applications. Kollmannsberger, Philip; Fabry, Ben in Review of Scientific Instruments (2007). 78(11) 114301--114301.