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How mechanobiology orchestrates the iterative and reciprocal ECM-cell cross-talk that drives microtissue growth

Benn MC, Pot SA, Moeller J, Yamashita T, Fonta CM, Orend G, Kollmannsberger P, Vogel V

Science Advances 9(13), eadd9275 (2023)

Multicellular dynamics on 3D scaffolds: Stress concentration is key to controlling complex microtissue morphology on engineered surfaces (Preprint)

Matsuzawa R, Matsuo A, Fukamachi S, Takeuchi M, Nishina T, Kollmannsberger P, Sudo R, Okuda S, Yamashita T

bioRxiv 530721 (2023)

Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales (Review)

Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo E, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska L, Kurniawan NA, Papantoniou I, Laurent Pieuchot, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC

Advanced Materials, 2206110 (2023)

Predicting Microenvironment in CXCR4- and FAP-Positive Solid Tumors—A Pan-Cancer Machine Learning Workflow for Theranostic Target Structures

Marquardt A, Hartrampf P, Kollmannsberger P, Solimando AG, Meierjohann S, Kübler H, Bargou R, Schilling B, Serfling SE, Buck A, Werner RA, Lapa C, Krebs M

Cancers 15(2), 392 (2023)



Single-molecule fluorescence microscopy demonstrates fast dynamics of the variant surface glycoprotein coat on living trypanosomes (Preprint)

Schwebs M, Paul T,  Glogger M, Forster L, Morriswood B, Teßmar J, Groll J, Engstler M, Kollmannsberger P, Fenz S

bioRxiv 502583 (2022)

Endogenous tagging of Unc-13 reveals nanoscale reorganization at active zones during presynaptic homeostatic potentiation

Dannhäuser S, Mrestani A, Gundelach F, Pauli M, Komma F, Kollmannsberger P, Sauer M, Heckmann M, Paul MM

Frontiers in Cellular Neuroscience 16:1074304 (2022)

ReCSAI: recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy

Reinhard S, Helmerich DA, Boras D, Sauer M, Kollmannsberger P

BMC Bioinformatics 23, 530 (2022)

Ultrastructural analysis of wildtype and RIM1α knock-out active zones in a large cortical synapse

Lichter K, Paul M, Pauli M, Schoch S, Kollmannsberger P, Stigloher C, Heckmann M, Siren A-L

​​​​​Cell Reports 40 (12), 111382 (2022)

Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors–Dependencies and Novel Pitfalls

Marquardt A, Kollmannsberger P, Krebs M, Knott M, Solimando AG, Kerscher A

​​​​​Genes 13(8), 1335 (2022)

Detecting ice artefacts in processed macromolecular diffraction data with machine learning

Nolte K, Gao Y, Stäb S, Kollmannsberger P, Thorn A

Acta Crystallographica D 78(2) (2022)



Fourier Ring Correlation and anisotropic kernel density estimation improve deep learning based SMLM reconstruction of microtubules

Berberich A, Kurz A, Reinhard S, Paul TJ, Burd PR, Sauer M, Kollmannsberger P

Frontiers in Bioinformatics 1:752788 (2021)       Code

Active zone compaction correlates with presynaptic homeostatic potentiation

Mrestani A, Pauli M, Kollmannsberger P, Repp F, Kittel RJ, Eilers J, Doose S, Sauer M, Sirén AL, Heckmann M, Paul MM

​​​​​Cell Reports 37(1) (2021)

Structural analysis of the C. elegans dauer larval anterior sensilla by Focused Ion Beam-Scanning Electron Microscopy

Britz S, Markert SM, Witvliet D, Steyer AM, Troeger S, Mulcahy B, Kollmannsberger P, Schwab Y, Zhen M, Stigloher C

Frontiers in Neuroanatomy 15:732520 (2021)      Data

Defining the Basis of Cyanine Phototruncation Enables a New Approach to Single Molecule Localization Microscopy

Matikonda S, Helmerich D, Meub M, Beliu G, Kollmannsberger P, Greer A, Sauer M, Schnermann M

ACS Central Science, 1c00483 (2021)

Identifying New Potential Biomarkers in Adrenocortical Tumors Based on mRNA Expression Data Using Machine Learning

Marquardt A, Landwehr LS, Ronchi CL, Dalmazi G, Riester A, Kollmannsberger P, Altieri B, Fassnacht M, Sbiera S

Cancers 13(18), 4671 (2021)

Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections

Pauli M, Paul MM, Proppert S, Sharifi M, Repp F, Kollmannsberger P, Sauer M, Heckmann M, Siren AL

Communications Biology, 4, 407 (2021)

Subgroup-independent mapping of renal cell carcinoma–machine learning reveals prognostic mitochondrial gene signature beyond histopathologic boundaries

Marquardt A, Solimando AG, Kerscher A, Bittrich M, Kalogirou C, Kübler H, Rosenwald A, Bargou R, Kollmannsberger P, Schilling B, Meierjohann S, Krebs M

Frontiers in Oncology 15(11), 621278 (2021)



DeepCLEM: automated registration for correlative light and electron microscopy using deep learning (Preprint)

Seifert R, Markert SM, Britz S, Perschin V, Erbacher C, Stigloher S, Kollmannsberger P

F1000Research 2020, 9:1275 (2020)       Code

Biological network growth in complex environments: a computational framework

Paul TJ, Kollmannsberger P

​​​​​PLOS Computational Biology, 16(11), e1008003 (2020)        Code

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐EM Maps

Mostosi P, Schindelin H, Kollmannsberger P, Thorn A

Angewandte Chemie Int. Ed., 59(35), 14788–14795 (2020)        Code

Efficient Classification of White Blood Cell Leukemia with Improved Swarm Optimization of Deep Features

Sahlol AT, Kollmannsberger P, Ewees AA

Scientific Reports 10, 2536 (2020)        Code



Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules

Spindler MC, Redolfi J, Helmprobst F, Kollmannsberger P, Stigloher C, Benavente R

Communications Biology, 2, 376 (2019)

Surface tension determines tissue shape and growth kinetics

Ehrig S, Schamberger B, Bidan CM, West A, Jacobi C, Lam K, Kollmannsberger P, Petersen A, Tomancak P, Kommareddy K, Fischer FD, Fratzl P, Dunlop JWC

Science Advances 5, eaav9394 (2019)

Towards a connectomic description of the osteocyte lacunocanalicular network in bone (Review)

Weinkamer R, Kollmannsberger P, Fratzl P

Current Osteoporosis Reports 17, 186–194 (2019)



Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning

Kaltdorf KV, Theiss M, Markert SM, Zhen M, Dandekar T, Stigloher C, Kollmannsberger P

PLOS one 13, e0205348 (2018)

Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts

Kollmannsberger P, Bidan CM, Dunlop JWC, Fratzl P, Vogel V.

Science Advances 4, eaao4881 (2018)



Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone

Repp F, Kollmannsberger P, Roschger A, Berzlanovich A, Gruber GM, Roschger P, Wagermaier W, Weinkamer R

Journal of Structural Biology 199, 177–186 (2017)

The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone

Kollmannsberger P, Kerschnitzki M, Repp F, Wagermaier W, Weinkamer R, Fratzl P

New Journal of Physics 19, 073019 (2017)

Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons

Repp F, Kollmannsberger P, Roschger A, Kerschnitzki M, Berzlanovich A, Gruber GM, Roschger P, Wagermaier W, Weinkamer R

Bone Reports 6:101-108 (2017)

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

Kaltdorf KV, Schulze K, Helmprobst F, Kollmannsberger P, Dandekar T, Stigloher C

PLOS Computational Biology 13, 1-21 (2017)



How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics

Avalos Vizcarra I, Hosseini V, Kollmannsberger P, Meier S, Weber SS, Arnoldini M, Ackermann M, Vogel V

Scientific Reports 6, 18109 (2016)

Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces

Yamashita T, Kollmannsberger P, Mawatari K, Kitamori T, Vogel V

Acta Biomaterialia. 45, 85 - 97 (2016)

Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth

Bidan CM, Kollmannsberger P, Gering V, Ehrig S, Joly P, Petersen A, Vogel V, Fratzl P, Dunlop JWC

Journal of The Royal Society Interface. 13,20160136 (2016)



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

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 (2014)

Möller J, Emge P, Avalos Vizcarra I, Kollmannsberger P, Vogel V, Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces. New Journal of Physics 15 125016 (2013)

Lukas C, Ruffoni D, Lambers FM, Schulte FA, Kuhn G, Kollmannnsberger P, Weinkamer R, Müller R, Mineralization kinetics in murine trabecular bone quantified by time-lapsed in vivo micro-computed tomographyBone 56(1) 55-60 (2013)

Kerschnitzki M*, Kollmannsberger P*, Burghammer M. Duda GN, 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 (2013)

Bidan CM, Kommareddy KP, Rumpler M, Kollmannsberger P, Fratzl P, Dunlop JWC, Geometry as a Factor for Tissue Growth: Towards Shape Optimization of Tissue Engineering Scaffolds. Advanced Healthcare Materials 2(1) 186-194 (2013)

Bidan CM, Kommareddy KP, Rumpler M, Kollmannsberger P, Bréchet YJM, Fratzl P, Dunlop JWC, How Linear Tension Converts to Curvature: Geometric Control of Bone Tissue GrowthPLOS one 7(5): e36336 (2012)

Lukas C, Kollmannsberger P, Ruffoni D, Roschger P, Fratzl P, Weinkamer R, The Heterogeneous Mineral Content of Bone-Using Stochastic Arguments to Overcome Experimental Limitations. Journal of Statistical Physics 144(2) 316-331 (2011)

Kollmannsberger P*, Bidan CM*, Dunlop JWC, Fratzl P, The physics of tissue patterning and extracellular matrix organisation: How cells join forces. Soft Matter 7, 9549-9560 (2011) (Peer-Reviewed Review)

Kollmannsberger P, Fabry B, Linear and Nonlinear Rheology of Living Cells. Annual Review of Materials Research 41, 75-97 (2011) (Peer-Reviewed Review)

Kollmannsberger P, Mierke CT, Fabry B, Nonlinear viscoelasticity of adherent cells is controlled by cytoskeletal tension. Soft Matter 7, 3127-3132 (2011)

Mierke CT, Kollmannsberger P, Zitterbart DP, Diez G, Koch TM, Marg S, Ziegler WH, Goldmann WH, Fabry B, Vinculin Facilitates Cell Invasion into Three-dimensional Collagen Matrices. Journal of Biological Chemistry 285, 13121-13130 (2010)

Kollmannsberger P, Fabry B, Active soft glassy rheology of adherent cellsSoft Matter 5, 1771-1774 (2009)

Lorenz C, Brunner JG, Kollmannsberger P, Jaafar L, Fabry B, Virtanen S, Effect of surface pre-treatments on biocompatibility of magnesium. Acta Biomateralia 5, 2783-2789 (2009)

Diez G, Kollmannsberger P, Mierke CT, Koch TM, Vali H, Fabry B, Goldmann WH, Anchorage of Vinculin to Lipid Membranes Influences Cell Mechanical Properties. Biophysical Journal 97, 3105-3112 (2009)

Kasza KE, Nakamura F, Hu S, Kollmannsberger P, Bonakdar N, Fabry B, Stossel TP, Wang N, Weitz DA, Filamin A Is Essential for Active Cell Stiffening but not Passive Stiffening under External Force. Biophysical Journal 96, 4326-4335 (2009)

Rosel D, Brabek J, Tolde O, Mierke CT, Zitterbart DP, Raupach C, Bicanova K, Kollmannsberger P, Pankova D, Vesely D, Fabry B, Up-regulation of Rho/ROCK signaling in sarcoma cells drives invasion and increased generation of protrusive forces. Molecular Cancer Research 6 (2008)

Mierke CT, Zitterbart DP, Kollmannsberger P, Raupach C, Schlötzer-Schrehardt U, Goecke TW, Behrens J, Fabry B, Breakdown of the endothelial barrier function in tumor cell transmigration. Biophysical Journal 94, 2832-2846 (2008)

Mierke CT*, Kollmannsberger P*, Zitterbart DP, Smith J, Fabry B, Goldmann WH, Mechanocoupling and regulation of contractility by the vinculin tail domainBiophysical Journal 94, 661-670 (2008)

Kollmannsberger P, Fabry B, High-force magnetic tweezers with force feedback for biological applicationsReviews of Scientific Instruments 78, 114301. (2007)