iMOL Publications

2025

  • Gravitational forces and matrix stiffness modulate the invasiveness of breast cancer cells in bioprinted spheroids. Breideband L, Wächtershäuser KN, Sarkar R, Puspathasan M, Stelzer EHK, Pampaloni F. Mater Today Bio. 2025, 31:101640. https://dx.doi.org/10.1016/j.mtbio.2025.101640
  • The slit diaphragm in Drosophila features a bi-layered, fishnet-like architecture. Moser D, Lang, K, Birtasu AN, Scheffer MP, Helmstädter M, Hermle T, Frangakis AS. bioRxiv 2025. https://doi.org/10.1101/2025.03.06.641875
  • Denoising diffusion models for high-resolution microscopy image restoration. Osuna-Vargas P, Wehrheim MH, Zinz L, Rahm J, Balakrishnan A, Kaminer A, Heilemann M, Kaschube M 2025 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV). 2025, pp 4320-4330, https://ieeexplore.ieee.org/document/10943369
  • Disease-adaptive drug delivery to the inflamed intestinal mucosa using poly(lactic-co-glycolic acid)-cyclodextrin hybrid nanocarriers. Schreiner J, Brettner FEB, Steigert S, Haessler A, Mols R, Gier S, Jung N, Vogel-Kindgen S, Muschert S, Augustijns P, Windbergs M. Advanced Therapeutics 2025, 8, 2400368. https://dx.doi.org/https://doi.org/10.1002/adtp.202400368

 

2024

  • Camera paths, modeling, and image processing tools for ArtiaX. Ermel UH, Roth P, Wehrheim MH, Moser D, Frangakis AS. bioRxiv 2024, 2024.09.23.614454. https://dx.doi.org/10.1101/2024.09.23.614454
  • Molecular architecture of the kidney slit diaphragm revealed by cryo-electron tomography: FR-PO756. Birtasu AN, Wieland K, Grahammer F, Frangakis A. Journal of the American Society of Nephrology 2024, 35, https://dx.doi.org/10.1681/ASN.2024cmcke0a1
  • Localization of albumin with correlative super resolution light- and electron microscopy in the kidney. Birtasu AN, Ermel UH, Rahm JV, Seybert A, Flottmann B, Heilemann M, Grahammer F, Frangakis AS. bioRxiv 2024, 2024.09.16.613238. https://dx.doi.org/10.1101/2024.09.16.613238
  • Anti-inflammatory effects of cyclodextrin nanoparticles enable macrophage repolarization and reduce inflammation. Brettner FEB, Gier S, Haessler A, Schreiner J, Vogel-Kindgen S, Windbergs M. Discover Nano 2024, 19, 211. https://dx.doi.org/10.1186/s11671-024-04175-6
  • Tobacco stalk nanofibrillated cellulose: An eco-friendly binder on fluidized bed granulation. Garcia KR, Beck RCR, Haessler A, Windbergs M, Paese K, Weiss-Angeli V, dos Santos V, Koester LS. Journal of Drug Delivery Science and Technology 2024, 102, 106370. https://dx.doi.org/https://doi.org/10.1016/j.jddst.2024.106370
  • Mapping cellular stress and lipid dysregulation in Alzheimer-related progressive neurodegeneration using label-free Raman microscopy. Haessler A, Candlish M, Hefendehl JK, Jung N, Windbergs M. Communications Biology 2024, 7, 1514. https://dx.doi.org/10.1038/s42003-024-07182-6
  • The Aβ(42):Aβ(40) ratio modulates aggregation in beta-amyloid oligomers and drives metabolic changes and cellular dysfunction. Haessler A, Gier S, Jung N, Windbergs M. Frontiers in Cellular Neuroscience 2024, 18, 1516093. https://dx.doi.org/10.3389/fncel.2024.1516093
  • Structural characterization of an essential lipoprotein of Mycoplasma pneumoniae. Keles I, Manger S, Mantanya MS, Frangakis AS. bioRxiv 2024, 2024.09.05.611430. https://dx.doi.org/10.1101/2024.09.05.611430
  • Vascular FLRT2 regulates venous-mediated angiogenic expansion and CNS barriergenesis. Llaó-Cid C, Peguera B, Kobialka P, Decker L, Vogenstahl J, Alivodej N, Srivastava S, Jin J, Kirchmaier BC, Milla C, Schlierbach H, Schänzer A, Acker T, Segarra M, Acker-Palmer A. Nature Communications 2024, 15, 10372. https://dx.doi.org/10.1038/s41467-024-54570-x
  • Open-hardware solutions for light sheet microscopy specimen chambers. Golden A, Colombelli J, Stelzer EHK, Pampaloni F. bioRxiv 2024, 2024.08.22.609188. https://dx.doi.org/10.1101/2024.08.22.609188
  • Light sheet-based laser patterning bioprinting produces long-term viable full-thickness skin constructs. Hafa L, Breideband L, Ramirez Posada L, Torras N, Martinez E, Stelzer EHK, Pampaloni F.  Advanced Materials 2024, 36, 2306258. https://dx.doi.org/https://doi.org/10.1002/adma.202306258
  • Robust virtual staining of landmark organelles. Liu Z, Hirata Miyasaki E, Pradeep S, Rahm JV, Foley C, Chandler T, Ivanov IE, Woosley HO, Lao T, Balasubramanian A, Liu C, Leonetti MD, Arias C, Jacobo A, Mehta SB. bioRxiv 2024, 2024.05.31.596901. https://dx.doi.org/10.1101/2024.05.31.596901
  • Efficient encoding of aversive location by CA3 long-range projections. Nikbakht N, Pofahl M, Miguel-López A, Kamali F, Tchumatchenko T, Beck H. Cell Reports 2024, 43, 113957. https://dx.doi.org/https://doi.org/10.1016/j.celrep.2024.113957
  • Denoising diffusion models for high-resolution microscopy image restoration. Osuna-Vargas P, Wehrheim MH, Zinz L, Rahm J, Balakrishnan A, Kaminer A, Heilemann M, Kaschube M. arXiv 2024, 2409.12078. https://dx.doi.org/10.48550/arXiv.2409.12078
  • Spatio-temporal segmentation of contraction waves in the extra-embryonic membranes of the red flour beetle. Pereyra M, Golden M, Lange Z, Golden A, Strobl F, Stelzer EHK, Matthaeus F. bioRxiv 2024, 2024.08.23.609389. https://dx.doi.org/10.1101/2024.08.23.609389
  • Fast and long-term super-resolution imaging of endoplasmic reticulum nano-structural dynamics in living cells using a neural network. Rahm JV, Balakrishnan A, Wehrheim M, Kaminer A, Glogger M, Kessler LF, Kaschube M, Barth H-D, Heilemann M. Small Science 2024, 2400385. https://dx.doi.org/https://doi.org/10.1002/smsc.202400385
  • Correlating topographic imaging and Raman spectroscopy to investigate wound re-epithelialization. Vestweber PK, Ederer IA, Rieger UM, Stelzer EHK, Planz V, Windbergs M. Journal of Investigative Dermatology 2024. https://dx.doi.org/10.1016/j.jid.2024.08.031
  • The interplay of Pseudomonas aeruginosa and Staphylococcus aureus in dual-species biofilms impacts development, antibiotic resistance and virulence of biofilms in in vitro wound infection models. Vestweber PK, Wächter J, Planz V, Jung N, Windbergs M. PLOS ONE 2024, 19. https://dx.doi.org/10.1371/journal.pone.0304491
  • Reliability of variability and complexity measures for task and task‐free BOLD fMRI. Wehrheim MH, Faskowitz J, Schubert A-L, & Fiebach CJ. Human Brain Mapping 2024, 45, 10: e26778. https://doi.org/10.1002/hbm.26778

2023

  • The molecular architecture of the kidney slit diaphragm. Birtasu AN, Wieland K, Ermel UH, Rahm JV, Scheffer MP, Flottmann B, Heilemann M, Grahammer F, Frangakis AS. bioRxiv 2023, 2023.10.27.564405. https://dx.doi.org/10.1101/2023.10.27.564405
  • Biased activation of the receptor tyrosine kinase HER2. Catapano C, Rahm JV, Omer M, Teodori L, Kjems J, Dietz MS, Heilemann M. Cellular and Molecular Life Sciences 2023, 80, 158. https://dx.doi.org/10.1007/s00018-023-04806-8
  • The devil’s in the variability: a multidimensional analysis of EEG signal dynamics and their relation to behaviour. García Alanis J, Nunez M, Wehrheim M, Fiebach C, Löffler C, Schubert A-L. psyRxiv 2023, https://dx.doi.org/10.31234/osf.io/4ug3y
  • Unraveling molecular composition in biological samples – Systematic evaluation of statistical methods for the analysis of hyperspectral Raman data. Haessler A, Jung N, Windbergs M. Analytical Chemistry 2023, 95, 17646-17653. https://dx.doi.org/10.1021/acs.analchem.3c03368 (Front Cover)
  • Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag. Jang S, Narayanasamy KK, Rahm JV, Saguy A, Kompa J, Dietz MS, Johnsson K, Shechtman Y, Heilemann M. Biophysical Reports 2023, 3, 100123. https://dx.doi.org/https://doi.org/10.1016/j.bpr.2023.100123
  • P116 from Mycoplasma is a self-sufficient lipid uptake and delivery machinery. Manger S, Arghittu SM, Sprankel L, Meier-Credo J, Wieland K, Schwalm MP, Bublak D, Knapp S, Langer J, Covino R, Frangakis AS. bioRxiv 2023, 2023.10.24.563710. https://dx.doi.org/10.1101/2023.10.24.563710
  • DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning. Saguy A, Alalouf O, Opatovski N, Jang S, Heilemann M, Shechtman Y. Nature Methods 2023, 20, 1939-1948. https://dx.doi.org/10.1038/s41592-023-01966-0
  • Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium. Sprankel L, Scheffer MP, Manger S, Ermel UH, Frangakis AS. PLoS Pathogens 2023, 19, e1011761. https://dx.doi.org/10.1371/journal.ppat.1011761
  • Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Sprankel L, Vizarraga D, Martín J, Manger S, Meier-Credo J, Marcos M, Julve J, Rotllan N, Scheffer MP, Escolà-Gil JC, Langer JD, Piñol J, Fita I, Frangakis AS. Nature Structural & Molecular Biology 2023, 30, 321-329. https://dx.doi.org/10.1038/s41594-023-00922-y
  • Utilizing 2D-region-based CNNs for automatic dendritic spine detection in 3D live cell imaging. Vogel FW, Alipek S, Eppler J-B, Osuna-Vargas P, Triesch J, Bissen D, Acker-Palmer A, Rumpel S, Kaschube M. Scientific Reports 2023, 13, 20497. https://dx.doi.org/10.1038/s41598-023-47070-3
  • Imitating the microenvironment of native biofilms using nanofibrous scaffolds to emulate chronic wound infections. Wächter J*, Vestweber PK*, Jung N, Windbergs M. Journal of Materials Chemistry B 2023, 11, 3212-3225. https://dx.doi.org/10.1039/D2TB02700C
  • Unravelling host-pathogen interactions by biofilm infected human wound models. Wächter J*, Vestweber PK*, Planz V, Windbergs M. Biofilm 2023, 6, 100164. https://dx.doi.org/https://doi.org/10.1016/j.bioflm.2023.100164
  • Few temporally distributed brain connectivity states predict human cognitive abilities. Wehrheim MH, Faskowitz J, Sporns O, Fiebach CJ, Kaschube M, Hilger K. NeuroImage 2023, 277, 120246. https://doi.org/10.1016/j.neuroimage.2023.120246
  • Reliability of variability and complexity measures for task and task-free BOLD fMRI. Wehrheim MH, Faskowitz J, Schubert A-L, Fiebach CJ. psyRxiv 2023, https://dx.doi.org/10.31234/osf.io/ves2t

2022

  • ArtiaX: an electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Ermel UH, Arghittu SM, Frangakis AS. Protein Science 2022, e4472. https://dx.doi.org/https://doi.org/10.1002/pro.4472
  • Mean curvature motion facilitates the segmentation and surface visualization of electron tomograms. Frangakis AS. Journal of Structural Biology 2022, 214, 107833. https://dx.doi.org/https://doi.org/10.1016/j.jsb.2022.107833
  • SEDDS-loaded mucoadhesive fiber patches for advanced oromucosal delivery of poorly soluble drugs. Friedl JD, Walther M, Vestweber PK, Wachter J, Knoll P, Joergensen AM, Bernkop-Schnuerch A, Windbergs M. Journal of Controlled Release 2022, 348, 692-705. https://dx.doi.org/10.1016/j.jconrel.2022.06.023
  • Biochemical characterization of cell-free synthesized human β1 adrenergic receptor cotranslationally inserted into nanodiscs. Köck Z, Ermel U, Martin J, Morgner N, Achilleas Frangakis S, Dötsch V, Hilger D, Bernhard F. Journal of Molecular Biology 2022, 167687. https://doi.org/10.1016/j.jmb.2022.167687
  • Receptor tyrosine kinase MET ligand-interaction classified via machine learning from single-particle tracking data. Malkusch S, Rahm JV, Dietz MS, Heilemann M, Sibarita J-B, Lötsch J. Molecular Biology of the Cell 2022, 33, ar60. https://dx.doi.org/10.1091/mbc.E21-10-0496
  • Fast DNA-PAINT imaging using a deep neural network. Narayanasamy KK, Rahm JV, Tourani S, Heilemann M. Nature Communications 2022, 13, 5047. https://dx.doi.org/10.1038/s41467-022-32626-0
  • Upgrading a consumer stereolithographic 3D printer to produce a physiologically relevant model with human liver cancer organoids. Breideband L, Wächtershäuser KN, Hafa L, Wieland K, Frangakis AS, Stelzer EHK, Pampaloni F. Advanced Materials Technologies 2022, 7, 2200029. https://dx.doi.org/https://doi.org/10.1002/admt.202200029

2021

  • CRISPR/Cas12a-mediated labeling of MET receptor enables quantitative single-molecule imaging of endogenous protein organization and dynamics. Baldering TN, Karathanasis C, Harwardt M-LIE, Freund P, Meurer M, Rahm JV, Knop M, Dietz MS, Heilemann M. iScience 2021, 24, 101895-101895. https://dx.doi.org/10.1016/j.isci.2020.101895
  • Therapy of infected wounds: overcoming clinical challenges by advanced drug delivery systems. Kaiser P, Wachter J, Windbergs M. Drug Delivery and Translational Research 2021, 11, 1545-1567. https://dx.doi.org/10.1007/s13346-021-00932-7
  • Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy. Manger S, Ermel UH, Frangakis AS. Communications Biology 2021, 4, 234. https://dx.doi.org/10.1038/s42003-021-01752-8
  • QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis. Pereyra M, Drusko A, Krämer F, Strobl F, Stelzer EHK, Matthäus F. BMC Bioinformatics 2021, 22, 579. https://dx.doi.org/10.1186/s12859-021-04474-0
  • Diffusion state transitions in single-particle trajectories of MET receptor tyrosine kinase measured in live cells. Rahm JV, Malkusch S, Endesfelder U, Dietz MS, Heilemann M. Frontiers in Computer Science 2021, 3, https://dx.doi.org/10.3389/fcomp.2021.757653
  • Imaging the fibroblast growth factor receptor network on the plasma membrane with DNA-assisted single-molecule super-resolution microscopy. Schröder MS, ML IEH, Rahm JV, Li Y, Freund P, Dietz MS, Heilemann M. Methods 2021, 193, 38-45. https://dx.doi.org/10.1016/j.ymeth.2020.05.004

*shared first authorship