iMOL Publications


  • 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.
  • 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.
  • 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,



  • 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.
  • 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.
  • 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,
  • 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. (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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Unravelling host-pathogen interactions by biofilm infected human wound models. Wächter J*, Vestweber PK*, Planz V, Windbergs M. Biofilm 2023, 6, 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.
  • Reliability of variability and complexity measures for task and task-free BOLD fMRI. Wehrheim MH, Faskowitz J, Schubert A-L, Fiebach CJ. psyRxiv 2023,



  • 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.
  • Mean curvature motion facilitates the segmentation and surface visualization of electron tomograms. Frangakis AS. Journal of Structural Biology 2022, 214, 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.
  • 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.
  • 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.
  • Fast DNA-PAINT imaging using a deep neural network. Narayanasamy KK, Rahm JV, Tourani S, Heilemann M. Nature Communications 2022, 13, 5047.



  • 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.
  • 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.
  • Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy. Manger S, Ermel UH, Frangakis AS. Communications Biology 2021, 4, 234.
  • 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.
  • 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,
  • 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.

*shared first authorship