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Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics.

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Probing coenzyme A homeostasis with semisynthetic biosensors.

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STED imaging of endogenously tagged ARF GTPases reveals their distinct nanoscale localizations.

Wong-Dilworth, L., Rodilla-Ramirez, C., Fox, E., Restel, S. D., Stockhammer, A., Adarska, P. & Bottanelli, F.

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The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion.

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The GAPDH redox switch safeguards reductive capacity and enables survival of stressed tumour cells.

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Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa.

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Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock.

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An antagonism between Spinophilin and Syd-1 operates upstream of memory-promoting presynaptic long-term plasticity.

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3-Mercaptopyruvate sulfur transferase is a protein persulfidase.

Pedre, B., Talwar, D., Barayeu, U., Schilling, D., Luzarowski, M., Sokolowski, M., Glatt, S. & Dick, T. P.

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Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora.

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Competition for cysteine acylation by C16:0 and C18:0 derived lipids is a global phenomenon in the proteome.

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The role of an amphiphilic helix and transmembrane region in the efficient acylation of the M2 protein from influenza virus.

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Scientific Reports 13, 18928,


Machine learning coarse-grained potentials of protein thermodynamics.

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CaMKII autophosphorylation can occur between holoenzymes without subunit exchange.

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One Scaffold, Two Conformations: The Ring-Flip of the Messenger InsP8 Occurs under Cytosolic Conditions.

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In vivo characterization of the bacterial intramembrane-cleaving protease RseP using the heme binding tag-based assay iCliPSpy.

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Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics.

Krämer, A., Durumeric, A. E. P., Charron, N. E., Chen, Y., Clementi, C. & Noé, F.

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Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy.

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Systematic functional analysis of rab GTPases reveals limits of neuronal robustness to environmental challenges in flies.

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From Bench to Bedside and Back Again: Translating Circadian Science to Medicine.

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IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion.

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A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway.

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Quantification of Dolichyl Phosphates Using Phosphate Methylation and Reverse-Phase Liquid Chromatography-High Resolution Mass Spectrometry.

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Unc13A dynamically stabilizes vesicle priming at synaptic release sites for short-term facilitation and homeostatic potentiation.

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Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag.

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A general method for the development of multicolor biosensors with large dynamic ranges.

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Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels.

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Sphingolipid subtypes differentially control proinsulin processing and systemic glucose homeostasis.

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Spontaneous neurotransmission at evocable synapses predicts their responsiveness to action potentials.

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Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca2+ channels drives sustained active zone potentiation.

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Branch point strength controls species-specific CAMK2B alternative splicing and regulates LTP.

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Nutrient-regulated control of lysosome function by signaling lipid conversion.

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3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning.

Dyhr, M. C. A., Sadeghi, M., Moynova, R., Knappe, C., Kepsutlu Çakmak, B., Werner, S., Schneider, G., McNally, J., Noé, F. & Ewers, H.

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Antisense Transcription of the Neurospora Frequency Gene Is Rhythmically Regulated by CSP-1 Repressor but Dispensable for Clock Function.

Cemel, I. A., Diernfellner, A. C. R. & Brunner, M.

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Synaptotagmin 1-triggered lipid signaling facilitates coupling of exo- and endocytosis.

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Hydropersulfides inhibit lipid peroxidation and ferroptosis by scavenging radicals.

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Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics.

Arts, M., Garcia Satorras, V., Huang, C.-W., Zügner, D., Federici, M., Clementi, C., Noé, F., Pinsler, R. & van den Berg, R.

Journal of chemical theory and computation 19, 6151-6159,


Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor.

Altuzar, J., Notbohm, J., Stein, F., Haberkant, P., Hempelmann, P., Heybrock, S., Worsch, J., Saftig, P. & Höglinger, D.

Proceedings of the National Academy of Sciences of the United States of America 120, e2213886120,


An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor.

Aguirre, T., Dornan, G. L., Hostachy, S., Neuenschwander, M., Seyffarth, C., Haucke, V., Schütz, A., Kries, J. P. & Fiedler, D.

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MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.

Abualrous, E. T., Stolzenberg, S., Sticht, J., Wieczorek, M., Roske, Y., Günther, M., Dähn, S., Boesen, B. B., Calvo, M. M., Biese, C., Kuppler, F., Medina-García, Á., Álvaro-Benito, M., Höfer, T., Noé, F. & Freund, C.

Nature Chemical Biology 19, 1196-1204,


Precise measurement of nanoscopic septin ring structures with deep learning-assisted quantitative superresolution microscopy.

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Recruitment of a splicing factor to the nuclear lamina for its inactivation.

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Syntaxin-1A modulates vesicle fusion in mammalian neurons via juxtamembrane domain dependent palmitoylation of its transmembrane domain.

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Glypican-1 drives unconventional secretion of fibroblast growth factor 2.

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Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa.

Singh, A., Li, C., Diernfellner, A. C. R., Höfer, T. & Brunner, M.

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Commonly Used Alkylating Agents Limit Persulfide Detection by Converting Protein Persulfides into Thioethers.

Schilling, D., Barayeu, U., Steimbach, R. R., Talwar, D., Miller, A. K. & Dick, T. P.

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Antagonistic control of active surface integrins by myotubularin and phosphatidylinositol 3-kinase C2β in a myotubular myopathy model.

Samsó, P., Koch, P. A., Posor, Y., Lo, W.-T., Belabed, H., Nazare, M., Laporte, J. & Haucke, V.

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Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8.

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Local synthesis of the phosphatidylinositol-3,4-bisphosphate lipid drives focal adhesion turnover.

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Tissue-Specific CRISPR-Cas9 Screening in Drosophila.

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Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.

Poetz, F., Lebedeva, S., Schott, J., Lindner, D., Ohler, U. & Stoecklin, G.

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Venn diagram analysis overestimates the extent of circadian rhythm reprogramming.

Pelikan, A., Herzel, H., Kramer, A. & Ananthasubramaniam, B.

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Quantum dynamics using path integral coarse-graining.

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Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals.

Marzoll, D., Serrano, F. E., Shostak, A., Schunke, C., Diernfellner, A. C. R. & Brunner, M.

Proceedings of the National Academy of Sciences of the United States of America 119,


Neurospora casein kinase 1a recruits the circadian clock protein FRQ via the C-terminal lobe of its kinase domain.

Marzoll, D., Serrano, F. E., Diernfellner, A. C. R. & Brunner, M.

FEBS letters 596, 1881-1891,


Deep learning to decompose macromolecules into independent Markovian domains.

Mardt, A., Hempel, T., Clementi, C. & Noé, F.

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Monitoring Virus-Induced Stress Granule Dynamics Using Long-Term Live-Cell Imaging.

Magg, V., Klein, P. & Ruggieri, A.

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Cholesterol promotes clustering of PI(4,5)P2 driving unconventional secretion of FGF2.

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Endosomal phosphatidylinositol 3-phosphate controls synaptic vesicle cycling and neurotransmission.

Liu, G.-T., Kochlamazashvili, G., Puchkov, D., Müller, R., Schultz, C., Mackintosh, A. I., Vollweiter, D., Haucke, V. & Soykan, T.

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Phosphoinositide Conversion Inactivates R-RAS and Drives Metastases in Breast Cancer.

Li, H., Prever, L., Hsu, M. Y., Lo, W.-T., Margaria, J. P., Santis, M. C., Zanini, C., Forni, M., Novelli, F., Pece, S., Di Fiore, P. P., Porporato, P. E., Martini, M., Belabed, H., Nazare, M., Haucke, V., Gulluni, F. & Hirsch, E.

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Allosteric stabilization of calcium and phosphoinositide dual binding engages several synaptotagmins in fast exocytosis.

Kobbersmed, J. R. L., Berns, M. M. M., Ditlevsen, S., Sørensen, J. B. & Walter, A. M.

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Temporal control of the integrated stress response by a stochastic molecular switch.

Klein, P., Kallenberger, S. M., Roth, H., Roth, K., Ly-Hartig, T. B. N., Magg, V., Aleš, J., Talemi, S. R., Qiang, Y., Wolf, S., Oleksiuk, O., Kurilov, R., Di Ventura, B., Bartenschlager, R., Eils, R., Rohr, K., Hamprecht, F. A., Höfer, T., Fackler, O. T., Stoecklin, G. & Ruggieri, A.

Science advances 8, eabk2022,


Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function.

Jang, W., Puchkov, D., Samsó, P., Liang, Y., Nadler-Holly, M., Sigrist, S. J., Kintscher, U., Liu, F., Mamchaoui, K., Mouly, V. & Haucke, V.

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Deeptime: a Python library for machine learning dynamical models from time series data.

Hoffmann, M., Scherer, M., Hempel, T., Mardt, A., Silva, B., Husic, B. E., Klus, S., Wu, H., Kutz, N., Brunton, S. L. & Noé, F.

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Image-Based Screening for Stress Granule Regulators.

Hoerth, K., Eiermann, N., Beneke, J., Erfle, H. & Stoecklin, G.

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Preferential translation of p53 target genes.

Hisaoka, M., Schott, J., Bortecen, T., Lindner, D., Krijgsveld, J. & Stoecklin, G.

RNA biology 19, 437-452,


Defective lipid signalling caused by mutations in PIK3C2B underlies focal epilepsy.

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Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy.

Glogger, M., Wang, D., Kompa, J., Balakrishnan, A., Hiblot, J., Barth, H.-D., Johnsson, K. & Heilemann, M.

ACS nano 16, 17991-17997,


Engineered HaloTag variants for fluorescence lifetime multiplexing.

Frei, M. S., Tarnawski, M., Roberti, M. J., Koch, B., Hiblot, J. & Johnsson, K.

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Live-Cell Fluorescence Lifetime Multiplexing Using Synthetic Fluorescent Probes.

Frei, M. S., Koch, B., Hiblot, J. & Johnsson, K.

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Mitochondrial Inhibition by Sodium Azide Induces Assembly of eIF2α Phosphorylation-Independent Stress Granules in Mammalian Cells.

Eiermann, N., Stoecklin, G. & Jovanovic, B.

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Inter-layer and inter-subject variability of diurnal gene expression in human skin.

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Sortase-Mediated Multi-Fragment Assemblies by Ligation Site Switching.

Bierlmeier, J., Álvaro-Benito, M., Scheffler, M., Sturm, K., Rehkopf, L., Freund, C. & Schwarzer, D.

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A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing.

Bergfort, A., Preußner, M., Kuropka, B., Ilik, İ. A., Hilal, T., Weber, G., Freund, C., Aktaş, T., Heyd, F. & Wahl, M. C.

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The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling.

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Circadian rhythms in septic shock patients.

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Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.

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Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins.

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