Publications

2026

Journal Article

Glushkova, D.; Böhm, S.; Beck, M.: Systematic membrane thickness variation across cellular organelles revealed by cryo-ET. Journal of Cell Biology 225 (1), e202504053 (2026)

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2025

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Mineev, K. S.; Gande, S. L.; Wenzel, A.; Linhard, V.; Andrews-Clark, H.; Witt, K.; Köster, S.; Segarra, M.; McDowell, M. A.; Acker-Palmer, A. et al.; Schwalbe, H.: Structural Role of Conformational Heterogeneity and Juxtamembrane Regions in the Ephrin A1 Interactions With the EphA2 Receptor Ligand-binding Domain. Journal of Molecular Biology 437 (24), 169454 (2025)

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Kompa, J.; Dornfeld, L. J.; Porzberg, N.; Jang, S.; Zedlitz, S.; Lilje, S. H.; Catapano, C.; Jocher, D.; Merk, L.; Hoege, C. et al.; Mao, R.; Wilhelm, J.; Dietz, M. S.; Tarnawski, M.; Hiblot, J.; Hyman, A. A.; Heilemann, M.; Johnsson, K.: Fast, Bright, and Reversible Fluorescent Labeling of Rhodamine-Binding Proteins. Journal of the American Chemical Society (accepted)

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Okuda, E. K.; Kessler, L. F.: A new rapid-degradation system combined with super-resolution microscopy. Nature Reviews Molecular Cell Biology 26 (12), p. 904 (2025)

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Berrevoets, E. S.; Kessler, L. F.; Balakrishnan, A.; Okuda, E. K.; Müller-McNicoll, M.; Rieger, B.; Stallinga, S.; Heilemann, M.: Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body. Nature Communications 16, 10689 (2025)

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Rosenkranz, N.; Birtasu, A. N.; Wieland, K.; Rehm, L.; Sharma, R.; Vats, A.; Manger, S.; Srivastava, A.; Bhattacharya, A.; Hummer, G. et al.; Frangakis, A. S.; Gottschalk, A.: In situ structure of a gap junction-stomatin complex. Science Advances 11 (45), eaea8596 (2025)

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Grabarczyk, D. B.; Aird, E. J.; Reznikow, V.; Kirchgatterer, P. C.; Ehrmann, J. F.; Kurzbauer, R.; Bell, L. E.; Kellner, M. J.; Aggarwal, R.; Schleiffer, A. et al.; Faas, V.; Deszcz, L.; Meinhart, A.; Versteeg, G. A.; Penninger, J. M.; Stelzl, L. S.; Gaidt, M. M.; Tessmer, I.; Corn, J. E.; Clausen, T.: A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles. Cell 188 (21), pp. 5995 - 6011 (2025)

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Majtner, T.; Kreysing, J. P.; Tuijtel, M.; Cruz-León, S.; Liu, J.; Hummer, G.; Beck, M.; Turoňová, B.: cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography. Communications Biology 8, 1443 (2025)

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Manger, S.; Arghittu, S. M.; Sprankel, L.; Meier-Credo, J.; Wieland, K.; Bublak, D.; Langer, J. D.; Covino, R.; Frangakis, A. S.: How does Mycoplasma pneumoniae scavenge lipids from its host membranes? Science Advances 11 (40), eady4746 (2025)

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Brdar, A.; Osterburg, C.; Münick, P.; Machel, A. C.; Rathore, R.; Osterburg, S.; Yüksel, B.; Schäfer, B.; Desch, K.; Langer, J. D. et al.; Dikic, I.; Dötsch, V.: p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners. eLife 13, RP103537 (2025)

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Kaulich, E.; Waselenchuk, Q.; Fürst, N.; Desch, K.; Mosbacher, J.; Ciirdaeva, E.; Juengling, M.; Ray, R.; Nassim-Assir, B.; Tushev, G. et al.; Langer, J. D.; Schuman, E. M.: An integrated transcriptomic and proteomic map of the mouse hippocampus at synaptic resolution. Nature Communications 16, 7942 (2025)

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Pedersen, K. B.; Ingólfsson, H. I.; Ramirez-Echemendia, D. P.; Borges-Araújo, L.; Andreasen, M. D.; Empereur-mot, C.; Melcr, J.; Ozturk, T. N.; Bennett, W. F. D.; Kjølbye, L. R. et al.; Brasnett, C.; Corradi, V.; Khan, H. M.; Cino, E. A.; Crowley, J.; Kim, H.; Fábián, B.; Borges-Araújo, A. C.; Pavan, G. M.; Launay, G.; Lolicato, F.; Wassenaar, T. A.; Melo, M. N.; Thallmair, S.; Carpenter, T. S.; Monticelli, L.; Tieleman, D. P.; Schiøtt, B.; Souza, P. C. T.; Marrink, S. J.: The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior. ACS Central Science 11 (9), pp. 1598 - 1610 (2025)

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Agip, A.-N. A.; Ornelas, P.; Yang, T.-J.; Uboldi, E.; Häder, S.; McDowell, M.; Kühlbrandt, W.: Structures of Chaetomium thermophilum TOM complexes with bound preproteins. Proceedings of the National Academy of Sciences of the United States of America 122 (29), e2507279122 (2025)

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Okuda, E. K.; Kessler, L. F.; Arnold, B.; Riegger, R. J.; Hernández Cañás, M. C.; Zebrowska, E.; Bakisoglu, C.; Rudigier, M.; Krost, C.; Nagasse, H. Y. et al.; Keiten-Schmitz, J.; Müller, S.; Stanek, D.; Dormann, D.; Zarnack, K.; Heilemann, M.; Müller-McNicoll, M.: Rapid depletion and super-resolution microscopy reveal dual roles of SRSF5 in coordinating nuclear speckle-paraspeckle crosstalk during cellular stress. Nucleic Acids Research 53, gkaf713 (2025)

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Perez-Rivera, E.; Plasencia, C.; Ros, U.: The Multifaceted Role of Calcium Signaling in Regulated Necrosis. Biomolecules 15 (6), 854 (2025)

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Münick, P.; Strubel, A.; Balourdas, D.-I.; Funk, J. S.; Mernberger, M.; Osterburg, C.; Dreier, B.; Schaefer, J. V.; Tuppi, M.; Yüksel, B. et al.; Schäfer, B.; Knapp, S.; Plückthun, A.; Stiewe, T.; Joerger, A. C.; Dötsch, V.: DARPin-induced reactivation of p53 in HPV-positive cells. Nature Structural & Molecular Biology 32 (5), pp. 790 - 801 (2025)

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Taniguchi, R.; Orniacki, C.; Kreysing, J. P.; Zila, V.; Zimmerli, C. E.; Böhm, S.; Turoňová, B.; Kräusslich, H.-G.; Doye, V.; Beck, M.: Nuclear pores safeguard the integrity of the nuclear envelope. Nature Cell Biology 27 (5), pp. 762 - 775 (2025)

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Cook, A. S. I.; Chen, M.; Nguyen, T. N.; Cabezudo, A. C.; Khuu, G.; Rao, S.; Garcia, S. N.; Yang, M.; Iavarone, A. T.; Ren, X. et al.; Lazarou, M.; Hummer, G.; Hurley, J. H.: Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Science 388 (6743), eadl3787 (2025)

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Poveda Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R.: Janus-like behavior of intrinsically disordered regions in reticulophagy. Autophagy 21 (3), pp. 681 - 683 (2025)

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Bailey, H. J.; Eisert, J.; Kazi, R.; Gerhartz, J.; Pieńkowska, D. E.; Dressel, I.; Vollrath, J.; Kondratov, I.; Matviyuk, T.; Tolmachova, N. et al.; Shah, V. J.; Giuliani, G.; Mosler, T.; Geiger, T. M.; Esteves, A. M.; Santos, S. P.; Sousa, R. L.; Bandeiras, T. M.; Leibrock, E.-M.; Bauer, U.; Leuthner, B.; Langer, J. D.; Wegener, A. A.; Nowak, R. P.; Sorrell, F. J.; Đikić, I.: An engineered cereblon optimized for high throughput screening and molecular glue discovery. Cell Chemical Biology 32 (2), pp. 363 - 376.e10 (2025)

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Kreysing, J. P.; Heidari, M.; Zila, V.; Cruz-León, S.; Obarska-Kosinska, A.; Laketa, V.; Rohleder, L.; Welsch, S.; Köfinger, J.; Turoňová, B. et al.; Hummer, G.; Kräusslich, H.-G.; Beck, M.: Passage of the HIV capsid cracks the nuclear pore. Cell 188 (4), pp. 930 - 943.e21 (2025)

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Hoffmann, P. C.; Kim, H.; Obarska-Kosinska, A.; Kreysing, J. P.; Andino-Frydman, E.; Cruz-León, S.; Margiotta, E.; Cernikova, L.; Kosinski, J.; Turoňová, B. et al.; Hummer, G.; Beck, M.: Nuclear pore permeability and fluid flow are modulated by its dilation state. Molecular Cell 85 (3), pp. 537 - 554.e11 (2025)

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Cutts, E. E.; Tetiker, D.; Kim, E.; Aragon, L.: Molecular mechanism of condensin I activation by KIF4A. The EMBO Journal 44 (3), pp. 682 - 704 (2025)

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Yin, M. D.; Lemaire, O. N.; Rosas Jiménez, J. G.; Belhamri, M.; Shevchenko, A.; Hummer, G.; Wagner, T.; Murphy, B. J.: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Science 387 (6733), pp. 498 - 504 (2025)

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Catapano, C.; Dietz, M. S.; Kompa, J.; Jang, S.; Freund, P.; Johnsson, K.; Heilemann, M.: Long-term single-molecule tracking in living cells using weak-affinity protein labeling. Angewandte Chemie, International Edition in English 64 (1), e202413117 (2025)

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Rahm, J. V.; Balakrishnan, A.; Wehrheim, M.; Kaminer, A.; Glogger, M.; Kessler, L. F.; Kaschube, M.; Barth, H.-D.; Heilemann, M.: Fast and Long-Term Super-Resolution Imaging of Endoplasmic Reticulum Nano-structural Dynamics in Living Cells Using a Neural Network. Small science 5 (1), 2400385 (2025)

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2024

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Herhaus, L.; Gestal-Mato, U.; Eapen, V. V.; Mačinković, I.; Bailey, H. J.; Prieto-Garcia, C.; Misra, M.; Jacomin, A.-C.; Ammanath, A. V.; Bagarić, I. et al.; Michaelis, J.; Vollrath, J.; Bhaskara, R. M.; Bündgen, G.; Covarrubias-Pinto, A.; Husnjak, K.; Zöller, J.; Gikandi, A.; Ribičić, S.; Bopp, T.; van der Heden van Noort, G. J.; Langer, J. D.; Weigert, A.; Harper, J. W.; Mancias, J. D.; Đikić, I.: IRGQ-mediated autophagy in MHC class I quality control promotes tumor immune evasion. Cell 187 (7), pp. 7285 - 7302 (2024)

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Rosas Jiménez, J. G.; Fábián, B.; Hummer, G.: Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water. Journal of Chemical Theory and Computation 20 (24), pp. 11068 - 11081 (2024)

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Sieber, A.; Parr, M.; Ehr, J. v.; Dhamotharan, K.; Kielkowski, P.; Brewer, T.; Schäpers, A.; Krafczyk, R.; Qi, F.; Schlundt, A. et al.; Frishman, D.; Lassak, J.: EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences. Nature Communications 15, 10465 (2024)

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Dubach, V. R. A.; San Segundo-Acosta, P.; Murphy, B. J.: Structural and mechanistic insights into Streptococcus pneumoniae NADPH oxidase. Nature Structural & Molecular Biology 31 (11), pp. 1769 - 1777 (2024)

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Li, Y.; Arghittu, S. M.; Dietz, M. S.; Hella, G. J.; Haße, D.; Ferraris, D. M.; Freund, P.; Barth, H.-D.; Iamele, L.; de Jonge, H. et al.; Niemann, H. H.; Covino, R.; Heilemann, M.: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in cells. Nature Communications 15, 9486 (2024)

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Sushkin, M. E.; Jung, M.; Lemke, E. A.: Tuning the Functionality of Designer Translating Organelles with Orthogonal tRNA Synthetase/tRNA Pairs. Journal of Molecular Biology 436 (21), 168728 (2024)

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Poveda-Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R. M.: Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy. Proceedings of the National Academy of Sciences of the United States of America 121 (44), e2408071121 (2024)

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Schartel, L.; Jann, C.; Wierczeiko, A.; Butto, T.; Mündnich, S.; Marchand, V.; Motorin, Y.; Helm, M.; Gerber, S.; Lemke, E. A.: Selective RNA pseudouridinylation in situ by circular gRNAs in designer organelles. Nature Communications 15, 9177 (2024)

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Ehr, J. v.; Oberstrass, L.; Yazgan, E.; Schnaubelt, L. I.; Blümel, N.; McNicoll, F.; Weigand, J. E.; Zarnack, K.; Müller-McNicoll, M.; Korn, S. M. et al.; Schlundt, A.: Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. Journal of Biological Chemistry 300 (7), 107457 (2024)

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Ri, K.; Weng, T.-H.; Claveras Cabezudo, A.; Jösting, W.; Zhang, Y.; Bazzone, A.; Leong, N. C. P.; Welsch, S.; Doty, R. T.; Gursu, G. et al.; Lim, T. J. Y.; Schmidt, S. L.; Abkowitz, J. L.; Hummer, G.; Wu, D.; Nguyen, L. N.; Safarian, S.: Molecular mechanism of choline and ethanolamine transport in humans. Nature 630, pp. 501 - 508 (2024)

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Cruz-León, S.; Majtner, T.; Hoffmann, P. C.; Kreysing, J. P.; Kehl, S.; Tuijtel, M.; Schaefer, S. L.; Geißler, K.; Beck, M.; Turoňová, B. et al.; Hummer, G.: High-confidence 3D template matching for cryo-electron tomography. Nature Communications 15, 3992 (2024)

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Tuijtel, M.; Cruz-León, S.; Kreysing, J. P.; Welsch, S.; Hummer, G.; Beck, M.; Turoňová, B.: Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances 10 (17), eadk6285 (2024)

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Arnold, B.; Riegger, R. J.; Okuda, E. K.; Slišković, I.; Keller, M.; Bakisoglu, C.; McNicoll, F.; Zarnack, K.; Müller-McNicoll, M.: hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. Journal of Cell Biology 223 (2), e202304030 (2024)

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Martinez-Mayorga, K.; Rosas-Jiménez, J. G.; Gonzalez-Ponce, K.; López-López, E.; Neme, A.; Medina-Franco, J. L.: The pursuit of accurate predictive models of the bioactivity of small molecules. Chemical Science 15 (6), pp. 1938 - 1952 (2024)

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2023

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Trebino, T. E.; Markusic, B.; Nan, H.; Banerjee, S.; Wang, Z.: Unveiling the domain-specific and RAS isoform-specific details of BRAF kinase regulation. eLife 12, RP88836 (2023)

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Gul, M.; Yuksel, B.; Bulut, H.; DeMirci, H.: Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography. Acta Crystallographica Section D: Structural Biology 79 (11), pp. 1010 - 1017 (2023)

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Hanson, S. M.; Scholüke, J.; Liewald, J.; Sharma, R.; Ruse, C.; Engel, M.; Schüler, C.; Klaus, A.; Arghittu, S. M.; Baumbach, F. et al.; Seidenthal, M.; Dill, H.; Hummer, G.; Gottschalk, A.: Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB 33 (16), pp. 3423 - 3435.e5 (2023)

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Jang, S.; Narayanasamy, K. K.; Rahm, J. V.; Saguy, A.; Kompa, J.; Dietz, M. S.; Johnsson, K.; Shechtman, Y.; Heilemann, M.: Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag. Biophysical Reports 3 (3), 100123 (2023)

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Saguy, A.; Alalouf, O.; Opatovski, N.; Jang, S.; Heilemann, M.; Shechtman, Y.: DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning. Nature Methods 20 (12), pp. 1939 - 1948 (2023)

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Goretzki, B.; Wiedemann, C.; McCray, B. A.; Schäfer, S. L.; Jansen, J.; Tebbe, F.; Mitrovic, S.-A.; Nöth, J.; Cabezudo, A. C.; Donohue, J. K. et al.; Jeffries, C. M.; Steinchen, W.; Stengel, F.; Sumner, C. J.; Hummer, G.; Hellmich, U. A.: Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications 14, 4165 (2023)

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Xing, H.; Taniguchi, R.; Khusainov, I.; Kreysing, J. P.; Welsch, S.; Turoňová, B.; Beck, M.: Translation dynamics in human cells visualized at high resolution reveal cancer drug action. Science 381 (6653), pp. 70 - 75 (2023)

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Ehr, J. v.; Korn, S. M.; Weiß, L.; Schlundt, A.: ¹H, ¹³C, ¹⁵N backbone chemical shift assignments of the extended ARID domain in human AT-rich interactive domain protein 5a (Arid5a). Biomolecular NMR Assignments 17 (1), pp. 121 - 127 (2023)

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Korn, S. M.; Ehr, J. v.; Dhamotharan, K.; Tants, J.-N.; Abele, R.; Schlundt, A.: Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein. International Journal of Molecular Sciences 24 (4), 3286 (2023)

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2022

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Hoffmann, P. C.; Kreysing, J. P.; Khusainov, I.; Tuijtel, M.; Welsch, S.; Beck, M.: Structures of the eukaryotic ribosome and its translational states in situ. Nature Communications 13, 7435 (2022)

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Publications

Journal Article (50)

Thesis - PhD (1)