Max-Planck-Institut für Multidisziplinäre Naturwissenschaften

Publikationen

Zeitschriftenartikel (12830)

1.

Zeitschriftenartikel

Scodellaro, R.; Zschüntzsch, J.; Hell, A.-K.; Alves, F.: A first explainable-AI-based workflow integrating forward-forward and backpropagation-trained networks of label-free multiphoton microscopy images to assess human biopsies of rare neuromuscular disease. Computer Methods and Programs in Biomedicine 265, 108733 (2025)

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2.

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Campbell, C. T.; Fingerhut, J.; Wodtke, A. M.: Experimental Energies of Formation Reactions for Adsorbates on Late Transition Metal Surfaces: A Database Update. Surface Science 756, 122714 (2025)

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Ali, T. T.; Merghani, M.; Al-Azzani, M.; Gatzemeier, L. M.; Hoppert, M.; Kaloyanova, D.; Outeiro, T. F.; Neumann, P.; Popova, B.; Braus, G. H.: Rationally designed peptides inhibit the formation of α-synuclein fibrils and oligomers. European Journal of Medicinal Chemistry 289, 117452 (2025)

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Budde, K.; Lange, C.; Reimann, M.; Zielinski, N.; Meiwes, L.; Köhler, N.; Reimann, M.; Avsar, K.; DiNardo, A.; Goldmann, T. et al.; Günther, G.; Hoelscher, M.; Ibraim, E.; Kalsdorf, B.; Kaufmann, S. H. E.; Köhler, N.; Mandalakas, A. M.; Maurer, F. P.; Müller, M.; Olaru, I. D.; Popa, C.; Rachow, A.; Rolling, T.; Salzer, H. J.F.; Carballo, P. S.; Schuhmann, M.; Schaub, D.; Spinu, V.; Terhalle, E.; Unnewehr, M.; Zielinski, N.; Heyckendorf, J.; Lange, C.; Carballo, P. S.: A novel method for detecting Lipoarabinomannan in urine with the promise of meeting the WHO target product profile for the diagnosis of tuberculosis. Tuberculosis 152, 102619 (2025)

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5.

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Wilson, C. J.; Gapsys, V.; de Groot, B. L.: Improving pK_a Predictions with Reparameterized Force Fields and Free Energy Calculations. Journal of Chemical Theory and Computation 21 (8), S. 4095 - 4106 (2025)

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6.

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Thongdee, N.; Alaniz, M. M.; Samatova, E.; Zhong, A.; Esnault, C.; Zhang, H.; Dale, R. K.; Rodnina, M. V.; Storz, G.: Modulation of protein activity by small RNA base pairing internal to coding sequences. Molecular Cell (2025)

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7.

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Feuermann, M.; Mi, H.; Gaudet, P.; Muruganujan, A.; Lewis, S. E.; Ebert, D.; Mushayahama, T.; Aleksander, S. A.; Balhoff, J.; Carbon, S. et al.; Cherry, J. M.; Drabkin, H. J.; Harris, N. L.; Hill, D. P.; Lee, R.; Logie, C.; Moxon, S.; Mungall, C. J.; Sternberg, P. W.; Van Auken, K.; Ramsey, J.; Siegele, D. A.; Chisholm, R. L.; Fey, P.; Giglio, M.; Nadendla, S.; Antonazzo, G.; Attrill, H.; Brown, N. H.; Garapati, P. V.; Marygold, S.; Ahmed, S. H.; Asanitthong, P.; Buitrago, D. L.; Erdol, M. N.; Gage, M. C.; Huang, S.; Kadhum, M. A.; Li, K. Y. C.; Long, M.; Michalak, A.; Pesala, A.; Pritazahra, A.; Saverimuttu, S. C. C.; Su, R.; Xu, Q.; Lovering, R. C.; Blake, J.; Christie, K.; Corbani, L.; Dolan, M. E.; Ni, L.; Sitnikov, D.; Smith, C.; Lera-Ramirez, M.; Rutherford, K.; Wood, V.; D’Eustachio, P.; Demos, W. M.; De Pons, J. L.; Dwinell, M. R.; Hayman, G. T.; Kaldunski, M. L.; Kwitek, A. E.; Laulederkind, S. J. F.; Smith, J. R.; Tutaj, M. A.; Vedi, M.; Wang, S.-J.; Engel, S. R.; Karra, K.; Miyasato, S. R.; Nash, R. S.; Skrzypek, M. S.; Weng, S.; Wong, E. D.; Achsel, T.; Andres-Alonso, M.; Bagni, C.; Bayés, À.; Biederer, T.; Brose, N.; Chua, J. J. E.; Coba, M. P.; Cornelisse, L. N.; de Juan-Sanz, J.; Goldschmidt, H. L.; Gundelfinger, E. D.; Huganir, R. L.; Imig, C.; Jahn, R.; Jung, H.; Kaeser, P. S.; Kim, E.; Koopmans, F.; Kreutz, M. R.; Lipstein, N.; MacGillavry, H. D.; McPherson, P. S.; O’Connor, V.; Pielot, R.; Ryan, T. A.; Sala, C.; Sheng, M.; Smalla, K.-H.; Smit, A. B.; Toonen, R. F.; van Weering, J. R. T.; Verhage, M.; Verpelli, C.; Bakker, E.; Berardini, T. Z.; Reiser, L.; Auchincloss, A.; Axelsen, K.; Argoud-Puy, G.; Blatter, M.-C.; Boutet, E.; Breuza, L.; Bridge, A.; Casals-Casas, C.; Coudert, E.; Estreicher, A.; Famiglietti, M. L.; Gos, A.; Gruaz-Gumowski, N.; Hulo, C.; Hyka-Nouspikel, N.; Jungo, F.; Le Mercier, P.; Lieberherr, D.; Masson, P.; Morgat, A.; Pedruzzi, I.; Pourcel, L.; Poux, S.; Rivoire, C.; Sundaram, S.; Bowler-Barnett, E.; Bye-A-Jee, H.; Denny, P.; Ignatchenko, A.; Ishtiaq, R.; Lock, A.; Lussi, Y.; Magrane, M.; Martin, M. J.; Orchard, S.; Raposo, P.; Speretta, E.; Tyagi, N.; Warner, K.; Zaru, R.; Chan, J.; Diamantakis, S.; Raciti, D.; Fisher, M.; James-Zorn, C.; Ponferrada, V.; Zorn, A.; Ramachandran, S.; Ruzicka, L.; Westerfield, M.; Thomas, P. D.: A compendium of human gene functions derived from evolutionary modelling. Nature 640, S. 146 - 154 (2025)

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8.

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Amaro, R. E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P. C.; Bonomi, M.; Bowman, G. R.; Bryce, R. A. et al.; Bussi, G.; Carloni, P.; Case, D. A.; Cavalli, A.; Chang, C.-E. A.; Cheatham, T. E.; Cheung, M. S.; Chipot, C.; Chong, L. T.; Choudhary, P.; Cisneros, G. A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T. D.; Dal Peraro, M.; de Groot, B. L.; Delemotte, L.; De Vivo, M.; Essex, J. W.; Fraternali, F.; Gao, J.; Gelpí, J. L.; Gervasio, F. L.; González-Nilo, F. D.; Grubmüller, H.; Guenza, M. G.; Guzman, H. V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J. H.; Jha, S.; Jiao, W.; Jorgensen, W. L.; Kamerlin, S. C. L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y. L.; Luque, F. J.; Lynch, C. I.; MacKerell, A. D.; Magistrato, A.; Marrink, S. J.; Martin, H.; McCammon, J. A.; Merz, K.; Moliner, V.; Mulholland, A. J.; Murad, S.; Naganathan, A. N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O’Mara, M. L.; Ondrechen, M. J.; Onuchic, J. N.; Onufriev, A.; Osuna, S.; Palermo, G.; Panchenko, A. R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J. R.; Pettitt, B. M.; Pietropaolo, A.; Piquemal, J.-P.; Poma, A. B.; Praprotnik, M.; Ramos, M. J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Rothlisberger, U.; Sanbonmatsu, K. Y.; Schlick, T.; Shaytan, A. K.; Simmerling, C.; Smith, J. C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tieleman, D. P.; Tikhonova, I. G.; Tirado-Rives, J.; Tuñón, I.; van der Kamp, M. W.; van der Spoel, D.; Velankar, S.; Voth, G. A.; Wade, R.; Warshel, A.; Welborn, V. V.; Wetmore, S. D.; Wheeler, T. J.; Wong, C. F.; Yang, L.-W.; Zacharias, M.; Orozco, M.: The need to implement FAIR principles in biomolecular simulations. Nature Methods 22, S. 641 - 645 (2025)

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9.

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Cormican, J. A.; Medfai, L.; Wawrzyniuk, M.; Pašen, M.; Afrache, H.; Fourny, C.; Khan, S.; Gneiße, P.; Soh, W. T.; Timelli, A. et al.; Nolfi, E.; Pannekoek, Y.; Cope, A.; Urlaub, H.; Sijts, A. J.A. M.; Mishto, M.; Liepe, J.: PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes. Molecular & Cellular Proteomics 24 (4), 100937 (2025)

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10.

Zeitschriftenartikel

Gobran, M.; Politi, A. Z.; Welp, L. M.; Jakobi, J.; Urlaub, H.; Lenart, P.: PLK1 inhibition delays mitotic entry revealing changes to the phosphoproteome of mammalian cells early in division. The EMBO Journal 44 (7), S. 1891 - 1920 (2025)

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11.

Zeitschriftenartikel

Lange, F.; Ratz, M.; Dohrke, J.-N.; Le Vasseur, M.; Wenzel, D.; Ilgen, P.; Riedel, D.; Jakobs, S.: In situ architecture of the human prohibitin complex. Nature Cell Biology 27, S. 633 - 640 (2025)

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12.

Zeitschriftenartikel

Liu, S.; Xu, D.; Cai, C.; Zhang, X. C.; Andreas, L. B.; Wang, Z.; Song, Q.; Wang, J.; Picu, C. R.; Zhang, K.: Transition Behavior of Cellulose Nanocrystal Networks Induced by Nanoconfined Water. Advanced Energy and Sustainability Research 6 (4), 2400319 (2025)

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13.

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Schneeberger, S.; Kim, S. J.; Geesdorf, M. N.; Friebel, E.; Eede, P.; Jendrach, M.; Boltengagen, A.; Braeuning, C.; Ruhwedel, T.; Hülsmeier, A. J. et al.; Gimber, N.; Foerster, M.; Obst, J.; Andreadou, M.; Mundt, S.; Schmoranzer, J.; Prokop, S.; Kessler, W.; Kuhlmann, T.; Möbius, W.; Nave, K.-A.; Hornemann, T.; Becher, B.; Edgar, J. M.; Karaiskos, N.; Kocks, C.; Rajewsky, N.; Heppner, F. L.: Interleukin-12 signaling drives Alzheimer’s disease pathology through disrupting neuronal and oligodendrocyte homeostasis. Nature aging 5, S. 622 - 641 (2025)

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14.

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Garg, V.; Möbius, W.; Heinrich, R.; Ruhwedel, T.; Perera, R. P.; Scholz, P.; Ischebeck, T.; Salinas, G.; Dullin, C.; Göpfert, M. C. et al.; Engelmann, J.; Dosch, R.; Geurten, B. R. H.: Patient-specific mutation of a contact site protein Tomm70 causes neurodegeneration in a zebrafish model. Disease Models & Mechanisms (2025)

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15.

Zeitschriftenartikel

Jain, N.; Chacinska, A.; Rehling, P.: Understanding mitochondrial protein import: a revised model of the presequence translocase. Trends in Biochemical Sciences (2025)

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16.

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Weller, C.; Bartok, O.; McGinnis, C. S.; Palashati, H.; Chang, T.-G.; Malko, D.; Shmueli, M. D.; Nagao, A.; Hayoun, D.; Murayama, A. et al.; Sakaguchi, Y.; Poulis, P.; Khatib, A.; Erlanger Avigdor, B.; Gordon, S.; Cohen Shvefel, S.; Zemanek, M. J.; Nielsen, M. M.; Boura-Halfon, S.; Sagie, S.; Gumpert, N.; Yang, W.; Alexeev, D.; Kyriakidou, P.; Yao, W.; Zerbib, M.; Greenberg, P.; Benedek, G.; Litchfield, K.; Petrovich-Kopitman, E.; Nagler, A.; Oren, R.; Ben-Dor, S.; Levin, Y.; Pilpel, Y.; Rodnina, M. V.; Cox, J.; Merbl, Y.; Satpathy, A. T.; Carmi, Y.; Erhard, F.; Suzuki, T.; Buskirk, A. R.; Olweus, J.; Ruppin, E.; Schlosser, A.; Samuels, Y.: Translation dysregulation in cancer as a source for targetable antigens. Cancer Cell (2025)

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17.

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Peralta, M. A.; Negro, M. F.; Aguirre, E. N. B.; Santi, M. D.; Ortega, M. G.: Antifungal and Anti-tyrosinase Activities of Dalea Species Extracts: Differential Biological Effects and Their Correlation with Phytochemical Content via UPLC-MS/MS Profiling. Revista Brasileira de Farmacognosia (2025)

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18.

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Singh, P.; Brand, J. N.; Schärer, L.: Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate. BMC Biology 23, 87 (2025)

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19.

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Sinha, S.; Wodtke, A. M.; Saalfrank, P.: When carbon monoxide goes “upside down”: vibrational signatures of CO at NaCl(100) from ab initio molecular dynamics. Physical Chemistry Chemical Physics 27, S. 7929 - 7942 (2025)

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20.

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Domröse, T.; da Camara Silva, L.; Ropers, C.: Megahertz cycling of ultrafast structural dynamics enabled by nanosecond thermal dissipation. Applied Physics Letters 126 (12), 123104 (2025)

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21.

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Daguano Gastaldi, V.; Hindermann, M.; Wilke, J. B. H.; Ronnenberg, A.; Arinrad, S.; Kraus, S.; Wildenburg, A.-F.; Ntolkeras, A.; Provost, M. J.; Ye, L. et al.; Curto, Y.; Cortés-Silva, J.-A.; Butt, U. J.; Nave, K.-A.; Miskowiak, K. W.; Ehrenreich, H.: A comprehensive and standardized pipeline for automated profiling of higher cognition in mice. Cell Reports Methods 5 (3), 101011 (2025)

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22.

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Lin, K.-H.; Ranjan, M.; Lipstein, N.; Brose, N.; Neher, E.; Taschenberger, H.: Number and relative abundance of synaptic vesicles in functionally distinct priming states determine synaptic strength and short‐term plasticity. The Journal of Physiology (2025)

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23.

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Koss, D. J.; Todd, O.; Menon, H.; Anderson, Z.; Yang, T.; Findlay, L.; Graham, B.; Palmowski, P.; Porter, A.; Morrice, N. et al.; Walker, L.; Attems, J.; Ghanem, S. S.; El-Agnaf, O.; LeBeau, F. E.; Erskine, D.; Outeiro, T. F.: A reciprocal relationship between markers of genomic DNA damage and alpha-synuclein pathology in dementia with Lewy bodies. Molecular Neurodegeneration 20, 34 (2025)

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24.

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Singh, S.; Gapsys, V.; Aldeghi, M.; Schaller, D.; Rangwala, A. M.; White, J. B.; Bluck, J. P.; Scheen, J.; Glass, W. G.; Guo, J. et al.; Hayat, S.; de Groot, B. L.; Volkamer, A.; Christ, C. D.; Seeliger, M. A.; Chodera, J. D.: Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding. The Journal of Physical Chemistry B 129 (11), S. 2882 - 2902 (2025)

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25.

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Laurent, C.; Poncet, G.; Herskovits, T.; Alves de Sousa, R.; Le Corre, L.; Al-Azzani, M.; Koenig, A.; Birman, S.; Outeiro, T. F.; Mansuy, D. et al.; Dairou, J.: Inhibition of the Parkinson’s Disease-Related Protein DJ-1 by Endogenous Neurotoxins of the 1,2,3,4-Tetrahydroisoquinoline Family. ACS Chemical Neuroscience 16 (6), S. 1034 - 1042 (2025)

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26.

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Sasmita, A. O.; Ong, E. C.; Nazarenko, T.; Mao, S.; Komarek, L.; Thalmann, M.; Hantakova, V.; Spieth, L.; Berghoff, S. A.; Barr, H. J. et al.; Hingerl, M.; Börensen, F.; Hirrlinger, J.; Simons, M.; Stevens, B.; Depp, C.; Nave, K.-A.: Parental origin of transgene modulates amyloid-β plaque burden in the 5xFAD mouse model of Alzheimer’s disease. Neuron 113 (6), S. 838 - 846.e4 (2025)

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27.

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Blom, K.; Makarov, D. E.; Godec, A.: Hallmarks of deception in asset-exchange models. Physical Review Research 7, 013279 (2025)

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28.

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Ferrari, D. P.; Cobanoglu, O.; Sayedipour, S.; Luna, O.; Ferkel, S. A. M.; Agorku, D.; Perez, Y.; Cruz, L. J.; Albericio, F.; Trottein, F. et al.; Alves, F.; Markus, M. A.; Ramos Gomes, F.: Anti-Tumor Efficacy of a Mesothelin-Based Nanovaccine in a KPC Orthotopic Mouse Model of Pancreatic Cancer. Vaccines 13 (3), 314 (2025)

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29.

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Ainatzi, S.; Kaufmann, S. V.; Silbern, I.; Georgiev, S. V.; Lorenz, S.; Rizzoli, S. O.; Urlaub, H.: Ca²⁺-triggered (de)ubiquitination events in synapses. Molecular & Cellular Proteomics, 100946 (2025)

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30.

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Kabinger, F.; Doze, V.; Schmitzová, J.; Lidschreiber, M.; Dienemann, C.; Cramer, P.: Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr. Proceedings of the National Academy of Sciences of the United States of America 122 (10), e2419854122 (2025)

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31.

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Schaeper, J. J.; Kampshoff, C. A.; Wolf, B. J.; Roos, L.; Michanski, S.; Ruhwedel, T.; Eckermann, M.; Meyer, A.; Jeschke, M.; Wichmann, C. et al.; Moser, T.; Salditt, T.: 3D virtual histology of rodent and primate cochleae with multi-scale phase-contrast X-ray tomography. Scientific Reports 15, 7933 (2025)

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32.

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Sala, F. A.; Ditter, K.; Dybkov, O.; Urlaub, H.; Hillen, H. S.: Structural basis of Nipah virus RNA synthesis. Nature Communications 16, 2261 (2025)

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supplementary-material

33.

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Dieball, C.; Godec, A.: Perspective: Time irreversibility in systems observed at coarse resolution. The Journal of Chemical Physics 162, 090901 (2025)

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34.

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Papantonis, A.; Oudelaar, A. M.: Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome. Annual Review of Genomics and Human Genetics (2025)

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35.

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Barreira-Silva, P.; Lian, Y.; Kaufmann, S. H. E.; Moura-Alves, P.: The role of the AHR in host–pathogen interactions. Nature Reviews Immunology 25, S. 178 - 194 (2025)

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36.

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Faul, N.; Chen, S.-Y.; Lamberz, C.; Bruckner, M.; Dienemann, C.; Burg, T. P.: Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives. Journal of Structural Biology 217 (1), 108179 (2025)

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37.

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Fries, L. M.; Moll, D.; Mei, R.; Hune, T. L. K.; Elsaßer, J.; Glöggler, S.: Assessing a hyperpolarized [1-¹³C]-labeled alanine derivative enhanced via parahydrogen for in vivo studies. Journal of Magnetic Resonance Open 22, 100183 (2025)

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38.

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Furukawa, K.; Ikoma, Y.; Niino, Y.; Hiraoka, Y.; Tanaka, K.; Miyawaki, A.; Hirrlinger, J.; Matsui, K.: Dynamics of Neuronal and Astrocytic Energy Molecules in Epilepsy. Journal of Neurochemistry 169 (3), e70044 (2025)

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39.

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Kim, W.; Mirdita, M.; Karin, E. L.; Gilchrist, C.; Schweke, H.; Söding, J.; Levy, E.; Steinegger, M.: Rapid and sensitive protein complex alignment with Foldseek-Multimer. Nature Methods 22, S. 469 - 472 (2025)

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40.

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Macarrón-Palacios, V.; Hubrich, J.; do Rego Barros Fernandes Lima, M. A.; Metzendorf, N. G.; Kneilmann, S.; Trapp, M.; Acuna, C.; Patrizi, A.; D’Este, E.; Kilimann, M. W.: Paralemmin-1 controls the nanoarchitecture of the neuronal submembrane cytoskeleton. Science Advances 11 (10), eadt3724 (2025)

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41.

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Putko, P.; Romero, J. A.; Pantoja, C. F.; Zweckstetter, M.; Kazimierczuk, K.; Zawadzka-Kazimierczuk, A.: Using temperature coefficients to support resonance assignment of intrinsically disordered proteins. Journal of Biomolecular NMR 79, S. 59 - 65 (2025)

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42.

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Fendler, N. L.; Ly, J.; Welp, L. M.; Lu, D.; Schulte, F.; Urlaub, H.; Vos, S. M.: Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing. Nucleic Acids Research 53 (4), gkae1273 (2025)

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43.

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Li, Y.; Fischer, P.; Wang, M.; Zhou, Q.; Song, A.; Yuan, R.; Meng, W.; Chen, F. X.; Lührmann, R.; Lau, B. et al.; Hurt, E.; Cheng, J.: Structural insights into spliceosome fidelity: DHX35–GPATCH1- mediated rejection of aberrant splicing substrates. Cell Research (2025)

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44.

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Reilly, C. S.; Auerbach, D. J.; Zhang, L.; Guo, H.; Beck, R. D.: Quantum interference observed in state-resolved molecule-surface scattering. Science 387 (6737), S. 962 - 967 (2025)

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45.

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Meling, A.; Yamin, T.; Kandratsenka, A.; Sharoni, A.; Schäfer, T.; Rahinov, I.: Vibrational Energy Transfer upon the Collision of NO with VO₂ Thin Films across the Insulator-to-Metal Transition. The Journal of Physical Chemistry A 129 (8), S. 1993 - 2005 (2025)

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46.

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Sailer, A.-L.; Brendel, J.; Chernev, A.; König, S.; Bischler, T.; Gräfenhan, T.; Urlaub, H.; Gophna, U.; Marchfelder, A.: Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system. Frontiers in Microbiology 16, 1543464 (2025)

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47.

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Ahrens, F. M.; do Prado, P. F.V.; Hillen, H. S.; Pfannschmidt, T.: The plastid-encoded RNA polymerase of plant chloroplasts. Trends in Plant Science (2025)

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48.

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Briand, E.; Kohnke, B.; Kutzner, C.; Grubmüller, H.: Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications. Journal of Chemical Theory and Computation 21 (4), S. 1762 - 1786 (2025)

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49.

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Flores-León, M.; Outeiro, T. F.: Expanding our understanding of synucleinopathies: proteinopathy, proteinopenia, and lipidopathy. The FEBS Journal (2025)

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50.

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Singh, M.; Leddy, S. M.; Iñiguez, L. P.; Bendall, M. L.; Nixon, D. F.; Feschotte, C.: Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. Genome Biology 26, 28 (2025)

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