Publications of the Institute

Figueiredo, A. Q.; Domingos, I. F.; Carvalho, L. B.; Wisniewski, J. R.; Korentzelos, D.; Quiroga-Garza, G.; Dhir, R.; Lodeiro, C.; Capelo, J. L.; Santos, H. M.: Novel tissue markers in renal neoplasms using molar-scale quantitative proteomics via the total protein approach normalised with protein deglycase DJ-1 (PARK7). Talanta 297 (Part A), 128558 (2026)

Garriga, F.; Codina-Benaiges, J.; Yeste, M.; Llavanera, M.: Calcium homeostasis role in preserving sperm function and metabolic activity during liquid storage of pig semen. Theriogenology 249, 117638 (2026)

Albrecht, V.; Müller-Reif, J. B.; Brennsteiner, V.; Mann, M.: A Simplified Perchloric Acid Workflow With Neutralization (PCA N) for Democratizing Deep Plasma Proteomics at Population Scale. Molecular & Cellular Proteomics 24 (11), 101071 (2025)

Chen, D.; Hartout, P.; Pellizzoni, P.; Oliver, C.; Borgwardt, K.: Endowing protein language models with structural knowledge. Bioinformatics 41 (11), btaf582 (2025)

Mund, C.; Sinha, A.; Aderhold, A.; Mateska, I.; Hagag, E.; Traikov, S.; Gercken, B.; Soto, A.; Pollock, J.; Arndt, L. et al.; Woelk, M.; Werner, N.; Fodelianaki, G.; Subramanian, P.; Chung, K.-J.; Grossklaus, S.; Langner, M.; Elgendy, M.; Grinenko, T.; Wielockx, B.; Dahl, A.; Gericke, M.; Blueher, M.; Coskun, U.; Voehringer, D.; Fedorova, M.; Peitzsch, M.; Murray, P. J.; Chavakis, T.; Alexaki, V. I.: A key role of polyamine metabolism in adipose tissue homeostasis that regulates obesity. Metabolism-Clinical and Experimental 172, 156358 (2025)

Kiss, L.: Decoding ubiquitin signals inside cells. Nature Reviews Molecular Cell Biology, p. 1 - 1 (2025)

Iermak, I.; Wilson-Eisele, N. R.; Kurscheidt, K.; Loukeri, M.-J.; Basquin, J.; Bonneau, F.; Langer, L. M.; Keidel, A.; Conti, E.: Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast. Cell Reports 44 (10), 116415 (2025)

Nielsen, A. B.; Fjordside, L.; Drici, L.; Ottenheijm, M. E.; Rasmussen, C.; Henningsson, A. J.; Harritshoj, L. H.; Mann, M.; Mens, H.; Lebech, A.-M. et al.; Albrechtsen, N. J. W.: The diagnostic potential of proteomics and machine learning in Lyme neuroborreliosis. Nature Communications 16 (1), 9322 (2025)

Alpi, A. F.; Chrustowicz, J.; Sherpa, D.; Schulman, B. A.: The many faces of the GID/CTLH E3 ligase complex. Biochemical Society Transactions 53 (5), pp. 1351 - 1364 (2025)

Menon, A. A.; Gansen, B.; Mulder, H.; Neely, M. L.; Papavasileiou, P.; Salisbury, M. L.; Southern, B. D.; Hesslinger, C.; Leonard, T. B.; Meissner, F. et al.; Todd, J. L.: Mass spectrometry-based peripheral blood proteomics for biomarker discovery in idiopathic pulmonary fibrosis. Respiratory Research 26 (1), 294 (2025)

Krohn, J.-H.; Mamot, A.; Kaletta, N.; Qutbuddin, Y.; Schwille, P.: Fluorescence correlation spectroscopy for particle sizing: A notorious challenge. Biophysical Journal 124 (20), pp. 3319 - 3328 (2025)

Wallmann, G.; Skowronek, P.; Brennsteiner, V.; Lebedev, M.; Thielert, M.; Steigerwald, S.; Kotb, M.; Despard, O.; Heymann, T.; Zhou, X.-X. et al.; Strauss, M. T.; Ammar, C.; Willems, S.; Schwörer, M.; Zeng, W.-F.; Mann, M.: AlphaDIA enables DIA transfer learning for feature-free proteomics. Nature Biotechnology (2025)

Dyall-Smith, M.: Archaeal symbioses all the way down. Nature Microbiology (2025)

Thielert, M.; Villalba, A.; Brennsteiner, V.; Wahle, M.; Ammar, C.; Brunner, A.-D.; Fouque, A.; Lourenco, C.; Oshima, M.; Rachdi, L. et al.; Staels, W.; Mann, M.; Scharfmann, R.: Decoding adult murine pancreatic islet cell diversity through cell type-resolved proteomics and phosphoproteomics. Communications Biology 8 (1), 1483 (2025)

Gimpel, A. L.; Fan, B.; Chen, D.; Wölfle, L. O. D.; Horn, M.; Meng-Papaxanthos, L.; Antkowiak, P. L.; Stark, W. J.; Christen, B.; Borgwardt, K. et al.; Grass, R. N.: Predicting sequence-specific amplification efficiency in multi-template PCR with deep learning. Nature Communications 16, 9187 (2025)

Sachweh, J.; Börmel, M.; Klumpe, S.; Becker, A.; Taniguchi, R.; Kubańska, M. A.; Pintschovius, V.; Kaindl, E.; Plitzko, J. M.; Wilfling, F. et al.; Beck, M.; Hampoelz, B.: The small GTPase Ran defines nuclear pore complex asymmetry. Cell 188 (21), pp. 5931 - 5946 (2025)

Shenkman, M.; Ogen-Shtern, N.; Patel, C.; Saad, H.; Groisman, B.; Pasmanik-Chor, M.; Schermann, S. M.; Körner, R.; Lederkremer, G. Z.: Oligosaccharyltransferase Is Involved in Targeting to ER-Associated Degradation. Cells 14 (20), 1593 (2025)

Tomaz da Silva, P.; Karollus, A.; Hingerl, J.; Galindez, G. S. T.; Wagner, N.; Hernandez-Alias, X.; Incarnato, D.; Gagneur, J.: Nucleotide dependency analysis of genomic language models detects functional elements. Nature Genetics 57 (10), pp. 2589 - 2602 (2025)

Guinart, A.; Qutbuddin, Y.; Ryabchun, A.; Krohn, J.-H.; Schwille, P.; Feringa, B. L.: Elucidating the physicochemical processes of light-activated rotary motors embedded in lipid membranes. Chem 11 (10), 102574 (2025)

Sewald, L.; Molke, N.; Tabak, W. W. A.; Haak, A.; Najdzion, M.; Geiss‐Friedlander, R.; Hellerschmied, D.; Huber, R.; Kaiser, M.: A PhotocagedN‐Phosphonopiperidinone as a Selective Photo‐Cleavable DPP8/9 Inhibitor. ChemBioChem: A European Journal of Chemical Biology 26 (19), e202500558 (2025)