Student Publications

Krimmel, M.; Hartout, P.; Borgwardt, K.; Chen, D.: PolyGraph Discrepancy: A Classifier-Based Metric for Graph Generation. arXiv (2026)

Larrea-Sebal, A.; Dai, C.; Brenes, A. J.; Korff, K.; Neely, B. A.; Geyer, P. E.; Dagley, L. F.; Unwin, R. D.; Naba, A.; MacCoss, M. J. et al.; Guo, T.; Deutsch, E. W.; Martin, C.; Schwenk, J. M.; Perez-Riverol, Y.: Blood proteomics: Insights from public data. Genome Biology 27, 81 (2026)

Weiss, C. A. M.; Brown, L. A.; Miranda, L.; Pellizzoni, P.; Steigerwald, S.; Remmert, K.; Hernandez, J. M.; Borgwardt, K.; Kleiner, D. E.; Ben-Moshe, S. et al.; Rosenberger, F. A.; Porat-Shliom, N.; Mann, M.: Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture. Nature Metabolism 8, pp. 741 - 756 (2026)

Kurscheidt, K.; Theunissen, S.; Pasquali, N.; Becker, K.; Boehm, V.; Conti, E.; Gehring, N. H.: Composite SMG5-SMG6 PIN domain formation is essential for NMD. Nature Communications 17, 1934 (2026)

Kaech, B.; Wyss, L.; Borgwardt, K.; Grassow, G.: Refine Drugs, Don’t Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery. 14th International Conference on Learning Representations (ICLR 2026) (2026)

Pellizzoni, P.; Schulz, T. H.; Borgwardt, K.: Gelato: Graph Edit Distance via Autoregressive Neural Combinatorial Optimization. 14th International Conference on Learning Representations (ICLR 2026) (2026)

von Scheidt, M.; Adkar, S. S.; Krefting, J.; Hoermann, G.; Meggendorfer, M.; Bauer, S.; Mitchell, S.; Pugach, I.; Friess, C.; Ma, A. et al.; Hao, K.; Steigerwald, S.; Wahle, M.; Kessler, T.; Schwab, M.; Voll, F.; Mokry, M.; Sofokleous, C.; Palm, K. C. A.; Bongiovanni, D.; Fleig, J.; Oldenbuettel, L.; Chen, Z.; Hecker, J. S.; Bassermann, F.; Maegdefessel, L.; Graw, M.; Ruusalepp, A.; Hilgendorf, I.; Leuschner, F.; Sager, H. B.; Heimlich, J. B.; Koenig, W.; Cremer, S.; Leistner, D. M.; Abplanalp, W. T.; Dimmeler, S.; Zeiher, A. M.; van der Laan, S. W.; Pasterkamp, G.; Braun, C.; Jaiswal, S.; Kovacic, J. C.; Kern, W.; Haferlach, C.; Mann, M.; Cassese, S.; Kastrati, A.; Haferlach, T.; Leeper, N. J.; Björkegren, J. L. M.; Schunkert, H.: Clonal haematopoiesis of indeterminate potential and mortality in coronary artery disease. European Heart Journal 47 (4), ehaf602, pp. 453 - 469 (2026)

Rawat, A.; Vu, D. T.; Erbacher, C.; Stigloher, C.; Uceyler, N.; Metousis, A.; Mann, M.; Briese, M.; Sendtner, M.: Proteomic analysis of isolated nerve terminals from NaV1.9 knockout mice reveals pathways relevant for pain perception. Pain 166 (12), pp. 770 - 787 (2025)

Vorontsov, I. E.; Kozin, I.; Abramov, S.; Boytsov, A.; Jolma, A.; Albu, M.; Ambrosini, G.; Faltejskova, K.; Gralak, A. J.; Gryzunov, N. et al.; Inukai, S.; Kolmykov, S.; Kravchenko, P.; Kribelbauer-Swietek, J. F.; Laverty, K. U.; Nozdrin, V.; Patel, Z. M.; Penzar, D.; Plescher, M.-L.; Pour, S. E.; Razavi, R.; Yang, A. W. H.; Yevshin, I.; Zinkevich, A.; Weirauch, M. T.; Bucher, P.; Deplancke, B.; Fornes, O.; Grau, J.; Grosse, I.; Kolpakov, F. A.; Barazandeh, M.; Brechalov, A.; Deng, Z.; Fathi, A.; Hu, C.; Lambert, S. A.; Salnikov, M.; Yellan, I.; Zheng, H.; Meshcheryakov, G.; Nikonov, M.; Kamenets, V.; Vlasov, A.; Hernandez-Corchado, A.; Najafabadi, H. S.; Morris, Q.; Chen, X.; Makeev, V. J.; Hughes, T. R.; Kulakovskiy, I. V.: Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors. Communications Biology 8 (1), 1545 (2025)

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

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)

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)

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)

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)

Unterauer, E. M.; Schentarra, E.-M.; Pachmayr, I.; Tashrin, T.; Kwon, J.; Strauss, S.; Jevdokimenko, K.; Kowalewski, R.; Opazo, F.; Fornasiero, E. F. et al.; Masullo, L. A.; Jungmann, R.: Left-handed DNA for efficient highly multiplexed imaging at single-protein resolution. Nature Communications 16, 8773 (2025)

Heaton, G. R.; Li, X.; Li, X.; Zhou, X.; Zhang, Y.; Vu, D. T.; Oeller, M.; Karayel, O.; Hoang, Q. Q.; Kars, M. E. et al.; Kamath, N.; Wang, M.; Tarassishin, L.; Mann, M.; Peter, I.; Yue, Z.: Targeting specific kinase substrates rescues increased colitis severity induced by the Crohn's disease-linked LRRK2-N2081D variant. The Journal of Clinical Investigation 135 (19), e190017 (2025)

Masullo, L. A.; Almahayni, K.; Pachmayr, I.; Honsa, M.; Heinze, L.; Fritsche, S.; Grabmayr, H.; Jungmann, R.; Möckl, L.: Ångström-resolution imaging of cell-surface glycans. Nature Nanotechnology 20, pp. 1457 - 1463 (2025)

Rodschinka, G.; Forcelloni, S.; Kühner, F. M.; Wani, S.; Riemenschneider, H.; Edbauer, D.; Behrens, A.; Nedialkova, D. D.: Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control. Nature Structural & Molecular Biology 32, pp. 1932 - 1946 (2025)

Yuste-Checa, P.; Carvajal, A. I.; Mi, C.; Paatz, S.; Hartl, F.-U.; Bracher, A.: Structural analyses define the molecular basis of clusterin chaperone function. Nature Structural & Molecular Biology 32, pp. 2035 - 2045 (2025)