Publications of the Institute

Bone, R. A.; Lowndes, M. P.; Raineri, S.; Riveiro, A.; Lundregan, S. L.; Dall, M.; Sulek, K.; Romero, J. A. H.; Malzard, L.; Koigi, S. et al.; Heckenbach, I. J.; Solis-Mezarino, V.; Voelker-Albert, M.; Vasilopoulou, C.; Meier, F.; Trusina, A.; Mann, M.; Nielsen, M.; Treebak, J. T.; Brickman, J. M.: Altering metabolism programs cell identity via NAD+-dependent deacetylation. The EMBO Journal 44 (11), pp. 3056 - 3084 (2025)

Skowronek, P.; Wallmann, G.; Wahle, M.; Willems, S.; Mann, M.: An accessible workflow for high-sensitivity proteomics using parallel accumulation–serial fragmentation (PASEF). Nature Protocols 20, pp. 1700 - 1729 (2025)

Olabisi-Adeniyi, E.; McAlister, J. A.; Ferretti, D.; Cox, J.; Geddes-McAlister, J.: ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus. Journal of Proteome Research 24 (6), pp. 2698 - 2708 (2025)

Zhou, H.; Hutchings, J.; Shiozaki, M.; Zhao, X.; Doolittle, L. K.; Yang, S.; Yan, R.; Jean, N.; Riggi, M.; Yu, Z. et al.; Villa, E.; Rosen, M. K.: Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America 122 (19), e2426449122 (2025)

Loreau, V.; Koolhaas, W. H.; Chan, E. H.; De Boissier, P.; Brouilly, N.; Avosani, S.; Sane, A.; Pitaval, C.; Reiter, S.; Luis, N. M. et al.; Mangeol, P.; von Philipsborn, A. C.; Rupprecht, J.-F.; Goerlich, D.; Habermann, B. H.; Schnorrer, F.: Titin-dependent biomechanical feedback tailors sarcomeres to specialized muscle functions in insects. Science Advances 11 (19), eads8716 (2025)

Fu, J.; Ji, X.; Chen, D.; Hu, G.; Li, S.; Feng, X.: AdvMixUp: Adversarial MixUp Regularization for Deep Learning. IEEE Transactions on Neural Networks and Learning Systems (2025)

Masullo, L. A.; Kowalewski, R.; Honsa, M.; Heinze, L.; Xu, S.; Steen, P. R.; Grabmayr, H.; Baudrexel, I.; Reinhardt, S. C. M.; Perovic, A. et al.; Kwon, J.; Oxley, E. P.; Dickins, R. A.; Bastings, M. M. C.; Parish, I. A.; Jungmann, R.: Spatial and stoichiometric in situ analysis of biomolecular oligomerization at single-protein resolution. Nature Communications 16 (1), 4202 (2025)

Ogger, P. P.; Murray, P. J.: Dissecting inflammation in the immunemetabolomic era. Cellular and Molecular Life Sciences 82, 182 (2025)

Xu, R.; Li, K.; Chen, A.; Chen, Y.; Sheng, R.; Chen, C.; Qin, H.; Zhang, W.; Liu, Y.; Rodriguez, H. V. et al.; Kanaparti, D.; Zhu, B.: Responses of Soil Microbial Communities to Abandoned Paddy Fields With Different Fertilization Histories. Land Degradation & Development 36 (6), pp. 1820 - 1833 (2025)

Perez-Riverol, Y.; Bittremieux, W.; Noble, W. S.; Martens, L.; Bilbao, A.; Lazear, M. R.; Gruening, B.; Katz, D. S.; MacCoss, M. J.; Dai, C. et al.; Eng, J. K.; Bouwmeester, R.; Shortreed, M. R.; Audain, E.; Sachsenberg, T.; Van Goey, J.; Wallmann, G.; Wen, B.; Kall, L.; Fondrie, W. E.: Open-Source and FAIR Research Software for Proteomics. Journal of Proteome Research 24 (5), pp. 2222 - 2234 (2025)

Pesch, G.; Piseddu, I.; Gaertig, J.; Kramer, N.; Kramer, R.; Schulz, T. U.; Zwiebel, M.; Ledderose, S.; Retzlaff, J.; Eckstein, M. et al.; Schett, G.; Kammerbauer, C.; Schmitt, C.; Kumbrink, J.; Erdmann, M.; Kruis, W.; Dougan, M.; Mayerle, J.; French, L. E.; Vera, J.; Nordmann, T. M.; Mann, M.; Klauschen, F.; Anz, D.; Heinzerling, L.: Deep immune phenotyping reveals distinct immunopathogenesis in checkpoint inhibitor-induced colitis compared to ulcerative colitis. Cancer Immunology Research (2025)

Klumpe, S.; Senti, K. A.; Beck, F.; Sachweh, J.; Hampoelz, B.; Ronchi, P.; Oorschot, V.; Brandstetter, M.; Yeroslaviz, A.; Briggs, J. A. G. et al.; Brennecke, J.; Beck, M.; Plitzko, J. M.: In-cell structure and snapshots of copia retrotransposons in intact tissue by cryoelectron tomography. Cell 188 (8), pp. 2094 - 2110.e18 (2025)

Klumpe, S.; Senti, K. A.; Beck, F.; Sachweh, J.; Hampoelz, B.; Ronchi, P.; Oorschot, V.; Brandstetter, M.; Yeroslaviz, A.; Briggs, J. A. G. et al.; Brennecke, J.; Beck, M.; Plitzko, J. M.: In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET. Cell 188 (8), pp. 2094 - 2110 (2025)

Cimen, C.; Siemer, P.; Sattler, J.; Voss, A.; Berends, M. S.; Hamprecht, A.: Performance of disk diffusion, gradient test, and VITEK 2 for carbapenem susceptibility testing in OXA-48-like carbapenemase-producing Enterobacterales: a comparative study. Journal of Clinical Microbiology 63 (5), e01893-24 (2025)

Jeong, T. Y.; Yoon, D. E.; Kim, S. P.; Yang, J.; Lim, S.-Y.; Ok, S.; Ju, S.; Park, J.; Lee, S. B.; Park, S.-J. et al.; Kim, S.; Lee, H.; Lee, D.; Kang, S. K.; Lee, S. E.; Kim, H. S.; Seong, J. K.; Kim, K.: An innovative approach using CRISPR-ribonucleoprotein packaged in virus-like particles to generate genetically engineered mouse models. Nature Communications 16, 3451 (2025)

Kiss, L.; James, L. C.; Schulman, B. A.: UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains. Molecular Cell 85 (7), pp. 1467 - 1476 (2025)

Sewald, L.; Tabak, W. W. A.; Fehr, L.; Zolg, S.; Najdzion, M.; Verhoef, C. J. A.; Podlesainski, D.; Geiss-Friedlander, R.; Lammens, A.; Kaschani, F. et al.; Hellerschmied, D.; Huber, R.; Kaiser, M.: Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors. Nature Communications 16 (1), 3208 (2025)

Stacey, J. C. V.; Hrebík, D.; Nand, E.; Shetty, S. D.; Qu, K.; Boicu, M.; Anders-Össwein, M.; Uchil, P. D.; Dick, R. A.; Mothes, W. et al.; Kräusslich, H.-G.; Müller, B.; Briggs, J. A. G.: The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation. Nature 640 (8057), pp. 258 - 264 (2025)

Archer, D.; Pérez-Muñoz, M. E.; Tollenaar, S.; Veniamin, S.; Hotte, N.; Cheng, C. C.; Nieves, K.; Oh, J.-H.; Morceli, L.; Muncner, S. et al.; Barreda, D. R.; Krishnamoorthy, G.; Power, C.; van Pijkeren, J.-P.; Walter, J.: A secondary metabolite of Limosilactobacillus reuteri R2lc drives strain-specific pathology in a spontaneous mouse model of multiple sclerosis. Cell Reports 44 (3), 115321 (2025)

Del-Pozo-Rodriguez, J.; Tilly, P.; Lecat, R.; Vaca, H. R.; Mosser, L.; Brivio, E.; Balla, T.; Gomes, M. V.; Ramos-Morales, E.; Schwaller, N. et al.; Salinas-Giegé, T.; VanNoy, G.; England, E. M.; Kern Lovgren, A.; O’Leary, M.; Chopra, M.; Ojeda, N. M.; Toosi, M. B.; Eslahi, A.; Alerasool, M.; Mojarrad, M.; Pais, L. S.; Yeh, R. C.; Gable, D. L.; Hashem, M. O.; Abdulwahab, F.; Rakiz Alqurashi, M.; Sbeih, L. Z.; Adas Blanco, O. A.; Khater, R. A.; Oprea, G.; Rad, A.; Alzaidan, H.; Aldhalaan, H.; Tous, E.; Alsagheir, A.; Alowain, M.; Tamim, A.; Alfayez, K.; Alhashem, A.; Alnuzha, A.; Kamel, M.; Al-Awam, B. S.; Elnaggar, W.; Almenabawy, N.; O'Donnell-Luria, A.; Neil, J. E.; Gleeson, J. G.; Walsh, C. A.; Alkuraya, F. S.; AlAbdi, L.; Elkhateeb, N.; Selim, L.; Srivastava, S.; Nedialkova, D. D.; Drouard, L.; Romier, C.; Bayam, E.; Godin, J. D.: ADAT3variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration. Brain (2025)