Publications of the Institute

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)

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)

Carvajal-Patiño, J. G.; Mallet, V.; Becerra, D.; Vasquez, L. F. N.; Oliver, C.; Waldispühl, J.: RNAmigos2: Accelerated structure-based RNA virtual screening with deep graph learning. Nature Communications 16 (1), 2799 (2025)

Pousa, S.; Ramos-Bermudez, P. E.; Besada, V.; Cabrales-Rico, A.; Cruz, O. G.; Garay, H. E.; Rodriguez-Mallon, A.; Zettl, K.; Wiśniewski, J. R.; Gonzalez, L. J.: Characterization by LC-MS/MS analysis of KLH vaccine conjugated with a tick antigen peptide. Analyst 150 (6), pp. 1091 - 1102 (2025)

Unterauer, E.; Schentarra, E.-M.; Jevdokimenko, K.; Boushehri, S. S.; Marr, C.; Opazo, F.; Fornasiero, E. F.; Jungmann, R.: Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons. Star Protocols 6 (1), 103637 (2025)

Becker, M.; Kälin, S.; Neubig, A. H.; Lauber, M.; Opaleva, D.; Hipp, H.; Salb, V. K.; Ott, V. B.; Legutko, B.; Kälin, R. E. et al.; Hippich, M.; Scherm, M. G.; Nascimento, L. F. R.; Serr, I.; Hosp, F.; Nikolaev, A.; Mohebiany, A.; Krueger, M.; Flachmeyer, B.; Pfaffl, M. W.; Haase, B.; Yi, C. X.; Dietzen, S.; Bopp, T.; Woods, S. C.; Waisman, A.; Weigmann, B.; Mann, M.; Tschöp, M. H.; Daniel, C.: Regulatory T cells in the mouse hypothalamus control immune activation and ameliorate metabolic impairments in high-calorie environments. Nature Communications 16, 2744 (2025)

Gupta, M.; Kurth, T.; Heinemann, F.; Schwille, P.; Keil, S.; Knopf, F.; Brand, M.: Fine-tuning of Fgf8 morphogen gradient by heparan sulfate proteoglycans in the extracellular matrix. Biophysical Journal 124 (6), pp. 996 - 1010 (2025)

Jerala, R.; Vidmar, S.; Šmidlehner, T.; Aupič, J.; Strmšek, Ž.; Ljubetič, A.; Xiao, F.; Hu, G.; Liu, C.; Beck, F. et al.; Erdmann, P. S.: Beyond Dimerization: Harnessing Tetrameric Coiled‐Coils for Nanostructure Assembly. Angewandte Chemie International Edition 64 (12), e202422075 (2025)