Alliance Research
The seven Alliance institutions work jointly on flagship projects, promoting synergies and exchanging expertise. Their research focuses on the following strategic areas:
- Genomic Health Research, particularly in the field of cancer research
- Synthetic Immunology, which makes it possible to precisely analyze and modify immune processes at the cellular level
- Interinstitutional Early Clinical Trial Units (I-ECTU) to foster collaboration between academia and industry, especially in early-phase clinical studies
- Cardio-Vascular Science, which focuses on cardiovascular diseases
- Multi-Omics Spatially Resolved Analyses, offering new insights into cellular mechanisms through molecular tissue analysis
- AI in Health, integrating AI methods with biomedical data to accelerate the translation of research into clinical practice
MULTI-SPACE is an interinstitutional technology platform housing state-of-the art instrumentations, currently mainly located at both the EMBL Heidelberg and BioQuant of Heidelberg University.
The focus areas of this project are genomic cancer research, research into the phenotypic effects of the composition of the human microbiome, and the field of infection biology in the context of dynamic mutation development of the SARS-CoV-2 and other pathogenic genomes, including new technology development in these areas.
Early Clinical Trials are of central importance in the development and implementation of current preclinical concepts in precision medicine, e.g., in the application of innovative drugs, RNA- or cell-based therapies, new drugs or brain stimulation treatments for mental disorders, and in the development of low-invasive diagnostics.
Ploidy and Organ Physiology; RNA Splicing in Cardiac Disease; Mechanisms of Cardiac Regeneration and Repair; AngioRhytms in Health and Disease.
Innovative methods of analysis based on artificial intelligence and machine learning have found their way into all research areas and are already enabling transformative developments in health research.
Synthetic immunology allows to analyze and modify central processes of immune recognition with highest precision at the single cell level. Using DNA nanotechnology and microfluidics, precision and high-throughput tools for characterizing and programming immune cells are being developed.
Microfluidics is an emerging field and is finding use in various disciplines. These range from understanding flow mechanisms, to the generation of synthetic cells with droplet-based microfluidics, continuous flow microfluidics to complex organ-on-a-chip models.
The Alliance promotes community and capacity building for research infrastructure scientists working in core facilities and technology platforms at Alliance institutions.
A successful joint technology development is part of the planned expanded collaboration between the two electron microscopy facilities on the Heidelberg campus.
The Zeiss Arivis Vision 4D software now provides a variety of tools for creating pipelines for cell and particle tracking in 3D microscopy - the Alliance supported its use on campus.
The Alliance contributes to the development of broad patient-tailored T cell monitoring and TCR discoveries for therapeutic purposes.
In-depth investigation of the consequences of the alterations in the NAD-ome may open novel avenues for the identification of biomarkers and personalized treatment options for Glioblastoma patients.
A standardized method for testing the effects of pesticides on mosquito larvae reveals new insights into resistance patterns and identifies potential strategies for controlling resistant populations.
A new comprehensive dipeptide-metabolome quantification method via UPLC-MS/MS
Publications
The interinstitutional efforts across the Alliance have resulted in a diverse set of publications. From groundbreaking discoveries to innovative methodologies, these papers give a glimpse into our commitment to advancing research and technology development in the life sciences, with the goal of continuously improving human health and healthcare. Explore a selection of Alliance preprints and publications below.
Babin-Ebell Gonçalves, A., Mao, Y., Baljkas, T., Wiedmann, F., Eis, L., Pilz, F., Winkler, M., Kürschner-Zacharias, S. W., Hoffarth, M., Funaya, C., Shahidi, R., Géraud, C., Wu, C.-C., Schmidt, C., Goerdt, S., Reiners-Koch, P.-S., & Singhal, M. (2025). A perfusion-independent high-throughput method to isolate liver sinusoidal endothelial cells. Communications Biology, 8(1), 22. https://doi.org/10.1038/s42003-025-07458-5
Bencun, M., Spreyer, L., Boileau, E., Eschenbach, J., Frey, N., Dieterich, C., & Völkers, M. (2025). A novel uORF regulates folliculin to promote cell growth and lysosomal biogenesis during cardiac stress. Scientific Reports, 15(1), 1–15. https://doi.org/10.1038/s41598-025-87107-3
Butavand, D. R., Nagel, J., Feld, G. B., & Steib, S. (2025). High intensity exercise before sleep boosts memory encoding the next morning. BioRxiv, 2025.01.20.633862. https://doi.org/10.1101/2025.01.20.633862
Chih, Y.-C., Dietsch, A. C., Koopmann, P., Ma, X., Agardy, D. A., Zhao, B., de Roia, A., Kourtesakis, A., Kilian, M., Krämer, C., Suwala, A. K., Stenzinger, M., Boenig, H., Blum, A., Pienkowski, V. M., Aman, K., Becker, J. P., Feldmann, H., Bunse, T., … Bunse, L. (2025). Vaccine-induced T cell receptor T cell therapy targeting a glioblastoma stemness antigen. Nature Communications, 16(1), 1–16. https://doi.org/10.1038/s41467-025-56547-w
Lim, B., Kamal, A., Gomez Ramos, B., Adrian Segarra, J. M., Ibarra, I. L., Dignas, L., Kindinger, T., Volz, K., Rahbari, M., Rahbari, N., Poisel, E., Kafetzopoulou, K., Böse, L., Breinig, M., Heide, D., Gallage, S., Barragan Avila, J. E., Wiethoff, H., Berest, I., … Mall, M. (2025). Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis. Nature Genetics, 13, 1–12. https://doi.org/10.1038/s41588-025-02081-w
Lutz, R., Poos, A. M., Solé-Boldo, L., John, L., Wagner, J., Prokoph, N., Baertsch, M. A., Vonficht, D., Palit, S., Brobeil, A., Mechtersheimer, G., Hildenbrand, N., Hemmer, S., Steiger, S., Horn, S., Pepke, W., Spranz, D. M., Rehnitz, C., Sant, P., … Weinhold, N. (2025). Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma. Science Immunology, 10(104), eadp6667. https://doi.org/10.1126/SCIIMMUNOL.ADP6667
Nalin, A., Fulman, N., Wilke, E. C., Ludwig, C., Zipf, A., Lantieri, C., Vignali, V., & Simone, A. (2025). Evaluation of accessibility disparities in urban areas during disruptive events based on transit real data. Communications in Transportation Research, 5, 100160. https://doi.org/10.1016/j.commtr.2024.100160
Nooij, S., Plomp, N., Sanders, I. M. J. G., Schout, L., van der Meulen, A. E., Terveer, E. M., Norman, J. M., Karcher, N., Larralde, M. F., Vossen, R. H. A. M., Kloet, S. L., Faber, K. N., Harmsen, H. J. M., Zeller, G. F., Kuijper, E. J., Smits, W. K., & Ducarmon, Q. R. (2025). Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status. Nature Communications, 16(1), 1–14. https://doi.org/10.1038/s41467-025-56449-x
Potel, C. M., Burtscher, M. L., Garrido-Rodriguez, M., Brauer-Nikonow, A., Becher, I., le Sueur, C., Typas, A., Zimmermann, M., & Savitski, M. M. (2025). Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco). Nature Structural & Molecular Biology 2025, 1–16. https://doi.org/10.1038/s41594-025-01485-w
Roberti, M. P., Charoentong, P., Lyu, Y., Meyer, M., Eichmüller, S. B., Schmidt, P., Momburg, F., Cetin, M., Hartmann, F., Valous, N. A., Stenzinger, A., Michel, L., Lichter, P., Schneeweiss, A., Thewes, V., Fremd, C., Zörnig, I., & Jäger, D. (2025). Isolation of a tumor neoantigen specific CD8+ TCR from a skin biopsy of a vaccination site. OncoImmunology, 14(1). https://doi.org/10.1080/2162402X.2025.2457793
Sachse, M., & Stellos, K. (2025). Synbiotics and Gut-Heart Axis in Cardiometabolic Disease. JACC: Basic to Translational Science, 10(1), 16–19. https://doi.org/10.1016/J.JACBTS.2024.11.008
Thiel, V., Renders, S., Panten, J., Dross, N., Bauer, K., Azorin, D., Henriques, V., Vogel, V., Klein, C., Leppä, A.-M., Barriuso Ortega, I., Schwickert, J., Ourailidis, I., Mochayedi, J., Mallm, J.-P., Müller-Tidow, C., Monyer, H., Neoptolemos, J., Hackert, T., … Trumpp, A. (2025). Characterization of single neurons reprogrammed by pancreatic cancer. Nature. https://doi.org/10.1038/s41586-025-08735-3
Afting, C., Walther, T., Drozdowski, O. M., Schlagheck, C., Schwarz, U. S., Wittbrodt, J., & Göpfrich, K. (2024). DNA microbeads for spatio-temporally controlled morphogen release within organoids. Nature Nanotechnology, 19(12), 1849–1857. https://doi.org/10.1038/s41565-024-01779-y
Amponsah-Offeh, M., Tual-Chalot, S., & Stellos, K. (2024). Repurposing of an antiasthmatic drug may reduce NETosis and myocardial ischaemia/reperfusion injury. European Heart Journal, 45(18), 1681–1683. https://doi.org/10.1093/eurheartj/ehae201
Baghai Arassi, M., Karcher, N., Mastrorilli, E., Gross, M., Brauer-Nikonow, A., Hackett, R., Czock, D., Tönshoff, B., Zeller, G., & Zimmermann, M. (2024). Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants. BioRxiv. https://doi.org/10.1101/2024.03.28.586928
Barwig, C., Sonn, A., Spratte, T., Mishra, A., Blasco, E., Selhuber-Unkel, C., & Pashapour, S. (2024). Two-photon direct laser writing of pNIPAM actuators in microchannels for dynamic microfluidics. Advanced Intelligent Systems, 6(7), 2300829. https://doi.org/10.1002/aisy.202300829
Boverhoff, D., Kool, J., Pijnacker, R., Ducarmon, Q. R., Zeller, G., Shetty, S., Sie, S., Mulder, A. C., van der Klis, F., Franz, E., Mughini-Gras, L., van Baarle, D., & Fuentes, S. (2024). Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands. Cell Reports, 43(9), 114729. https://doi.org/10.1016/j.celrep.2024.114729
Bunse, L., Michel, J., Sanghvi, K., Rosenbauer, J., Humbs, L., Grudzenski-Theis, S., Sachs, V., Jähne, K., Degenhardt, K., Frölich, L., Herms, J., Fatar, M., & Platten, M. (2024). Type-I interferon drives T-cell responses to amyloid-beta in the central nervous system. Research Square. https://doi.org/10.21203/rs.3.rs-5140494/v1
Burtscher, M. L., Gade, S., Garrido-Rodriguez, M., Rutkowska, A., Werner, T., Eberl, H. C., Petretich, M., Knopf, N., Zirngibl, K., Grandi, P., Bergamini, G., Bantscheff, M., Fälth-Savitski, M., & Saez-Rodriguez, J. (2024). Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Molecular Systems Biology, 20(4), 458-474. https://doi.org/10.1038/s44320-024-00025-w
Castro, I. de, Schuster, L., Patiño-Gomez, C., Glavas, D., Udupa, A., Vázquez, M. R., Symens, T., Tulcan, G., Heinze, J., las, H. J. de, Reinhardt, R., Trojanowski, J., Harz, H., Stumberger, G., Leonhardt, H., Schirmer, E., Saka, S., Laketa, V., & Lusic, M. (2024). Nucleoporin Nup153 docks the splicing machinery to the nuclear pore for efficient mRNA processing. BioRxiv. https://doi.org/10.1101/2024.09.30.615666
Cirrincione, A. M., Poos, A. M., Ziccheddu, B., Kaddoura, M., Baertsch, M. A., Maclachlan, K., Chojnacka, M., Diamond, B., John, L., Reichert, P., Huhn, S., Blaney, P., Gagler, D., Rippe, K., Zhang, Y. M., Dogan, A., Lesokhin, A. M., Davies, F., Goldschmidt, H., … Maura, F. (2024). The biological and clinical impact of deletions before and after large chromosomal gains in multiple myeloma. Blood, 144(7), 771–783. https://doi.org/10.1182/blood.2024024299
Ciurli, A., Mohammed, Y., Ammon, C., Derks, R. J. E., Olivier-Jimenez, D., Ducarmon, Q. R., Slingerland, M., Neefjes, J., & Giera, M. (2024). Spatially and temporally resolved metabolome of the human oral cavity. iScience, 27(2). https://doi.org/10.1016/j.isci.2024.108884
Clarke, B., Holtkamp, E., Öztürk, H., Mück, M., Wahlberg, M., Meyer, K., Munzlinger, F., Brechtmann, F., Hölzlwimmer, F. R., Lindner, J., Chen, Z., Gagneur, J., & Stegle, O. (2024). Integration of variant annotations using deep set networks boosts rare variant association testing. Nature Genetics, 56(10), 2271–2280. https://doi.org/10.1038/s41588-024-01919-z
Constanty, F., Wu, B., Wei, K.-H., Lin, I.-T., Dallmann, J., Guenther, S., Lautenschlaeger, T., Priya, R., Lai, S.-L., Stainier, D. Y. R., & Beisaw, A. (2024). Border-zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration. BioRxiv, 2024.03.12.584570. https://doi.org/10.1101/2024.03.12.584570
Cosenza, M. R., Gaiatto, A., Erarslan Uysal, B., Andrades Delgado, Á., Sautter, N. L., Jendrusch, M. A., Zumalave Duro, S., Rausch, T., Halavatyi, A., Geissen, E.-M., Hasenfeld, P., Cortes-Ciriano, I., Kulozik, A., Pepperkok, R., & Korbel, J. O. (2024). Origins of de novo chromosome rearrangements unveiled by coupled imaging and genomics. BioRxiv. https://doi.org/10.1101/2024.08.15.607890
Costea, J., Rauwolf, K. K., Zafferani, P., Rausch, T., Mathioudaki, A., Zaugg, J., Schrappe, M., Eckert, C., Escherich, G., Bourquin, J. P., Bornhauser, B., Kulozik, A. E., & Korbel, J. O. (2024). Role of stem-like cells in chemotherapy resistance and relapse in pediatric T cell acute lymphoblastic leukemia. BioRxiv. https://doi.org/10.1101/2024.06.24.600391
Ducarmon, Q. R., Karcher, N., Tytgat, H. L. P., Delannoy-Bruno, O., Pekel, S., Springer, F., Schudoma, C., & Zeller, G. (2024). Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman. BioRxiv, 2024.01.08.574624. https://doi.org/10.1101/2024.01.08.574624
Ducarmon, Q., Grundler, F., Giannopoulou, C., Loumé, A., Karcher, N., Larralde, M., Romano, S., MacArthur, M., Mitchell, S., Toledo, F. W. de, Zeller, G., & Mesnage, R. (2024). Long-term fasting remodels gut microbial metabolism and host metabolism. BioRxiv, 2024.04.19.590209. https://doi.org/10.1101/2024.04.19.590209
Dupouy, B., Cotos, L., Binder, A., Slavikova, L., Rottmann, M., Mäser, P., Jacquemin, D., Ganter, M., Davioud-Charvet, E., & Elhabiri, M. (2024). Click Coupling of Flavylium Dyes with Plasmodione Analogues: Towards New Redox-Sensitive Pro-Fluorophores. Chemistry : A European Journal, e202403691. https://doi.org/10.1002/chem.202403691
Foltyn-Dumitru, M., Mahmutoglu, M. A., Brugnara, G., Kessler, T., Sahm, F., Wick, W., Heiland, S., Bendszus, M., Vollmuth, P., & Schell, M. (2024). Shape matters: Unsupervised exploration of IDH-wildtype glioma imaging survival predictors. European Radiology. https://doi.org/10.1007/s00330-024-11042-6
Fulman, N., Grinblat, Y., & Benenson, I. (2024). A project-based view of urban dynamics: Analyzing ‘leapfrogging’ and fringe development in Israel. Cities, 148, 104908. https://doi.org/10.1016/J.CITIES.2024.104908
Fulman, N., Memduhoğlu, A., & Zipf , A. (2024). Distortions in Judged Spatial Relations in Large Language Models. Professional Geographer, 703–711. https://doi.org/10.1080/00330124.2024.2372792
Gandara, L., Jacoby, R., Laurent, F., Spatuzzi, M., Vlachopoulos, N., Borst, N. O., Ekmen, G., Potel, C. M., Garrido-Rodriguez, M., Böhmert, A. L., Misunou, N., Bartmanski, B. J., Li, X. C., Kutra, D., Hériché, J. K., Tischer, C., Zimmermann-Kogadeeva, M., Ingham, V. A., Savitski, M. M., … Crocker, J. (2024). Pervasive sublethal effects of agrochemicals on insects at environmentally relevant concentrations. Science, 386(6720), 446–453. https://doi.org/10.1126/science.ado0251
Georgiopoulos, G., Athanasopoulos, S., Mavraganis, G., Konstantaki, C., Papaioannou, M., Delialis, D., Angelidakis, L., Sachse, M., Papoutsis, D., Cavlan, B., Tual-Chalot, S., Zervas, G., Sopova, K., Mitrakou, A., Stellos, K., & Stamatelopoulos, K. (2024). Incremental value of blood-based markers of liver fibrosis in cardiovascular risk stratification. Journal of Clinical Endocrinology & Metabolism. https://doi.org/10.1210/clinem/dgae619
Göpfrich, K., Platten, M., Frischknecht, F., & Fackler, O. T. (2024). Bottom-up synthetic immunology. Nature Nanotechnology, 19(11), 1587–1596. https://doi.org/10.1038/s41565-024-01744-9
Grimes, K., Jeong, H., Amoah, A., Xu, N., Niemann, J., Raeder, B., Hasenfeld, P., Stober, C., Rausch, T., Benito, E., Jann, J.-C., Nowak, D., Emini, R., Hoenicka, M., Liebold, A., Ho, A., Shuai, S., Geiger, H., Sanders, A. D., & Korbel, J. O. (2024). Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells. Nature Genetics, 56(6), 1134–1146. https://doi.org/10.1038/s41588-024-01754-2
Grundler, F., Ducarmon, Q. R., Holley, A., Knufinke, M., Strathmeyer, S., Heelemann, S., Geyer, R., Tellez, B. M., MacArthur, M. R., Zeller, G., Toledo, F. W. de, & Mesnage, R. (2024). Health benefits of a five-day at-home modified fasting program: a randomised controlled trial. MedRxiv, 2024.11.01.24316348. https://doi.org/10.1101/2024.11.01.24316348
Gründer, G., Brand, M., Mertens, L. J., Jungaberle, H., Kärtner, L., Scharf, D. J., Spangemacher, M., & Wolff, M. (2024). Treatment with psychedelics is psychotherapy: Beyond reductionism. The Lancet Psychiatry, 11(3), 231–236. https://doi.org/10.1016/S2215-0366(23)00363-2
Ibarra-Arellano, M. A., Caprio, L. A., Hada, A., Stotzem, N., Cai, L., Shah, S., Melms, J. C., Wünneman, F., Izar, B., & Schapiro, D. (2024). micronuclAI: Automated quantification of micronuclei for assessment of chromosomal instability. BioRxiv. https://doi.org/10.1101/2024.05.24.595722
Kahmann, J., Nörenberg, D., Papavassiliu, T., Dar, S. U. H., Engelhardt, S., Schoenberg, S. O., Froelich, M. F., & Ayx, I. (2024). Combined conventional factors and the radiomics signature of coronary plaque texture could improve cardiac risk prediction. Insights into Imaging, 15(1), 113–170. https://doi.org/10.1186/s13244-024-01759-9
Kors, S., & Schlaitz, A. L. (2024). Dynamic remodelling of the endoplasmic reticulum for mitosis. Journal of Cell Science, 137(22), 261444. https://doi.org/10.1242/jcs.261444
Köhler, N., Würf, V., Rose, T. D., & Pauling, J. K. (2024). Identification and Integration of Key-Metabolic Reactions from Untargeted Metabolomics. BioRxiv, 2023.05.15.540613. https://doi.org/10.1101/2023.05.15.540613
Li, C.-P., Jakob, J., Menge, F., Reißfelder, C., Hohenberger, P., & Yang, C. (2024). Comparing ChatGPT-3.5 and ChatGPT-4’s alignments with the German evidence-based S3 guideline for adult soft tissue sarcoma. IScience, 27(12), 111493. https://doi.org/10.1016/j.isci.2024.111493
Lim, B., Domsch, K., Mall, M., & Lohmann, I. (2024). Canalizing cell fate by transcriptional repression. Molecular Systems Biology, 20(3), 144–161. https://doi.org/10.1038/s44320-024-00014-z
Mahara, S., Prüssing, S., Smialkovska, V., Krall, S., Holliman, S., Blum, B., Dachtler, V., Borgers, H., Sollier, E., Plass, C., & Feldmann, A. (2024). Transient promoter interactions modulate developmental gene activation. Molecular Cell, 84(23), 4486–4502.e7. https://doi.org/10.1016/j.molcel.2024.10.005
Meyer, M., Parpoulas, C., Barthélémy, T., Becker, J. P., Charoentong, P., Lyu, Y., Börsig, S., Bulbuc, N., Tessmer, C., Weinacht, L., Ibberson, D., Schmidt, P., Pipkorn, R., Eichmüller, S. B., Steinberger, P., Lindner, K., Poschke, I., Platten, M., Fröhling, S., … Momburg, F. (2024). MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Frontiers in Immunology, 14, 1294565. https://doi.org/10.3389/fimmu.2023.1294565
Moeller, H. v, L’Etoile-Goga, A., Vincenzi, L., Norlin, A., Barbaglia, G. S., Runte, G. C., Kaare-Rasmussen, J. T., & Johnson, M. D. (2024). Retention of blue-green cryptophyte organelles by Mesodinium rubrum and their effects on photophysiology and growth. The Journal of Eukaryotic Microbiology, e13066. https://doi.org/10.1111/jeu.13066
Müller, S., Lieb, K., Streit, F., Awasthi, S., Wagner, S., Frank, J., Müller, M. B., Tadic, A., Heilmann-Heimbachi, S., Hoffmanni, P., Mavaranij, L., Schmidtj, B., Rietschela, M., Witta, S. H., Zillich, L., & Engelmann, J. (2024). Common polygenic variation in the early medication change (EMC) cohort affects disorder risk, but not the antidepressant treatment response. Journal of Affective Disorders, 363, 542–551. https://doi.org/10.1016/j.jad.2024.07.138
Müller-Dott, S., Jaehnig, E. J., Munchic, K. P., Jiang, W., Yaron-Barir, T. M., Savage, S. R., Garrido-Rodriguez, M., Johnson, J. L., Lussana, A., Petsalaki, E., Lei, J. T., Dugourd, A., Krug, K., Cantley, L. C., Mani, D. R., Zhang, B., & Saez-Rodriguez, J. (2024). Comprehensive evaluation of phosphoproteomic-based kinase activity inference. BioRxiv. https://doi.org/10.1101/2024.06.27.601117
Nooij, S., Plomp, N., Sanders, I. M. J. G., Schout, L., Meulen, A. E. van der, Terveer, E. M., Norman, J. M., Karcher, N., Larralde, M. F., Vossen, R. H. A. M., Kloet, S. L., Faber, K. N., Harmsen, H. J. M., Zeller, G. F., Kuijper, E. J., Smits, W. K., & Ducarmon, Q. R. (2024). Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status. BioRxiv, 2024.06.27.600998. https://doi.org/10.1101/2024.06.27.600998
Paiardi, G., Ferraz, M., Rusnati, M., & Wade, R. C. (2024). The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming. Proceedings of the National Academy of Sciences, 121(43), e2404892121. https://doi.org/10.1073/pnas.2404892121
Park, Y. W., Choi, K. S., Foltyn-Dumitru, M., Brugnara, G., Banan, R., Kim, S., Han, K., Park, J. E., Kessler, T., Bendszus, M., Krieg, S., Wick, W., Sahm, F., Choi, S. H., Kim, H. S., Chang, J. H., Kim, S. H., Wongsawaeng, D., Pollock, J. M., … Ahn, S. S. (2024). Incorporating Supramaximal Resection into Survival Stratification of IDH-wildtype Glioblastoma: A Refined Multi-institutional Recursive Partitioning Analysis. Clinical Cancer Research, 30(21), 4866–4875. https://doi.org/10.1158/1078-0432.CCR-23-3845
Paton, V., Flores, R. O. R., Gabor, A., Badia-i-Mompel, P., Tanevski, J., Garrido-Rodriguez, M., & Saez-Rodriguez, J. (2024). Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results. Nucleic Acids Research, 52(14), 8100–8111. https://doi.org/10.1093/nar/gkae552
Paton, V., Türei, D., Ivanova, O., Müller-Dott, S., Rodriguez-Mier, P., Venafra, V., Perfetto, L., Garrido-Rodriguez, M., & Saez-Rodriguez, J. (2024). NetworkCommons: Bridging data, knowledge and methods to build and evaluate context-specific biological networks. BioRxiv. https://doi.org/10.1101/2024.11.22.624823
Pedraz-Petrozzi, B., Spangemacher, M., Deicher, A., Drews, L., Defert, J., Silva-Colmenero, A. Y., Wein, P., Riedinger, E., Gründer, G., Gilles, M., Sartorius, A., & Reinwald, J. R. (2024). Baseline monocyte count predicts symptom improvement during intravenous ketamine therapy in treatment-resistant depression: A single-arm open-label observational study. Frontiers in Psychiatry, 15, 1415505. https://doi.org/10.3389/fpsyt.2024.1415505
Rademacher, A., Huseynov, A., Bortolomeazzi, M., Wille, S. J., Schumacher, S., Sant, P., Keitel, D., Okonechnikov, K., Ghasemi, D. R., Pajtler, K. W., Mallm, J.-P., & Rippe, K. (2024). Comparison of spatial transcriptomics technologies using tumor cryosections. BioRxiv. https://doi.org/10.1101/2024.04.03.586404
Reeve, M. P., Loomis, S., Nissilä, E., Rausch, T., Zheng, Z., Parolo, P. D. B., Ben-Isvy, D., Aho, E., Cesetti, E., Okunuki, Y., McLaughlin, H., Mäkelä, J., FinnGen, Kurki, M., Talkowski, M. E., Korbel, J. O., Connor, K., Meri, S., Daly, M. J., & Runz, H. (2024). Loss of CFHR5 function reduces the risk for age-related macular degeneration. MedRxiv, 2024.11.11.24317117. https://doi.org/10.1101/2024.11.11.24317117
Riabov, V., Xu, Q. Y., Schmitt, N., Streuer, A., Ge, G., Bolanos, L., Wunderlich, M., Jann, J. C., Wein, A., Altrock, E., Demmerle, M., Mukherjee, S., Ali, A. M., Rapp, F., Nowak, V., Weimer, N., Oblaender, J., Palme, I., Göl, M., … Nowak, D. (2024). ASXL1 mutations are associated with a response to alvocidib and 5-azacytidine combination in myelodysplastic neoplasms. Haematologica, 109(5), 1426–1438. https://doi.org/10.3324/haematol.2023.282921
Sachse, M., & Stellos, K. (2024). Unraveling the RNA code: a uridine RNA modification drives glycoRNA biogenesis. Signal Transduction and Targeted Therapy, 9(1), 334. https://doi.org/10.1038/s41392-024-02056-z
Schubert, M. C., Soyka, S. J., Tamimi, A., Maus, E., Schroers, J., Wißmann, N., Reyhan, E., Tetzlaff, S. K., Yang, Y., Denninger, R., Peretzke, R., Beretta, C., Drumm, M., Heuer, A., Buchert, V., Steffens, A., Walshon, J., McCortney, K., Heiland, S., … Venkataramani, V. (2024). Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis. Nature Communications, 15(1), 1–21. https://doi.org/10.1038/s41467-024-51432-4
Smirnov, P., Przybilla, M. J., Simovic-Lorenz, M., Parra, R. G., Susak, H., Ratnaparkhe, M., Wong, J. K. L., Körber, V., Mallm, J. P., Philippos, G., Sill, M., Kolb, T., Kumar, R., Casiraghi, N., Okonechnikov, K., Ghasemi, D. R., Maaß, K. K., Pajtler, K. W., Jauch, A., … Ernst, A. (2024). Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability. Nature Communications 2024 15:1, 15(1), 1–20. https://doi.org/10.1038/s41467-024-54547-w
Spangemacher, M., Mertens, L. J., Färber, L. v., Jungaberle, A., Jungaberle, H., & Gründer, G. (2024). Psilocybin as a disease-modifying drug—a salutogenic approach in psychiatry. Deutsches Ärzteblatt International, 121, 868–874. https://doi.org/10.3238/arztebl.m2024.0224
Streuer, A., Jann, J. C., Boch, T., Mossner, M., Riabov, V., Schmitt, N., Altrock, E., Xu, Q. Y., Demmerle, M., Nowak, V., Oblaender, J., Palme, I., Weimer, N., Rapp, F., Metzgeroth, G., Hecht, A., Hoeger, T., Merz, C., Hofmann, W. K., … Nowak, D. (2024). Treatment with the apoptosis inhibitor Asunercept reduces clone sizes in patients with lower risk myelodysplastic neoplasms. Annals of Hematology, 103(4), 1221–1233. https://doi.org/10.1007/s00277-024-05664-5
Sun, D., Ng, S. W., Zheng, Y., Xie, S., Schwan, N., Breuer, P., Hoffmann, D. C., Michel, J., Azorin, D. D., Boonekamp, K. E., Winkler, F., Wick, W., Boutros, M., Li, Y., & Johnsson, K. (2024). Molecular recording of cellular protein kinase activity with chemical labeling. BioRxiv. https://doi.org/10.1101/2024.09.11.611894
Tetzlaff, S. K., Reyhan, E., Layer, N., Bengtson, C. P., Heuer, A., Schroers, J., Faymonville, A. J., Langeroudi, A. P., Drewa, N., Keifert, E., Wagner, J., Soyka, S. J., Schubert, M. C., Sivapalan, N., Pramatarov, R. L., Buchert, V., Wageringel, T., Grabis, E., Wißmann, N., … Venkataramani, V. (2024). Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing. Cell, 188, 1–22. https://doi.org/10.1016/j.cell.2024.11.002
Tran, M. P., Chakraborty, T., Poppleton, E., Monari, L., Giessler, F., & Göpfrich, K. (2024). Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells. BioRxiv, 2024.06.12.598448. https://doi.org/10.1101/2024.06.12.598448
Tual-Chalot, S., & Stellos, K. (2024). First-in-human gene editing for lipid lowering: The initial results. Cardiovascular Research, 120(4), e5–e8. https://doi.org/10.1093/cvr/cvae037
van Linthout, S., Stellos, K., Giacca, M., Bertero, E., Cannata, A., Carrier, L., Garcia-Pavia, P., Ghigo, A., González, A., Haugaa, K. H., Imazio, M., Lopes, L. R., Most, P., Pollesello, P., Schunkert, H., Streckfuss-Bömeke, K., Thum, T., Tocchetti, C. G., Tschöpe, C., … Heymans, S. (2024). State of the art and perspectives of gene therapy in heart failure: A scientific statement of the Heart Failure Association of the ESC, the ESC Council on Cardiovascular Genomics and the ESC Working Group on Myocardial & Pericardial Diseases. European Journal of Heart Failure. https://doi.org/10.1002/ejhf.3516
Weinmann, R., Udupa, A., Nickels, J. F., Frank, L., Knotz, C., & Rippe, K. (2024). HP1 binding creates a local barrier against transcription activation and persists during chromatin decondensation. BioRxiv, 2024.12.09.627308. https://doi.org/10.1101/2024.12.09.627308
Wiedmann, F., & Schmidt, C. (2024). Novel drug therapies for atrial fibrillation. Nature Reviews Cardiology, 21(5), 275–276. https://doi.org/10.1038/s41569-024-01004-2
Wolff, M., Evens, R., Mertens, L. J., Schmidt, C., Beck, J., Rutrecht, H., Cherniak, A. D., Gründer, G., & Jungaberle, H. (2024). Measuring psychotherapeutic processes in the context of psychedelic experiences: Validation of the General Change Mechanisms Questionnaire (GCMQ). Journal of Psychopharmacology, 38(5), 432–457. https://doi.org/10.1177/02698811241249698
Wünnemann, F., Sicklinger, F., Bestak, K., Nimo, J., Thiemann, T., Amrute, J., Nordbeck, M., Hartmann, N., Ibarra-Arellano, M. A., Tanevski, J., Heine, C., Frey, N., Lavine, K. J., Coscia, F., Saez-Rodriguez, J., Leuschner, F., & Schapiro, D. (2024). Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration. BioRxiv. https://doi.org/10.1101/2024.05.20.594955
Zaremba, B., Fallahshahroudi, A., Schneider, C., Schmidt, J., Sarropoulos, I., Leushkin, E., Berki, B., van Poucke, E., Jensen, P., Senovilla-Ganzo, R., Hervas-Sotomayor, F., Trost, N., Lamanna, F., Sepp, M., García-Moreno, F., & Kaessmann, H. (2024). Developmental origins and evolution of pallial cell types and structures in birds. BioRxiv, 2024.04.30.591857. https://doi.org/10.1101/2024.04.30.591857
Burtscher, M. L., Gade, S., Garrido-Rodriguez, M., Rutkowska, A., Werner, T., Eberl, H. C., Petretich, M., Knopf, N., Zirngibl, K., Grandi, P., Bergamini, G., Bantscheff, M., Fälth-Savitski, M., & Saez-Rodriguez, J. (2023). Integration of Thermal Proteome Profiling with phosphoproteomic and transcriptomic data via mechanistic network models decodes the molecular response to PARP inhibition. BioRxiv, 2023.08.15.553354. https://doi.org/10.1101/2023.08.15.553354
Ducarmon, Q. R., Grundler, F., le Maho, Y., de Toledo, F. W., Zeller, G., Habold, C., & Mesnage, R. (2023). Remodelling of the intestinal ecosystem during caloric restriction and fasting. Trends in Microbiology, 31(8), 832–844. https://doi.org/10.1016/j.tim.2023.02.009
Friedrich, M., Hahn, M., Michel, J., Sankowski, R., Kilian, M., Kehl, N., Günter, M., Bunse, T., Pusch, S., von Deimling, A., Wick, W., Autenrieth, S. E., Prinz, M., Platten, M., & Bunse, L. (2023). Dysfunctional dendritic cells limit antigen-specific T cell response in glioma. Neuro-Oncology, 25(2), 263–276. https://doi.org/10.1093/neuonc/noac138
Maneta, E., Aivalioti, E., Tual-Chalot, S., Emini Veseli, B., Gatsiou, A., Stamatelopoulos, K., & Stellos, K. (2023). Endothelial dysfunction and immunothrombosis in sepsis. Frontiers in Immunology, 14, 1144229. https://doi.org/10.3389/fimmu.2023.1144229
Melde, K., Kremer, H., Shi, M., Seneca, S., Frey, C., Platzman, I., Degel, C., Schmitt, D., Schölkopf, B., & Fischer, P. (2023). Compact holographic sound fields enable rapid one-step assembly of matter in 3D. Science Advances, 9(6), eadf6182. https://doi.org/10.1126/sciadv.adf6182
Okonechnikov, K., Camgöz, A., Chapman, O., Wani, S., Park, D. E., Hübner, J. M., Chakraborty, A., Pagadala, M., Bump, R., Chandran, S., Kraft, K., Acuna-Hidalgo, R., Reid, D., Sikkink, K., Mauermann, M., Juarez, E. F., Jenseit, A., Robinson, J. T., Pajtler, K. W., … Chavez, L. (2023). 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature Communications 2023 14:1, 14(1), 1–16. https://doi.org/10.1038/s41467-023-38044-0
Poppleton, E., Urbanek, N., Chakraborty, T., Griffo, A., Monari, L., & Göpfrich, K. (2023). RNA origami: Design, simulation and application. RNA Biology, 20(1), 510–524. https://doi.org/10.1080/15476286.2023.2237719
Xu, Q., Altrock, E., Schmitt, N., Streuer, A., Rapp, F., Nowak, V., Obländer, J., Weimer, N., Palme, I., Göl, M., Hofmann, W.-K., Nowak, D., & Riabov, V. (2023). In Silico Pan-Cancer Analysis Reveals Prognostic Role of the Erythroferrone (ERFE) Gene in Human Malignancies. International Journal of Molecular Sciences, 24(2), 1725. https://doi.org/10.3390/ijms24021725
Xu, Q., Streuer, A., Jann, J.-C., Altrock, E., Schmitt, N., Flach, J., Sens-Albert, C., Rapp, F., Wolf, J., Nowak, V., Weimer, N., Obländer, J., Palme, I., Kuzina, M., Jawhar, A., Darwich, A., Weis, C.-A., Marx, A., Wuchter, P., … Nowak, D. (2023). Inhibition of lysyl oxidases synergizes with 5-azacytidine to restore erythropoiesis in myelodysplastic and myeloid malignancies. Nature Communications, 14(1), 1497. https://doi.org/10.1038/s41467-023-37175-8
Bergmann, A. M., Donau, C., Späth, F., Jahnke, K., Göpfrich, K., & Boekhoven, J. (2022). Evolution and single-droplet analysis of fuel-driven compartments by droplet-based microfluidics. Angewandte Chemie International Edition, 61(32), e202203928. https://doi.org/10.1002/anie.202203928
Bunse, L., Bunse, T., Krämer, C., Chih, Y. C., & Platten, M. (2022). Clinical and translational advances in glioma immunotherapy. Neurotherapeutics, 19(6), 1799–1817. https://doi.org/10.1007/s13311-022-01313-9
Lu, K. H.-N., Michel, J., Kilian, M., Aslan, K., Qi, H., Kehl, N., Jung, S., Sanghvi, K., Lindner, K., Zhang, X.-W., Green, E. W., Poschke, I., Ratliff, M., Bunse, T., Sahm, F., von Deimling, A., Wick, W., Platten, M., & Bunse, L. (2022). T cell receptor dynamic and transcriptional determinants of T cell expansion in glioma-infiltrating T cells. Neuro-Oncology Advances, 4(1), vdac140. https://doi.org/10.1093/noajnl/vdac140
Mertens, L. J., Koslowski, M., Betzler, F., Evens, R., Gilles, M., Jungaberle, A., Jungaberle, H., Majić, T., Ströhle, A., Wolff, M., Wellek, S., & Gründer, G. (2022). Methodological challenges in psychedelic drug trials: Efficacy and safety of psilocybin in treatment-resistant major depression (EPIsoDE) – Rationale and study design. Neuroscience Applied, 1, 100104. https://doi.org/10.1016/j.nsa.2022.100104