Publications (selection)

Bauer, H. F., Delling, J. P., Bockmann, J., Boeckers, T. M., & Schön, M. (2022). Development of sex- and genotype-specific behavioral phenotypes in a Shank3 mouse model for neurodevelopmental disorders. Front Behav Neurosci, 16, 1051175. https://doi.org/10.3389/fnbeh.2022.1051175 

Garrido, D., Beretta, S., Grabrucker, S., Bauer, H. F., Bayer, D., Sala, C., Verpelli, C., Roselli, F., Bockmann, J., Proepper, C., Catanese, A., & Boeckers, T. M. (2022). Shank2/3 double knockout-based screening of cortical subregions links the retrosplenial area to the loss of social memory in autism spectrum disorders. Mol Psychiatry, 27(12), 4994-5006. doi.org/10.1038/s41380-022-01756-8 

Hall, D., Giaimo, B. D., Park, S. S., Hemmer, W., Friedrich, T., Ferrante, F., Bartkuhn, M., Yuan, Z., Oswald, F., Borggrefe, T., Rual, J. F., & Kovall, R. A. (2022). The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3. Nucleic Acids Res, 50(22), 13083-13099. doi.org/10.1093/nar/gkac1137 

Müssel, C., Ikonomi, N., Werle, S. D., Weidner, F. M., Maucher, M., Schwab, J. D., & Kestler, H. A. (2022). CANTATA-prediction of missing links in Boolean networks using genetic programming. Bioinformatics, 38(21), 4893-4900. doi.org/10.1093/bioinformatics/btac623 

Nicolò, A., Amendt, T., El Ayoubi, O., Young, M., Finzel, S., Senel, M., Voll, R. E., & Jumaa, H. (2022). Rheumatoid factor IgM autoantibodies control IgG homeostasis. Front Immunol, 13, 1016263. doi.org/10.3389/fimmu.2022.1016263 

Pérez Arévalo, A., Lutz, A. K., Atanasova, E., & Boeckers, T. M. (2022). Trans-cardiac perfusion of neonatal mice and immunofluorescence of the whole body as a method to study nervous system development. PLoS One, 17(10), e0275780. doi.org/10.1371/journal.pone.0275780 

Perez-Correa, J.-F., Tharmapalan, V., Geiger, H., & Wagner, W. (2022). Epigenetic Clocks for Mice Based on Age-Associated Regions That are Conserved Between Mouse Strains and Human [Original Research]. Frontiers in Cell and Developmental Biology, Volume 10 - 2022. doi.org/10.3389/fcell.2022.902857 

Sehring, I., Mohammadi, H. F., Haffner-Luntzer, M., Ignatius, A., Huber-Lang, M., & Weidinger, G. (2022). Zebrafish fin regeneration involves generic and regeneration-specific osteoblast injury responses. Elife, 11. doi.org/10.7554/eLife.77614 

Sommer, D., Rajkumar, S., Seidel, M., Aly, A., Ludolph, A., Ho, R., Boeckers, T. M., & Catanese, A. (2022). Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons. Front Mol Neurosci, 15, 894230. doi.org/10.3389/fnmol.2022.894230 
 

Aly, A., Laszlo, Z. I., Rajkumar, S., Demir, T., Hindley, N., Lamont, D. J., Lehmann, J., Seidel, M., Sommer, D., Franz-Wachtel, M., Barletta, F., Heumos, S., Czemmel, S., Kabashi, E., Ludolph, A., Boeckers, T. M., Henstridge, C. M., & Catanese, A. (2023). Integrative proteomics highlight presynaptic alterations and c-Jun misactivation as convergent pathomechanisms in ALS. Acta Neuropathol, 146(3), 451-475. doi.org/10.1007/s00401-023-02611-y 

Arora, A., Kolberg, J. E., Srinivasachar Badarinarayan, S., Savytska, N., Munot, D., Müller, M., Krchlíková, V., Sauter, D., & Bansal, V. (2023). SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses. Mob DNA, 14(1), 11. doi.org/10.1186/s13100-023-00299-1 

Atanasova, E., Arévalo, A. P., Graf, I., Zhang, R., Bockmann, J., Lutz, A. K., & Boeckers, T. M. (2023). Immune activation during pregnancy exacerbates ASD-related alterations in Shank3-deficient mice. Mol Autism, 14(1), 1. doi.org/10.1186/s13229-022-00532-3 

Bocova, L., Hubens, W., Engel, C., Koschmieder, S., Jost, E., & Wagner, W. (2023). Quantification of hematopoietic stem and progenitor cells by targeted DNA methylation analysis. Clin Epigenetics, 15(1), 105. doi.org/10.1186/s13148-023-01521-w 

Burkert, N., Roy, S., Häusler, M., Wuttke, D., Müller, S., Wiemer, J., Hollmann, H., Oldrati, M., Ramirez-Franco, J., Benkert, J., Fauler, M., Duda, J., Goaillard, J. M., Pötschke, C., Münchmeyer, M., Parlato, R., & Liss, B. (2023). Deep learning-based image analysis identifies a DAT-negative subpopulation of dopaminergic neurons in the lateral Substantia nigra. Commun Biol, 6(1), 1146. doi.org/10.1038/s42003-023-05441-6 

Caratti, G., Stifel, U., Caratti, B., Jamil, A. J. M., Chung, K.-J., Kiehntopf, M., Gräler, M. H., Blüher, M., Rauch, A., & Tuckermann, J. P. (2023). Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance. Nature Communications, 14(1), 2271. https://doi.org/10.1038/s41467-023-37831-z

 
Catanese, A., Rajkumar, S., Sommer, D., Masrori, P., Hersmus, N., Van Damme, P., Witzel, S., Ludolph, A., Ho, R., Boeckers, T. M., & Mulaw, M. (2023). Multiomics and machine-learning identify novel transcriptional and mutational signatures in amyotrophic lateral sclerosis. Brain, 146(9), 3770-3782. doi.org/10.1093/brain/awad075 

Handwerk, L., Schreier, H. K., Kraft, D., Shreder, K., Hemmersbach, R., Hauslage, J., Bonig, H., Wiesmüller, L., Fournier, C., & Rall-Scharpf, M. (2023). Simulating Space Conditions Evokes Different DNA Damage Responses in Immature and Mature Cells of the Human Hematopoietic System. Int J Mol Sci, 24(18). doi.org/10.3390/ijms241813761 

Harms, M., Fabech Hansson, R., Gilg, A., Almeida-Hernández, Y., Löffler, J., Rodríguez-Alfonso, A., Habib, M. M. W., Albers, D., Ahmed, N. S., Abadi, A. H., Winter, G., Rasche, V., Beer, A. J., Weidinger, G., Preising, N., Ständker, L., Wiese, S., Sanchez-Garcia, E., Zelikin, A. N., & Münch, J. (2023). Development of N-Terminally Modified Variants of the CXCR4-Antagonistic Peptide EPI-X4 for Enhanced Plasma Stability. J Med Chem, 66(22), 15189-15204. doi.org/10.1021/acs.jmedchem.3c01128 

Iben, S. (2023). To aggregate or not to aggregate - Is it a matter of the ribosome? Bioessays, 45(7), e2200230. doi.org/10.1002/bies.202200230 

Jacobi, H., Vieri, M., Bütow, M., Namasu, C. Y., Flüter, L., Costa, I. G., Maié, T., Lindemann-Docter, K., Chatain, N., Beier, F., Huber, M., Wagner, W., Crysandt, M., Brümmendorf, T. H., & Schemionek, M. (2023). Myelofibrosis at diagnosis is associated with the failure of treatment-free remission in CML patients. Front Pharmacol, 14, 1212392. doi.org/10.3389/fphar.2023.1212392 

Khalid, F., Phan, T., Qiang, M., Maity, P., Lasser, T., Wiese, S., Penzo, M., Alupei, M., Orioli, D., Scharffetter-Kochanek, K., & Iben, S. (2023). TFIIH mutations can impact on translational fidelity of the ribosome. Hum Mol Genet, 32(7), 1102-1113. doi.org/10.1093/hmg/ddac268 

Krüger, J., Fischer, A., Breunig, M., Allgöwer, C., Schulte, L., Merkle, J., Mulaw, M. A., Okeke, N., Melzer, M. K., Morgenstern, C., Azoitei, N., Seufferlein, T., Barth, T. F., Siebert, R., Hohwieler, M., & Kleger, A. (2023). DNA methylation-associated allelic inactivation regulates Keratin 19 gene expression during pancreatic development and carcinogenesis. J Pathol, 261(2), 139-155. doi.org/10.1002/path.6156 

Mansilla, S. F., Bertolin, A. P., Venerus Arbilla, S., Castaño, B. A., Jahjah, T., Singh, J. K., Siri, S. O., Castro, M. V., de la Vega, M. B., Quinet, A., Wiesmüller, L., & Gottifredi, V. (2023). Polymerase iota (Pol ι) prevents PrimPol-mediated nascent DNA synthesis and chromosome instability. Science Advances, 9(15), eade7997. doi.org/doi:10.1126/sciadv.ade7997 

Merz, S., Breunig, M., Melzer, M. K., Heller, S., Wiedenmann, S., Seufferlein, T., Meier, M., Krüger, J., Mulaw, M. A., Hohwieler, M., & Kleger, A. (2023). Single-cell profiling of GP2-enriched pancreatic progenitors to simultaneously create acinar, ductal, and endocrine organoids. Theranostics, 13(6), 1949-1973. doi.org/10.7150/thno.78323 

Miralles, A. J., Unger, N., Kannaiyan, N., Rossner, M. J., & Dimou, L. (2023). Analysis of the GPR17 receptor in NG2-glia under physiological conditions unravels a new subset of oligodendrocyte progenitor cells with distinct functions. Glia, 71(6), 1536-1552. doi.org/10.1002/glia.24356 

Pan, L., Mulaw, M. A., Gout, J., Guo, M., Zarrin, H., Schwarz, P., Baumann, B., Seufferlein, T., Wagner, M., & Oswald, F. (2023). RBPJ Deficiency Sensitizes Pancreatic Acinar Cells to KRAS-Mediated Pancreatic Intraepithelial Neoplasia Initiation. Cell Mol Gastroenterol Hepatol, 16(5), 783-807. doi.org/10.1016/j.jcmgh.2023.07.013 

Pflumm, D., Seidel, A., Klein, F., Groß, R., Krutzke, L., Kochanek, S., Kroschel, J., Münch, J., Stifter, K., & Schirmbeck, R. (2023). Heterologous DNA-prime/protein-boost immunization with a monomeric SARS-CoV-2 spike antigen redundantizes the trimeric receptor-binding domain structure to induce neutralizing antibodies in old mice [Original Research]. Frontiers in Immunology, Volume 14 - 2023. doi.org/10.3389/fimmu.2023.1231274 

Puri, D., Maaßen, C., Varona Baranda, M., Zeevaert, K., Hahnfeld, L., Hauser, A., Fornero, G., Elsafi Mabrouk, M. H., & Wagner, W. (2023). CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs. Front Cell Dev Biol, 11, 1302448. doi.org/10.3389/fcell.2023.1302448 

Puri, D., & Wagner, W. (2023). Epigenetic rejuvenation by partial reprogramming. Bioessays, 45(4), e2200208. doi.org/10.1002/bies.202200208 

Rebehn, L., Khalaji, S., KleinJan, F., Kleemann, A., Port, F., Paul, P., Huster, C., Nolte, U., Singh, K., Kwapich, L., Pfeil, J., Pula, T., Fischer-Posovszky, P., Scharffetter-Kochanek, K., & Gottschalk, K.-E. (2023). The weakness of senescent dermal fibroblasts. Proceedings of the National Academy of Sciences, 120(34), e2301880120. doi.org/doi:10.1073/pnas.2301880120 

Salz, L., Seitz, A., Schäfer, D., Franzen, J., Holzer, T., Garcia-Prieto, C. A., Bürger, I., Hardt, O., Esteller, M., & Wagner, W. (2023). Culture expansion of CAR T cells results in aberrant DNA methylation that is associated with adverse clinical outcome. Leukemia, 37(9), 1868-1878. doi.org/10.1038/s41375-023-01966-1 

Schlett, J. S., Mettang, M., Skaf, A., Schweizer, P., Errerd, A., Mulugeta, E. A., Hein, T. M., Tsesmelis, K., Tsesmelis, M., Büttner, U. F. G., Wendt, H., Abaei, A., Rasche, V., Prex, V., Nespoli, E., Alami, N. O., Tews, D., Walther, P., Yilmazer-Hanke, D.,…Baumann, B. (2023). NF-κB is a critical mediator of post-mitotic senescence in oligodendrocytes and subsequent white matter loss. Mol Neurodegener, 18(1), 24. doi.org/10.1186/s13024-023-00616-5 

Schmidt, M., Zeevaert, K., Elsafi Mabrouk, M. H., Goetzke, R., & Wagner, W. (2023). Epigenetic biomarkers to track differentiation of pluripotent stem cells. Stem Cell Reports, 18(1), 145-158. doi.org/10.1016/j.stemcr.2022.11.001 

Seidel, M., Rajkumar, S., Steffke, C., Noeth, V., Agarwal, S., Roger, K., Lipecka, J., Ludolph, A., Guerrera, C. I., Boeckers, T., & Catanese, A. (2023). Propranolol reduces the accumulation of cytotoxic aggregates in C9orf72-ALS/FTD in vitro models. Curr Res Neurobiol, 5, 100105. doi.org/10.1016/j.crneur.2023.100105 

Stifel, U., Vogel, F., Caratti, G., Reincke, M., & Tuckermann, J. (2023). Unique Gene Expression Signature in Periadrenal Adipose Tissue Identifies a High Blood Pressure Group in Patients With Cushing Syndrome. Hypertension, 80(11), 2333-2344. doi.org/10.1161/hypertensionaha.123.21185 

Stirmlinger, N., Delling, J. P., Pfänder, S., & Boeckers, T. M. (2023). Elevation of SHANK3 Levels by Antisense Oligonucleotides Directed Against the 3'-UTR of the Human SHANK3 mRNA. Nucleic Acid Ther, 33(1), 58-71. doi.org/10.1089/nat.2022.0048 
Tuckermann, J., & Fischer-Posovszky, P. (2023). Energy saver: Monocytes hibernate in bone marrow upon fasting. Cell Metab, 35(5), 734-736. doi.org/10.1016/j.cmet.2023.04.008 

Vieri, M., Tharmapalan, V., Kalmer, M., Baumeister, J., Nikolić, M., Schnitker, M., Kirschner, M., Flosdorf, N., de Toledo, M. A. S., Zenke, M., Koschmieder, S., Brümmendorf, T. H., Beier, F., & Wagner, W. (2023). Cellular aging is accelerated in the malignant clone of myeloproliferative neoplasms. Blood Cancer J, 13(1), 164. doi.org/10.1038/s41408-023-00936-1 

Weidner, F. M., Rossini, M., Ankerhold, J., & Kestler, H. A. (2023). A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems. STAR Protoc, 4(3), 102438. doi.org/10.1016/j.xpro.2023.102438 

Weidner, F. M., Schwab, J. D., Wölk, S., Rupprecht, F., Ikonomi, N., Werle, S. D., Hoffmann, S., Kühl, M., & Kestler, H. A. (2023). Leveraging quantum computing for dynamic analyses of logical networks in systems biology. Patterns (N Y), 4(3), 100705. doi.org/10.1016/j.patter.2023.100705 

Wlaschek, M., Singh, K., Maity, P., & Scharffetter-Kochanek, K. (2023). The skin of the naked mole-rat and its resilience against aging and cancer. Mech Ageing Dev, 216, 111887. doi.org/10.1016/j.mad.2023.111887 

Woelfle, S., Pedro, M. T., Wagner, J., Schön, M., & Boeckers, T. M. (2023). Expression profiles of the autism-related SHANK proteins in the human brain. BMC Biol, 21(1), 254. doi.org/10.1186/s12915-023-01712-0 

Yazar, V., Kühlwein, J. K., Knehr, A., Grozdanov, V., Ekici, A. B., Ludolph, A. C., & Danzer, K. M. (2023). Impaired ATF3 signaling involves SNAP25 in SOD1 mutant ALS patients. Sci Rep, 13(1), 12019. doi.org/10.1038/s41598-023-38684-8 

Yildiz, B., Schiedt, L., Mulaw, M., Bockmann, J., Jesse, S., Lutz, A. K., & Boeckers, T. M. (2023). Shank3 related muscular hypotonia is accompanied by increased intracellular calcium concentrations and ion channel dysregulation in striated muscle tissue. Front Cell Dev Biol, 11, 1243299. doi.org/10.3389/fcell.2023.1243299 

Zeevaert, K., Goetzke, R., Elsafi Mabrouk, M. H., Schmidt, M., Maaßen, C., Henneke, A. C., He, C., Gillner, A., Zenke, M., & Wagner, W. (2023). YAP1 is essential for self-organized differentiation of pluripotent stem cells. Biomater Adv, 146, 213308. doi.org/10.1016/j.bioadv.2023.213308 

Zhu, G., Khalid, F., Zhang, D., Cao, Z., Maity, P., Kestler, H. A., Orioli, D., Scharffetter-Kochanek, K., & Iben, S. (2023). Ribosomal Dysfunction Is a Common Pathomechanism in Different Forms of Trichothiodystrophy. Cells, 12(14). https://doi.org/10.3390/cells12141877 

Auger, J.-P., Zimmermann, M., Faas, M., Stifel, U., Chambers, D., Krishnacoumar, B., Taudte, R. V., Grund, C., Erdmann, G., Scholtysek, C., Uderhardt, S., Ben Brahim, O., Pascual Maté, M., Stoll, C., Böttcher, M., Palumbo-Zerr, K., Mangan, M. S. J., Dzamukova, M., Kieler, M.,…Krönke, G. (2024). Metabolic rewiring promotes anti-inflammatory effects of glucocorticoids. Nature, 629(8010), 184-192. https://doi.org/10.1038/s41586-024-07282-7 

Bongiovanni, C., Bueno-Levy, H., Posadas Pena, D., Del Bono, I., Miano, C., Boriati, S., Da Pra, S., Sacchi, F., Redaelli, S., Bergen, M., Romaniello, D., Pontis, F., Tassinari, R., Kellerer, L., Petraroia, I., Mazzeschi, M., Lauriola, M., Ventura, C., Heermann, S.,…D'Uva, G. (2024). BMP7 promotes cardiomyocyte regeneration in zebrafish and adult mice. Cell Rep, 43(5), 114162. doi.org/10.1016/j.celrep.2024.114162 

Caspers, J., Ritter, A., Bahrami, B., Hoock, S. C., Roth, S., Friemel, A., Oswald, F., Louwen, F., Kreis, N. N., & Yuan, J. (2024). Involvement of RBP-J interacting and tubulin-associated protein in the distribution of protein regulator of cytokinesis 1 in mitotic spindles. Front Cell Dev Biol, 12, 1472340. doi.org/10.3389/fcell.2024.1472340 

Dallmeier, D., Braisch, J., Denkinger, M., Koenig, W., & Rothenbacher, D. (2024). Three-year changes in high-sensitivity cardiac troponin-T and total mortality in older adults. Sci Rep, 14(1), 28412. doi.org/10.1038/s41598-024-78641-7 

Delling, J. P., Bauer, H. F., Gerlach-Arbeiter, S., Schön, M., Jacob, C., Wagner, J., Pedro, M. T., Knöll, B., & Boeckers, T. M. (2024). Combined expansion and STED microscopy reveals altered fingerprints of postsynaptic nanostructure across brain regions in ASD-related SHANK3-deficiency. Mol Psychiatry, 29(10), 2997-3009. doi.org/10.1038/s41380-024-02559-9 

Elsafi Mabrouk, M. H., Zeevaert, K., Henneke, A. C., Maaßen, C., & Wagner, W. (2024). Substrate elasticity does not impact DNA methylation changes during differentiation of pluripotent stem cells. Cytotherapy, 26(9), 1046-1051. doi.org/10.1016/j.jcyt.2024.03.485 

Flosdorf, N., Böhnke, J., de Toledo, M. A. S., Lutterbach, N., Lerma, V. G., Graßhoff, M., Olschok, K., Gupta, S., Tharmapalan, V., Schmitz, S., Götz, K., Schüler, H. M., Maurer, A., Sontag, S., Küstermann, C., Seré, K., Wagner, W., Costa, I. G., Brümmendorf, T. H.,…Zenke, M. (2024). Proinflammatory phenotype of iPS cell-derived JAK2 V617F megakaryocytes induces fibrosis in 3D in vitro bone marrow niche. Stem Cell Reports, 19(2), 224-238. doi.org/10.1016/j.stemcr.2023.12.011 

Ioannidis, V., Pandey, R., Bauer, H. F., Schön, M., Bockmann, J., Boeckers, T. M., & Lutz, A. K. (2024). Disrupted extracellular matrix and cell cycle genes in autism-associated Shank3 deficiency are targeted by lithium. Mol Psychiatry, 29(3), 704-717. doi.org/10.1038/s41380-023-02362-y 

Iyer-Bierhoff, A., Wieczorek, M., Peter, S. M., Ward, D., Bens, M., Vettorazzi, S., Guehrs, K.-H., Tuckermann, J. P., & Heinzel, T. (2024). Acetylation-induced proteasomal degradation of the activated glucocorticoid receptor limits hormonal signaling. iScience, 27(2), 108943. doi.orghttps://doi.org/10.1016/j.isci.2024.108943 

Kumar, S., Vassallo, J. D., Nattamai, K. J., Hassan, A., Vollmer, A., Karns, R., Sacma, M., Nemkov, T., D'Alessandro, A., & Geiger, H. (2024). Rejuvenation of the reconstitution potential and reversal of myeloid bias of aged HSCs upon pH treatment. Aging Cell, 23(10), e14324. doi.org/10.1111/acel.14324 

Lausser, L., Szekely, R., & Kestler, H. A. (2024). Permutation-invariant linear classifiers. Machine Learning, 113(10), 7195-7221. doi.org/10.1007/s10994-024-06561-8 

Lehmann, J., Aly, A., Steffke, C., Fabbio, L., Mayer, V., Dikwella, N., Halablab, K., Roselli, F., Seiffert, S., Boeckers, T. M., Brenner, D., Kabashi, E., Mulaw, M., Ho, R., & Catanese, A. (2024). Heterozygous knockout of Synaptotagmin13 phenocopies ALS features and TP53 activation in human motor neurons. Cell Death & Disease, 15(8), 560. doi.org/10.1038/s41419-024-06957-3 

Long, S., Zheng, Y., Deng, X., Guo, J., Xu, Z., Scharffetter-Kochanek, K., Dou, Y., & Jiang, M. (2024). Maintaining mitochondrial DNA copy number mitigates ROS-induced oocyte decline and female reproductive aging. Communications Biology, 7(1), 1229. doi.org/10.1038/s42003-024-06888-x 

Majewska, J., Agrawal, A., Mayo, A., Roitman, L., Chatterjee, R., Sekeresova Kralova, J., Landsberger, T., Katzenelenbogen, Y., Meir-Salame, T., Hagai, E., Sopher, I., Perez-Correa, J. F., Wagner, W., Maimon, A., Amit, I., Alon, U., & Krizhanovsky, V. (2024). p16-dependent increase of PD-L1 stability regulates immunosurveillance of senescent cells. Nat Cell Biol, 26(8), 1336-1345. doi.org/10.1038/s41556-024-01465-0 

Ogrodnik, M., Carlos Acosta, J., Adams, P. D., d’Adda di Fagagna, F., Baker, D. J., Bishop, C. L., Chandra, T., Collado, M., Gil, J., Gorgoulis, V., Gruber, F., Hara, E., Jansen-Dürr, P., Jurk, D., Khosla, S., Kirkland, J. L., Krizhanovsky, V., Minamino, T., Niedernhofer, L. J.,…Demaria, M. (2024). Guidelines for minimal information on cellular senescence experimentation in vivo. Cell, 187(16), 4150-4175. doi.orghttps://doi.org/10.1016/j.cell.2024.05.059 

Papismadov, N., Levi, N., Roitman, L., Agrawal, A., Ovadya, Y., Cherqui, U., Yosef, R., Akiva, H., Gal, H., & Krizhanovsky, V. (2024). p21 regulates expression of ECM components and promotes pulmonary fibrosis via CDK4 and Rb. Embo j, 43(22), 5360-5380. doi.org/10.1038/s44318-024-00246-7 

Rachmian, N., Medina, S., Cherqui, U., Akiva, H., Deitch, D., Edilbi, D., Croese, T., Salame, T. M., Ramos, J. M. P., Cahalon, L., Krizhanovsky, V., & Schwartz, M. (2024). Identification of senescent, TREM2-expressing microglia in aging and Alzheimer's disease model mouse brain. Nat Neurosci, 27(6), 1116-1124. doi.org/10.1038/s41593-024-01620-8 

Schmidt, M., Maié, T., Cramer, T., Costa, I. G., & Wagner, W. (2024). Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer. Clin Epigenetics, 16(1), 164. doi.org/10.1186/s13148-024-01783-y 

Schuster, T., Amoah, A., Vollmer, A., Marka, G., Niemann, J., Saçma, M., Sakk, V., Soller, K., Vogel, M., Grigoryan, A., Wlaschek, M., Scharffetter-Kochanek, K., Mulaw, M., & Geiger, H. (2024). Quantitative determination of the spatial distribution of components in single cells with CellDetail. Nat Commun, 15(1), 10250. doi.org/10.1038/s41467-024-54638-8 

Sehring, I., & Weidinger, G. (2024). Wound healing: Surprising support from distant sources. Curr Biol, 34(16), R774-r776. https://doi.org/10.1016/j.cub.2024.07.007

Steffke, C., Agarwal, S., Kabashi, E., & Catanese, A. (2024). Overexpression of Toxic Poly(Glycine-Alanine) Aggregates in Primary Neuronal Cultures Induces Time-Dependent Autophagic and Synaptic Alterations but Subtle Activity Impairments. Cells, 13(15), 1300. www.mdpi.com/2073-4409/13/15/1300 

Tharmapalan, V., & Wagner, W. (2024). Biomarkers for aging of blood - how transferable are they between mice and humans? Exp Hematol, 140, 104600. doi.org/10.1016/j.exphem.2024.104600 

Wagner, M., Zhu, G., Khalid, F., Phan, T., Maity, P., Lupu, L., Agyeman-Duah, E., Wiese, S., Lindenberg, K. S., Schön, M., Landwehrmeyer, G. B., Penzo, M., Kochanek, S., Scharffetter-Kochanek, K., Mulaw, M., & Iben, S. (2024). General loss of proteostasis links Huntington disease to Cockayne syndrome. Neurobiol Dis, 201, 106668. doi.org/10.1016/j.nbd.2024.106668 

Weidner, F. M., Ikonomi, N., Werle, S. D., Schwab, J. D., & Kestler, H. A. (2024). GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks. Bioinformatics, 40(1). doi.org/10.1093/bioinformatics/btae007 
 

Aghapour, M., Heuvel, F. O., Fröhlich, A., Heinzl, A., Maity, P., Singh, K., Wang, Y., Cheng, J., Roselli, F., & Scharffetter-Kochanek, K. (2025). Traumatic Brain Injury Induces Early Barrier Protective Responses in Incisional Skin Wounds Accelerating Cutaneous Wound Healing. Wound Repair Regen, 33(5), e70079. https://doi.org/10.1111/wrr.70079

Basu, A., Farsam, V., Singh, K., Crisan, D., Treiber, N., Schneider, L. A., Huber, M., Engelmeyer, J. I., Schumacher, B., Maity, P., Brandt, D., Jastroch, M., Mauch, C., Geiger, H., Kletsas, D., & Scharffetter-Kochanek, K. (2025). Senescent Fibroblasts Drive Melanoma Progression Through GCP-2 Induced CREB Phosphorylation Enhancing Glycolysis. Aging Cell, e70239. https://doi.org/10.1111/acel.70239

Boehm, F. J., Fritzenschaft, L., Braig, S., Denkinger, M., Rothenbacher, D., & Dallmeier, D. (2025). Sex- and system-specific analysis of blood-based biomarkers and frailty in older adults-the Activity and Function of the Elderly study. Age Ageing, 54(9). https://doi.org/10.1093/ageing/afaf255

Böhm, M., Stegemann, A., Paus, R., Kleszczyński, K., Maity, P., Wlaschek, M., & Scharffetter-Kochanek, K. (2025). Endocrine Controls of Skin Aging. Endocrine Reviews, 46(3), 349-375. https://doi.org/10.1210/endrev/bnae034

Braig, S., Denkinger, M. D., Dallmeier, D., Klenk, J., & Rothenbacher, D. (2025). Social isolation, loneliness and the relationship with serum biomarkers, functional parameters and mortality in older adults. Aging Clin Exp Res, 37(1), 140. https://doi.org/10.1007/s40520-025-03041-4

Bopp, V., LeeBae, J., Oeckl, P., Kühlwein, J. K., Grozdanov, V., Kiechle, M., Mayer, B., Möhrle, B., Geiger, H., & Danzer, K. M. (2025). Targeting Cdc42 improves motor phenotype in Parkinson's disease mice and reveals age-dependent susceptibility to α-synuclein. iScience, 28(12), 114217. doi.org/10.1016/j.isci.2025.114217 
 

Coßmann, J., Kos, P. I., Varamogianni-Mamatsi, V., Assenheimer, D. S., Bischof, T. A., Kuhn, T., Vomhof, T., Papantonis, A., Giorgetti, L., & Gebhardt, J. C. M. (2025). Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis. Nat Commun, 16(1), 1833. https://doi.org/10.1038/s41467-025-56889-5

Ehrmann, A. S., Quijada-Álamo, M., Close, V., Guo, M., Carracoi, V., Pérez-Carretero, C., Corchete, L. A., Friedrich, T., Giaimo, B. D., Yosifov, D. Y., Bloehdorn, J., Rodríguez-Sánchez, A., Tausch, E., Schneider, C., Döhner, H., Kietzmann, T., Borggrefe, T., Stilgenbauer, S., Oswald, F.,…Mertens, D. (2025). NOTCH1 signaling is dysregulated by loss of the deubiquitinase USP28 with del(11q), uncovering USP28 inhibition as novel therapeutic target in CLL. Leukemia. https://doi.org/10.1038/s41375-025-02632-4

 

Fritzenschaft, L., Boehm, F., Rothenbacher, D., Denkinger, M., & Dallmeier, D. (2025). Association of blood biomarkers with frailty-A mapping review. Ageing Res Rev, 109, 102761. https://doi.org/10.1016/j.arr.2025.102761

Guo, M., Memis, T., Ehrmann, A. S., Pittrof, A., Baumann, B., Ferrante, F., Tausch, E., Fischer, K., Döhner, H., Borggrefe, T., Stilgenbauer, S., Pannicke, U., Schwarz, K., Mertens, D., & Oswald, F. (2025). A noncoding mutation in the NOTCH1 gene initiates oncogenic NOTCH signaling via wild-type NICD stabilization in CLL. Blood. https://doi.org/10.1182/blood.2025028529

Huynh, D., Hoffmeister, P., Friedrich, T., Zhang, K., Bartkuhn, M., Ferrante, F., Giaimo, B. D., Kovall, R. A., Borggrefe, T., Oswald, F., & Gebhardt, J. C. M. (2025). Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding. Nat Commun, 16(1), 1259. https://doi.org/10.1038/s41467-025-56515-4

Krchlikova, V., Lu, Y., & Sauter, D. (2025). Viral influencers: deciphering the role of endogenous retroviral LTR12 repeats in cellular gene expression. J Virol, 99(2), e0135124. https://doi.org/10.1128/jvi.01351-24

Kunath, P., Pflumm, D., Moehrle, B., Sakk, V., Seidel, A., Münch, J., Geiger, H., & Schirmbeck, R. (2025). Old hematopoietic stem cells retain competence to reconstitute a youthful B cell system that is highly responsive to protein-based vaccination. Immun Ageing, 22(1), 14. https://doi.org/10.1186/s12979-025-00507-x

Lang, J., Bergner, T., Zinngrebe, J., Lepelley, A., Vill, K., Leiz, S., Wlaschek, M., Wagner, M., Scharffetter-Kochanek, K., Fischer-Posovszky, P., Read, C., Crow, Y. J., Hirschenberger, M., & Sparrer, K. M. J. (2025). Distinct pathogenic mutations in ARF1 allow dissection of its dual role in cGAS-STING signalling. EMBO reports, 26(9), 2232-2261. https://doi.org/https://doi.org/10.1038/s44319-025-00423-7

Liesenfelder, S., Elsafi Mabrouk, M. H., Iliescu, J., Baranda, M. V., Mizi, A., Perez-Correa, J. F., Wessiepe, M., Papantonis, A., & Wagner, W. (2025). Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape. Nat Aging, 5(6), 997-1009. https://doi.org/10.1038/s43587-025-00841-1

Maier, J., Schwab, J. D., Werle, S. D., Marienfeld, R., Stilgenbauer, S., Möller, P., Ikonomi, N., & Kestler, H. A. (2025). CLL to Richter syndrome: Integrating network strategies with experiments elucidating disease drivers and personalized therapies. Science Advances, 11(37), eadu7705. https://doi.org/doi:10.1126/sciadv.adu7705

Majewska, J., & Krizhanovsky, V. (2025). GD3 ganglioside checkpoints in immune surveillance of senescent cells. Nat Aging, 5(2), 182-183. https://doi.org/10.1038/s43587-025-00803-7

Mennerich, D., Ashok, Y., Vela-Rodríguez, C., Hentilä, H. I., Rall-Scharpf, M., Wiesmüller, L., Prunskaite-Hyyryläinen, R., Lehtiö, L., & Kietzmann, T. (2025). The E3 ubiquitin ligase DTX3L and the deubiquitinase USP28 fine-tune DNA repair through mutual regulation of their protein levels. iScience, 28(8), 112990. https://doi.org/10.1016/j.isci.2025.112990

Mensching, L., Beiersdorfer, M., Schloer, S., Köllmann, S., Reinsberg, F., Padoan, B., Fittje, P., Trenkner, T., Zaayenga, A., Martrus, G., Almahfoud, M., Stürzel, C. M., Sauter, D., Kirchhoff, F., Schulze Zur Wiesch, J., Altfeld, M., Garcia-Beltran, W. F., & Hoelzemer, A. (2025). HIV-1 infection of macrophages differentially primes NK-cell cytotoxicity and proinflammatory cytokine production. iScience, 28(7), 112879. https://doi.org/10.1016/j.isci.2025.112879

Munot, D., Lu, Y., Haußmann, I., Najjar, G., Baur, C., Singh, M., Günes, C., Sauter, D., & Arora, A. (2025). Antagonistic regulation of LINE-1/Alu elements and their repressor APOBEC3B in cellular senescence. Mob DNA, 16(1), 39. https://doi.org/10.1186/s13100-025-00378-5

Olari, L. R., Liu, S., Arnold, F., Kühlwein, J., Gil Miró, M., Updahaya, A. R., Stürzel, C., Thal, D. R., Walther, P., Sparrer, K. M. J., Danzer, K. M., Münch, J., & Kirchhoff, F. (2025). α-Synuclein fibrils enhance HIV-1 infection of human T cells, macrophages and microglia. Nat Commun, 16(1), 813. https://doi.org/10.1038/s41467-025-56099-z

Perez-Correa, J. F., Stiehl, T., Marioni, R. E., Corley, J., Cox, S. R., Costa, I. G., & Wagner, W. (2025). Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age. Genome Biol, 26(1), 103. https://doi.org/10.1186/s13059-025-03562-1

Rall-Scharpf, M., Schlotter, D., Koch, P., Szafranski, K., Groth, M., Sahm, A., Biber, S., Castaño, Bryan A., Heitmeir, B., Zengerling, F., Deniz, M., Dallmeier, D., Braig, S., Bonig, H., Milyavsky, M., Pospiech, H., & Wiesmüller, L. (2025). Replication stress responses in human lymphocytes change sex-specifically during aging. Nucleic Acids Research, 53(11). https://doi.org/10.1093/nar/gkaf498

 

Rossini M, Weidner FM, Ankerhold J, Kestler HA. A novel quantum algorithm for efficient attractor search in gene regulatory networks. Patterns 6(9): 101295, 2025. https://doi.org/10.1016/j.patter.2025.101295

Schönfelder, J., El Ayoubi, O., Havryliuk, O., Groß, R., Seidel, A., Bakchoul, T., Münch, J., Jumaa, H., & Setz, C. S. (2025). Mimicking immune complexes for efficient antibody responses. Front Immunol, 16, 1570487. https://doi.org/10.3389/fimmu.2025.1570487

Singh, K., Koroma, A. K., Pandey, R. K., Wang, Y., Cheng, J., Haas, P., Aghapour, M., Krug, L., Hainzl, A., Wlaschek, M., Maity, P., & Scharffetter-Kochanek, K. (2025). Restoring Histone Acetylation Accelerates Diabetic Wound Repair by Improving the Spatiotemporal Dynamics of Macrophages. Adv Sci (Weinh), e04920. https://doi.org/10.1002/advs.202504920

Stolnicu, A., Eckhardt-Bellmann, P., Kestler, A. M. R., & Kestler, H. A. (2025). Identification of ordinal relations and alternative suborders within high-dimensional molecular data. Front Bioinform, 5, 1665892. https://doi.org/10.3389/fbinf.2025.1665892

Stolnicu, A., Ikonomi, N., Eckhardt-Bellmann, P., Kraus, J. M., & Kestler, H. A. (2025). Robust signalling entropy estimation for biological process characterisation. Brief Bioinform, 26(3). https://doi.org/10.1093/bib/bbaf269

Tharmapalan, V., Du Marchie Sarvaas, M., Bleichert, M., Wessiepe, M., & Wagner, W. (2025). Senolytic compounds reduce epigenetic age of blood samples in vitro. npj Aging, 11(1), 6. https://doi.org/10.1038/s41514-025-00199-z

Thiam, P., Schwenker, F., & Kestler, H. A. (2025). Dealing with Class Overlap Through Cluster-Based Sample Weighting. Computers, 14(11), 457. https://www.mdpi.com/2073-431X/14/11/457

Vasudevarao, M. D., Posadas Pena, D., Ihle, M., Bongiovanni, C., Maity, P., Geissler, D., Mohammadi, H. F., Rall-Scharpf, M., Niemann, J., Mommersteeg, M. T. M., Redaelli, S., Happ, K., Wu, C. C., Beisaw, A., Scharffetter-Kochanek, K., D'Uva, G., Malek Mohammadi, M., Wiesmüller, L., Geiger, H., & Weidinger, G. (2025). BMP signaling promotes zebrafish heart regeneration via alleviation of replication stress. Nat Commun, 16(1), 1708. https://doi.org/10.1038/s41467-025-56993-6

Vonficht, D., Jopp-Saile, L., Yousefian, S., Flore, V., Simó Vesperinas, I., Teuber, R., Avanesyan, B., Luo, Y., Röthemeier, C., Grünschläger, F., Fernandez-Vaquero, M., Fregona, V., Ordoñez-Rueda, D., Schmalbrock, L. K., Deininger, L., Yamachui Sitcheu, A. J., Gu, Z., Funk, M. C., Mikut, R.,…Haas, S. (2025). Ultra-high-scale cytometry-based cellular interaction mapping. Nature Methods, 22(9), 1887-1899. https://doi.org/10.1038/s41592-025-02744-w

Wlaschek, M., Maity, P., Koroma, A. K., Geiger, H., Singh, K., & Scharffetter-Kochanek, K. (2025). Imbalanced redox dynamics induce fibroblast senescence leading to impaired stem cell pools and skin aging. Free Radic Biol Med, 233, 292-301. doi.org/10.1016/j.freeradbiomed.2025.03.024