Journal Article (3226)

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Abdullaev, E.; Haridoss, D. A.; Arndt, P. F.: Predicting the methylation status of CpG islands from read distribution biases. BMC Genomics 26, 973 (2025)
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Kraft, K.; Murphy, S.; Jones, M. G.; Shi, Q.; Bhargava-Shah, A.; Luong, C.; Hung, K. L.; He, B. J.; Li, R.; Park, S. K. et al.; Montgomery, M. T.; Weiser, N. E.; Wang, Y.; Luebeck, J.; Bafna, V.; Boeke, J. D.; Mischel, P. S.; Boettiger, A. N.; Chang, H. Y.: Enhancer activation from transposable elements in extrachromosomal DNA. Nature Cell Biology (2025)
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Lin, Y.-Y.; Breuer, K.; Weichenhan, D.; Lafrenz, P.; Sarnataro, A.; Wilk, A.; Chepeleva, M.; Mücke, O.; Schönung, M.; Petermann, F. et al.; Kensche, P. R.; Weiser, L.; Thommen, .; Giacomelli, G.; Nordstroem, K.; Gonzalez-Avalos, E.; Merkel, A.; Kretzmer, H.; Fischer, J.; Krämer, S.; Iskar, M.; Wolf, S.; Buchhalter, I.; Esteller, M.; Lawerenz, C.; Twardziok, S.; Zapatka, M.; Hovestadt, V.; Schlesner, M.; Schulz, M. H.; Hoffmann, S.; Gerhause, C.; Walter, J.; Hartmann, M.; Lipka, D. B.; Assenov, Y.; Bock, C.; Plass, C.; Toth, R.; Lutsik, P.: Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard. Nucleic Acids Research 53 (2025)
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Funk, E. M.; Jafree, D. J.; Hansmeier, N. R.; Abad Baucells, C.; Behncke, R. Y.; Pomeranz, G.; Kolatsi-Joannou, M.; Mason, W. J.; Moulding, D.; Russell, L. G. et al.; Subramanian, A.; Ulferts, S.; Wilson, L.; Long, D. A.; Hägerling, R.: Nanobody Immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice. Journal of Nanobiotechnology 23, 667 (2025)
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Cifuentes Fontanals, L.; Tonello, E.; Siebert, H.: Node and edge control strategy identification via trap spaces in Boolean networks. BMC Bioinformatics 24, 494 (2025)
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Schwämmle, T.; Noviello, G.; Kanata, E.; Froehlich, J. J.; Bothe, A. M.; Martitz, A.; Altay, A.; Scouarnec, J.; Feng, V.-Y.; Mallie, H. et al.; Vingron, M.; Schulz, E. G.: Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus. Nature Structural & Molecular Biology (2025)
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Key, J.; Almaguer-Mederos, L.-E.; Kandi, A. R.; Fellenz, M.; Gispert, S.; Köpf, G.; Meierhofer, D.; Deller, T.; Auburger, G.: Conditional ATXN2L-Null in Adult Frontal Cortex CamK2a+ Neurons Does Not Cause Cell Death but Restricts Spontaneous Mobility and Affects the Alternative Splicing Pathway. Cells 14, p. 1532 (2025)
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Demir, S.; Kessler, T.; Hotes, A.; Häberle, B.; Hiyama, E.; Hishiki, T.; Indersie, E.; Branchereau, S.; Vokuhl, C.; Dorel, M. et al.; Lehrach, H.; Lange, B.; Cairo, S.; Kappler, R.: Mechanistic models position ceritinib as a nuclear integrity disrupting therapy in pediatric liver tumors. Journal of Experimental & Clinical Cancer Research 44, 268 (2025)
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Rübsam, F. N. M.; Liuwei, W.; Sun, Y.; Patel, B. I.; van der Toorn, W.; Piechotta, M.; Dieterich, C.; von Kleist, M.; Ehrenhofer-Murra, A. E.: MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers. Nucleic Acids Research (2025)
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Jacobs, J.; Lyubenova, H.; Potelle, S.; Kopp, J.; Gerin, I.; Chan, W. L.; Rodriguez de los Santos, M.; Hülsemann, W.; Mensah, M. A.; Cormier-Daire, V. et al.; Joosten, M.; Bruggenwirth, H. T.; Stuurman, K. E.; Miranda, V.; Campeau, P. M.; Wittler, L.; Graff, J.; Mundlos, S.; Ibrahim, D. M.; Van Schaftingen, E.; Fischer-Zirnsak, B.; Kornak, U.; Ehmke, N.; Bommer, G. T.: A missing enzyme-rescue metabolite as cause of a rare skeletal dysplasia. Nature (2025)
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Wang, L.; Riediger, L.; Rao, Q.; Xu, X.; Nie, Y.; Zhou, Y.; Zhang, J.; Tang, P.; Wang, W.; Tacke, F. et al.; Guillot, A.; Vallier, L.; Talon, I.; Li, W.; Yang, Y.; Haag, R.; Ma, N.: Tunable Synthetic Hydrogel Modulates Hepatic Lineage Specification of Human Liver Organoid. Advanced Functional Materials (2025)
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Biswas, A.; Muñoz, O.; Kim, K.; Hoege, C.; Lorton, B. M.; Nikolay, R.; Kraushar, M. L.; Shechter, D.; Guck, J.; Zaburdaev, V. et al.; Reber, S.: Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes. Nature Communications 16, 7597 (2025)
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Campana, P. A.; Prasse, P.; Herwig, R.; Scheffer, T.: PanThera: predictive analysis of higher-order combination therapies using deep neural networks. Briefings in Bioinformatics (2025)
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Kapmaz, M.; Keske, Ş.; Tekin, S.; Doğan, Ö.; İrkören, P.; Ataç, N.; Vatansever, C.; Albayrak, Ö.; Genç, Z.; Madran, B. et al.; Dönmez, H. E.; Özer, B.; Aksu, E. D.; Başkurt, D.; Berkkan, M.; Güldan, M.; Bakır, V. O.; Gönen, M.; Can, F.; Ergönül, Ö.: The Analysis of Missed Antibiotic De-Escalation Opportunities in Gram-Negative Bloodstream Infections. Antibiotics 14, p. 800 (2025)
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Garrett, A.; Kalscheuer, V. M.; Figueroa, R. R.; Palmer, E. E.; Morgan, A. T.: CLCN4‐Related Neurodevelopmental Condition: Characterization of Speech and Language Abilities. American Journal of Medical Genetics Part A (2025)
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Loyal, L.; Jürchott, K.; Reimer, U.; Meyer‐Arndt, L.; Henze, L.; Mages, N.; Kostrzanowski, J.; Reus, B.; Mangold, M.; Kruse, B. et al.; Dingeldey, M.; Sawitzki, B.; Michel, J.; Grossegesse, M.; Schnatbaum, K.; Wenschuh, H.; Nitsche, A.; Lachmann, N.; Timmermann, B.; Giesecke-Thiel, C.; Braun, J.; Kern, F.; Thiel, A.: Aging and Viral Evolution Impair Immunity Against Dominant Pan‐Coronavirus‐Reactive T Cell Epitope. European Journal of Immunology 55 (2025)
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Bauer, C.; Dang, L. T. D.; van den Beucken, T.; Herwig, R.: Systematic analysis of hepatotoxicity: combining literature mining and AI language models. Frontiers in Artificial Intelligence (2025)
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Stremmel, N.; Lemke, O.; Textoris‐Taube, K.; Ludwig, D.; Mülleder, M.; Muenzner, J.; Ralser, M.: An INS-1 832/13 ß-Cell Proteome Highlights the Rapid Regulation of Fatty Acid Biosynthesis in Glucose-Stimulated Insulin Secretion. PROTEOMICS 25, pp. 13 - 26 (2025)
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Guckelberger, P.; Haut, L.; Tornisiello, R.; Kretzmer, H.; Meissner, A.: HELLS is required for maintaining proper DNA modification at human satellite repeats. Genome Biology (26) (2025)
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Hetzel, S.; Hodis , E.; Torlai Triglia, E.; Kovacsovics, A.; Steinmann , K.; Gnirke, A.; Cui, M.; McQuaid, D.; Weigert, R.; Pohl, G. et al.; Muzumdar, M. D.; Leyvraz, S.; Keilholz, U.; Yaspo, M.-L.; Regev, A.; Kretzmer, H.; Smith, Z.; Meissner, A.: Direct genetic transformation bypasses tumor-associated DNA methylation alterations. Genome Biology (26) (2025)
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