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Enukashvily, N. I. ; Ponomartsev, N. V. ; Ketkar, A. ; Suezov, R. ; Chubar, A. V. ; Prjibelski, A. D. ; Shafranskaya, D. D. ; Elmshäuser, S. ; Keber, C. U. ; Stefanova, V. N. ; Akopov, A. L. ; Klingmüller, U. ; Pfefferle, P. I. ; Stiewe, T. ; Lauth, M. ; Brichkina, A. I. Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis.
Cell death & disease 14 (1 ), 19 (2023 ) [10.1038/s41419-023-05553-1] 2023
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Polenkowski, M. ; Allister, A. B. ; Burbano de Lara, S. ; Pierce, A. ; Geary, B. ; El Bounkari, O. ; Wiehlmann, L. ; Hoffmann, A. ; Whetton, A. D. ; Tamura, T. ; Tran, D. D. H. THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate.
iScience 26 (1 ), 105784 (2023 ) [10.1016/j.isci.2022.105784] 2023
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Wolf, S. D. ; Ehlting, C. ; Müller-Dott, S. ; Poschmann, G. ; Petzsch, P. ; Lautwein, T. ; Wang, S. ; Helm, B. ; Schilling, M. ; Saez-Rodriguez, J. ; Vucur, M. ; Stühler, K. ; Köhrer, K. ; Tacke, F. ; Dooley, S. ; Klingmüller, U. ; Luedde, T. ; Bode, J. G. Hepatocytes reprogram liver macrophages involving control of TGF-? activation, influencing liver regeneration and injury.
Hepatology communications 7 (8 ), e0208 (2023 ) [10.1097/HC9.0000000000000208] 2023
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Hammad, S. ; Ogris, C. ; Othman, A. ; Erdoesi, P. ; Schmidt-Heck, W. ; Biermayer, I. ; Helm, B. ; Gao, Y. ; Pioro?ska, W. ; Holland, C. H. ; D'Alessandro, L. A. ; de la Torre, C. ; Sticht, C. ; Al Aoua, S. ; Theis, F. J. ; Bantel, H. ; Ebert, M. P. ; Klingmüller, U. ; Hengstler, J. G. ; Dooley, S. ; Mueller, N. S. Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation.
Cell death & disease 14 (7 ), 414 (2023 ) [10.1038/s41419-023-05855-4] 2023
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Polenkowski, M. ; Allister, A. B. ; Burbano de Lara, S. ; Soltau, M. ; Kendre, G. ; Tran, D. D. H. Mapping alternative polyadenylation in human cells using direct RNA sequencing technology.
STAR Protocols 4 (3 ), 102420 (2023 ) [10.1016/j.xpro.2023.102420] 2023
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Samarin, J. (First author) ; Fabrowski, P. (First author) ; Kurilov, R. ; Nuskova, H. ; Hummel-Eisenbeiss, J. ; Pink, H. ; Li, N. ; Weru, V. ; Alborzinia, H. ; Yildiz, U. ; Grob, L. ; Täubert, M. J. ; Czech, M. ; Morgen, M. ; Brandstädter, C. ; Becker, K. ; Mao, L. ; Jayavelu, A. K. ; Goncalves, A. ; Uhrig, U. ; Seiler, J. S. ; Lyu, Y. ; Diederichs, S. ; Klingmüller, U. ; Muckenthaler, M. ; Kopp-Schneider, A. ; Teleman, A. ; Miller, A. ; Gunkel, P. N. (Last author) Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs.
Redox Biology 62 , 102639 (2023 ) [10.1016/j.redox.2023.102639] 2023
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Heming, S. (First author) ; Hansen, P. (First author) ; Vlasov, A. ; Schwörer, F. ; Schaumann, S. ; Frolovaite, P. ; Lehmann, W.-D. ; Timmer, J. ; Schilling, M. ; Helm, B. (Last author) ; Klingmüller, U. (Last author) MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics.
Bioinformatics advances 2 (1 ), vbac004 (2022 ) [10.1093/bioadv/vbac004] 2022
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Gegner, H. M. ; Naake, T. ; Dugourd, A. ; Müller, T. ; Czernilofsky, F. ; Kliewer, G. ; Jäger, E. ; Helm, B. ; Kunze-Rohrbach, N. ; Klingmüller, U. ; Hopf, C. ; Müller-Tidow, C. ; Dietrich, S. ; Saez-Rodriguez, J. ; Huber, W. ; Hell, R. ; Poschet, G. ; Krijgsveld, J. (Last author) Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis
Frontiers in molecular biosciences 9 , 961448 (2022 ) [10.3389/fmolb.2022.961448] 2022
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Baur, K. ; Abdullah, Y. ; Mandl, C. ; Hölzl-Wenig, G. ; Shi, Y. ; Edelkraut, U. ; Khatri, P. ; Hagenston, A. M. ; Irmler, M. ; Beckers, J. ; Ciccolini, F. A novel stem cell type at the basal side of the subventricular zone maintains adult neurogenesis
EMBO reports 23 (9 ), e54078 (2022 ) [10.15252/embr.202154078] 2022
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Gründing, A. R. ; Schneider, M. A. ; Richtmann, S. ; Kriegsmann, M. ; Winter, H. ; Martinez-Delgado, B. ; Varona, S. ; Liu, B. ; DeLuca, D. S. ; Held, J. ; Wrenger, S. ; Muley, T. ; Meister, M. ; Welte, T. ; Janciauskiene, S. Lung Adenocarcinoma Cell Sensitivity to Chemotherapies: A Spotlight on Lipid Droplets and SREBF1 Gene.
Cancers 14 (18 ), 4454 (2022 ) [10.3390/cancers14184454] 2022
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Chakraborty, S. (First author) ; Andrieux, G. ; Kastl, P. ; Adlung, L. ; Altamura, S. ; Boehm, M. E. ; Schwarzmüller, L. ; Abdullah, Y. ; Wagner, M.-C. ; Helm, B. ; Gröne, H.-J. ; Lehmann, W.-D. ; Boerries, M. ; Busch, H. ; Muckenthaler, M. U. ; Schilling, M. ; Klingmüller, U. (Last author) Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo.
Cell reports 40 (12 ), 111360 (2022 ) [10.1016/j.celrep.2022.111360] 2022
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Dehlke, K. ; Krause, L. ; Tyufekchieva, S. ; Murtha-Lemekhova, A. ; Mayer, P. ; Vlasov, A. ; Klingmüller, U. ; Mueller, N. S. ; Hoffmann, K. Predicting liver regeneration following major resection.
Scientific reports 12 (1 ), 13396 (2022 ) [10.1038/s41598-022-16968-9] 2022
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Budelmann, D. ; Laue, H. ; Weiss, N. ; Dahmen, U. ; D?Alessandro, L. A. ; Biermayer, I. ; Klingmüller, U. ; Ghallab, A. ; Hassan, R. ; Begher-Tibbe, B. ; Hengstler, J. G. ; Schwen, L. O. Automated Detection of Portal Fields and Central Veins in Whole-Slide Images of Liver Tissue
Journal of pathology informatics 13 , 100001 (2022 ) [10.1016/j.jpi.2022.100001] 2022
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D'Alessandro, L. A. (First author) ; Klingmüller, U. ; Schilling, M. (Last author) Deciphering signal transduction networks in the liver by mechanistic mathematical modelling.
Biochemical journal 479 (12 ), 1361 - 1374 (2022 ) [10.1042/BCJ20210548] 2022
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Theobald, V. ; Benjamin, N. ; Seyfarth, H.-J. ; Halank, M. ; Schneider, M. A. ; Richtmann, S. ; Hinderhofer, K. ; Xanthouli, P. ; Egenlauf, B. ; Seeger, R. ; Hoeper, M. M. ; Jonigk, D. ; Grünig, E. ; Eichstaedt, C. A. Reduction of BMPR2 mRNA Expression in Peripheral Blood of Pulmonary Arterial Hypertension Patients: A Marker for Disease Severity?
Genes 13 (5 ), 759 (2022 ) [10.3390/genes13050759] 2022
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Polenkowski, M. ; Burbano de Lara, S. (First author) ; Allister, A. B. ; Nguyen, T. N. Q. ; Tamura, T. ; Tran, D. D. H. Identification of Novel Micropeptides Derived from Hepatocellular Carcinoma-Specific Long Noncoding RNA.
International journal of molecular sciences 23 (1 ), 58 (2021 ) [10.3390/ijms23010058] 2021
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Adlung, L. (First author) ; Stapor, P. ; Tönsing, C. ; Schmiester, L. ; Schwarzmüller, L. E. ; Postawa, L. ; Wang, D. ; Timmer, J. ; Klingmüller, U. ; Hasenauer, J. ; Schilling, M. (Last author) Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells.
Cell reports 36 (6 ), 109507 (2021 ) [10.1016/j.celrep.2021.109507] 2021
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Mohapatra, S. R. (First author) ; Sadik, A. ; Sharma, S. ; Poschet, G. ; Gegner, H. M. ; Lanz, T. V. ; Lucarelli, P. ; Klingmüller, U. ; Platten, M. ; Heiland, I. ; Opitz, C. (Last author) Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine Production.
Frontiers in immunology 12 , 590532 (2021 ) [10.3389/fimmu.2021.590532] 2021
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Robichon, K. (First author) ; Maiwald, T. ; Schilling, M. ; Schneider, A. ; Willemsen, J. ; Salopiata, F. ; Teusel, M. T. ; Kreutz, C. ; Ehlting, C. ; Huang, J. ; Chakraborty, S. ; Huang, X. ; Damm, G. ; Seehofer, D. ; Lang, P. A. ; Bode, J. G. ; Binder, M. ; Bartenschlager, R. ; Timmer, J. ; Klingmüller, U. (Last author) Identification of Interleukin1? as an Amplifier of Interferon alpha-induced Antiviral Responses.
PLoS pathogens 16 (10 ), e1008461 - (2020 ) [10.1371/journal.ppat.1008461] 2020
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Wessels, S. ; Muley, T. ; Christopoulos, P. ; Meister, M. ; Heinzmann-Groth, I. ; Warth, A. ; Herpel, E. ; Hummler, S. ; Klingmüller, U. ; Kuon, J. ; Heussel, C.-P. ; Eberhardt, R. ; Herth, F. J. F. ; Winter, H. ; Bischoff, H. ; Stenzinger, A. ; Reck, M. ; Huber, R. M. ; Thomas, M. ; Schneider, M. A. Comprehensive serial biobanking in advanced NSCLC: feasibility, challenges and perspectives.
Translational Lung Cancer Research 9 (4 ), 1000 - 1014 (2020 ) [10.21037/tlcr-20-137] 2020
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Gremke, N. ; Polo, P. ; Dort, A. ; Schneikert, J. ; Elmshäuser, S. ; Brehm, C. ; Klingmüller, U. ; Schmitt, A. ; Reinhardt, H. C. ; Timofeev, O. ; Wanzel, M. ; Stiewe, T. mTOR-mediated cancer drug resistance suppresses autophagy and generates a druggable metabolic vulnerability.
Nature Communications 11 (1 ), 4684 (2020 ) [10.1038/s41467-020-18504-7] 2020
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Kok, F. K. (First author) ; Rosenblatt, M. ; Teusel, M. (First author) ; Nizharadze, T. ; Goncalves Magalhaes, V. ; Dächert, C. ; Maiwald, T. ; Vlasov, A. ; Wäsch, M. ; Tyufekchieva, S. ; Hoffmann, K. ; Damm, G. ; Seehofer, D. ; Boettler, T. ; Binder, M. ; Timmer, J. ; Schilling, M. (Last author) ; Klingmüller, U. (Last author) Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction.
Molecular systems biology 16 (7 ), e8955 (2020 ) [10.15252/msb.20198955] 2020
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Nilsson, A. ; Haanstra, J. R. ; Engqvist, M. ; Gerding, A. ; Bakker, B. M. ; Klingmüller, U. ; Teusink, B. ; Nielsen, J. Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.
Proceedings of the National Academy of Sciences of the United States of America 117 (19 ), 10294-10304 (2020 ) [10.1073/pnas.1919250117] 2020
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Duerr, J. ; Leitz, D. H. W. ; Szczygiel, M. (First author) ; Dvornikov, D. ; Fraumann, S. G. ; Kreutz, C. ; Zadora, P. ; Seyhan Agircan, A. ; Konietzke, P. ; Engelmann, T. A. ; Hegermann, J. ; Mulugeta, S. ; Kawabe, H. ; Knudsen, L. ; Ochs, M. ; Rotin, D. ; Muley, T. ; Kreuter, M. ; Herth, F. J. F. ; Wielpütz, M. O. ; Beers, M. F. ; Klingmüller, U. ; Mall, M. A. Conditional deletion of Nedd4-2 in lung epithelial cells causes progressive pulmonary fibrosis in adult mice.
Nature Communications 11 (1 ), 2012 (2020 ) [10.1038/s41467-020-15743-6] 2020
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Kim-Wanner, S.-Z. (First author) ; Assenov, Y. ; Nair, M. B. ; Weichenhan, D. ; Benner, A. ; Becker, N. ; Landwehr, K. ; Kuner, R. ; Sültmann, H. ; Esteller, M. ; Koch, I. ; Lindner, M. ; Meister, M. ; Thomas, M. ; Bieg, M. ; Klingmueller, U. ; Schlesner, M. ; Warth, A. ; Brors, B. ; Seifried, E. ; Bonig, H. ; Plass, C. ; Risch, A. ; Muley, T. Genome-wide DNA methylation profiling in early stage I lung adenocarcinoma reveals predictive aberrant methylation in the promoter region of the long non-coding RNA PLUT - an exploratory study.
Journal of thoracic oncology 15 (8 ), 1338-1350 (2020 ) [10.1016/j.jtho.2020.03.023] 2020
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Giustarini, G. ; Huppelschoten, S. ; Barra, M. ; Oppelt, A. ; Wagenaar, L. ; Weaver, R. J. ; Bol-Schoenmakers, M. ; Smit, J. ; van de Water, B. ; Klingmueller, U. ; Pieters, R. The hepatotoxic fluoroquinolone trovafloxacin disturbs TNF- and LPS-induced p65 nuclear translocation in vivo and in vitros.
Toxicology and applied pharmacology 391 , 114915 (2020 ) [10.1016/j.taap.2020.114915] 2020
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Weaver, R. J. ; Blomme, E. A. ; Chadwick, A. E. ; Copple, I. M. ; Gerets, H. H. J. ; Goldring, C. E. ; Guillouzo, A. ; Hewitt, P. G. ; Ingelman-Sundberg, M. ; Jensen, K. G. ; Juhila, S. ; Klingmüller, U. ; Labbe, G. ; Liguori, M. J. ; Lovatt, C. A. ; Morgan, P. ; Naisbitt, D. J. ; Pieters, R. H. H. ; Snoeys, J. ; van de Water, B. ; Williams, D. P. ; Park, B. K. Managing the challenge of drug-induced liver injury: a roadmap for the development and deployment of preclinical predictive models.
Nature reviews / Drug discovery Drug discovery [...] 19 (2 ), 131-148 (2020 ) [10.1038/s41573-019-0048-x] 2020
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