Petrov, L.; Brumhard, S.; Wisniewski, S.; Georg, P.; Hillus, D.; Hiller, A.; Astaburuaga-Garcia, R.; Blüthgen, N.; Wyler, E.; Vogt, K.; Dey, H-P.; von Stillfried, S.; Iwert, C.; Bülow, R. D.; Märkl, B.; Maas, L.; Langner, C.; Meyer, T.; Loske, J.; Eils, R.; Lehmann, I.; Ondruschka, B.; Ralser, M.; Trimpert, J.; Boor, P.; Bedoui, S.; Meisel, C.; Mall, M. A.; Corman, V. M.; Sander, L. E.; Röhmel, J. and Sawitzki, B. Rewired type I IFN signaling is linked to age-dependent differences in COVID-19. bioRxiv, 2024.doi
Aust, O.; Blanc, E.; LÜthen, M.; Hollek, V.; Astaburuaga-Garcia, R.; Klinger, B.; Trinks, A.; Beule, D.; Papke, B.; Horst, D.; Blüthgen, N.; Sers, C.; Der, C. and Morkel, M. Reporter-based screening identifies RAS-RAF stabilizing mutations as drivers of resistance to broad-spectrum RAS inhibition in colorectal cancer. bioRxiv, 2024.doi
Kassem, G. El; Sieber, A.; Klinger, B.; Uhlitz, F.; Steinbrecht, D.; Bentum, M. v.; Hillmer, J.; Schlichting, J. v.; Schäfer, R.; Blüthgen, N. and Boettcher, M. Targeted Perturb-seq Reveals EGR1 and FOS as Key Regulators of the Transcriptional RAF-MAPK Response. bioRxiv, 2024.doi
Schmiedel, J.; Marks, D. S.; Lehner, B. and Blüthgen, N. Noise control is a primary function of microRNAs and post-transcriptional regulation. bioRxiv, 2017/168641, 2017.doi
Journal papers
2024
Steinbrecht, D.; Minia, I.; Milek, M.; Meisig, J.; Blüthgen, N. and Landthaler, M. Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting. Molecular Systems Biology, online: 1-26, 2024.doipubmed
Klinger, B; Rausch, I; Sieber, A; Kutz, H; Kruse, V; Kirchner, M; Mertins, P; Kieser, A; Blüthgen, N * and *, K. D Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network. PLoS Comput Biol, 20: e1012488, 2024.doipubmed
Weii, T T; Blanc, E; Peidli, S; Bischoff, P; Trinks, A; Horst, D; Sers, C; Blüthgen, N; Beule, D; Morkel, M and Obermayer, B High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment. Int J Cancer, 155: 1655-1669, 2024.doipubmed
Ihlow, J; Penter, L; Vuong, L G; Bischoff, P; Obermayer, B; Trinks, A; Blau, O; Behnke, A; Conrad, T; Morkel, M; Wu, C J; Westermann, J; Bullinger, L; von Brünneck, A C; Blüthgen, N; Horst, D and Praktiknjo, S D Diagnosing recipient- vs. donor-derived posttransplant myelodysplastic neoplasm via targeted single-cell mutational profiling. Med, 2024.doipubmed
Astaburuaga-García, R.; Sell, T; Mutlu, S; Sieber, A; Lauber, K and Blüthgen, N Removal of Unwanted Covariance in mass cytometry data. Bioinformatics, online: btae669, 2024.doipubmed
Peidli, S.; Nouailles, G.; Wyler, E.; Adler, J. M.; Kunder, S.; Voß, A.; Kazmierski, J.; Pott, F.; Pennitz, P.; Postmus, D.; Alves, L. G. T.; Goffinet, C.; Gruber, A. D.; Blüthgen, N.; Witzenrath, M.; Trimpert, J.; Landthaler, M. and Praktiknjo, S. D. Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19. Cell Reports, 43 (6): 114328, 2024.doi
Del Olmo, M; Legewie, S; Brunner, M; Höfer, T; Kramer, A; Blüthgen, N and Herzel, H Network switches and their role in circadian clocks. J Biol Chem, 300: 107220, 2024.doipubmed
Peidli, S.; Green, T. D.; Shen, C.; Gross, T.; Min, J.; Garda, S.; Yuan, Bo; Schumacher, L. J.; Taylor-King, J. P.; Marks, D. S.; Luna, A. *; Blüthgen, N. * and Sander, C. * scPerturb: harmonized single-cell perturbation data. Nature Methods, 2024.doi
Fischer, M. M. and Blüthgen, N. On minimising tumoural growth under treatment resistance. Journal of Theoretical Biology, 579: 111716, 2024.doi
2023
Sultana, Z.; Dorel, M.; Klinger, B.; Sieber, A.; Dunkel, I.; Blüthgen, N. * and Schulz, E. G * Modeling unveils sex differences of signaling networks in mouse embryonic stem cells. Molecular Systems Biology, early online: e11510, 2023.doi
Zschaeck, S; Klinger, B; van den Hoff, J; Cegla, P; Apostolova, I; Kreissl, M C; Cholewiński, W; Kukuk, E; Strobel, H; Amthauer, H; Blüthgen, N; Zips, D and Hofheinz, F Combination of tumor asphericity and an extracellular matrix-related prognostic gene signature in non-small cell lung cancer patients. Sci Rep., 13: 20840, 2023.doipubmed
Kassuhn, W; Cutillas, P R; Kessler, M; Sehouli, J; Braicu, E I; Blüthgen, N * and Kulbe, H * In Silico Analysis Predicts Nuclear Factors NR2F6 and YAP1 as Mesenchymal Subtype-Specific Therapeutic Targets for Ovarian Cancer Patients. Cancers (Basel), 15: 3155, 2023.doipubmed
Sell, T.; Klotz, C.; Fischer, M. M.; Astaburuaga-García, R.; Krug, S.; Drost, J.; Clevers, H.; Sers, C.; Morkel, M. and Blüthgen, N. Oncogenic signaling is coupled to colorectal cancer cell differentiation state. Journal of Cell Biology, 222 (6), 2023.doi
Nouailles, G.; Adler, J. M; Pennitz, P.; Peidli, S.; Teixeira Alves, L. G.; Baumgardt, M.; Bushe, J.; Voss, A.; Langenhagen, A.; Langner, C.; Martin Vidal, R.; Pott, F.; Kazmierski, J.; Ebenig, A.; Lange, M. V; M"uhlebach, M. D; Goekeri, C.; Simmons, S.; Xing, Na; Abdelgawad, A.; Herwig, S.; Cichon, G.; Niemeyer, D.; Drosten, C.; Goffinet, C.; Landthaler, M.; Blüthgen, N.; Wu, H.; Witzenrath, M.; Gruber, A. D; Praktiknjo, S. D; Osterrieder, N.; Wyler, E.; Kunec, D. and Trimpert, J. Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nat Microbiol, 2023.doipubmed
Keyl, P; Bischoff, P; Dernbach, G; Bockmayr, M; Fritz, R; Horst, D; Blüthgen, N; Montavon, G; Müller, KR and Klauschen, F Single-cell gene regulatory network prediction by explainable AI. Nucleic Acids Res, 51: e20, 2023.doipubmed
Fischer, M. M. and Blüthgen, N. On tumoural growth and treatment under cellular dedifferentiation. Journal of Theoretical Biology, 557: 111327, 2023.doi
2022
Aguilar, C.; Pauzuolis, M.; Pompaiah, M.; Vafadarnejad, E.; Arampatzi, P.; Fischer, M.; Narres, D.; Neyazi, M.; Kayisoglu, Ö.; Sell, T.; Blüthgen, N.; Morkel, M.; Wiegering, A.; Germer, C. T.; Kircher, S.; Rosenwald, A.; Saliba, A. E. and Bartfeld, S. Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis. Nat Commun, 13 (1): 5878, 2022.pubmed
Bosdriesz, E.; Fernandes Neto, J. M.; Sieber, A.; Bernards, R.; Blüthgen, N. and Wessels, L. F. A. Identifying mutant-specific multi-drug combinations using comparative network reconstruction. iScience, 25 (8): 104760, 2022.pubmed
Seidel, F.; Cherianidou, A.; Kappenberg, F.; Marta, M.; Dreser, N.; Blum, J.; Waldmann, T.; Blüthgen, N.; Meisig, J.; Madjar, K.; Henry, M.; Rotshteyn, T.; Scholtz-Illigens, A.; Marchan, R.; Edlund, K.; Leist, M.; Rahnenführer, J.; Sachinidis, A. and Hengstler, J. G. High accuracy classification of developmental toxicants by in vitro tests of human neuroepithelial and cardiomyoblast differentiation. Cells, 11 (21): 3404, 2022.pubmed
Nell, P.; Kattler, K.; Feuerborn, D.; Hellwig, B.; Rieck, A.; Salhab, A.; Lepikhov, K.; Gasparoni, G.; Thomitzek, A.; Belgasmi, K.; Blüthgen, N.; Morkel, M.; Küppers-Munther, B.; Godoy, P.; Hay, D. C.; Cadenas, C.; Marchan, R.; Vartak, N.; Edlund, K.; Rahnenführer, J.; Walter, J. and Hengstler, J. G. Identification of an FXR-modulated liver-intestine hybrid state in iPSC-derived hepatocyte-like cells. J Hepatol, 77 (5): 1386-1398, 2022.pubmed
Berlak, M.; Tucker, E.; Dorel, M.; Winkler, A.; McGearey, A.; Rodriguez-Fos, E.; da Costa, B. M.; Barker, K.; Fyle, E.; Calton, E.; Eising, S.; Ober, K.; Hughes, D.; Koutroumanidou, E.; Carter, P.; Stankunaite, R.; Proszek, P.; Jain, N.; Rosswog, C.; Dorado-Garcia, H.; Molenaar, J. J.; Hubank, M.; Barone, G.; Anderson, J.; Lang, P.; Deubzer, H. E.; Künkele, A.; Fischer, M.; Eggert, A.; Kloft, C.; Henssen, A. G.; Boettcher, M.; Hertwig, F.; Blüthgen, N.; Chesler, L. and Schulte, J. H. Mutations in ALK signaling pathways conferring resistance to ALK inhibitor treatment lead to collateral vulnerabilities in neuroblastoma cells. Mol Cancer, 21 (1): 126, 2022.pubmed
Neumann, M.; Xu, X.; Smaczniak, C.; Schumacher, J.; Yan, W.; Blüthgen, N.; Greb, T.; Jönsson, H.; Traas, J.; Kaufmann, K. and Muino, J. M. A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data. Nat Commun, 13 (1): 2838, 2022.pubmed
Cherianidou, A.; Seidel, F.; Kappenberg, F.; Dreser, N.; Blum, J.; Waldmann, T.; Blüthgen, N.; Meisig, J.; Madjar, K.; Henry, M.; Rotshteyn, T.; Marchan, R.; Edlund, K.; Leist, M.; Rahnenführer, J.; Sachinidis, A. and Hengstler, J. G. Classification of Developmental Toxicants in a Human iPSC Transcriptomics-Based Test. Chem Res Toxicol, 35 (5): 760-773, 2022.pubmed
Wyler, E.; Adler, J. M.; Eschke, K.; Teixeira Alves, G.; Peidli, S.; Pott, F.; Kazmierski, J.; Michalick, L.; Kershaw, O.; Bushe, J.; Andreotti, S.; Pennitz, P.; Abdelgawad, A.; Postmus, D.; Goffinet, C.; Kreye, J.; Reincke, S. M.; Prüss, H.; Blüthgen, N.; Gruber, A. D.; Kuebler, W. M.; Witzenrath, M.; Landthaler, M.; Nouailles, G. and Trimpert, J. Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single-cell transcriptomics. Mol Ther, 30 (5): 1952-1965, 2022.pubmed
Georg, P. *; Astaburuaga-Garcia, R. *; Bonaguro, L. *; Brumhard, S.; Michalick, L.; Lippert, L. J.; Kostevc, T.; Gäbel, C.; Schneider, M.; Streitz, M.; Demichev, V.; Gemünd, I.; Barone, M.; Tober-Lau, P.; Helbig, E. T.; Hillus, D.; Petrov, L.; Stein, J.; Dey, H-P.; Paclik, D.; Iwert, C.; Mülleder, M.; Aulakh, S. K.; Djudjaj, S.; Bülow, R. D.; Mei, H. E.; Schulz, A. R.; Thiel, A.; Hippenstiel, S.; Saliba, A-E.; Eils, R.; Lehmann, I.; Mall, M. A.; Stricker, S.; Röhmel, J.; Corman, V. M.; Beule, D.; Wyler, E.; Landthaler, M.; Obermayer, B.; von Stillfried, S.; Boor, P.; Demir, M.; Wesselmann, H.; Suttorp, N.; Uhrig, A.; Müller-Redetzky, H.; Nattermann, J.; Kuebler, W. M.; Meisel, C.; Ralser, M.; Schultze, J. L.; Aschenbrenner, A. C.; Thibeault, C.; Kurth, F.; Sander, L. E. *; Blüthgen, N. * and Sawitzki, B. * Complement activation induces excessive T cell cytotoxicity in severe COVID-19. Cell, 185: 493-512, 2022.doi
Fischer, M M; H, H. and Blüthgen, N Mathematical modelling identifies conditions for maintaining and escaping feedback control in the intestinal epithelium. Scientific Reports, 12: 5569, 2022.doipubmed
Wyler, E; Adler, J M; Eschke, K; Alves, G T; Peidli, S; Pott, F; Kazmierski, J; Michalick, L; Kershaw, O; Bushe, J; Andreotti, S; Pennitz, P; Abdelgawad, A; Postmus, D; Goffinet, C; Kreye, J; Reincke, S M; Prüss, H; Blüthgen, N; Gruber, A D; Kuebler, W M; Witzenrath, M; Landthaler, M; Nouailles, G and Trimpert, J Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single cell transcriptomics. Mol Ther, online first, 2022.doipubmed
Bischoff, P; Trinks, A; Wiederspahn, J; Obermayer, B; Pett, JP; Jurmeister, P; Elsner, A; Dziodzio, T; Rückert, JC; Neudecker, J; Falk, C; Beule, D; Sers, C; Morkel, M; Horst, D; Klauschen, F and Blüthgen, N The single-cell transcriptional landscape of lung carcinoid tumors. Int J Cancer, early online, 2022.doipubmed
Simon, T; Riemer, P; Jarosch, A; Detjen, K; Di Domenico, A. B. F; Menne, A; Khouja, S; Monjé, N; Childs, LH; Lenze, D; Leser, U; Rossner, F; Morkel, M; Blüthgen, N; Pavel, M; Horst, D; Capper, D; Marinoni, I; Perren, A; Mamlouk, S and Sers, C DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors. Genome Med, 14: 24, 2022.doipubmed
2021
Schoetz, U; Klein, D; Hess, J; Shnayien, S; Spoerl, S; Orth, M; Mutlu, S; Hennel, R; Sieber, A; Ganswindt, U; Luka, B; Thomsen, A R; Unger, K; Jendrossek, V; Zitzelsberger, H; Blüthgen, N; Belka, C; Unkel, S; Klinger, B * and Lauber, K * Early senescence and production of senescence-associated cytokines are major determinants of radioresistance in head-and-neck squamous cell carcinoma. Cell Death Dis., 12: 1162, 2021.doipubmed
Dorel, M; Klinger, B; Mari, T; Toedling, J; Blanc, E; Messerschmidt, C; Nadler-Holly, M; Ziehm, M; Sieber, A; Hertwig, F; Beule, D; Eggert, A; Schulte, J H; Selbach, M and Blüthgen, N Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance. PLoS Comput Biol, 17: e1009515, 2021.doipubmed
Uhlitz, F *; Bischoff, P *; Peidli, S *; Sieber, A; Trinks, A; Lüthen, M; Obermayer, B; Blanc, E; Ruchiy, Y; Sell, T; Mamlouk, S; Arsie, R; Wei, T T; Klotz-Noack, K; Schwarz, R F; Sawitzki, B; Kamphues, C; Beule, D; Landthaler, M; Sers, C; Horst, D; Blüthgen, N * and Morkel, M * Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med., 13: e14123, 2021.doipubmed
Krämer, B.; Knoll, R.; Bonaguro, L.; ToVinh, M.; Raabe, J.; Astaburuaga-García, R.; Schulte-Schrepping, J.; Kaiser, K. M.; Rieke, G. J.; Bischoff, J.; Monin, M. B.; Hoffmeister, C.; Schlabe, S.; De Domenico, E.; Reusch, N.; Händler, K.; Reynolds, G.; Blüthgen, N.; Hack, G.; Finnemann, C.; Nischalke, H. D.; Strassburg, C. P.; Stephenson, E.; Su, Y.; Gardner, L.; Yuan, D.; Chen, D.; Goldman, J.; Rosenstiel, P.; Schmidt, S. V.; Latz, E.; Hrusovsky, K.; Ball, A. J.; Johnson, J. M.; Koenig, P. A.; Schmidt, F. I.; Haniffa, M.; Heath, J. R.; Kümmerer, B. M.; Keitel, V.; Jensen, B.; Stubbemann, P.; Kurth, F.; Sander, L. E.; Sawitzki, B.; Aschenbrenner, A. C.; Schultze, J. L. and Nattermann, J. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity, 54: 2650-2669, 2021.doipubmed
Kuhn, N; Klinger, B; Uhlitz, F; Sieber, A; Rivera, M; Klotz-Noack, K; Fichtner, I; Hoffmann, J; Blüthgen, N; Falk, C; Sers, C and Schäfer, R Mutation-specific effects of NRAS oncogenes in colorectal cancer cells. Adv Biol Regul., 79: 100778, 2021.doipubmed
Kassuhn, W; Klein, O; Darb-Esfahani, S; Lammert, H; Handzik, S; Taube, ET; Schmitt, WD; Keunecke, C; Horst, D; Dreher, F; George, J; Bowtell, DD; Dorigo, O; Hummel, M; Sehouli, J; Blüthgen, N; Kulbe, H and Braicu, EI Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging. Cancers, 13: 1512, 2021.doipubmed
2020
Meisig, J.; Dreser, N.; Kapitza, M.; Henry, M.; Rotshteyn, T.; Rahnenführer, J.; Hengstler, J. G.; Sachinidis, A.; Waldmann, T.; Leist, M. and Blüthgen, N. Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation. Nucleic Acids Res: 12577-12592, 2020.doipubmed
Denkena, J.; Zaisser, A.; Merz, B.; Klinger, B.; Kuhl, D.; Blüthgen, N. and Hermey, G. Neuronal activity regulates alternative exon usage. Mol Brain, 13 (1): 148, 2020.doi
Gross, T. and Blüthgen, N. Identifiability and experimental design in perturbation studies. Bioinformatics, 36: i482-i489, 2020.pubmed
Thole, T. M.; Toedling, J.; Sprüssel, A.; Pfeil, S.; Savelyeva, L.; Capper, D.; Messerschmidt, C.; Beule, D.; Groeneveld-Krentz, S.; Eckert, C.; Gambara, G.; Henssen, A. G.; Finkler, S.; Schulte, J. H.; Sieber, A.; Blüthgen, N.; Regenbrecht, C. R. A.; Künkele, A.; Lodrini, M.; Eggert, A. and Deubzer, H. E. Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model. Int J Cancer, 146 (4): 1031-1041, 2020.pubmed
Klotz-Noack, K.; Klinger, B.; Rivera, M.; Bublitz, N.; Uhlitz, F.; Riemer, P.; Lüthen, M.; Sell, T.; Kasack, K.; Gastl, B.; Ispasanie, S. S.S.; Simon, T.; Janssen, N.; Schwab, M.; Zuber, J.; Horst, D.; Blüthgen, N.; Schäfer, R.; Morkel, M. and Sers, C. SFPQ Depletion Is Synthetically Lethal with BRAFV600E in Colorectal Cancer Cells. Cell Reports, 32 (12): 108184, 2020.doi
Gastl, B.; Klotz-Noack, K.; Klinger, B.; Ispasanie, S.; Salib, K. H. F.; Zuber, J.; Mamlouk, S.; Bublitz, N.; Blüthgen, N.; Horst, D.; Morkel, M.; Schäfer, R. and Sers, C. Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe. Cell Death Dis, 11 (7): 499, 2020.pubmed
Rydenfelt, M. *; Klinger, B. *; Klünemann, M. and Blüthgen, N. SPEED2: inferring upstream pathway activity from differential gene expression. Nucleic Acids Research, 48: W307-W312, 2020.doi
Benary, M. *; Bohn, S. *,; Lüthen, M.; Nolis, I.; Blüthgen, N. * and Loewer, A. * Disentangling pro-mitotic signaling during cell cycle progression using time-resolved single-cell imaging. Cell reports, 31: 107514, 2020.doi
Saez-Rodriguez, J. and Blüthgen, N. Personalized signaling models for personalized treatments. Molecular Systems Biology, 16: e9042, 2020.doipubmed
Granada, AE; Jiménez, A; Stewart-Ornstein, J; Blüthgen, N; Reber, S; Jambhekar, A and Lahav, G The effects of proliferation status and cell cycle phase on the responses of single cells to chemotherapy. Mol Biol Cell.: mbcE19090515, 2020.doipubmed
Dreser, N; Madjar, K; Holzer, AK; Kapitza, M; Scholz, C; Kranaster, P; Gutbier, S; Klima, S; Kolb, D; Dietz, C; Trefzer, T; Meisig, J; van Thriel, C; Henry, M; Berthold, MR; Blüthgen, N; Sachinidis, A; Rahnenführer, J; Hengstler, JG; Waldmann, T and Leist, M. Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances. Arch Toxicol., 94: 151-171, 2020.doipubmed
2019
Brandt, R. *; Sell, T. *; Lüthen, M.; Uhlitz, F.; Klinger, B.; Riemer, P.; Giesecke-Thiel, C.; Schulze, S.; El-Shimy, I. A.; Kunkel, D.; Fauler, B.; Mielke, T.; Mages, N.; Herrmann, B. G; Sers, C.; Blüthgen, N. * and Morkel, M. * Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium. Nature communications, 10 (1): 2919, 2019.doi
Rydenfelt, M.; Wongchenko, M.; Klinger, B.; Yan, Y. and Blüthgen, N. The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs. Life science alliance, 2 (4): e201900445, 2019.doipubmed
Gross, T.; Wongchenko, M.; Yan, Y. and Blüthgen, N. Robust network inference using response logic. Bioinformatics, 35: i634–i642, 2019.doi
Hood, F. E. *; Klinger, B. *; Newlaczyl, A. U.; Sieber, A.; Dorel, M.; Oliver, S. P.; Coulson, J. M.; Blüthgen, N. * and Prior, I. A. * Isoform-specific Ras signaling is growth factor dependent. Molecular Biology of the Cell, 30: 1051-1128, 2019.doipubmed
2018
Klinger, B and Blüthgen, N Reverse engineering gene regulatory networks by modular response analysis – a benchmark. Essays In Biochemistry, 62: 535-547, 2018.doi
Witzel, F. and Blüthgen, N. When more is less: Dual phosphorylation protects signaling off-state against overexpression. Biophysical Journal, 115: 1383-1392, 2018.doi
Dorel, M.; Klinger, B.; Sieber, A.; Prahallad, A.; Gross, T.; Bosdriesz, E.; Wessels, L. and Blüthgen, N. Modelling Signalling Networks from Perturbation Data. Bioinformatics, 34: 4079-4086, 2018.doipubmed
Ünal, B.; Kiel, C.; Benisty, H.; Campbell, A.; Pickering, K.; Blüthgen, N.; Sansom, O. and Serrano, L. Systems level expression correlation of Ras GTPase regulators. Cell Communication and Signaling, 16: 46, 2018.doi
Bosdriesz, E; A, A P.; Klinger, B; Sieber, A; Bosma, A; Bernards, R; Blüthgen, N. and Wessels, L F A Comparative Network Reconstruction using mixed integer programming. Bioinformatics, 34: i997-i1004, 2018.doipubmed
Meisig, J. and Blüthgen, N. The gene regulatory network of mESC differentiation - a benchmark for reverse engineering methods. Philosophical Transactions B, 373: 20170222, 2018.doipubmed
Godoy, P; Schmidt-Heck, W; Hellwig, B; Nell, P; Feuerborn, D; Rahnenführer, J; Kattler, K; Walter, J; Blüthgen, N and Hengstler, J G Assessment of stem cell differentiation based on genome-wide expression profiles. Philosophical Transactions B, 373: 20170221, 2018.doipubmed
Apweiler, R.; Beissbarth, T.; Berthold, M. R; Blüthgen, N.; Burmeister, Y.; Dammann, O.; Deutsch, A.; Feuerhake, F.; Franke, A.; Hasenauer, J.; Hoffmann, S.; Höfer, T.; Jansen, P. Lm; Kaderali, L.; Klingmüller, U.; Koch, I.; Kohlbacher, O.; Kuepfer, L.; Lammert, F.; Maier, D.; Pfeifer, N.; Radde, N.; Rehm, M.; Roeder, I.; Saez-Rodriguez, J.; Sax, U.; Schmeck, B.; Schuppert, A.; Seilheimer, B.; Theis, F. J; Vera, J. and Wolkenhauer, O. Whither systems medicine?. Experimental & molecular medicine, 50 (3): e453, 2018.doipubmed
Schubert, M.; Klinger, B.; Klünemann, M.; Sieber, A.; Uhlitz, F.; Sauer, S.; Garnett, M.; Blüthgen, N. and Saez-Rodriguez, J. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nature Communications, 9: 20, 2018.doipubmed
2017
Cantini, L.; Calzone, L.; Martignetti, L.; Rydenfelt, M.; Blüthgen, N.; Barillot, E. and Zinovyev, A. Classification of gene signatures for their information value and functional redundancy. npj Systems Biology and Applications, 4: 2, 2017.doipubmed
Ünal, E B.; Uhlitz, F. and Blüthgen, N. A compendium of ERK targets. FEBS Letters, 591: 2607–2615, 2017.doi
Uhlitz, F.; Sieber, A.; Wyler, E.; Fritsche-Guenther, R.; Meisig, J.; Landthaler, M.; Klinger, B. and Blüthgen, N. An immediate-late gene expression module decodes ERK signal duration. Molecular Systems Biology, 13: 928, 2017.doi
Hermey, G.; Blüthgen, N. and Kuhl, D. Neuronal activity-regulated alternative mRNA splicing. Int. J. Biochem. Cell Biol., 91: 184-193, 2017.doipubmed
Riemer, P.; Rydenfelt, M.; Marks, M.; Eunen, K. v.; Thedieck, K.; Herrmann, B.; Blüthgen, N.; Sers, C. and Morkel, M. Oncogenic β-Catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids. Journal of Cell Biology, 216: 1567, 2017.doi
Eduati, F.; Doldàn-Martelli, V.; Klinger, B.; Cokelaer, T.; Sieber, A.; Kogera, F.; Dorel, M.; Garnett, M. J.; Blüthgen, N. * and Saez-Rodriguez, J. * Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models. Cancer Research, 77: 3364–75, 2017.doi
Zhan, Z; Mariani, L; Barozzi, I; Schulz, E G; Blüthgen, N.; Stadler, M; Tiana, G and Giorgetti, L Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Research, 27: 479-490, 2017.doi
Blüthgen, N.; Bentum, M. v.; Merz, B.; Kuhl, D. and Hermey, G. Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo. Scientific Reports, 7: 45101, 2017.doi
2016
Fritsche-Günther, R; Witzel, F; Kempa, S; Brummer, T; Sers, C and Blüthgen, N. Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis. Oncotarget, 7: 7960-9, 2016.doi
Hoelting, L.; Klima, S.; Karreman, C.; Grinberg, M.; Meisig, J.; Henry, M.; Rotshteyn, T.; Rahnenfuhrer, J.; Blüthgen, N.; Sachinidis, A.; Waldmann, T. and Leist, M. Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants. Stem Cells Transl Med, 5 (4): 476-487, 2016.pubmed
Godoy, P.; Widera, A.; Schmidt-Heck, W.; Campos, G.; Meyer, C.; Cadenas, C.; Reif, R.; Stöber, R.; Hammad, S.; Pütter, L.; Gianmoena, K.; Marchan, R.; Ghallab, A.; Edlund, K.; Nüssler, A.; Thasler, W. E; Damm, G.; Seehofer, D.; Weiss, T. S; Dirsch, O.; Dahmen, U.; Gebhardt, R.; Chaudhari, U.; Meganathan, K.; Sachinidis, A.; Kelm, J.; Hofmann, U.; Zahedi, R. P; Guthke, R.; Blüthgen, N.; Dooley, S. and Hengstler, J. G Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Archives of toxicology, 90: 2513-2529, 2016.pubmed
Rohwer, N.; Bindel, F.; Grimm, C.; Lin, S. J; Wappler, J.; Klinger, B.; Blüthgen, N.; Du Bois, I.; Schmeck, B.; Lehrach, H.; de Graauw, M.; Goncalves, E.; Saez-Rodriguez, J.; Tan, P.; Grabsch, H. I; Prigione, A.; Kempa, S. and Cramer, T. Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget, 7 (6): 6693-6710, 2016.doi
Michna, A.; Braselmann, H.; Selmansberger, M.; Dietz, A.; Hess, J.; Gomolka, M.; Hornhardt, S.; Blüthgen, N.; Zitzelsberger, H. and Unger, K. Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data. PloS one, 11 (8): e0160791, 2016.doi
Shinde, V.; Perumal Srinivasan, S.; Henry, M.; Rotshteyn, T.; Hescheler, J.; Rahnenfuhrer, J.; Grinberg, M.; Meisig, J.; Blüthgen, N.; Waldmann, T.; Leist, M.; Hengstler, J. G. and Sachinidis, A. Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells. Stem Cell Research and Therapy, 7 (1): 190, 2016.doi
Schulthess, P.; Löffler, A.; Vetter, S.; Kreft, L.; Schwarz, M; Braeuning, A. * and Blüthgen, N. * Signal Integration by the CYP1A1 Promoter – A Quantitative Study. Nucleic Acids Research, 43: 5318-30, 2015.doipubmed
Witzel, F; Fritsche-Guenther, R; Lehmann, N; Sieber, A and Blüthgen, N Analysis of impedance-based cellular growth assays. Bioinformatics, 31: 1258-1266, 2015.doipubmed
Schmiedel, J.M.; Klemm, S.; Zheng, Y.; Sahay, A.; Blüthgen, N. *; Marks, D.S. * and Oudenaarden, A.v. * MicroRNA control of protein expression noise. Science, 348: 128-132, 2015.doipubmed
Murakawa, Y.; Hinz, M.; Mothes, J.; Schuetz, A.; Uhl, M.; Wyler, E.; Yasuda, T.; Mastrobuoni, G.; Friedel, C.; Dölken, L.; Kempa, S.; Schmidt-Supprian, M.; Blüthgen, N.; Backofen, R.; Heinemann, U.; Wolf, J.; Scheidereit, C. and Landthaler, M. RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. Nature communications, 6: 7367, 2015.doipubmed
Thomas, P.; Durek, P.; Solt, I.; Klinger, B.; Witzel, F.; Schulthess, P.; Mayer, Y.; Tikk, D.; Blüthgen, N. * and Leser, U * Computer-assisted curation of a human regulatory core network from the biological literature. Bioinformatics, 31: 1258-1266, 2015.doipubmed
Rempel, E; Hoelting, L; Waldmann, T; Balmer, N V; Schildknecht, S; M, G.; Das Gaspar, J A; Shinde, V; Stöber, R; Marchan, R; van Thriel, C; Liebing, J; Meisig, J; Blüthgen, N; Sachinidis, A; Rahnenführer, J; Hengstler, J G and M, L. A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors. Arch Toxicol, 89: 1599-618, 2015.doipubmed
Staudacher, J.; Naarmann-de Vries, I.; Ujvari, S.; Klinger, B.; Kasim, M.; Benko, E.; Ostareck-Lederer, A.; Ostareck, D.; Bondke Persson, A.; Lorenzen, S.; Meier, J.; Blüthgen, N.; Persson, P.; Henrion-Caude, A.; Mrowka, R. and Fähling, M. Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Research, 43: 3219-3236, 2015.doipubmed
Bastiaens, P.; Birtwistle, M.; Blüthgen, N.; Bruggeman, F.; Cho, K-H.; Cosentino, C.; Fuente, A. de la; Hoek, J.; Kiyatkin, A.; Klamt, S.; Kolch, W.; Legewie, S.; Mendes, P.; Naka, T.; Santra, T.; Sontag, E.; Westerhoff, H. and Kholodenko, B. Silence on the relevant literature and errors in implementation. Nature Biotechnology, 33: 336-339, 2015.doipubmed
Amos, M.; Axmann, I. M.; Blüthgen, N.; de la Cruz, F.; Jaramillo, A.; Rodriguez-Paton, A. and Simmel, F. Bacterial computing with engineered populations. Philos Trans A, 373 (2046), 2015.pubmed
2014
Schulz, E. G; Meisig, J.; Nakamura, T.; Okamoto, I.; Sieber, A.; Picard, C.; Borensztein, M.; Saitou, M.; Blüthgen, N. and Heard, E. The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network. Cell stem cell, 14 (2): 203-216, 2014.doipubmed
Klinger, B. and Blüthgen, N. Consequences of feedback in signal transduction for targeted therapies. Biochem. Soc. Trans., 42: 770-775, 2014.doipubmed
Killig, M.; Friedrichs, B.; Meisig, J.; Gentilini, C.; Blüthgen, N.; Loddenkemper, C.; Labopin, M.; Basara, N.; Pfrepper, C.; Niederwieser, D. W.; Uharek, L. and Romagnani, C. Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation. Eur. J. Immunol., 44: 2822-34, 2014.doipubmed
2013
Hermey, G.; Mahlke, C.; Gutzmann, J.; Schreiber, J.; Blüthgen, N. and Kuhl, D. Genome-wide profiling of the activity-dependent hippocampal transcriptome. PLOS One, 8: e76903, 2013.doi
Bentele, K.; Saffert, P.; Rauscher, R.; Ignatova, Z. and Blüthgen, N. Efficient translation initiation dictates codon usage at gene start. Molecular Systems Biology, 9: 675, 2013.doipubmed
Klinger, B.; Sieber, A.; Fritsche-Guenther, R.; Witzel, F.; Berry, L.; Schumacher, D.; Yan, Y.; Durek, P.; Merchant, M.; Schäfer, R.; Sers, C. and Blüthgen, N. Network quantification of EGFR signaling unveils potential for targeted combination therapy. Molecular Systems Biology, 9: 673, 2013.doipubmed
Glatzer, T.; Killig, M.; Meisig, J.; Ommert, I.; Babic, M. L-E. M.; Paclik, D.; Blüthgen, N.; Seidl, R.; Seifarth, C.; Gröne, J.; Lenarz, M.; Stölzel, K.; Fugmann, D.; Porgador, A.; Hauser, A.; Karlas, A. and Romagnani, C. RORγt+ innate lymphoid cells acquire a pro-inflammatory program upon engagement of the activating receptor NKp44. Immunity, 38: 1223-1235, 2013.doi
Witzel, F.; Maddison, L.E. and Blüthgen, N How Scaffolds shape MAPK signalling: What we know and opportunities for systems approaches. Frontiers in Systems Biology, 3: 475, 2012.doipubmed
Fähling, M; Persson, A B.; Klinger, B; Benko, E; Steege, A; Kasim, M; Patzak, A; Persson, PB; Wolf, G; Blüthgen, N and Mrowka, R Multi-level regulation of HIF-1 signalling by TTP. Mol Biol Cell, 23: 4129-4141, 2012.doipubmed
Stelniec, I; Legewie, S; Tchernitsa, O; Witzel, F; Klinger, B; Sers, C; Herzel, H; Blüthgen, N. * and Schäfer, R. * Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS. Molecular Systems Biology, 8: 601, 2012.doipubmed
Nora, EP; Lajoie, BR; Schulz, EG; Giorgetti, L; Okamoto, I; Servant, N; Piolot, T; Berkum, NL v.; Meisig, J; Sedat, J; Gribnau, J; Barillot, E; Blüthgen, N; Dekker, J * and Heard, E * Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 485: 381-385, 2012.doipubmed
2011
Fritsche-Guenther, R.; Witzel, F.; Sieber, A.; Herr, R.; Schmidt, N.; Braun, S.; Brummer, T.; Sers, C. and Blüthgen, N. Strong negative feedback from Erk to Raf confers robustness to MAPK signalling. Mol Syst Biol, 7: 489, 2011.doipubmed
Schulthess, P. and Blüthgen, N. From Reaction Networks to Information Flows -- Using Modular Response Analysis to Track Information in Signalling Networks. Methods in Enzymology, 500: 397-409, 2011.doipubmed
2010
Jürchot, K.; Kunban, R-J.; Krecht, T.; Blüthgen, N.; Stein, U.; Walther, W.; Friese, C.; Kielbasa, S. M; Ungethüm, U.; Lund, P.; Knösel, T.; Kemmner, W.; Morkel, M.; Fritzmann, J.; Schlag, P. M.; Birchmeier, W.; Krueger, T.; Sperling, S.; Sers, C.; Royer, H-D.; Herzel, H. and Schäfer, R. Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells. PLoS Genetics, 6: e1001231, 2010.doi
Kielbasa, SM; Klein, H.; Roider, H.; Vingron, M. and Blüthgen, N TransFind - Predicting transcriptional regulators for gene sets. Nucleic Acids Research, 38: W275-W280, 2010.doi
Kielbasa, SM; Blüthgen, N; Fahling, M, and Mrowka, R Targetfinder.org: a resource for systematic discovery of transcription factor target genes. Nucleic Acids Research, 38: W233-W238, 2010.doi
Parikh, J; Klinger, B; Xia, Y; Marto, JA and Blüthgen, N Discovering causal signaling pathways through gene expression patterns. Nucleic Acids Research, 38: W109-W117, 2010.doi
Blüthgen, N. Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction. Molecular Biosystems, 6: 1277-1284, 2010.doi
Wolkenhauer, O.; Auffray, C.; Baltrusch, S.; Blüthgen, N.; Byrne, H.; Cascante, M.; Ciliberto, A.; Dale, T.; Drasdo, D.; Fell, D.; Ferrell, J. E; Gallahan, D.; Gatenby, R.; Günther, U.; Harms, B. D; Herzel, H.; Junghanss, C.; Kunz, M.; Leeuwen, I. v.; Lenormand, P.; Levi, F.; Linnebacher, M.; Lowengrub, J.; Maini, P. K; Malik, A.; Rateitschak, K.; Sansom, O.; Sch"afer, R.; Schürrle, K.; Sers, C.; Schnell, S.; Shibata, D.; Tyson, J.; Vera, J.; White, M.; Zhivotovsky, B. and Jaster, R. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res, 70 (1): 12-3, 2010.doipubmed
2009
Blüthgen, N.; Legewie, S.; Kielbasa, S. M; Schramme, A.; Tchernitsa, O.; Keil, J.; Solf, A.; Vingron, M.; Sch"afer, R.; Herzel, H. and Sers, C. A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts. FEBS J, 276 (4): 1024-35, 2009.doipubmed
Wolkenhauer, O; Fell, D; Meyts, P De; Blüthgen, N; Herzel, H; Nov`ere, N Le; Höfer, T; Schürrle, K and Leeuwen, I v. SysBioMed report: Advancing systems biology for medical applications. IET systems biology, 3 (3): 131, 2009.doipubmed
Bruggeman, F. J; Blüthgen, N. and Westerhoff, H. V Noise management by molecular networks. PLoS Comput Biol, 5 (9): e1000506, 2009.doipubmed
2008
Herzel, H. and Blüthgen, N. Mathematical models in mammalian cell biology. Genome Biol, 9 (70er): 316, 2008.doipubmed
Bevilacqua, A.; Wilkinson, S. J; Dimelow, R.; Murabito, E.; Rehman, S.; Nardelli, M.; Eunen, K. v.; Rossell, S.; Bruggeman, F. J; Blüthgen, N.; Vos, D. De; Bouwman, J.; Bakker, B. M and Westerhoff, H. V Vertical systems biology: from DNA to flux and back. SEB experimental biology series, 61: 65-91, 2008.pubmed
Mrowka, R.; Blüthgen, N. and F"ahling, M. Seed-based systematic discovery of specific transcription factor target genes. FEBS J, 275 (12): 3178-92, 2008.doipubmed
Legewie, S.; Herzel, H.; Westerhoff, H. V and Blüthgen, N. Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol, 4: 190, 2008.doipubmed
Blüthgen, N. and Legewie, S. Systems analysis of MAPK signal transduction. Essays Biochem, 45: 95-107, 2008.doipubmed
Herrgaard, M. J; Swainston, N.; Dobson, P.; Dunn, W. B; Arga, K Y. c.; Arvas, M.; Blüthgen, N.; Borger, S.; Costenoble, R.; Heinemann, M.; Hucka, M.; Nov`ere, N. Le; Li, P.; Liebermeister, W.; Mo, M. L; Oliveira, A. P.; Petranovic, D.; Pettifer, S.; Simeonidis, E.; Smallbone, K.; Spasi'c, I.; Weichart, D.; Brent, R.; Broomhead, D. S; Westerhoff, H. V; Kirdar, B.; Penttil"a, M.; Klipp, E.; Palsson, B. O; Sauer, U.; Oliver, S. G; Mendes, P.; Nielsen, J. and Kell, D. B A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol, 26 (10): 1155-60, 2008.doipubmed
2007
Legewie, S.; Schoeberl, B.; Blüthgen, N. and Herzel, H. Competing docking interactions can bring about bistability in the MAPK cascade. Biophys J, 93 (7): 2279-88, 2007.doipubmed
Bluthgen, N.; Menzel, F.; Hovestadt, T.; Fiala, B. and Blüthgen, N. Specialization, constraints, and conflicting interests in mutualistic networks. Curr Biol, 17 (4): 341-6, 2007.doipubmed
Mrowka, R.; Steege, A.; Kaps, C.; Herzel, H.; Thiele, B. J; Persson, P. B and Blüthgen, N. Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity. Nucleic Acids Res, 35 (15): 5120-9, 2007.doipubmed
2006
Bandapalli, O. R.; Geheeb, M.; Kobelt, D.; Kuehnle, K.; Elezkurtaj, S.; Herrmann, J.; Gressner, A. M; Weiskirchen, R.; Beule, D.; Blüthgen, N.; Herzel, H.; Franke, C. and Brand, K. Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases. Int J Cancer, 118 (1): 74-89, 2006.doipubmed
Bluthgen, N.; Menzel, F. and Blüthgen, N. Measuring specialization in species interaction networks. BMC Ecol, 6: 9, 2006.doipubmed
Legewie, S.; Blüthgen, N. and Herzel, H. Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol, 2 (9): e120, 2006.doipubmed
Blüthgen, N.; Bruggeman, F. J; Legewie, S.; Herzel, H.; Westerhoff, H. V and Kholodenko, B. N Effects of sequestration on signal transduction cascades. FEBS J, 273 (5): 895-906, 2006.doipubmed
Blüthgen, N. Sequestration shapes the response of signal transduction cascades. IUBMB Life, 58 (11): 659-63, 2006.doipubmed
2005
Blüthgen, N.; Kielbasa, S. M and Herzel, H. Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res, 33 (1): 272-9, 2005.doipubmed
Legewie, S.; Blüthgen, N.; Sch"afer, R. and Herzel, H. Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction. PLoS Comput Biol, 1 (5): e54, 2005.doipubmed
Kleinschmidt, M.; Grundmann, O.; Blüthgen, N.; Mösch, H-U. and Braus, G. H Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions. Mol Genet Genomics, 273 (5): 382-93, 2005.doipubmed
Legewie, S.; Blüthgen, N. and Herzel, H. Quantitative analysis of ultrasensitive responses. FEBS J, 272 (16): 4071-9, 2005.doipubmed
2004
Blüthgen, N.; Kielbasa, S. M; Cajavec, B. and Herzel, H. HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics, 20 (1): 125-6, 2004.pubmed
Blüthgen, N. and Herzel, H. How robust are switches in intracellular signaling cascades?. J Theor Biol, 225 (3): 293-300, 2003.pubmed
2000
Bluthgen, N.; Verhaagh, M; Goit'ia, W and Blüthgen, N. Ant nests in tank bromeliads--an example of non-specific interaction. Insectes sociaux, 2000.pubmed