Publications

2017

  1. Ünal, E B., Uhlitz, F. and Blüthgen, N.
    A compendium of ERK targets.
    FEBS Letters, 591: 2607–2615, 2017. doi.. 
  2. 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.. 
  3. Hermey, G., Blüthgen, N. and Kuhl, D.
    Neuronal activity-regulated alternative mRNA splicing.
    Int. J. Biochem. Cell Biol., 91: 184-193, 2017. pubmed..  doi.. 
  4. 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.. 
  5. 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.. 
  6. 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.. 
  7. 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

  1. 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.. 
  2. Hoelting, L., Klima, S., Karreman, C., Grinberg, M., Meisig, J., Henry, M., Rotshteyn, T., Rahnenfuhrer, J., Bluthgen, 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.. 
  3. 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.. 
  4. Rohwer, N., Bindel, F., Grimm, C., Lin, S. J, Wappler, J., Klinger, B., Blüthgen, N., I., Du B., Schmeck, B., Lehrach, H., M., de G., 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.. 
  5. 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.. 
  6. Shinde, V., S., Perumal S., Henry, M., Rotshteyn, T., Hescheler, J., Rahnenfuhrer, J., Grinberg, M., Meisig, J., Bluthgen, 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.. 

2015

  1. Blüthgen, N.
    Signaling output: it's all about timing and feedbacks.
    Molecular Systems Biology, 11: 843, 2015. pubmed..  doi.. 
  2. 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. pubmed..  doi.. 
  3. Witzel, F, Fritsche-Guenther, R, Lehmann, N, Sieber, A and Blüthgen, N.
    Analysis of impedance-based cellular growth assays.
    Bioinformatics, 31: 1258-1266, 2015. pubmed..  doi.. 
  4. 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. pubmed..  doi.. 
    (see also Perspective
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  5. 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. pubmed..  doi.. 
  6. 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. pubmed..  doi.. 
  7. Dreser, N., Zimmer, B., Dietz, C., Sugis, E., Pallocca, G., Nyffeler, J., Meisig, J., Bluthgen, N., Berthold, M. R., Waldmann, T. and Leist, M.
    Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling.
    Neurotoxicology, 50: 56-70, 2015. pubmed..  doi.. 
  8. Rempel, E, Hoelting, L, Waldmann, T, Balmer, N V, Schildknecht, S, M, G., A, Das G. J, Shinde, V, Stöber, R, Marchan, R, C, van T., 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. pubmed..  doi.. 
  9. Staudacher, J., I., Naarmann-de V., Ujvari, S., Klinger, B., Kasim, M., Benko, E., Ostareck-Lederer, A., Ostareck, D., A., Bondke P., 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. pubmed..  doi.. 
  10. Bastiaens, P., Birtwistle, M., Blüthgen, N., Bruggeman, F., Cho, K., 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. pubmed..  doi.. 
  11. Amos, M., Axmann, I. M., Bluthgen, N., F., de la C., Jaramillo, A., Rodriguez-Paton, A. and Simmel, F.
    Bacterial computing with engineered populations.
    Philos Trans A, 373 (2046), 2015. pubmed.. 

2014

  1. 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. pubmed..  doi.. 
    (see preview
  2. Klinger, B. and Blüthgen, N.
    Consequences of feedback in signal transduction for targeted therapies.
    Biochem. Soc. Trans., 42: 770-775, 2014. pubmed..  doi.. 
  3. Killig, M., Friedrichs, B., Meisig, J., Gentilini, C., Bluthgen, 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. pubmed..  doi.. 

2013

  1. 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.. 
  2. Bentele, K., Saffert, P., Rauscher, R., Ignatova, Z. and Bluthgen, N.
    Efficient translation initiation dictates codon usage at gene start.
    Molecular Systems Biology, 9: 675, 2013. pubmed..  doi.. 
  3. 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. pubmed..  doi.. 
  4. Glatzer, T., Killig, M., Meisig, J., Ommert, I., Babic, M. L. 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.. 
  5. Blüthgen, N and Legewie, S.
    Robustness of signal transduction pathways.
    Cellular and Molecular Life Sciences, 70: 2259-2269, 2013. pubmed..  doi..  full text.. 

2012

  1. 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. pubmed..  doi.. 
  2. 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. pubmed..  doi..  full text.. 
  3. 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. pubmed..  doi..  full text.. 
  4. 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. pubmed..  doi.. 
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2011

  1. 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. pubmed..  doi..  full text.. 
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  2. 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. pubmed..  doi..  full text.. 

2010

  1. Jürchot, K., Kunban, R., 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., 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..  full text.. 
  2. 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..  full text.. 
  3. 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..  full text.. 
  4. 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..  full text.. 
  5. Blüthgen, N.
    Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction.
    Molecular Biosystems, 6: 1277 - 1284, 2010. doi.. 
  6. 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., Schäfer, 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. pubmed..  doi.. 

2009

  1. Blüthgen, N., Legewie, S., Kielbasa, S. M, Schramme, A., Tchernitsa, O., Keil, J., Solf, A., Vingron, M., Schäfer, 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. pubmed..  doi..  full text.. 
  2. Wolkenhauer, O, Fell, D, Meyts, P De, Blüthgen, N, Herzel, H, Novère, 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. pubmed..  doi..  full text.. 
  3. Bruggeman, F. J, Blüthgen, N. and Westerhoff, H. V.
    Noise management by molecular networks.
    PLoS Comput Biol, 5 (9): e1000506, 2009. pubmed..  doi.. 

2008

  1. Herzel, H. and Blüthgen, N.
    Mathematical models in mammalian cell biology.
    Genome Biol, 9 (70er): 316, 2008. pubmed..  doi..  full text.. 
  2. 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..  full text.. 
  3. Mrowka, R., Blüthgen, N. and Fähling, M.
    Seed-based systematic discovery of specific transcription factor target genes.
    FEBS J, 275 (12): 3178-92, 2008. pubmed..  doi..  full text.. 
  4. 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. pubmed..  doi..  full text.. 
  5. Blüthgen, N. and Legewie, S.
    Systems analysis of MAPK signal transduction.
    Essays Biochem, 45: 95-107, 2008. pubmed..  doi..  full text.. 
  6. 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., Novère, 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., Penttilä, 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. pubmed..  doi..  full text.. 

2007

  1. 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. pubmed..  doi..  full text.. 
  2. Blüthgen, 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. pubmed..  doi..  full text.. 
    (Cover story / Dispatch
  3. 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. pubmed..  doi..  full text.. 

2006

  1. 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. pubmed..  doi..  full text.. 
  2. Blüthgen, N., Menzel, F. and Blüthgen, N.
    Measuring specialization in species interaction networks.
    BMC Ecol, 6: 9, 2006. pubmed..  doi..  full text.. 
  3. 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. pubmed..  doi..  full text.. 
    (Editor's Choice in Science 314: 389
  4. 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. pubmed..  doi..  full text.. 
    (2nd most read paper in FEBS J 2006
  5. Blüthgen, N.
    Sequestration shapes the response of signal transduction cascades.
    IUBMB Life, 58 (11): 659-63, 2006. pubmed..  doi..  full text.. 

2005

  1. Blüthgen, N., Kielbasa, S. M and Herzel, H.
    Inferring combinatorial regulation of transcription in silico.
    Nucleic Acids Res, 33 (1): 272-9, 2005. pubmed..  doi..  full text.. 
  2. Legewie, S., Blüthgen, N., Schäfer, R. and Herzel, H.
    Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction.
    PLoS Comput Biol, 1 (5): e54, 2005. pubmed..  doi..  full text.. 
  3. Blüthgen, N., Brand, K., Cajavec, B., Swat, M., Herzel, H. and Beule, D.
    Biological profiling of gene groups utilizing Gene Ontology.
    Genome informatics International Conference on Genome Informatics, 16 (1): 106-15, 2005. pubmed..  full text.. 
  4. Kleinschmidt, M., Grundmann, O., Blüthgen, N., Mösch, H. and Braus, G. H.
    Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions.
    Mol Genet Genomics, 273 (5): 382-93, 2005. pubmed..  doi..  full text.. 
  5. Legewie, S., Blüthgen, N. and Herzel, H.
    Quantitative analysis of ultrasensitive responses.
    FEBS J, 272 (16): 4071-9, 2005. pubmed..  doi..  full text.. 

2004

  1. 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..  full text.. 
  2. Kielbase, S. M, Blüthgen, N., Sers, C., Schäfer, R. and Herzel, H.
    Prediction of cis-regulatory elements of coregulated genes.
    Genome informatics International Conference on Genome Informatics, 15 (1): 117-24, 2004. pubmed..  full text.. 

2003

  1. Blüthgen, N. and Herzel, H.
    How robust are switches in intracellular signaling cascades?.
    J Theor Biol, 225 (3): 293-300, 2003. pubmed..  full text.. 

2000

  1. Blüthgen, N., Verhaagh, M, Goit'ia, W and Blüthgen, N.
    Ant nests in tank bromeliads--an example of non-specific interaction.
    Insectes sociaux, 2000. pubmed..  full text.. 

* Joint First or Last Author