Publications

Journal Papers

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.. 
    (evaluated in Faculty of 1000 as Must Read) 
  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.. 

Books / Conference Papers

2008

  1. Bevilacqua, A., Wilkinson, S. J., Dimelow, R., Murabito, E., Rehman, S., Nardelli, M., Eunen, K. v., Rossell, S., Bruggeman, F. J., Bluthgen, N., Vos, D. de, Bouwman, J., Bakker, B. M. and Westerhoff, H. V.
    Vertical systems biology: From DNA to flux and back.
    In Practical Systems Biology, pages 65-92, Taylor and Francis, 2008. pubmed.. 

2007

  1. Blüthgen, N., Legewie, S., Herzel, H. and Kholodenko, B.
    Mechanisms generating ultrasensitivity, bistability and oscillation in signal transduction.
    In Introduction to Systems Biology, Sangdun Choi, 2007. doi..  full text.. 
  2. Blüthgen, N., Kielbasa, S. M. and Beule, D.
    Handling, comparing and interpreting gene groups.
    In Introduction to Systems Biology, Humana Press, 2007. doi..  full text.. 

2004

  1. Kielbasa, S. M., Blüthgen, N. and Herzel, H.
    Genome-wide analysis of functions regulated by sets of transcription factors.
    In German Conference on Bioinformatics 2004, pages 105-113, Gesellschaft für Informatik, 2004.

2001

  1. Blüthgen, N. and Herzel, H.
    MAP-Kinase-Cascade: Switch, Amplifier or Feedback Controller?.
    In 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks, pages 55-62, Logos Verlag, 2001.