Nils Blüthgen

Summary

Affiliation: Humboldt University
Country: Germany

Publications

  1. ncbi Sequestration shapes the response of signal transduction cascades
    Nils Blüthgen
    Molecular Neurobiology, Free University Berlin, and Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany
    IUBMB Life 58:659-63. 2006
  2. ncbi Effects of sequestration on signal transduction cascades
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Germany
    FEBS J 273:895-906. 2006
  3. ncbi A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    FEBS J 276:1024-35. 2009
  4. ncbi Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS
    Iwona Stelniec-Klotz
    Laboratory of Molecular Tumour Pathology, Institute of Pathology, Charite Universitatsmedizin Berlin, Berlin, Germany
    Mol Syst Biol 8:601. 2012
  5. ncbi HOMGL-comparing genelists across species and with different accession numbers
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, D 10115, Germany
    Bioinformatics 20:125-6. 2004
  6. ncbi Recurrent design patterns in the feedback regulation of the mammalian signalling network
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    Mol Syst Biol 4:190. 2008
  7. ncbi Competing docking interactions can bring about bistability in the MAPK cascade
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    Biophys J 93:2279-88. 2007
  8. ncbi Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 2:e120. 2006
  9. ncbi Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 1:e54. 2005
  10. ncbi Seed-based systematic discovery of specific transcription factor target genes
    Ralf Mrowka
    Paul Ehrlich Zentrum für Experimentelle Medizin, AG Systems Biology Computational Physiology, Tucholskystrasse 2, Berlin, Germany
    FEBS J 275:3178-92. 2008

Collaborators

Detail Information

Publications18

  1. ncbi Sequestration shapes the response of signal transduction cascades
    Nils Blüthgen
    Molecular Neurobiology, Free University Berlin, and Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany
    IUBMB Life 58:659-63. 2006
    ..However, sequestration due to high-affinity enzymes can shape the dynamics and steady-state behaviour of signal transduction cascades in different ways, some of which are discussed in this review...
  2. ncbi Effects of sequestration on signal transduction cascades
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Germany
    FEBS J 273:895-906. 2006
    ..We show that sequestration limits ultrasensitivity in this cascade and may thereby abolish the potential for oscillations induced by negative feedback...
  3. ncbi A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    FEBS J 276:1024-35. 2009
    ..Taken together, an integrated systems biological approach reveals that transcriptional negative feedback controls the kinetics and the extent of MAPK activation under both physiological and pathological conditions...
  4. ncbi Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS
    Iwona Stelniec-Klotz
    Laboratory of Molecular Tumour Pathology, Institute of Pathology, Charite Universitatsmedizin Berlin, Berlin, Germany
    Mol Syst Biol 8:601. 2012
    ..The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype...
  5. ncbi HOMGL-comparing genelists across species and with different accession numbers
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, D 10115, Germany
    Bioinformatics 20:125-6. 2004
    ..We illustrate the use of HOMGL with respect to microarray studies and promoter analysis. AVAILABILITY: http://homgl.biologie.hu-berlin.de/..
  6. ncbi Recurrent design patterns in the feedback regulation of the mammalian signalling network
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    Mol Syst Biol 4:190. 2008
    ....
  7. ncbi Competing docking interactions can bring about bistability in the MAPK cascade
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    Biophys J 93:2279-88. 2007
    ....
  8. ncbi Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 2:e120. 2006
    ..g., Casp3 and Casp9), the feedback mechanism described in this paper is likely to be a widespread principle on how cells achieve ultrasensitivity, bistability, and irreversibility...
  9. ncbi Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 1:e54. 2005
    ..Additionally, switch-like phenomena such as ultrasensitization are known to contribute to bistability, oscillations, noise reduction, and cellular heterogeneity...
  10. ncbi Seed-based systematic discovery of specific transcription factor target genes
    Ralf Mrowka
    Paul Ehrlich Zentrum für Experimentelle Medizin, AG Systems Biology Computational Physiology, Tucholskystrasse 2, Berlin, Germany
    FEBS J 275:3178-92. 2008
    ..We present a robust and reliable method to enhance the genome-wide prediction of specific transcription factor target genes that exploits the vast amount of expression information available in public databases today...
  11. ncbi Biological profiling of gene groups utilizing Gene Ontology
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Germany
    Genome Inform 16:106-15. 2005
    ..The software package GOSSIP implements our method and is made freely available at http://gossip.gene-groups.net/...
  12. ncbi Quantitative analysis of ultrasensitive responses
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University Berlin, Germany
    FEBS J 272:4071-9. 2005
    ..e. over the whole stimulus range) we introduce the integral-based relative amplification coefficient. Our relative amplification approach can easily be extended to monotonically decreasing, bell-shaped or nonsaturated responses...
  13. ncbi Mathematical models in mammalian cell biology
    Hanspeter Herzel
    Institute for Theoretical Biology, Humboldt University, Invalidenstrasse, 10115 Berlin, Germany
    Genome Biol 9:316. 2008
    ..A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008...
  14. ncbi Strong negative feedback from Erk to Raf confers robustness to MAPK signalling
    Raphaela Fritsche-Guenther
    Institute of Pathology, Charite Universitatsmedizin Berlin, Berlin, Germany
    Mol Syst Biol 7:489. 2011
    ..Surprisingly, robustness is provided through a fast post-translational mechanism although variation of Erk levels occurs on a timescale of days...
  15. ncbi Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells
    Karsten Jurchott
    Laboratory of Molecular Tumor Pathology, Universitatsmedizin Berlin, Berlin, Germany
    PLoS Genet 6:e1001231. 2010
    ..This suggests that MEK/ERK-dependent, YBX1-regulated target genes are involved in executing malignant properties...
  16. ncbi From reaction networks to information flow--using modular response analysis to track information in signaling networks
    Pascal Schulthess
    Institute of Pathology, Charite Universitatsmedizin Berlin, Chariteplatz 1, Berlin, Germany
    Methods Enzymol 500:397-409. 2011
    ....
  17. ncbi Prediction of cis-regulatory elements of coregulated genes
    Szymon M Kiełbase
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    Genome Inform 15:117-24. 2004
    ..Indications of overrepresented Elk-1 and AP-1 motifs are found via a comparison with shuffled sequences. In some promoters consistent predictions of clustered binding sites were obtained...
  18. ncbi How robust are switches in intracellular signaling cascades?
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University, Invalidenstrasse 43, D 10115 Berlin, Germany
    J Theor Biol 225:293-300. 2003
    ..Our results indicate that amplification of ultrasensitivity in cascades and multisite phosphorylation might be a design principle to achieve robust switches...