BORIS KHOLODENKO

Summary

Affiliation: Thomas Jefferson University
Country: USA

Publications

  1. doi The topology design principles that determine the spatiotemporal dynamics of G-protein cascades
    Mikhail A Tsyganov
    Institute of Theoretical and Experimental Biophysics, Pushchino, Moscow Region, Russia
    Mol Biosyst 8:730-43. 2012
  2. ncbi Quantification of short term signaling by the epidermal growth factor receptor
    B N Kholodenko
    Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
    J Biol Chem 274:30169-81. 1999
  3. ncbi Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    J Exp Biol 206:2073-82. 2003
  4. pmc Untangling the wires: a strategy to trace functional interactions in signaling and gene networks
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 99:12841-6. 2002
  5. ncbi MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?
    Boris N Kholodenko
    Dept of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    Trends Cell Biol 12:173-7. 2002
  6. pmc Diffusion control of protein phosphorylation in signal transduction pathways
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
    Biochem J 350:901-7. 2000
  7. ncbi Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
    Metab Eng 2:1-13. 2000
  8. ncbi Why cytoplasmic signalling proteins should be recruited to cell membranes
    B N Kholodenko
    Dept of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Trends Cell Biol 10:173-8. 2000
  9. ncbi Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Eur J Biochem 267:1583-8. 2000
  10. pmc Multistrip Western blotting to increase quantitative data output
    Edita Aksamitiene
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Electrophoresis 28:3163-73. 2007

Collaborators

  • Anatoly Kiyatkin
  • Hans V Westerhoff
  • O V Demin
  • Stefan Legewie
  • Nick I Markevich
  • Jan B Hoek
  • Nikolay M Borisov
  • Mikhail A Tsyganov
  • Herbert M Sauro
  • Frank J Bruggeman
  • Vijay Chickarmane
  • Edita Aksamitiene
  • Holger Conzelmann
  • Nils Blüthgen
  • Mark A Peletier
  • Walter Kolch
  • Julio Saez-Rodriguez
  • Ernst D Gilles
  • Hanspeter Herzel
  • Thomas Sauter

Detail Information

Publications21

  1. doi The topology design principles that determine the spatiotemporal dynamics of G-protein cascades
    Mikhail A Tsyganov
    Institute of Theoretical and Experimental Biophysics, Pushchino, Moscow Region, Russia
    Mol Biosyst 8:730-43. 2012
    ..This first, complete classification of all possible interaction circuitries systematically links topological design to the spatiotemporal dynamics of G-protein cascades, predicting and explaining experimentally observed behavior...
  2. ncbi Quantification of short term signaling by the epidermal growth factor receptor
    B N Kholodenko
    Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
    J Biol Chem 274:30169-81. 1999
    ..Quantitation of signaling network responses to growth factors allows us to assess how cells process information controlling their growth and differentiation...
  3. ncbi Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    J Exp Biol 206:2073-82. 2003
    ..We hypothesize that ligand-independent waves of receptor activation or/and traveling waves of phosphorylated kinases emerge to spread the signals over long distances...
  4. pmc Untangling the wires: a strategy to trace functional interactions in signaling and gene networks
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 99:12841-6. 2002
    ..The method is tested and illustrated by using computer-generated responses of a modeled mitogen-activated protein kinase cascade and gene network...
  5. ncbi MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?
    Boris N Kholodenko
    Dept of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
    Trends Cell Biol 12:173-7. 2002
    ..The proposed mechanism explains recent observations that MAPK activation can be strongly suppressed by various inhibitors of endocytosis...
  6. pmc Diffusion control of protein phosphorylation in signal transduction pathways
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
    Biochem J 350:901-7. 2000
    ..The kinase can contribute significantly to the control of the absolute value of the phospho-protein gradient...
  7. ncbi Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
    Metab Eng 2:1-13. 2000
    ..An explicit solution to this problem of engineering metabolism is then given in the form of a single matrix equation...
  8. ncbi Why cytoplasmic signalling proteins should be recruited to cell membranes
    B N Kholodenko
    Dept of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Trends Cell Biol 10:173-8. 2000
    ..We discuss an important structural constraint imposed by this mechanism on signal transduction proteins that might also account for the presence of adaptor proteins...
  9. ncbi Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
    B N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Eur J Biochem 267:1583-8. 2000
    ..The oscillations of the phosphorylation cascades and slow protein diffusion in the cytoplasm can lead to intracellular waves of phospho-proteins...
  10. pmc Multistrip Western blotting to increase quantitative data output
    Edita Aksamitiene
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Electrophoresis 28:3163-73. 2007
    ..Compared to the traditional methods, this approach provides a more economical, reproducible, and effective procedure, facilitating the generation of large amounts of high-quality quantifiable data...
  11. pmc Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades
    Nick I Markevich
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
    J Cell Biol 164:353-9. 2004
    ..Hence, bistability induced by multisite covalent modification may be a widespread mechanism of the control of protein activity...
  12. ncbi Quantitative analysis of signaling networks
    Herbert M Sauro
    Computational Biology, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
    Prog Biophys Mol Biol 86:5-43. 2004
    ..In this review, we will summarize the great versatility of the simple cascade cycle as a computational unit and towards the end give two examples, one prokaryotic chemotaxis circuit and the other, the eukaryotic MAPK cascade...
  13. ncbi Modular response analysis of cellular regulatory networks
    Frank J Bruggeman
    Department of Molecular Cell Physiology, BioCentrum Amsterdam, De Boelelaan 1087, The Netherlands
    J Theor Biol 218:507-20. 2002
    ..The approach is illustrated by two examples: (i) mitogenic signalling through the mitogen-activated protein kinase cascade in the epidermal growth factor receptor network and (ii) regulation of ammonium assimilation in Escherichia coli...
  14. pmc Untangling the signalling wires
    Boris N Kholodenko
    Nat Cell Biol 9:247-9. 2007
  15. pmc Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades
    Nick I Markevich
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Locust St, Philadelphia, PA 19107, USA
    Mol Syst Biol 2:61. 2006
    ..The finding of phosphorylation waves traveling with constant amplitude and high velocity may solve a long-standing enigma of survival signaling in developing neurons...
  16. ncbi Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation
    Vijay Chickarmane
    Keck Graduate Institute, 535 Watson Dr, Claremont, CA 91711, USA
    J Theor Biol 244:68-76. 2007
    ..In this case we obtain a ring oscillator. Both these networks illustrate the versatility of the multisite bistable network...
  17. 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...
  18. pmc A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks
    Holger Conzelmann
    Institute for System Dynamics and Control Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
    BMC Bioinformatics 7:34. 2006
    ..The number of possible species grows exponentially with the number of different docking sites and can easily reach several millions. Models accounting for this combinatorial variety become impractical for many applications...
  19. ncbi Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law
    Mark A Peletier
    Centrum voor Wiskunde en Informatica, Kruislaan 413, 1098 SJ Amsterdam, The Netherlands
    J Theor Biol 225:477-87. 2003
    ....
  20. pmc Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity
    Nikolay M Borisov
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
    Biophys J 89:951-66. 2005
    ..Our domain-oriented approach drastically reduces the number of states, processes, and kinetic parameters to be considered for quantification of complex signaling networks that propagate distinct physiological responses...
  21. pmc Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains
    Nikolay M Borisov
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
    Biosystems 83:152-66. 2006
    ..Thus, our results greatly facilitate quantitative analysis and computational modeling of multi-protein signaling networks...