BORIS KHOLODENKO

Summary

Affiliation: Thomas Jefferson University
Country: USA

Publications

  1. 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
  2. pmc Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses
    Marc R Birtwistle
    Department of Chemical Engineering, University of Delaware, Newark, DE, USA
    Mol Syst Biol 3:144. 2007
  3. pmc Systems-level interactions between insulin-EGF networks amplify mitogenic signaling
    Nikolay Borisov
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Mol Syst Biol 5:256. 2009
  4. 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
  5. pmc Positional information generated by spatially distributed signaling cascades
    Javier Muñoz-García
    School of Mathematical Sciences and Complex Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS Comput Biol 5:e1000330. 2009
  6. 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
  7. pmc Cell-signalling dynamics in time and space
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
    Nat Rev Mol Cell Biol 7:165-76. 2006
  8. pmc Four-dimensional dynamics of MAPK information processing systems
    Boris N Kholodenko
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Wiley Interdiscip Rev Syst Biol Med 1:28-44. 2009
  9. doi request reprint Giving space to cell signaling
    Boris N Kholodenko
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Cell 133:566-7. 2008
  10. doi request reprint Computational approaches for analyzing information flow in biological networks
    BORIS KHOLODENKO
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Sci Signal 5:re1. 2012

Research Grants

  1. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2000
  2. Receptor Tyrosine Kinase Signaling Networks
    BORIS KHOLODENKO; Fiscal Year: 2007
  3. Mechanisms of Central Autonomic Orchestration of Blood Pressure
    BORIS KHOLODENKO; Fiscal Year: 2007
  4. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2002
  5. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2004
  6. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2003
  7. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2006
  8. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2001
  9. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2005

Collaborators

Detail Information

Publications27

  1. 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...
  2. pmc Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses
    Marc R Birtwistle
    Department of Chemical Engineering, University of Delaware, Newark, DE, USA
    Mol Syst Biol 3:144. 2007
    ..Sensitivity analysis leads to the hypothesis that ERK activation is robust to parameter perturbation at high ligand doses, while Akt activation is not...
  3. pmc Systems-level interactions between insulin-EGF networks amplify mitogenic signaling
    Nikolay Borisov
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Mol Syst Biol 5:256. 2009
    ..Our results show the feasibility of using computational models to identify key target combinations and predict complex cellular responses to a mixture of external cues...
  4. 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...
  5. pmc Positional information generated by spatially distributed signaling cascades
    Javier Muñoz-García
    School of Mathematical Sciences and Complex Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS Comput Biol 5:e1000330. 2009
    ....
  6. 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...
  7. pmc Cell-signalling dynamics in time and space
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
    Nat Rev Mol Cell Biol 7:165-76. 2006
    ....
  8. pmc Four-dimensional dynamics of MAPK information processing systems
    Boris N Kholodenko
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Wiley Interdiscip Rev Syst Biol Med 1:28-44. 2009
    ....
  9. doi request reprint Giving space to cell signaling
    Boris N Kholodenko
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Cell 133:566-7. 2008
    ..In this issue, Neves et al. (2008) report how the propagation of spatial information is controlled by the shape of hippocampal neurons and feedback and feed-forward motifs of the beta-adrenergic receptor signaling pathway...
  10. doi request reprint Computational approaches for analyzing information flow in biological networks
    BORIS KHOLODENKO
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Sci Signal 5:re1. 2012
    ....
  11. 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...
  12. 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...
  13. 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...
  14. pmc Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle
    Nikolai P Kaimachnikov
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
    FEBS J 276:4102-18. 2009
    ..Our mathematical model helps to understand the puzzling experimental observations and suggests conditions where these different kinetic behaviors of SFKs can be tested experimentally...
  15. 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...
  16. pmc PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells
    Edita Aksamitiene
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
    Cell Signal 22:1369-78. 2010
    ..We discuss candidate proteins that can be involved in this activation circuitry and suggest that PDZ-Binding Kinase/T-LAK Cell-Originated Protein Kinase (PBK/TOPK) may play a role in mediating MEK-independent ERK activation...
  17. ncbi request reprint 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...
  18. ncbi request reprint Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model
    Gisela Moehren
    Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
    Biochemistry 41:306-20. 2002
    ..A combination of high-resolution experimental monitoring and molecular level kinetic modeling made it possible to quantitatively account for the temperature dependence of the integrative signaling responses...
  19. pmc Untangling the signalling wires
    Boris N Kholodenko
    Nat Cell Biol 9:247-9. 2007
  20. ncbi request reprint The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks
    Yoshiyuki Sakaki
    Syst Biol (Stevenage) 152:53-4. 2005
  21. ncbi request reprint 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...
  22. ncbi request reprint Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements
    Fernando Ortega
    Centre for Research in Theoretical Chemistry, Scientific Park of Barcelona, Spain
    FEBS J 273:3915-26. 2006
    ..Our results show that bistable behavior in covalent modification cascades relies not only on the structure and regulatory pattern of feedback/feedforward loops, but also on the kinetic characteristics of their component proteins...
  23. ncbi request reprint Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy
    Michael Andrec
    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 8087, USA
    J Theor Biol 232:427-41. 2005
    ..Our ideas are illustrated using the mitogen-activated protein kinase (MAPK) signaling network as an example...
  24. ncbi request reprint Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
    Eduardo Sontag
    Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA
    Bioinformatics 20:1877-86. 2004
    ..Here, we propose how these technologies can be utilized to infer the topology and strengths of connections among genes, proteins and metabolites by monitoring time-dependent responses of cellular networks to experimental interventions...
  25. ncbi request reprint 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...
  26. ncbi request reprint Modular interaction strengths in regulatory networks; an example
    Frank J Bruggeman
    Dept Molecular Cell Physiology, BioCentrum Amsterdam, The Netherlands
    Mol Biol Rep 29:57-61. 2002
    ..This is illustrated by a calculation for an example of a modular biochemical network...
  27. pmc Control analysis for autonomously oscillating biochemical networks
    Karin A Reijenga
    Department of Molecular Cell Physiology, BioCentrum Amsterdam, Faculty of Biology, Vrije Universiteit, NL 1081 HV Amsterdam, The Netherlands, EU
    Biophys J 82:99-108. 2002
    ..We show that the control of various oscillatory properties is distributed over the system enzymes in ways that differ among those properties. The models that are described in this paper can be accessed on http://jjj.biochem.sun.ac.za...

Research Grants10

  1. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2000
    ....
  2. Receptor Tyrosine Kinase Signaling Networks
    BORIS KHOLODENKO; Fiscal Year: 2007
    ....
  3. Mechanisms of Central Autonomic Orchestration of Blood Pressure
    BORIS KHOLODENKO; Fiscal Year: 2007
    ..The approach is to test these predictions at the level of effects on molecular processes involved in the physiological response, including feedback from gene regulatory responses. ..
  4. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2002
    ....
  5. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2004
    ....
  6. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2003
    ....
  7. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2006
    ....
  8. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2001
    ....
  9. RECEPTOR TYROSINE KINASE SIGNALING IN THE LIVER
    BORIS KHOLODENKO; Fiscal Year: 2005
    ....