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Boris Kholodenko

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Angela Baljuls; Boris N Kholodenko; Walter Kolch
It takes two to tango--signalling by dimeric Raf kinases.
Lan K Nguyen; Carsten C Scholz; Murtaza Tambuwala; Cormac T Taylor; Eoin P Cummins; Susan F Fitzpatrick; Boris N Kholodenko; Mario C Manresa; Ulrike Bruning; Miguel A S Cavadas; Alex Cheong
A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network.
Lan K Nguyen; Alexander von Kriegsheim; David R Croucher; David Matallanas; Boris N Kholodenko
Signalling by protein phosphatases and drug development: a systems-centred view.

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All Publications

2013: Angela Baljuls; Boris N Kholodenko; Walter Kolch
It takes two to tango--signalling by dimeric Raf kinases.
Molecular bioSystems 2013;9(4):551-8.
2013: Lan K Nguyen; Carsten C Scholz; Murtaza Tambuwala; Cormac T Taylor; Eoin P Cummins; Susan F Fitzpatrick; Boris N Kholodenko; Mario C Manresa; Ulrike Bruning; Miguel A S Cavadas; Alex Cheong
A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network.
Journal of cell science 2013;126(Pt 6):1454-63.
2013: Lan K Nguyen; Alexander von Kriegsheim; David R Croucher; David Matallanas; Boris N Kholodenko
Signalling by protein phosphatases and drug development: a systems-centred view.
The FEBS journal 2013;280(2):751-65.
2012: Marc R Birtwistle; Maciej Dobrzyński; Boris N Kholodenko; Alexander von Kriegsheim; Walter Kolch
Mammalian protein expression noise: scaling principles and the implications for knockdown experiments.
Molecular bioSystems 2012;8(11):3068-76.
2012: Till D Frank; Alex Cheong; Mariko Okada-Hatakeyama; Boris N Kholodenko
Catching transcriptional regulation by thermostatistical modeling.
Physical biology 2012;9(4):045007.
2012: MA Tsyganov; Walter Kolch; Boris N Kholodenko
The topology design principles that determine the spatiotemporal dynamics of G-protein cascades.
Molecular bioSystems 2012;8(3):730-43.
2012: Edita Aksamitiene; Anatoly Kiyatkin; Boris N Kholodenko
Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance.
Biochemical Society transactions 2012;40(1):139-46.
2012: Dirk Fey; David R Croucher; Walter Kolch; Boris N Kholodenko
Crosstalk and signaling switches in mitogen-activated protein kinase cascades.
Frontiers in physiology 2012;3():355.
2012: Marc R Birtwistle; Maciej Dobrzyński; Jan B Hoek; Anatoly Kiyatkin; Walter Kolch; Babatunde A Ogunnaike; Jens Rauch; Edita Aksamitiene; Boris N Kholodenko
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise.
BMC systems biology 2012;6():109.
2012: Till D Frank; Aimée M Carmody; Boris N Kholodenko
Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects.
PloS one 2012;7(4):e34439.
2011: Edita Aksamitiene; Jan B Hoek; Boris N Kholodenko; Sirisha Achanta; Walter Kolch; Anatoly Kiyatkin
Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signaling pathway in breast cancer cells.
Cellular signalling 2011;23(11):1794-805.
2010: Javier Muñoz-García; Boris N Kholodenko
Signalling over a distance: gradient patterns and phosphorylation waves within single cells.
Biochemical Society transactions 2010;38(5):1235-41.
2010: Edita Aksamitiene; Boris N Kholodenko; Walter Kolch; Jan B Hoek; Anatoly Kiyatkin
PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells.
Cellular signalling 2010;22(9):1369-78.
2010: Javier Muñoz-García; Boris N Kholodenko; Zoltán Neufeld
Formation of intracellular concentration landscapes by multisite protein modification.
Biophysical journal 2010;99(1):59-66.
2010: Boris N Kholodenko; John F Hancock; Walter Kolch
Signalling ballet in space and time.
Nature reviews. Molecular cell biology 2010;11(6):414-26.
2010: Takashi Nakakuki; Marc R Birtwistle; Yuko Saeki; Noriko Yumoto; Kaori Ide; Takeshi Nagashima; Lutz Brusch; Babatunde A Ogunnaike; Mariko Okada-Hatakeyama; Boris N Kholodenko
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.
Cell 2010;141(5):884-96.
2009: Boris N Kholodenko
Spatially distributed cell signalling.
FEBS letters 2009;583(24):4006-12.
2009: Nikolai P Kaimachnikov; Boris N Kholodenko
Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle.
The FEBS journal 2009;276(15):4102-18.
2009: Marc R Birtwistle; Boris N Kholodenko
Endocytosis and signalling: a meeting with mathematics.
Molecular oncology 2009;3(4):308-20.
2009: Boris N Kholodenko; Marc R Birtwistle
Four-dimensional dynamics of MAPK information processing systems.
Wiley interdisciplinary reviews. Systems biology and medicine 2009;1(1):28-44.
2009: Atsushi Suenaga; Mariko Hatakeyama; Anatoly Kiyatkin; Ravi Radhakrishnan; Makoto Taiji; Boris N Kholodenko
Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor.
Biophysical journal 2009;96(6):2278-88.
2009: Javier Muñoz-García; Zoltan Neufeld; Boris N Kholodenko
Positional information generated by spatially distributed signaling cascades.
PLoS computational biology 2009;5(3):e1000330.
2009: Nikolay Borisov; Edita Aksamitiene; Anatoly Kiyatkin; Stefan Legewie; Jan Berkhout; Thomas Maiwald; Nikolai P Kaimachnikov; Jens Timmer; Jan B Hoek; Boris N Kholodenko
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling.
Molecular systems biology 2009;5():256.
2009: Jörg Stelling; Boris N Kholodenko
Signaling cascades as cellular devices for spatial computations.
Journal of mathematical biology 2009;58(1-2):35-55.
2008: Boris N Kholodenko; Walter Kolch
Giving space to cell signaling.
Cell 2008;133(4):566-7.
2008: Boris N Kholodenko; Herbert M Sauro
Spatio-temporal dynamics of protein modification cascades.
SEB experimental biology series 2008;61():141-59.
2007: Edita Aksamitiene; Jan B Hoek; Boris N Kholodenko; Anatoly Kiyatkin
Multistrip Western blotting to increase quantitative data output.
Electrophoresis 2007;28(18):3163-73.
2007: Boris N Kholodenko
Untangling the signalling wires.
Nature cell biology 2007;9(3):247-9.
2007: Vijay Chickarmane; Boris N Kholodenko; Herbert M Sauro
Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation.
Journal of theoretical biology 2007;244(1):68-76.
2007: Marc R Birtwistle; Mariko Hatakeyama; Noriko Yumoto; Babatunde A Ogunnaike; Jan B Hoek; Boris N Kholodenko
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.
Molecular systems biology 2007;3():144.
2006: Fernando Ortega; Josep Lluís Garcés; Francesc Mas; Boris N Kholodenko; Marta Cascante
Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements.
The FEBS journal 2006;273(17):3915-26.
2006: Anatoly Kiyatkin; Edita Aksamitiene; Nick I Markevich; Nikolay M Borisov; Jan B Hoek; Boris N Kholodenko
Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops.
The Journal of biological chemistry 2006;281(29):19925-38.
2006: Nirupama Yalamanchili; Daniel E Zak; Babatunde A Ogunnaike; James S Schwaber; Andres Kriete; Boris N Kholodenko
Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.
Systems biology 2006;153(4):236-46.
2006: Boris N Kholodenko
Cell-signalling dynamics in time and space.
Nature reviews. Molecular cell biology 2006;7(3):165-76.
2006: Nils Blüthgen; Frank J Bruggeman; Stefan Legewie; Hanspeter Herzel; Hans V Westerhoff; Boris N Kholodenko
Effects of sequestration on signal transduction cascades.
The FEBS journal 2006;273(5):895-906.
2006: Nikolay M Borisov; Nick I Markevich; Jan B Hoek; Boris N Kholodenko
Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains.
Bio Systems 2006;83(2-3):152-66.
2006: Nick I Markevich; Mikhail A Tsyganov; Jan B Hoek; Boris N Kholodenko
Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades.
Molecular systems biology 2006;2():61.
2006: Holger Conzelmann; Julio Saez-Rodriguez; Thomas Sauter; Boris N Kholodenko; Ernst Dieter Gilles
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
BMC bioinformatics 2006;7():34.
2005: Nikolay M Borisov; Nick I Markevich; Jan B Hoek; Boris N Kholodenko
Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity.
Biophysical journal 2005;89(2):951-66.
2005: Yoshiyuki Sakaki; Boris N Kholodenko; Mariko Hatakeyama; Hiroaki Kitano; Walter Kolch; Pierre De Meyts; Yosef Yarden; Hans V Westerhoff; H Steven Wiley
The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks.
Systems biology 2005;152(2):53-4.
2005: Michael Andrec; Boris N Kholodenko; Ronald M Levy; Eduardo Sontag
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy.
Journal of theoretical biology 2005;232(3):427-41.
2004: Herbert M Sauro; Boris N Kholodenko
Quantitative analysis of signaling networks.
Progress in biophysics and molecular biology 2004;86(1):5-43.
2004: Eduardo Sontag; Anatoly Kiyatkin; Boris N Kholodenko
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data.
Bioinformatics (Oxford, England) 2004;20(12):1877-86.
2004: Nick I Markevich; Gisela Moehren; Oleg Demin; Anatoly Kiyatkin; Jan B Hoek; Boris N Kholodenko
Signal processing at the Ras circuit: what shapes Ras activation patterns?
Systems biology 2004;1(1):104-13.
2004: Atsushi Suenaga; Anatoly Kiyatkin; Mariko Hatakeyama; Noriyuki Futatsugi; Noriaki Okimoto; Yoshinori Hirano; Tetsu Narumi; Atsushi Kawai; Ryutaro Susukita; Takahiro Koishi; Hideaki Furusawa; Kenji Yasuoka; Naoki Takada; Yousuke Ohno; Makoto Taiji; Toshikazu Ebisuzaki; Jan B Hoek; Akihiko Konagaya; Boris N Kholodenko
Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.
The Journal of biological chemistry 2004;279(6):4657-62.
2004: Nick I Markevich; Jan B Hoek; Boris N Kholodenko
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades.
The Journal of cell biology 2004;164(3):353-9.
2003: Mark A Peletier; Hans V Westerhoff; Boris N Kholodenko
Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law.
Journal of theoretical biology 2003;225(4):477-87.
2003: Boris N Kholodenko
Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors.
The Journal of experimental biology 2003;206(Pt 12):2073-82.
2002: Frank J Bruggeman; Hans V Westerhoff; Jan B Hoek; Boris N Kholodenko
Modular response analysis of cellular regulatory networks.
Journal of theoretical biology 2002;218(4):507-20.
2002: Boris N Kholodenko; Anatoly Kiyatkin; Frank J Bruggeman; Eduardo Sontag; Hans V Westerhoff; Jan B Hoek
Untangling the wires: a strategy to trace functional interactions in signaling and gene networks.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(20):12841-6.
2002: Boris N Kholodenko
MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?
Trends in cell biology 2002;12(4):173-7.
2002: Gisela Moehren; Nick I Markevich; Oleg Demin; Anatoly Kiyatkin; Igor Goryanin; Jan B Hoek; Boris N Kholodenko
Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model.
Biochemistry 2002;41(1):306-20.
2002: Frank J Bruggeman; Boris N Kholodenko
Modular interaction strengths in regulatory networks; an example.
Molecular biology reports 2002;29(1-2):57-61.
2002: Karin A Reijenga; Hans V Westerhoff; Boris N Kholodenko; Jacky L Snoep
Control analysis for autonomously oscillating biochemical networks.
Biophysical journal 2002;82(1 Pt 1):99-108.
2001: Oleg Demin; I I Gorianin; Boris N Kholodenko; H V Westerhoff
[Kinetic modeling of energy metabolism and generation of active forms of oxygen in hepatocyte mitochondria].
Molekuliarnaia biologiia 2001;35(6):1095-104.
2000: Boris N Kholodenko; G C Brown; Jan B Hoek
Diffusion control of protein phosphorylation in signal transduction pathways.
The Biochemical journal 2000;350 Pt 3():901-7.
2000: A Marcinkeviciute; Vida Mildaziene; S Crumm; Oleg Demin; Jan B Hoek; Boris N Kholodenko
Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding.
The Biochemical journal 2000;349(Pt 2):519-26.
2000: Boris N Kholodenko; Jan B Hoek; H V Westerhoff
Why cytoplasmic signalling proteins should be recruited to cell membranes.
Trends in cell biology 2000;10(5):173-8.
2000: Boris N Kholodenko
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.
European journal of biochemistry / FEBS 2000;267(6):1583-8.
2000: Boris N Kholodenko; Hans V Westerhoff; James S Schwaber; M Cascante
Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes.
Metabolic engineering 2000;2(1):1-13.
1999: Boris N Kholodenko; Oleg Demin; Gisela Moehren; Jan B Hoek
Quantification of short term signaling by the epidermal growth factor receptor.
The Journal of biological chemistry 1999;274(42):30169-81.
1999: W C van Heeswijk; Barbara M Bakker; Bas Teusink; Boris N Kholodenko; Oscar J G Somsen; Jacky L Snoep; Hans V Westerhoff
Live control of the living cell.
Biochemical Society transactions 1999;27(2):261-4.
1998: Johann M Rohwer; Pieter W Postma; Boris N Kholodenko; Hans V Westerhoff
Implications of macromolecular crowding for signal transduction and metabolite channeling.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(18):10547-52.
1998: Jan B Hoek; Boris N Kholodenko
The intracellular signaling network as a target for ethanol.
Alcoholism, clinical and experimental research 1998;22(5 Suppl):224S-230S.
1998: Boris N Kholodenko; M Cascante; Jan B Hoek; Hans V Westerhoff; James S Schwaber
Metabolic design: how to engineer a living cell to desired metabolite concentrations and fluxes.
Biotechnology and bioengineering 1998;59(2):239-47.
1998: Boris N Kholodenko; Johann M Rohwer; M Cascante; Hans V Westerhoff
Subtleties in control by metabolic channelling and enzyme organization.
Molecular and cellular biochemistry 1998;184(1-2):311-20.
1998: Oleg Demin; Boris N Kholodenko; Vladimir P Skulachev
A model of O2.-generation in the complex III of the electron transport chain.
Molecular and cellular biochemistry 1998;184(1-2):21-33.
1997: Boris N Kholodenko; Jan B Hoek; Hans V Westerhoff; G C Brown
Quantification of information transfer via cellular signal transduction pathways.
FEBS letters 1997;414(2):430-4.
1997: G C Brown; J B Hoek; Boris N Kholodenko
Why do protein kinase cascades have more than one level?
Trends in biochemical sciences 1997;22(8):288.
1996: Martin Bier; Bas Teusink; Boris N Kholodenko; Hans V Westerhoff
Control analysis of glycolytic oscillations.
Biophysical chemistry 1996;62(1-3):15-24.
1996: V Mildaziene; R Baniene; Z Nauciene; A Marcinkeviciute; R Morkuniene; V Borutaite; Boris N Kholodenko; G C Brown
Ca2+ stimulates both the respiratory and phosphorylation subsystems in rat heart mitochondria.
The Biochemical journal 1996;320 ( Pt 1)():329-34.
1996: Boris N Kholodenko; G C Brown
Paradoxical control properties of enzymes within pathways: can activation cause an enzyme to have increased control?
The Biochemical journal 1996;314 ( Pt 3)():753-60.
1996: Boris N Kholodenko; H V Westerhoff; Marta Cascante
Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated.
The Biochemical journal 1996;313 ( Pt 3)():921-6.
1995: V Mildaziene; R Baniene; Z Nauciene; Barbara M Bakker; G C Brown; Hans V Westerhoff; Boris N Kholodenko
Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria.
Archives of biochemistry and biophysics 1995;324(1):130-4.
1995: Boris N Kholodenko; Dylan Molenaar; S Schuster; R Heinrich; Hans V Westerhoff
Defining control coefficients in non-ideal metabolic pathways.
Biophysical chemistry 1995;56(3):215-26.
1995: Boris N Kholodenko; S Schuster; Johann M Rohwer; Marta Cascante; Hans V Westerhoff
Composite control of cell function: metabolic pathways behaving as single control units.
FEBS letters 1995;368(1):1-4.
1995: Peter R Jensen; Jacky L Snoep; Dylan Molenaar; W C van Heeswijk; Boris N Kholodenko; A A van der Gugten; Hans V Westerhoff
Molecular biology for flux control.
Biochemical Society transactions 1995;23(2):367-70.
1995: Boris N Kholodenko; H M Sauro; Hans V Westerhoff; Marta Cascante
Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem.
Biochemistry and molecular biology international 1995;35(3):615-25.
1995: Boris N Kholodenko; Marta Cascante; Hans V Westerhoff
Control theory of metabolic channelling.
Molecular and cellular biochemistry 1995;143(2):151-68.
1995: Boris N Kholodenko; Hans V Westerhoff
The macroworld versus the microworld of biochemical regulation and control.
Trends in biochemical sciences 1995;20(2):52-4.
1994: Boris N Kholodenko; Hans V Westerhoff
Control theory of one enzyme.
Biochimica et biophysica acta 1994;1208(2):294-305.
1994: Boris N Kholodenko; H M Sauro; Hans V Westerhoff
Control by enzymes, coenzymes and conserved moieties. A generalisation of the connectivity theorem of metabolic control analysis.
European journal of biochemistry / FEBS 1994;225(1):179-86.
1994: Jacky L Snoep; Peter R Jensen; Philip Groeneveld; Dylan Molenaar; Boris N Kholodenko; Hans V Westerhoff
How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox.
Biochemistry and molecular biology international 1994;33(5):1023-32.
1994: Boris N Kholodenko; Hans V Westerhoff; G C Brown
Rate limitation within a single enzyme is directly related to enzyme intermediate levels.
FEBS letters 1994;349(1):131-4.
1994: Hans V Westerhoff; J H Hofmeyr; Boris N Kholodenko
Getting to the inside of cells using metabolic control analysis.
Biophysical chemistry 1994;50(3):273-83.
1994: Boris N Kholodenko; Marta Cascante; Hans V Westerhoff
Control theory of metabolic channelling.
Molecular and cellular biochemistry 1994;133-134():313-31.
1993: Boris N Kholodenko
Kinetic models of coupling between H+ and Na(+)-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: can a cell utilize both delta mu H+ and delta mu Na+ for ATP synthesis under in vivo conditions using the same enzyme?
Journal of bioenergetics and biomembranes 1993;25(3):285-95.
1993: V Borutaité; V Mildaziene; Z Katiliuté; Boris N Kholodenko; A Toleikis
The function of ATP/ADP translocator in the regulation of mitochondrial respiration during development of heart ischemic injury.
Biochimica et biophysica acta 1993;1142(1-2):175-80.
1993: Boris N Kholodenko; Oleg Demin; Hans V Westerhoff
'Channelled' pathways can be more sensitive to specific regulatory signals.
FEBS letters 1993;320(1):75-8.
1993: Boris N Kholodenko; Hans V Westerhoff
Metabolic channelling and control of the flux.
FEBS letters 1993;320(1):71-4.
1993: Karel van Dam; Johan Van der Vlag; Boris N Kholodenko; Hans V Westerhoff
The sum of the control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two.
European journal of biochemistry / FEBS 1993;212(3):791-9.
1992: Boris N Kholodenko; A E Lyubarev; B I Kurganov
Control of the metabolic flux in a system with high enzyme concentrations and moiety-conserved cycles. The sum of the flux control coefficients can drop significantly below unity.
European journal of biochemistry / FEBS 1992;210(1):147-53.
1989: V Borutaite; V Mildaziene; L Ivanoviene; Boris N Kholodenko; A Toleikis; A Praskevicius
The role of long-chain acyl-CoA in the damage of oxidative phosphorylation in heart mitochondria.
FEBS letters 1989;243(2):264-6.
1988: Boris N Kholodenko
How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control.
FEBS letters 1988;232(2):383-6.
1987: Boris N Kholodenko; V Zilinskiene; V Borutaite; L Ivanoviene; A Toleikis; A Praskevicius
The role of adenine nucleotide translocators in regulation of oxidative phosphorylation in heart mitochondria.
FEBS letters 1987;223(2):247-50.