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- Core Technologies
Professor Boris Kholodenko DSc, PhD, MS
Contact Details
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Biography:
Professor Boris Kholodenko is widely recognised and respected as an academic leader in the field of systems biology and predictive models of cellular functions (www.cellnetworks.org/). Boris Kholodenko graduated (with the distinction of summa cum laude) and received a Ph.D. in Biophysics from the Moscow Institute of Physics and Technology, Russia. Most recently Dr. Kholodenko was employed at the faculty of Thomas Jefferson University in Philadelphia, Pennsylvania, USA, where he was a Professor and Director of Computational Cell Biology. He developed the first systems biology model of the epidermal-growth-factor receptor signalling pathway, a novel principle for mechanistic modeling, referred to as a domain-oriented framework, discovered a novel systematic approach to unravel interaction 'maps' in signaling and gene networks from experimental data on steady-state and temporal responses to perturbations, predicted the existence of intracellular gradients of signaling activities that control both the living circuitry and cell communication and showed intricate dynamic behaviours of signalling systems in space and time including oscillations, bistability and travelling waves of phosphorylation signals. |
Research Interests
Research Projects
| Sponsor : Science Foundation Ireland (SFI) Title : Stokes Professorship Start Date / End Date : 31-JAN-09 / 30-JAN-14 |
| Sponsor : Higher Education Authority (HEA) Title : PRTLI 5: SimSci - Split Accounts School of Mathematical Sciences Start Date / End Date : 01-MAR-11 / 29-FEB-16 |
| Sponsor : Science Foundation Ireland (SFI) Title : Walton Fellowship: Dynamic rewiring of Rho family GTPase signalling fluxes in cancer cell invasion Start Date / End Date : 01-MAR-12 / 31-AUG-12 |
| Sponsor : AstraZeneca UK Ltd. Title : CRC50: Modelling synergistic combinations Start Date / End Date : 13-NOV-09 / 31-MAY-12 |
| Sponsor : RIKEN Title : Modeling and Experimental Studies of Cellular Signal Transduction Networks Start Date / End Date : 01-JUN-09 / 31-MAR-11 |
Current Postgraduate Students
| Elena Nikonova, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Cormac Mc Carthy, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Benedikt Minke, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Thawfeek Varusai, Doctor of Philosophy (PhD) - Thesis Supervisor |
Peer Reviewed Journals
| Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzynski M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN (2012) 'Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise'. BMC systems biology, 6 . [DOI] [Details] |
| Aksamitiene E, Kiyatkin A, Kholodenko BN (2012) 'Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance'. Biochemical Society Transactions, 40 (1):139-146. [DOI] [Details] |
| Tsyganov MA, Kolch W, Kholodenko BN (2012) 'The topology design principles that determine the spatiotemporal dynamics of G-protein cascades'. Molecular BioSystems, 8 (3):730-743. [DOI] [Details] |
| Birtwistle MR, Kriegsheim Av, Dobrzyſski M, Kholodenko BN, Kolch W (2012) 'Mammalian protein expression noise: scaling principles and the implications for knockdown experiments'. Molecular BioSystems, 8 (11):3068-3076. [DOI] [Details] |
| Muñoz-GarcÃa J, Neufeld Z, Kholodenko BN (2009) 'Positional information generated by spatially distributed signaling cascades'. PLoS computational biology, 5 (3). [DOI] [Details] |
| Sturm OE, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W (2010) 'The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier'. Science signaling, 3 (153). [DOI] [Details] | |||||||||
| Muñoz-GarcÃa J, Kholodenko BN (2010) 'Signalling over a distance: gradient patterns and phosphorylation waves within single cells'. Biochemical Society Transactions, 38 (5):1235-1241. [DOI] [Details] | |||||||||
| Muñoz-GarcÃa J, Kholodenko BN, Neufeld Z (2010) 'Formation of intracellular concentration landscapes by multisite protein modification'. Biophysical Journal, 99 (1):59-66. [DOI] [Details] | |||||||||
| Nguyen LK, Munoz-GarcÃa J, Maccario H, Ciechanover A, Kolch W, Kholodenko BN (2011) 'Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system'. PLoS computational biology, 7 (12). [DOI] [Details] | |||||||||
| Santra T, Kholodenko B, Kolch W (2012) 'An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells'. Frontiers in Modeling and Control of Breathing, 736 :59-80. [DOI] [Details] | |||||||||
| Frank TD, Cheong A, Okada-Hatakeyama M, Kholodenko BN (2012) 'Catching transcriptional regulation by thermostatistical modeling'. Physical Biology, 9 (4). [DOI] [Details] | |||||||||
| Kholodenko B, Yaffe MB, Kolch W (2012) 'Computational approaches for analyzing information flow in biological networks'. Science signaling, 5 (220). [DOI] [Details] | |||||||||
| Nguyen LK, Matallanas D, Croucher DR, von Kriegsheim A, Kholodenko BN (2012) 'Signalling by protein phosphatases and drug development: a systems-centred view'. The FEBS journal, . [DOI] [Details] | |||||||||
| Frank TD, Carmody AM, Kholodenko BN (2012) 'Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects'. PLoS ONE, 7 (4). [DOI] [Details] | |||||||||
| Fey D, Croucher DR, Kolch W, Kholodenko BN (2012) 'Crosstalk and signaling switches in mitogen-activated protein kinase cascades'. Frontiers in physiology, 3 . [DOI] [Details] | |||||||||
| Frank, TD; Cheong, A; Okada-Hatakeyama, M; Kholodenko, BN (2012) 'Catching transcriptional regulation by thermostatistical modeling'. Physical Biology, . [DOI] [Details] | |||||||||
| Frank, T.D., Carmody, A.M., Kholodenko, B.N. (2012) 'Versatility of cooperative transcriptional activation'. PLoS ONE, . [Details] | |||||||||
| Aksamitiene, E,Achanta, S,Kolch, W,Kholodenko, BN,Hoek, JB,Kiyatkin, A; (2011) '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, 23 :1794-1805. [DOI] [Details] | |||||||||
| Sturm, OE,Orton, R,Grindlay, J,Birtwistle, M,Vyshemirsky, V,Gilbert, D,Calder, M,Pitt, A,Kholodenko, B,Kolch, W; (2010) 'The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier'. Science signaling, 3 . [DOI] [Details] | |||||||||
| Munoz-Garcia, J,Kholodenko, BN; (2010) 'Signalling over a distance: gradient patterns and phosphorylation waves within single cells'. Biochemical Society Transactions, 38 :1235-1241. [DOI] [Details] | |||||||||
| Kholodenko BN, Hancock JF, Kolch W; (2010) 'Signalling ballet in space and time'. Nature reviews. Molecular cell biology, 11 (6):414-426. [DOI] [Details] | |||||||||
| Aksamitiene E, Kholodenko BN, Kolch W, Hoek JB, Kiyatkin A; (2010) 'PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells'. Cell, 22 (9):1369-1378. [DOI] [Details] | |||||||||
| Nakakuki, T,Birtwistle, MR,Saeki, Y,Yumoto, N,Ide, K,Nagashima, T,Brusch, L,Ogunnaike, BA,Okada-Hatakeyama, M,Kholodenko, BN; (2010) 'Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics'. Cell, 141 :884-896. [DOI] [Details] | |||||||||
| Aksamitiene, E.Aksamitiene, E.,Kholodenko, B. N.Kholodenko, B. N.,Kolch, W.Kolch, W.,Hoek, J. B.Hoek, J. B.,Kiyatkin, A.Kiyatkin, A.; (2010) 'PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells'. Cell Signal, 22 (99):1369-781369. [Details] | |||||||||
| Muñoz-García J, Kholodenko BN, Neufeld Z.; (2010) 'Formation of intracellular concentration landscapes by multisite protein modification'. Biophysical Journal, . [Details] | |||||||||
| Borisov N, Aksamitiene E, Kiyatkin A, Legewie S, Berkhout J, Maiwald T, Kaimachnikov NP, Timmer J, Hoek JB, Kholodenko BN; (2009) 'Systems-level interactions between insulin-EGF networks amplify mitogenic signaling'. Molecular systems biology, 5 . [DOI] [Details] | |||||||||
| Suenaga A, Hatakeyama M, Kiyatkin AB, Radhakrishnan R, Taiji M, Kholodenko BN; (2009) 'Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor'. Biophysical Journal, 96 (6):2278-2288. [DOI] [Details] | |||||||||
| Kaimachnikov NP, Kholodenko BN; (2009) 'Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle'. The FEBS journal, 276 (15):4102-4118. [DOI] [Details] | |||||||||
| Stelling J, Kholodenko BN; (2009) 'Signaling cascades as cellular devices for spatial computations'. Journal of mathematical biology, 58 (1-2):35-55. [DOI] [Details] | |||||||||
| Kholodenko BN, Birtwistle MR; (2009) 'Four-dimensional dynamics of MAPK information processing systems'. Wiley interdisciplinary reviews. Systems biology and medicine, 1 (1):28-44. [DOI] [Details] | |||||||||
| Birtwistle MR, Kholodenko BN; (2009) 'Endocytosis and signalling: a meeting with mathematics'. Molecular oncology, 3 (4):308-320. [DOI] [Details] | |||||||||
Kaimachnikov, N. P.Kaimachnikov, N. P.,Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle'. FEBS JFEBS JFEBS J, 276 (1515):4102-184102. [Details] |
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Suenaga, A.Suenaga, A.,Hatakeyama, M.Hatakeyama, M.,Kiyatkin, A. B.Kiyatkin, A. B.,Radhakrishnan, R.Radhakrishnan, R.,Taiji, M.Taiji, M.,Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor'. Biophys JBiophys JBiophys J, 96 (66):2278-882278. [Details] |
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Munoz-Garcia, J.Munoz-Garcia, J.,Neufeld, Z.Neufeld, Z.,Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Positional information generated by spatially distributed signaling cascades'. PLoS Comput BiolPLoS Comput BiolPLoS Comput Biol, 5 (33). [Details] |
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| Munoz-Garcia, J., Neufeld, Z. and Kholodenko, B. ; (2009) 'Positional Information Generated by Spatially Distributed Signaling Cascades'. PLoS Computational Biology, 5 (3). [DOI] [Details] | |||||||||
Kholodenko, B. N.Kholodenko, B. N.,Birtwistle, M. R.Birtwistle, M. R.; (2009) 'Four-dimensional dynamics of MAPK information processing systems'. Wiley Interdiscip Rev Syst Biol MedWiley Interdiscip Rev Syst Biol MedWiley Interdiscip Rev Syst Biol Med, 1 (11):28-4428. [Details] |
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Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Spatially distributed cell signalling'. FEBS LettFEBS LettFEBS Lett, 583 (2424):4006-124006. [Details] |
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Birtwistle, M. R.Birtwistle, M. R.,Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Endocytosis and signalling: a meeting with mathematics'. Mol OncolMol OncolMol Oncol, 3 (44):308-20308. [Details] |
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Borisov, N.Borisov, N.,Aksamitiene, E.Aksamitiene, E.,Kiyatkin, A.Kiyatkin, A.,Legewie, S.Legewie, S.,Berkhout, J.Berkhout, J.,Maiwald, T.Maiwald, T.,Kaimachnikov, N. P.Kaimachnikov, N. P.,Timmer, J.Timmer, J.,Hoek, J. B.Hoek, J. B.,Kholodenko, B. N.Kholodenko, B. N.; (2009) 'Systems-level interactions between insulin-EGF networks amplify mitogenic signaling'. Mol Syst BiolMol Syst BiolMol Syst Biol, 5 . [Details] |
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| Suenaga, A,Hatakeyama, M,Kiyatkin, AB,Radhakrishnan, R,Taiji, M,Kholodenko, BN; (2009) 'Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor'. Biophysical Journal, 96 :2278-2288. [DOI] [Details] | |||||||||
| Borisov, N,Aksamitiene, E,Kiyatkin, A,Legewie, S,Berkhout, J,Maiwald, T,Kaimachnikov, NP,Timmer, J,Hoek, JB,Kholodenko, BN; (2009) 'Systems-level interactions between insulin-EGF networks amplify mitogenic signaling'. Stem, 5 . [DOI] [Details] | |||||||||
| Kaimachnikov, NP,Kholodenko, BN; (2009) 'Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle'. FEBS Journal, 276 :4102-4118. [DOI] [Details] | |||||||||
| Munoz-Garcia, J,Neufeld, Z,Kholodenko, BN; (2009) 'Positional Information Generated by Spatially Distributed Signaling Cascades'. PLoS Computational Biology, 5 . [DOI] [Details] | |||||||||
| Kholodenko BN; (2009) 'Spatially distributed cell signalling'. FEBS Letters, 583 (24):4006-4012. [DOI] [Details] | |||||||||
| Kholodenko BN, Sauro HM; (2008) 'Spatio-temporal dynamics of protein modification cascades'. Experimental Biology, 61 :141-159. [Details] | |||||||||
| Borisov NM, Chistopolsky AS, Faeder JR, Kholodenko BN; (2008) 'Domain-oriented reduction of rule-based network models'. IET systems biology, 2 (5):342-351. [DOI] [Details] | |||||||||
| Kholodenko BN, Kolch W; (2008) 'Giving space to cell signaling'. Cell, 133 (4):566-567. [DOI] [Details] | |||||||||
| Kholodenko, B. N.Kholodenko, B. N.,Kolch, W.Kolch, W.; (2008) 'Giving space to cell signaling'. Cell, 133 (44):566-567566. [Details] | |||||||||
| Aksamitiene E, Hoek JB, Kholodenko B, Kiyatkin A; (2007) 'Multistrip Western blotting to increase quantitative data output'. Electrophoresis, 28 (18):3163-3173. [DOI] [Details] | |||||||||
| Chickarmane V, Kholodenko BN, Sauro HM; (2007) 'Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation'. Journal of Theoretical Biology, 244 (1):68-76. [DOI] [Details] | |||||||||
| Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN; (2007) 'Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses'. Molecular systems biology, 3 . [DOI] [Details] | |||||||||
| Kholodenko BN; (2007) 'Untangling the signalling wires'. Cell, 9 (3):247-249. [DOI] [Details] | |||||||||
| Kiyatkin A, Aksamitiene E, Markevich NI, Borisov NM, Hoek JB, Kholodenko BN; (2006) 'Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops'. Journal of Biological Chemistry, 281 (29):19925-19938. [DOI] [Details] | |||||||||
| Yalamanchili N, Zak DE, Ogunnaike BA, Schwaber JS, Kriete A, Kholodenko BN; (2006) 'Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach'. Systems biology, 153 (4):236-246. [Details] | |||||||||
| Kholodenko BN; (2006) 'Cell-signalling dynamics in time and space'. Nature reviews. Molecular cell biology, 7 (3):165-176. [DOI] [Details] | |||||||||
| Conzelmann H, Saez-Rodriguez J, Sauter T, Kholodenko BN, Gilles ED; (2006) 'A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks'. BMC Bioinformatics, 7 . [DOI] [Details] | |||||||||
| Markevich NI, Tsyganov MA, Hoek JB, Kholodenko BN; (2006) 'Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades'. Molecular systems biology, 2 . [DOI] [Details] | |||||||||
| Borisov NM, Markevich NI, Hoek JB, Kholodenko BN; (2006) 'Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains'. Bio Systems, 83 (2-3):152-166. [DOI] [Details] | |||||||||
| Andrec M, Kholodenko BN, Levy RM, Sontag E; (2005) 'Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy'. Journal of Theoretical Biology, 232 (3):427-441. [DOI] [Details] | |||||||||
| Borisov NM, Markevich NI, Hoek JB, Kholodenko BN; (2005) 'Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity'. Biophysical Journal, 89 (2):951-966. [DOI] [Details] | |||||||||
| Sakaki, Y.Sakaki, Y.,Kholodenko, B. N.Kholodenko, B. N.,Hatakeyama, M.Hatakeyama, M.,Kitano, H.Kitano, H.,Kolch, W.Kolch, W.,De, Meyts P.De, Meyts P.,Yarden, Y.Yarden, Y.,Westerhoff, H. V.Westerhoff, H. V.,Wiley, H. S.Wiley, H. S.; (2005) 'The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks'. Syst.Biol.(Stevenage.), 152 (22):53-5453. [Details] | |||||||||
| Sakaki Y, Kholodenko BN, Hatakeyama M, Kitano H, Kolch W, De Meyts P, Yarden Y, Westerhoff HV, Wiley HS; (2005) 'The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks'. Systems biology, 152 (2):53-54. [Details] | |||||||||
| Sontag E, Kiyatkin A, Kholodenko BN; (2004) 'Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data'. Bioinformatics (Oxford, England), 20 (12):1877-1886. [DOI] [Details] | |||||||||
| Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, Ebisuzaki T, Hoek JB, Konagaya A, Kholodenko BN; (2004) 'Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations'. Journal of Biological Chemistry, 279 (6):4657-4662. [DOI] [Details] | |||||||||
| Markevich NI, Hoek JB, Kholodenko BN; (2004) 'Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades'. Cell, 164 (3):353-359. [DOI] [Details] | |||||||||
| Sauro HM, Kholodenko BN; (2004) 'Quantitative analysis of signaling networks'. Progress in biophysics and molecular biology, 86 (1):5-43. [DOI] [Details] | |||||||||
| Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN; (2004) 'Signal processing at the Ras circuit: what shapes Ras activation patterns?'. Systems biology, 1 (1):104-113. [Details] | |||||||||
| Peletier MA, Westerhoff HV, Kholodenko BN; (2003) 'Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law'. Journal of Theoretical Biology, 225 (4):477-487. [Details] | |||||||||
| Kholodenko BN; (2003) 'Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors'. Experimental Biology, 206 (Pt 12):2073-2082. [Details] | |||||||||
| Reijenga KA, Westerhoff HV, Kholodenko BN, Snoep JL; (2002) 'Control analysis for autonomously oscillating biochemical networks'. Biophysical Journal, 82 (1 Pt 1):99-108. [DOI] [Details] | |||||||||
| Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB; (2002) '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, 99 (20):12841-12846. [DOI] [Details] | |||||||||
| Moehren G, Markevich N, Demin O, Kiyatkin A, Goryanin I, Hoek JB, Kholodenko BN; (2002) 'Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model'. Biochemistry, 41 (1):306-320. [Details] | |||||||||
| Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN; (2002) 'Modular response analysis of cellular regulatory networks'. Journal of Theoretical Biology, 218 (4):507-520. [Details] | |||||||||
| Kholodenko BN; (2002) 'MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?'. Cell, 12 (4):173-177. [Details] | |||||||||
| Bruggeman FJ, Kholodenko BN; (2002) 'Modular interaction strengths in regulatory networks; an example'. Molecular biology reports, 29 (1-2):57-61. [Details] | |||||||||
| De Atauri P, Acerenza L, Kholodenko BN, De La Iglesia N, Guinovart JJ, Agius L, Cascante M; (2001) 'Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase'. The Biochemical journal, 355 (Pt 3):787-793. [Details] | |||||||||
| Demin OV, Gorianin II, Kholodenko BN, Westerhoff HV; (2001) '[Kinetic modeling of energy metabolism and generation of active forms of oxygen in hepatocyte mitochondria]'. Molekuliarnaia biologiia, 35 (6):1095-1104. [Details] | |||||||||
| Marcinkeviciute A, Mildaziene V, Crumm S, Demin O, Hoek JB, Kholodenko B; (2000) 'Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding'. The Biochemical journal, 349 (Pt 2):519-526. [Details] | |||||||||
| Kholodenko BN, Hoek JB, Westerhoff HV; (2000) 'Why cytoplasmic signalling proteins should be recruited to cell membranes'. Cell, 10 (5):173-178. [Details] | |||||||||
| Kholodenko BN, Brown GC, Hoek JB; (2000) 'Diffusion control of protein phosphorylation in signal transduction pathways'. The Biochemical journal, 350 Pt 3 :901-907. [Details] | |||||||||
| Schuster S, Kholodenko BN, Westerhoff HV; (2000) 'Cellular information transfer regarded from a stoichiometry and control analysis perspective'. Bio Systems, 55 (1-3):73-81. [Details] | |||||||||
| Kholodenko BN; (2000) 'Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades'. European journal of biochemistry / FEBS, 267 (6):1583-1588. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV, Schwaber J, Cascante M; (2000) 'Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes'. Metabolic Engineering, 2 (1):1-13. [DOI] [Details] | |||||||||
| van Heeswijk WC, Bakker BM, Teusink B, Kholodenko BN, Somsen OJ, Snoep JL, Westerhoff HV; (1999) 'Live control of the living cell'. Biochemical Society Transactions, 27 (2):261-264. [Details] | |||||||||
| Brown GC, Kholodenko BN; (1999) 'Spatial gradients of cellular phospho-proteins'. FEBS Letters, 457 (3):452-454. [Details] | |||||||||
| Kholodenko BN, Demin OV, Moehren G, Hoek JB; (1999) 'Quantification of short term signaling by the epidermal growth factor receptor'. Journal of Biological Chemistry, 274 (42):30169-30181. [Details] | |||||||||
| Hoek JB, Kholodenko BN; (1998) 'The intracellular signaling network as a target for ethanol'. Alcoholism, clinical and experimental research, 22 (5 Suppl):1-1. [Details] | |||||||||
| Demin OV, Kholodenko BN, Skulachev VP; (1998) 'A model of O2.-generation in the complex III of the electron transport chain'. Cell, 184 (1-2):21-33. [Details] | |||||||||
| Kholodenko BN, Cascante M, Hoek JB, Westerhoff HV, Schwaber J; (1998) 'Metabolic design: how to engineer a living cell to desired metabolite concentrations and fluxes'. BIOTECHNOL BIOENG, 59 (2):239-247. [Details] | |||||||||
| Kholodenko BN, Rohwer JM, Cascante M, Westerhoff HV; (1998) 'Subtleties in control by metabolic channelling and enzyme organization'. Cell, 184 (1-2):311-320. [Details] | |||||||||
| Kholodenko BN, Schuster S, Garcia J, Westerhoff HV, Cascante M; (1998) 'Control analysis of metabolic systems involving quasi-equilibrium reactions'. Biochimica et biophysica acta, 1379 (3):337-352. [Details] | |||||||||
| Demin OV, Westerhoff HV, Kholodenko BN; (1998) 'Mathematical modelling of superoxide generation with the bc1 complex of mitochondria'. Biochemistry, 63 (6):634-649. [Details] | |||||||||
| Rohwer JM, Postma PW, Kholodenko BN, Westerhoff HV; (1998) 'Implications of macromolecular crowding for signal transduction and metabolite channeling'. Proceedings of the National Academy of Sciences of the United States of America, 95 (18):10547-10552. [Details] | |||||||||
| Kholodenko BN, Brown GC, Hoek JB; (1997) 'Why do protein kinase cascades have more than one level?'. Trends in Biochemical Sciences, 22 (8). [Details] | |||||||||
| Kholodenko BN, Hoek JB, Westerhoff HV, Brown GC; (1997) 'Quantification of information transfer via cellular signal transduction pathways'. FEBS Letters, 414 (2):430-434. [Details] | |||||||||
| Brown GC, Westerhoff HV, Kholodenko BN; (1996) 'Molecular control analysis: control within proteins and molecular processes'. Journal of Theoretical Biology, 182 (3):389-396. [DOI] [Details] | |||||||||
| Bier M, Teusink B, Kholodenko BN, Westerhoff HV; (1996) 'Control analysis of glycolytic oscillations'. Biophysical Chemistry, 62 (1-3):15-24. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV, Cascante M; (1996) 'Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated'. The Biochemical journal, 313 ( Pt 3) :921-926. [Details] | |||||||||
| Kholodenko BN, Brown GC; (1996) 'Paradoxical control properties of enzymes within pathways: can activation cause an enzyme to have increased control?'. The Biochemical journal, 314 ( Pt 3) :753-760. [Details] | |||||||||
| Mildaziene V, Baniene R, Nauciene Z, Marcinkeviciute A, Morkuniene R, Borutaite V, Kholodenko B, Brown GC; (1996) 'Ca2+ stimulates both the respiratory and phosphorylation subsystems in rat heart mitochondria'. The Biochemical journal, 320 ( Pt 1) :329-334. [Details] | |||||||||
| Kholodenko BN, Sakamoto N, Puigjaner J, Westerhoff HV, Cascante M; (1996) 'Strong control on the transit time in metabolic channelling'. FEBS Letters, 389 (2):123-125. [Details] | |||||||||
| Nartsissov IaR, Kholodenko BN; (1996) '[Control of the rate of the glucokinase reaction by its elementary stages]'. Biokhimiia (Moscow, Russia), 61 (7):1279-1284. [Details] | |||||||||
| Westerhoff HV, Kholodenko BN, Cascante M, Van Dam K; (1995) 'Elusive control'. Journal of bioenergetics and biomembranes, 27 (5):491-497. [Details] | |||||||||
| Jensen PR, Snoep JL, Molenaar D, van Heeswijk WC, Kholodenko BN, van der Gugten AA, Westerhoff HV; (1995) 'Molecular biology for flux control'. Biochemical Society Transactions, 23 (2):367-370. [Details] | |||||||||
| Kholodenko BN, Sauro HM, Westerhoff HV, Cascante M; (1995) 'Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem'. Biochemistry and Molecular Biology International, 35 (3):615-625. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV; (1995) 'The macroworld versus the microworld of biochemical regulation and control'. Trends in Biochemical Sciences, 20 (2):52-54. [Details] | |||||||||
| Mildaziene V, Baniene R, Nauciene Z, Bakker BM, Brown GC, Westerhoff HV, Kholodenko BN; (1995) 'Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria'. Archives of Biochemistry and Biophysics, 324 (1):130-134. [DOI] [Details] | |||||||||
| Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV; (1995) 'Defining control coefficients in non-ideal metabolic pathways'. Biophysical Chemistry, 56 (3):215-226. [Details] | |||||||||
| Kholodenko BN, Cascante M, Westerhoff HV; (1995) 'Control theory of metabolic channelling'. Cell, 143 (2):151-168. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV, Puigjaner J, Cascante M; (1995) 'Control in channelled pathways. A matrix method calculating the enzyme control coefficients'. Biophysical Chemistry, 53 (3):247-258. [Details] | |||||||||
| Kholodenko BN, Schuster S, Rohwer JM, Cascante M, Westerhoff HV; (1995) 'Composite control of cell function: metabolic pathways behaving as single control units'. FEBS Letters, 368 (1):1-4. [Details] | |||||||||
| Kholodenko BN, Sauro HM, Westerhoff HV; (1994) 'Control by enzymes, coenzymes and conserved moieties. A generalisation of the connectivity theorem of metabolic control analysis'. European journal of biochemistry / FEBS, 225 (1):179-186. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV; (1994) 'Control theory of one enzyme'. Biochimica et biophysica acta, 1208 (2):294-305. [Details] | |||||||||
| Snoep JL, Jensen PR, Groeneveld P, Molenaar D, Kholodenko BN, Westerhoff HV; (1994) 'How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox'. Biochemistry and Molecular Biology International, 33 (5):1023-1032. [Details] | |||||||||
| Kholodenko BN, Cascante M, Westerhoff HV; (1994) 'Control theory of metabolic channelling'. Cell, 133-134 :313-331. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV, Brown GC; (1994) 'Rate limitation within a single enzyme is directly related to enzyme intermediate levels'. FEBS Letters, 349 (1):131-134. [Details] | |||||||||
| Westerhoff HV, Hofmeyr JH, Kholodenko BN; (1994) 'Getting to the inside of cells using metabolic control analysis'. Biophysical Chemistry, 50 (3):273-283. [Details] | |||||||||
| Kholodenko BN, Westerhoff HV; (1993) 'Metabolic channelling and control of the flux'. FEBS Letters, 320 (1):71-74. [Details] | |||||||||
| Kholodenko BN, Cascante M, Westerhoff HV; (1993) 'Dramatic changes in control properties that accompany channelling and metabolite sequestration'. FEBS Letters, 336 (3):381-384. [Details] | |||||||||
| Kholodenko BN; (1993) '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, 25 (3):285-295. [Details] | |||||||||
| van Dam K, van der Vlag J, Kholodenko BN, Westerhoff HV; (1993) '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, 212 (3):791-799. [Details] | |||||||||
| Kholodenko BN, Demin OV, Westerhoff HV; (1993) ''Channelled' pathways can be more sensitive to specific regulatory signals'. FEBS Letters, 320 (1):75-78. [Details] | |||||||||
| Kholodenko BN, Lyubarev AE, Kurganov BI; (1992) '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, 210 (1):147-153. [Details] | |||||||||
| Kholodenko BN, Erlikh LI; (1989) '[Theory of metabolism regulation: a complete system of equations for regulation coefficients]'. Biofizika, 34 (5):802-807. [Details] | |||||||||
| Borutaite V, Mildaziene V, Ivanoviene L, Kholodenko B, Toleikis A, Praskevicius A; (1989) 'The role of long-chain acyl-CoA in the damage of oxidative phosphorylation in heart mitochondria'. FEBS Letters, 243 (2):264-266. [Details] | |||||||||
| Kholodenko BN; (1988) 'How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control'. FEBS Letters, 232 (2):383-386. [Details] | |||||||||
| Kholodenko BN; (1988) '[Control of molecular transformations in polyenzyme systems: quantitative theory of the regulation of metabolism]'. Molekuliarnaia biologiia, 22 (5):1238-1256. [Details] | |||||||||
| Kholodenko BN; (1988) '[A new theorem in the theory of metabolism regulation: how external parameters control the flow and concentration of metabolites]'. Biofizika, 33 (1):145-147. [Details] | |||||||||
| Kholodenko B, Zilinskiene V, Borutaite V, Ivanoviene L, Toleikis A, Praskevicius A; (1987) 'The role of adenine nucleotide translocators in regulation of oxidative phosphorylation in heart mitochondria'. FEBS Letters, 223 (2):247-250. [Details] | |||||||||
| Kholodenko BN; (1987) '[Degree of stability of metabolic chain with 1 feedback loop]'. Biofizika, 32 (3):424-428. [Details] | |||||||||
| Kholodenko BN; (1984) '[The mitochondrial carrier of adenylates controls ATP production in the physiological range of respiration rates]'. Biofizika, 29 (3):453-458. [Details] | |||||||||
| Kholodenko BN; (1984) 'Control of mitochondrial oxidative phosphorylation'. Journal of Theoretical Biology, 107 (2):179-188. [Details] | |||||||||
| Kholodenko BN; (1983) '[Power-law approximation and similarity properties of metabolic regulatory characteristics]'. Biofizika, 28 (4):674-681. [Details] | |||||||||
| Kholodenko BN, Geviksman KhV, Kholodov LE; (1982) '[Optical tactics of antibacterial therapy for the trigger model of the infection process]'. Biofizika, 27 (5):900-905. [Details] | |||||||||
| Dibrov BF, Zhabotinsky AM, Kholodenko BN; (1982) 'Dynamic stability of steady states and static stabilization in unbranched metabolic pathways'. Journal of mathematical biology, 15 (1):51-63. [Details] | |||||||||
| Ataullakhanov FI, Vitvitsky VM, Zhabotinsky AM, Pichugin AV, Kholodenko BN, Ehrlich LI; (1981) 'Regulation of glycolysis in human erythrocytes. The mechanism of ATP concentration stabilization'. Acta biologica et medica Germanica, 40 (7-8):991-997. [Details] | |||||||||
| Ataullakhanov FI, Vitvitsky VM, Zhabotinsky AM, Pichugin AV, Platonova OV, Kholodenko BN, Ehrlich LI; (1981) 'The regulation of glycolysis in human erythrocytes. The dependence of the glycolytic flux on the ATP concentration'. European journal of biochemistry / FEBS, 115 (2):359-365. [Details] | |||||||||
| Kholodenko BN; (1980) '[Stabilization of the relative concentration of ATP and invariants in the regulation of erythrocyte energy metabolism]'. Biofizika, 25 (2):258-264. [Details] | |||||||||
| Kholodenko BN; (1980) '[Biochemical individuality of humans and invariants of regulation. Scale invariance of the characteristic of glycolysis in erythrocytes]'. Biofizika, 25 (2):250-257. [Details] | |||||||||
| Kholodenko BN; (1979) '[Study of the dynamic behavior of the glycolytic system using the simplest model]'. Biofizika, 24 (4):640-645. [Details] | |||||||||
| Kholodenko BN; (1974) '[Nets of excitable elements. VII. Stabilization of the excitation level by inhibiting bonds]'. Biofizika, 19 (4):722-727. [Details] | |||||||||
| Kholodenko BN; (1974) '[Nets of excitable elements. IV. Nets of elements without refractoriness in continuous time]'. Biofizika, 19 (2):324-329. [Details] | |||||||||
| Kholodenko BN, Chetaev AN; (1973) '[Nets of excitable elements. 3. Ring-type nets]'. Biofizika, 18 (2):361-364. [Details] | |||||||||
| Kholodenko BN; (1972) '[Correlation of impulse currents for a neuron model with multiple inputs]'. Biofizika, 17 (1):175-177. [Details] | |||||||||
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