Boris Kholodenko is a Russian professor of Systems Biology at Systems Biology Ireland and Conway Institutes at University College Dublin, Ireland. He is also an adjunct professor at Thomas Jefferson University, Philadelphia where his group was behind the development of the first model of Epidermal growth factor receptor.
Boris Kholodenko graduated from Institute of Physics and Technology from Moscow, Russia where he got his Ph.D. He used to be a professor and director of Computational Cell Biology at Thomas Jefferson University in Philadelphia.
From 1982 to 2006 he was an author and coauthor of numerous scientific papers. He has 89 papers in his selected works:
Dibrov, B.F., Zhabotinsky, A.M. & Kholodenko, B.N. (1982). "Dynamic stability of steady states and static stabilization in unbranched metabolic pathways". J. Math. Biol. 15: 51–63. doi:10.1007/bf00275788. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N. (1983). "A model of energy metabolism of erythrocytes. Scale invariance of regulatory characteristics". Mathematical Modeling in Immunology and Medicine. North-Holland Publishing Company: 311–318.
Kholodenko, B.N. (1983). "Power law approximation and similarity properties of metabolic regulatory characteristics". Biophysics. Moscow. 28: 674–681.
Kholodenko, B.N. (1984). "Control of mitochondrial oxidative phosphorylation". J. Theor. Biol. 107: 179–188. doi:10.1016/s0022-5193(84)80020-x.
Kholodenko, B.; Zilinskiene V.; Borutaite V.; Ivanoviene L.; Toleikis A.; Praskevicius A. (1987). "The role of adenine nucleotide translocator in regulation of oxidative phosphorylation in heart mitochondria". FEBS Letters. 223: 247–250. doi:10.1016/0014-5793(87)80298-3.
Kholodenko, B.N. (1987). "Degree of stability of a metabolic chain with one feedback loop". Biophysics. Moscow. 32: 424–428.
Kholodenko B.N. (1988). "Control of molecular transformations in multienzyme systems: quantitative theory of metabolic regulation". Mol. Biol. Moscow. 22: 1238–1256.
Kholodenko, B.N. (1988). "How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control". FEBS Lett. 232: 383–386. doi:10.1016/0014-5793(88)80775-0.
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 of heart mitochondria". FEBS Lett. 243: 264–266. doi:10.1016/0014-5793(89)80141-3.
Kholodenko, B.N. (1991). "Kinetic models of coupling between proton translocation and ATP syntheshs/hydrolysis by FoF1-ATPases". J. Chem. Biochem. Kinetics. 1: 141–150.
Kholodenko, B.N.; Lyubarev, A.E.; Kurganov, B.I. (1992). "Control of the metabolic flux in the system with high enzyme concentrations and moiety-conserved cycles. The sum of the flux control coefficients can drop significantly below unity". Eur. J. Biochem. 210: 147–153. doi:10.1111/j.1432-1033.1992.tb17402.x.
Van Dam, K.; Van der Vlag, J.; Kholodenko, B.N.; Westerhoff, H.V. (1993). "The sum of the flux control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two". Eur. J. Biochem. 212: 791–799. doi:10.1111/j.1432-1033.1993.tb17720.x.
Kholodenko, B.N. & Westerhoff, H.V. (1993). "Metabolic channelling and control of the flux". FEBS Lett. 320: 71–74. doi:10.1016/0014-5793(93)81660-r.
Kholodenko, B.N. & Demin, O.V.; Westerhoff H.V. (1993). ""Channelled" pathways can be more sensitive to specific regulatory signals". FEBS Lett. 320: 75–78. doi:10.1016/0014-5793(93)81661-i. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N., Cascante, M. & Westerhoff, H.V. (1993). "Dramatic changes in control properties that accompany channelling and metabolite sequestration". FEBS Lett. 336: 381–384. doi:10.1016/0014-5793(93)80841-h. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N. (1993). "Control theory of "nonclassical" enzyme system and methods for the study of metabolic channeling". Biochemistry. Moscow. 58: 424–437.
Kholodenko, B.N. & Demin, O.V. (1993). "Parametric stabilization and dynamic stability of the steady-states in metabolic pathways. What are the optimal structures?". Biochemistry. Moscow. 58: 512–528.
Demin, O.V. & Kholodenko, B.N. (1993). "Structure of metabolic pathways that combine the high quality of end-product stabilization with high transition rates". Biochemistry. Moscow. 58: 997–1008.
Westerhoff, H.V.; Hofmeyr, J.-H.S.; Kholodenko, B.N. (1994). "Getting inside of cells using metabolic control analysis". Biophys. Chem. 50: 273–283. doi:10.1016/0301-4622(93)e0095-m.
Kholodenko, B.N., Cascante, M. & Westerhoff, H.V. (1994). "Control theory of metabolic channelling". Cellular bioenergetics: role of coupled creatine kinases. (Eds. V. Saks, R. Ventura-Clapier). Dordrecht-Boston: Kluwer Academic Publishers: 312–332. CS1 maint: Multiple names: authors list (link)
Snoep, J.L.; Jensen, P.R.; Groeneveld, P.; Molenaar, D.; Kholodenko, B.N.; Westerhoff, H.V. (1994). "How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox". Mol. Biol. Intern. 33: 1023–1032.
Kholodenko, B.N. & Westerhoff, H.V. (1994). "Control theory of one enzyme". Biochim. Biophys. Acta. 1208: 294–305. doi:10.1016/0167-4838(94)90116-3.
Kholodenko, B.N.; Sauro, H.M.; Westerhoff, H.V. (1994). "Control by enzymes, coenzymes and conserved moieties: a generalization of the connectivity theorem of metabolic control analysis". Eur. J. Biochem. 225: 179–186. doi:10.1111/j.1432-1033.1994.00179.x.
Kholodenko, B.N., Westerhoff, H.V. & Brown, G.C. (1994). "Rate limitation within a single enzyme is directly related to enzyme intermediate levels.". FEBS Lett. 349: 131–134. doi:10.1016/0014-5793(94)00617-2. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N., Cascante, M. & Westerhoff, H.V. (1995). "Control and regulation of channelled versus ideal pathways". Channelling and Intermediary Metabolism: 91–114. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N.; Schuster, S.; Rohwer, J. M.; Cascante, M.; Westerhoff, H.V. (1995). "Composite control of cell function: metabolic pathways behaving as single control units". FEBS Lett. 368: 1–4. doi:10.1016/0014-5793(95)00562-n.
Kholodenko, B.N.; Cascante, M.; Molenaar, D.; Demin, O.V.; Gugten van der, A.A.; Westerhoff, H.V. (1995). "Control theory of cell metabolism: towards more realistic "non-ideal" systems". J. Biol. Syst. 3: 145–154. doi:10.1142/s0218339095000149.
Cascante, M.; Melendez-Hevia, E.; Kholodenko, B.N.; Sicilia, J.; Kacser, H. (1995). "Control analysis of transit time for free and enzyme-bound metabolites". Biochem. J. 308: 895–899. doi:10.1042/bj3080895.
Mildaziene, V., Baniene, R., Nauciene, Z.; Bakker, B. M.; Westerhoff, H.V.; Brown, G.C.; Kholodenko, B.N. (1995). "Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria". Arch. Biochem. Biophys. 324: 130–134. doi:10.1006/abbi.1995.9918. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N.; Westerhoff, H.V.; Puigjaner, J.; Cascante, M. (1995). "Control in channelled pathways. A matrix method calculating the enzyme control coefficients". Biophys. Chem. 53: 247–258. doi:10.1016/0301-4622(94)00104-r.
Kholodenko, B.N. & Westerhoff, H.V. (1995). "The macro- versus microworld of biochemical regulation and control". Trends Biochem. Sci. 20: 52–54. doi:10.1016/s0968-0004(00)88955-0.
Kholodenko, B.N., Molenaar, D.; Schuster, S.; Heinrich, R.; Westerhoff, H.V. (1995). "Defining control coefficients in "non-ideal" metabolic pathways". Biophys. Chem. 56: 215–226. doi:10.1016/0301-4622(95)00039-z. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N. & Westerhoff, H.V. (1995). "Control theory of group-transfer pathways". Biochim. Biophys. Acta. 1229: 256–274. doi:10.1016/0005-2728(95)00014-a.
Kholodenko, B.N. & Westerhoff, H.V. (1995). "How to reveal various aspects of regulation in group-transfer pathways". Biochim. Biophys. Acta. 1229: 275–289. doi:10.1016/0005-2728(95)00013-9.
Kholodenko, B.N.; Sauro, H.M.; Westerhoff, H.V.; Cascante, M. (1995). "Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalized connectivity theorem". Biochem. Mol. Biol. Intern. 35: 615–625.
Jensen, P.R.; Snoep, J.L.; Molenaar, D.; Van Heeswijk, W.C.; Kholodenko, B.N.; Van der Gugten, A.A.; Westerhoff, H.V. (1995). "Molecular Biology for Flux Control Coefficients". Biochem. Soc. Trans. 23: 364–368.
Westerhoff, H.V., Kholodenko, B.N.; Cascante, M.; Van Dam, K. (1995). "Elusive control". J. Bioenerg. Biomembr. 27: 491–497. doi:10.1007/bf02110189. CS1 maint: Multiple names: authors list (link)
Cascante, M., Puigjaner, J. & Kholodenko, B.N. (1996). "Steady-state characterization of systems with moiety-conservations made easy". J.theor.Biol. 178: 1–6. doi:10.1006/jtbi.1996.0001. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N., Westerhoff, H.V. & Cascante, M. (1996). "Channelling and the concentration of bulk phase intermediates as cytosolic proteins get more concentrated". Biochem. J. 313: 921–926. doi:10.1042/bj3130921. CS1 maint: Multiple names: authors list (link)
Brown, G.C., Westerhoff, H.V. & Kholodenko, B.N. (1996). "Molecular control analysis: Control within proteins and molecular processes". J. Theor. Biol. 182: 389–396. doi:10.1006/jtbi.1996.0178. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N. & Brown, G.C. (1996). "Paradoxical properties of enzymes within pathways: can activation cause an enzyme to have increased control?". Biochem. J. 314: 753–760. doi:10.1042/bj3140753.
Kholodenko, B.N.; Sakamoto, N.; Puigjaner, J.; Westerhoff, H.V.; Cascante, M. (1996). "Strong control on the transit time in metabolic channelling". FEBS Lett. 389: 123–125. doi:10.1016/0014-5793(96)00532-7.
Bier M., Teusink B.; Kholodenko B.N.; Westerhoff H.V. (1996). "Control analysis of glycolytic oscillations". Biophys. Chem. 62: 15–24. doi:10.1016/s0301-4622(96)02195-3.
Mildaziene, V., Baniene, R.; Nauciene, Z.; Marcinkeviciute, A.; Borutaite, V.; Brown, G.C.; Kholodenko, B.N. (1996). "Calcium stimulates both respiratory and phosphosylation subsystem in heart mitochondria". Biochem. J. 320: 329–334. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Demin, O. V. & Westerhoff, H. V. (1997). "Control analysis of periodic phenomena in biological systems". J. Phys. Chem. 101: 2070–2081. doi:10.1021/jp962336u. CS1 maint: Multiple names: authors list (link)
Brown, G. C., Hoek, J.B. & Kholodenko, B. N. (1997). "Why do protein kinase cascades have more than one level?". Trends Biochem. Sci. 22: 288. doi:10.1016/s0968-0004(97)82216-5. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Hoek, J. B.; Westerhoff, H. W.; Brown, G. C. (1997). "Quantification of information transfer via cellular signal transduction pathways". FEBS Lett. 414: 430–434. doi:10.1016/s0014-5793(97)01018-1. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Rower, J.; Cascante, M.; Westerhoff, H. W. (1998). "Subtleties in control by metabolic channelling and enzyme organization". Mol. Cell. Biochem. 184: 311–320. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Shuster, S.; Garcia, J.; Westerhoff, H. W.; Cascante, M. (1998). "Control analysis of metabolic systems involving quasi-equilibrium reactions". Biochim. Biophys. Acta. 1379: 337–352. doi:10.1016/s0304-4165(97)00114-1. CS1 maint: Multiple names: authors list (link)
Westerhoff, H.V., Jensen, P.R.; Snoep, J.L.; Kholodenko, B.N. (1998). "Thermodynamics of complexity. The live cell". Thermochem. Acta. 309: 111–120. doi:10.1016/s0040-6031(97)00353-5. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Cascante, M.; Hoek, J. B.; Westerhoff, H. W.; Schwaber, J. (1998). "Metabolic design: how to engineer a living cell to desired metabolite concentrations and fluxes". Biotechnol. Bioeng. 59: 239–247. doi:10.1002/(sici)1097-0290(19980720)59:2<239::aid-bit11>3.0.co;2-9. CS1 maint: Multiple names: authors list (link)
Demin, O.V.; Kholodenko, B.N.; Skulachev, V.P. (1998). "A model of superoxide generation in the complex III of the electron transport chain". Mol. Cell. Biochem. 184: 21–33.
Rower, J., Postma, P.; Kholodenko, B.N.; Westerhoff, H. W. (1998). "Implications of macromolecular crowding for signal transduction and metabolic channeling". Proc. Natl. Acad. Sci. 95: 10547–10552. CS1 maint: Multiple names: authors list (link)
Brown, G. C. & Kholodenko, B. N. (1999). "Spatial gradients of cellular phospho-proteins". FEBS Lett. 457: 452–454. doi:10.1016/s0014-5793(99)01058-3.
Kholodenko, B.N., Demin, O.V.; Moehren, G.; Hoek, J.B. (1999). "Quantification of short-term signaling by the epidermal growth factor receptor". JBC. 274: 30169–30181. doi:10.1074/jbc.274.42.30169. CS1 maint: Multiple names: authors list (link)
Demin, O.V., Westerhoff, H. W. & Kholodenko, B.N. (1999). "Control analysis of stationary forced oscillations". J. Phys. Chem. B. 103: 10695–10710. doi:10.1021/jp991597b. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N. (2000). "Negative feedback and ultrasensitivity can bring about oscillations in the mitogen activated protein kinase cascades". Eur. J. Biochem. 267: 1583–1588. doi:10.1046/j.1432-1327.2000.01197.x.
Schuster, S., B. N. Kholodenko & H. V. Westerhoff (2000). "Cellular information transfer regarded from a stoichiometry and control analysis perspective". BioSystems. 55: 73–81. doi:10.1016/s0303-2647(99)00085-4. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N., Westerhoff, H. W.; Schwaber, J.; Cascante, M. (2000). "Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes". Metabolic Engineer. 2: 1–13. doi:10.1006/mben.1999.0132. CS1 maint: Multiple names: authors list (link)
Kholodenko, B.N., Hoek, J.B. & Westerhoff, H.V. (2000). "Why cytoplasmic signalling proteins should be recruited to cell membranes". Trends Cell Biol. 10: 173–178. doi:10.1016/s0962-8924(00)01741-4. CS1 maint: Multiple names: authors list (link)
Marcinkeviciute A.; Mildaziene V.; Crumm S.; Demin O.; Hoek, J.B.; Kholodenko, B. (2000). "Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding". Biochem. J. 349: 519–526. doi:10.1042/bj3490519.
Kholodenko, B. N.; G. C. Brown & Hoek, J.B. (2000). "Diffusion control of protein phosphorylation in signal transduction pathways". Biochem. J. 350: 901–907. doi:10.1042/0264-6021:3500901.
Markevich, N., Kiyatkin, A. B.; Zak D. E.; Pastorino, J. G.; Hoek, J. B.; Kholodenko, B. N. (2001). "Four-Dimensional Organization Of Cellular Signal Transduction Cascades". Pasadena, CA: Proceedings of the Second International Conference on System Biology: 141–147. CS1 maint: Multiple names: authors list (link)
De Atauri, P.; Acerenza, L.; Kholodenko, B. N.; De La Iglesia, N.; Guinovart, J. J.; 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". Biochem. J. 355: 787–793. doi:10.1042/bj3550787.
Moehren, G., Markevich, N., Demin, O.V.; Kiyatkin, A.; Hoek, J.B.; Kholodenko, B.N. (2002). "Temperature dependence of epidermal growth factor receptor signaling can be accounted for by a kinetic model". Biochemistry. 41: 306–320. doi:10.1021/bi011506c. CS1 maint: Multiple names: authors list (link)
Reijenga K.A., Westerhoff H.V.; Kholodenko B. N.; Snoep J. L. (2002). "Control Analysis for Autonomously Oscillating Biochemical Networks.". Biophys. J. 82: 99–108. PMC 1302452 . PMID 11751299. doi:10.1016/s0006-3495(02)75377-0.
Kholodenko, B.N. (2002). "Map kinase cascade signaling and endocytic trafficking: a marriage of convenience?". Trends Cell Biol. 12: 173–177. doi:10.1016/s0962-8924(02)02251-1.
Bruggeman, F. J. & Kholodenko, B. N. (2002). "Modular interaction strengths in regulatory networks; an example". Mol Biol. Rep. 29: 57–61.
Kholodenko B.N, Kiyatkin A, Bruggeman, F.; Sontag, E; Westerhoff, H.V.; Hoek, J. B. (2002). "Untangling the wires: A strategy to trace functional interactions in signaling and gene networks". Proc. Natl. Acad. Sci. USA. 20: 12841–12846. CS1 maint: Multiple names: authors list (link)
Bruggeman, F.J., Westerhoff, H.V.; Hoek, J. B.; Kholodenko, B. N. (2002). "Modular Response Analysis of Cellular Regulatory Networks". J. Theor. Biol. 218: 507–520. doi:10.1016/s0022-5193(02)93096-1. CS1 maint: Multiple names: authors list (link)
Kholodenko, B. N. (2003). "Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors". J. Exp. Biol. 206: 2073–2082. PMID 12756289. doi:10.1242/jeb.00298.
Peletier, M.A., Westerhoff, H. W. & Kholodenko, B. N. (2003). "Control of Spatially Heterogeneous Cellular Reaction Networks. A New Summation Law.". J. Theor. Biol. 225: 477–487. doi:10.1016/s0022-5193(03)00289-3. CS1 maint: Multiple names: authors list (link)
Westerhoff H.V. & Kholodenko B.N. (2003). "Metabolic Engineering, What it was and What it is.". Metabolic Engineering in the Post Genomic Era. Norfolk, England: Horizon Bioscience: 1–35.
Westerhoff H.V. & Kholodenko B.N. (2003). "Metabolic engineering in the postgenomic era: what it should become". Metabolic Engineering in the Post Genomic Era. Norfolk, England: Horizon Bioscience: 435–442.
Markevich, N., Hoek, J. B. & Kholodenko, B. N. (2004). "Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades". J. Cell Biology. 164: 353–359. PMC 2172246 . PMID 14744999. doi:10.1083/jcb.200308060. CS1 maint: Multiple names: authors list (link)
Sontag, E.; Kiyatkin, A.; Kholodenko, B. N. (2004). "Inferring Dynamic Architecture of Cellular Networks Using Time Series of Gene Expression, Protein and Metabolite Data". Bioinformatics. 20: 1877–1886. doi:10.1093/bioinformatics/bth173.
Sauro, H.M & Kholodenko, B.N. (2004). "Quantitative analysis of signaling networks". Prog Biophys Mol Biol. 86 (1): 5–43. doi:10.1016/j.pbiomolbio.2004.03.002.
Markevich, N. I.; Moehren, G.; Demin, O.; Kiyatkin, A.; Hoek, J. B.; Kholodenko, B. N. (2004). "Signal processing at the Ras circuit: What shapes Ras activation patterns?". IEE Systems Biology. 1: 104–113. doi:10.1049/sb:20045003.
Andrec, M.; Kholodenko, B.N.; Levy, R.M.; Sontag E (2005). "Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy". J. Theor. Biol. 232: 427–441. doi:10.1016/j.jtbi.2004.08.022.
Borisov N.M.; Markevich, N.I.; Hoek J.B.; Kholodenko, B.N. (2005). "Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity". Biophys J. 89: 951–966. doi:10.1529/biophysj.105.060533.
Bluthgen, N.; Bruggeman, F. J.; Legewie, S.; Herzel, H.; Westerhoff, H. V.; Kholodenko, B. N. (2006). "Effects of sequestration on signal transduction cascades". FEBS Journal. 273: 895–906. doi:10.1111/j.1742-4658.2006.05105.x.
Borisov, N. M.; Markevich, N. I.; Hoek, J. B.; Kholodenko, B. N. (2006). "Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains". Biosystems. 83: 152–66. doi:10.1016/j.biosystems.2005.03.006.
Conzelmann, H.; Saez-Rodriguez, J.; Sauter, T.; Kholodenko, B. N.; Gilles, E. D. (2006). "A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks". BMC Bioinformatics. 7 (34). doi:10.1186/1471-2105-7-34.
Kholodenko, B. N. (2006). "Cell-signalling dynamics in time and space". Nat Rev Mol Cell Biol. 7: 165–76. PMC 1679905 . PMID 16482094. doi:10.1038/nrm1838.
