Boris Kholodenko

Research & Publications
Biography

Coauthors

Anatoly Kiyatkin

Selected Publications

Control of cell state transitionsRukhlenko O, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher N, Kolch W, Kholodenko B. Control of cell state transitions. Nature 2022, 609: 975-985. PMID: 36104561, PMCID: PMC9644236, DOI: 10.1038/s41586-022-05194-y.
A systematic analysis of signaling reactivation and drug resistanceKholodenko B, Rauch N, Kolch W, Rukhlenko O. A systematic analysis of signaling reactivation and drug resistance. Cell Reports 2021, 35: 109157. PMID: 34038718, PMCID: PMC8202068, DOI: 10.1016/j.celrep.2021.109157.
Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migrationBolado-Carrancio A, Rukhlenko O, Nikonova E, Tsyganov M, Wheeler A, Garcia-Munoz A, Kolch W, von Kriegsheim A, Kholodenko B. Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. ELife 2020, 9: e58165. PMID: 32705984, PMCID: PMC7380942, DOI: 10.7554/elife.58165.
Scaffolding Protein Grb2-associated Binder 1 Sustains Epidermal Growth Factor-induced Mitogenic and Survival Signaling by Multiple Positive Feedback Loops*Kiyatkin A, Aksamitiene E, Markevich NI, Borisov NM, Hoek JB, Kholodenko BN. Scaffolding Protein Grb2-associated Binder 1 Sustains Epidermal Growth Factor-induced Mitogenic and Survival Signaling by Multiple Positive Feedback Loops*. Journal Of Biological Chemistry 2006, 281: 19925-19938. PMID: 16687399, PMCID: PMC2312093, DOI: 10.1074/jbc.m600482200.
Untangling the wires: A strategy to trace functional interactions in signaling and gene networksKholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB. 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: 12841-12846. PMID: 12242336, PMCID: PMC130547, DOI: 10.1073/pnas.192442699.
Reversing pathological cell states: the road less travelled can extend the therapeutic horizonKholodenko B, Kolch W, Rukhlenko O. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends In Cell Biology 2023, 33: 913-923. PMID: 37263821, PMCID: PMC10593090, DOI: 10.1016/j.tcb.2023.04.004.
Can Systems Biology Advance Clinical Precision Oncology?Rocca A, Kholodenko B. Can Systems Biology Advance Clinical Precision Oncology? Cancers 2021, 13: 6312. PMID: 34944932, PMCID: PMC8699328, DOI: 10.3390/cancers13246312.
Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBIDegasperi A, Nguyen L, Fey D, Kholodenko B. Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI. 2021, 2385: 91-115. PMID: 34888717, PMCID: PMC9446379, DOI: 10.1007/978-1-0716-1767-0_5.
Modeling the Nonlinear Dynamics of Intracellular Signaling NetworksRukhlenko O, Kholodenko B. Modeling the Nonlinear Dynamics of Intracellular Signaling Networks. Bio-protocol 2021, 11: e4089. PMID: 34395728, PMCID: PMC8329461, DOI: 10.21769/bioprotoc.4089.
Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosisChatterjee S, Yabaji S, Rukhlenko O, Bhattacharya B, Waligurski E, Vallavoju N, Ray S, Kholodenko B, Brown L, Beeler A, Ivanov A, Kobzik L, Porco J, Kramnik I. Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosis. IScience 2021, 24: 102845. PMID: 34381970, PMCID: PMC8333345, DOI: 10.1016/j.isci.2021.102845.
Reengineering protein-phosphorylation switchesKholodenko B, Okada M. Reengineering protein-phosphorylation switches. Science 2021, 373: 25-26. PMID: 34210865, PMCID: PMC8327301, DOI: 10.1126/science.abj5028.
Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungsSeidel C, Zhernovkov V, Cassidy H, Kholodenko B, Matallanas D, Cosnier F, Gaté L. Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs. Nanotoxicology 2020, 15: 238-256. PMID: 33332178, DOI: 10.1080/17435390.2020.1851418.
Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processingRukhlenko O, Kholodenko B, Kolch W. Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Current Opinion In Structural Biology 2020, 67: 61-68. PMID: 33126139, PMCID: PMC8062579, DOI: 10.1016/j.sbi.2020.09.007.
Acute Phase Response as a Biological Mechanism‐of‐Action of (Nano)particle‐Induced Cardiovascular DiseaseHadrup N, Zhernovkov V, Jacobsen N, Voss C, Strunz M, Ansari M, Schiller H, Halappanavar S, Poulsen S, Kholodenko B, Stoeger T, Saber A, Vogel U. Acute Phase Response as a Biological Mechanism‐of‐Action of (Nano)particle‐Induced Cardiovascular Disease. Small 2020, 16: e1907476. PMID: 32227434, DOI: 10.1002/smll.201907476.
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13DKennedy S, Jarboui M, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn M, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko B, Iglesias-Martinez L, Ryan C, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn D, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D. Nature Communications 2020, 11: 499. PMID: 31980649, PMCID: PMC6981206, DOI: 10.1038/s41467-019-14224-9.
An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced ToxicityZhernovkov V, Santra T, Cassidy H, Rukhlenko O, Matallanas D, Krstic A, Kolch W, Lobaskin V, Kholodenko B. An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced Toxicity. Toxicological Sciences 2019, 171: 303-314. PMID: 31271423, DOI: 10.1093/toxsci/kfz151.
Mapping connections in signaling networks with ambiguous modularityLill D, Rukhlenko O, Mc Elwee A, Kashdan E, Timmer J, Kholodenko B. Mapping connections in signaling networks with ambiguous modularity. Npj Systems Biology And Applications 2019, 5: 19. PMID: 31149348, PMCID: PMC6533310, DOI: 10.1038/s41540-019-0096-1.
Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstructionThomaseth C, Fey D, Santra T, Rukhlenko OS, Radde NE, Kholodenko BN. Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Scientific Reports 2018, 8: 16217. PMID: 30385767, PMCID: PMC6212399, DOI: 10.1038/s41598-018-34353-3.
How Combining Structurally Different RAF Inhibitors Can Open New Strides In Targeted Melanoma TherapyRauch J, Rukhlenko O, Kholodenko B. How Combining Structurally Different RAF Inhibitors Can Open New Strides In Targeted Melanoma Therapy. Science Trends 2018 DOI: 10.31988/scitrends.34642.
Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS SignalingRukhlenko OS, Khorsand F, Krstic A, Rozanc J, Alexopoulos LG, Rauch N, Erickson KE, Hlavacek WS, Posner RG, Gómez-Coca S, Rosta E, Fitzgibbon C, Matallanas D, Rauch J, Kolch W, Kholodenko BN. Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Systems 2018, 7: 161-179.e14. PMID: 30007540, PMCID: PMC6149545, DOI: 10.1016/j.cels.2018.06.002.
PO-136 Studying pathway interactions and dynamics to predict cell responses to chemotherapeutic treatment in breast cancer cellsTuffery L, Kholodenko B, Kolch W, Halasz M, Fey D. PO-136 Studying pathway interactions and dynamics to predict cell responses to chemotherapeutic treatment in breast cancer cells. ESMO Open 2018, 3: a279. DOI: 10.1136/esmoopen-2018-eacr25.660.
Reconstructing static and dynamic models of signaling pathways using Modular Response AnalysisSantra T, Rukhlenko O, Zhernovkov V, Kholodenko B. Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis. Current Opinion In Systems Biology 2018, 9: 11-21. DOI: 10.1016/j.coisb.2018.02.003.
Performance of objective functions and optimisation procedures for parameter estimation in system biology modelsDegasperi A, Fey D, Kholodenko BN. Performance of objective functions and optimisation procedures for parameter estimation in system biology models. Npj Systems Biology And Applications 2017, 3: 20. PMID: 28804640, PMCID: PMC5548920, DOI: 10.1038/s41540-017-0023-2.
Rac1 and RhoA: Networks, loops and bistabilityNguyen LK, Kholodenko BN, von Kriegsheim A. Rac1 and RhoA: Networks, loops and bistability. Small GTPases 2016, 9: 316-321. PMID: 27533896, PMCID: PMC5997137, DOI: 10.1080/21541248.2016.1224399.
HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC statusWeitsman G, Barber PR, Nguyen LK, Lawler K, Patel G, Woodman N, Kelleher MT, Pinder SE, Rowley M, Ellis PA, Purushotham AD, Coolen AC, Kholodenko BN, Vojnovic B, Gillett C, Ng T. HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status. Oncotarget 2016, 7: 51012-51026. PMID: 27618787, PMCID: PMC5239455, DOI: 10.18632/oncotarget.9963.
Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal dataFrank TD, Kiyatkin A, Cheong A, Kholodenko BN. Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data. Mathematical Medicine And Biology A Journal Of The IMA 2016, 34: 177-191. PMID: 27079221, DOI: 10.1093/imammb/dqw001.
On the personalised modelling of cancer signalling**Supported by EU FP7 grant “SynSignal” (No. 613879).Fey D, Kuehn A, Kholodenko B. On the personalised modelling of cancer signalling**Supported by EU FP7 grant “SynSignal” (No. 613879). IFAC-PapersOnLine 2016, 49: 312-317. DOI: 10.1016/j.ifacol.2016.12.145.
Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate TransactivationJambrina P, Rauch N, Pilkington R, Rybakova K, Nguyen L, Kholodenko B, Buchete N, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angewandte Chemie 2015, 128: 995-998. DOI: 10.1002/ange.201509272.
Abstract CN05-03: Personalized cancer diagnostics and therapeutics based on the computational modeling of signal transduction networksKolch W, Fey D, Halasz M, Rauch N, Munoz A, Pilkington R, Kholodenko B, Croucher D, Kennedy S, Hastings J, Westermann F, Dreidax D, Fischer M, Duffy D, Krstic A, Schwarzl T. Abstract CN05-03: Personalized cancer diagnostics and therapeutics based on the computational modeling of signal transduction networks. Molecular Cancer Therapeutics 2015, 14: cn05-03-cn05-03. DOI: 10.1158/1535-7163.targ-15-cn05-03.
Frequency modulation of ERK activation dynamics rewires cell fateRyu H, Chung M, Dobrzyński M, Fey D, Blum Y, Lee SS, Peter M, Kholodenko BN, Jeon NL, Pertz O. Frequency modulation of ERK activation dynamics rewires cell fate. Molecular Systems Biology 2015, 11: 838. PMID: 26613961, PMCID: PMC4670727, DOI: 10.15252/msb.20156458.
Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor EffectsKholodenko BN. Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects. Cell Reports 2015, 12: 1939-1949. PMID: 26344764, DOI: 10.1016/j.celrep.2015.08.014.
G Protein–Coupled Receptor Signaling Networks from a Systems PerspectiveRoth S, Kholodenko B, Smit M, Bruggeman F. G Protein–Coupled Receptor Signaling Networks from a Systems Perspective. Molecular Pharmacology 2015, 88: 604-616. PMID: 26162865, DOI: 10.1124/mol.115.100057.
Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant TransformationMilewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A. Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation. PLOS ONE 2015, 10: e0129859. PMID: 26065894, PMCID: PMC4466796, DOI: 10.1371/journal.pone.0129859.
Silence on the relevant literature and errors in implementationBastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN. Silence on the relevant literature and errors in implementation. Nature Biotechnology 2015, 33: 336-339. PMID: 25850052, DOI: 10.1038/nbt.3185.
Signalling mechanisms regulating phenotypic changes in breast cancer cellsVolinsky N, McCarthy CJ, von Kriegsheim A, Saban N, Okada-Hatakeyama M, Kolch W, Kholodenko BN. Signalling mechanisms regulating phenotypic changes in breast cancer cells. Bioscience Reports 2015, 35: e00178. PMID: 25643809, PMCID: PMC4370098, DOI: 10.1042/bsr20140172.
Network-based identification of feedback modules that control RhoA activity and cell migrationKim TH, Monsefi N, Song JH, von Kriegsheim A, Vandamme D, Pertz O, Kholodenko BN, Kolch W, Cho KH. Network-based identification of feedback modules that control RhoA activity and cell migration. Journal Of Molecular Cell Biology 2015, 7: 242-252. PMID: 25780058, DOI: 10.1093/jmcb/mjv017.
A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) networkNguyen LK, Cavadas MA, Scholz CC, Fitzpatrick SF, Bruning U, Cummins EP, Tambuwala MM, Manresa MC, Kholodenko BN, Taylor CT, Cheong A. A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network. Journal Of Cell Science 2015, 128: 422-422. PMID: 25589793, DOI: 10.1242/jcs.167304.
228 Her2–3 heterodimer is a new and better than HER2 IHC score for clinical outcome prognosisWeitsman G, Barber P, Lawler K, Gillett C, Woodman N, Kholodenko B, Nguyen L, Santra T, Vojnovic B, Ng T. 228 Her2–3 heterodimer is a new and better than HER2 IHC score for clinical outcome prognosis. European Journal Of Cancer 2014, 50: 77. DOI: 10.1016/s0959-8049(14)70354-5.
533: Proteomic profiling of N-Myc-associated proteins in neuroblastomaHalasz M, Santra T, Rodriguez J, Kholodenko B, Kolch W. 533: Proteomic profiling of N-Myc-associated proteins in neuroblastoma. European Journal Of Cancer 2014, 50: s133-s134. DOI: 10.1016/s0959-8049(14)50493-5.
Systems biology‐embedded target validation: improving efficacy in drug discoveryVandamme D, Minke BA, Fitzmaurice W, Kholodenko BN, Kolch W. Systems biology‐embedded target validation: improving efficacy in drug discovery. WIREs Mechanisms Of Disease 2013, 6: 1-11. PMID: 24214316, DOI: 10.1002/wsbm.1253.
Complexity of Receptor Tyrosine Kinase Signal ProcessingVolinsky N, Kholodenko BN. Complexity of Receptor Tyrosine Kinase Signal Processing. Cold Spring Harbor Perspectives In Biology 2013, 5: a009043. PMID: 23906711, PMCID: PMC3721286, DOI: 10.1101/cshperspect.a009043.
Systems medicine: helping us understand the complexity of diseaseVandamme D, Fitzmaurice W, Kholodenko B, Kolch W. Systems medicine: helping us understand the complexity of disease. QJM 2013, 106: 891-895. PMID: 23904523, DOI: 10.1093/qjmed/hct163.
Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2Reiterer V, Fey D, Kolch W, Kholodenko BN, Farhan H. Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: e2934-e2943. PMID: 23847209, PMCID: PMC3732994, DOI: 10.1073/pnas.1301985110.
A dynamic model of the hypoxia‐inducible factor (HIF) networkCheong A, Cavadas M, Nguyen L, Scholz C, Fitzpatrick S, Bruning U, Tambuwala M, Manresa M, Kholodenko B, Taylor C. A dynamic model of the hypoxia‐inducible factor (HIF) network. The FASEB Journal 2013, 27: 717.12-717.12. DOI: 10.1096/fasebj.27.1_supplement.717.12.
Control of the G- protein cascade dynamics by GDP dissociation inhibitorsNikonova E, Tsyganov MA, Kolch W, Fey D, Kholodenko BN. Control of the G- protein cascade dynamics by GDP dissociation inhibitors. Molecular Omics 2013, 9: 2454-2462. PMID: 23872884, DOI: 10.1039/c3mb70152b.
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noiseBirtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC Systems Biology 2012, 6: 109. PMID: 22920937, PMCID: PMC3484110, DOI: 10.1186/1752-0509-6-109.
Understanding Cell Fate Decisions by Identifying Crucial System DynamicsFey D, Croucher D, Kolch W, Kholodenko B. Understanding Cell Fate Decisions by Identifying Crucial System Dynamics. 2012, 83-104. DOI: 10.1007/978-88-470-2571-4_5.
Bimodal Protein Distributions in Heterogeneous Oscillating SystemsDobrzyński M, Fey D, Nguyen L, Kholodenko B. Bimodal Protein Distributions in Heterogeneous Oscillating Systems. 2012, 7605: 17-28. DOI: 10.1007/978-3-642-33636-2_3.
11 From benchside to byteside: what we can learn from computational modellingKolch W, Birtwistle M, Kholodenko B, Grindlay J, Sturm O, Orton R, Gilbert D, von Kriegsheim A. 11 From benchside to byteside: what we can learn from computational modelling. European Journal Of Cancer Supplements 2010, 8: 3. DOI: 10.1016/s1359-6349(10)70820-x.
1P295 Computational analysis of protein-protein interactions(Bioinformatics:Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan)Suenaga A, Okada M, Kholodenko B, Taiji M. 1P295 Computational analysis of protein-protein interactions(Bioinformatics:Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan). Seibutsu Butsuri 2010, 50: s72. DOI: 10.2142/biophys.50.s72_1.
Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycleKaimachnikov NP, Kholodenko BN. Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle. The FEBS Journal 2009, 276: 4102-4118. PMID: 19627364, PMCID: PMC2924194, DOI: 10.1111/j.1742-4658.2009.07117.x.
Four‐dimensional dynamics of MAPK information‐processing systemsKholodenko BN, Birtwistle MR. Four‐dimensional dynamics of MAPK information‐processing systems. WIREs Mechanisms Of Disease 2009, 1: 28-44. PMID: 20182652, PMCID: PMC2826817, DOI: 10.1002/wsbm.16.
Positional Information Generated by Spatially Distributed Signaling CascadesMuñoz-García J, Neufeld Z, Kholodenko BN. Positional Information Generated by Spatially Distributed Signaling Cascades. PLOS Computational Biology 2009, 5: e1000330. PMID: 19300504, PMCID: PMC2654021, DOI: 10.1371/journal.pcbi.1000330.
Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor ReceptorSuenaga A, Hatakeyama M, Kiyatkin AB, Radhakrishnan R, Taiji M, Kholodenko BN. Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor. Biophysical Journal 2009, 96: 2278-2288. PMID: 19289054, PMCID: PMC2717265, DOI: 10.1016/j.bpj.2008.11.018.
Systems‐level interactions between insulin–EGF networks amplify mitogenic signalingBorisov N, Aksamitiene E, Kiyatkin A, Legewie S, Berkhout J, Maiwald T, Kaimachnikov NP, Timmer J, Hoek JB, Kholodenko BN. Systems‐level interactions between insulin–EGF networks amplify mitogenic signaling. Molecular Systems Biology 2009, 5: 256-256. PMID: 19357636, PMCID: PMC2683723, DOI: 10.1038/msb.2009.19.
Domain-oriented reduction of rule-based network models.Borisov N, Chistopolsky A, Faeder J, Kholodenko B. Domain-oriented reduction of rule-based network models. IET Systems Biology 2008, 2: 342-51. PMID: 19045829, PMCID: PMC2628550, DOI: 10.1049/iet-syb:20070081.
Giving Space to Cell SignalingKholodenko BN, Kolch W. Giving Space to Cell Signaling. Cell 2008, 133: 566-567. PMID: 18485861, DOI: 10.1016/j.cell.2008.04.033.
Multi‐scale modeling of neuronal adaptation mediated by angiotensin II in the central regulation of blood pressureVadigepalli R, Nikolaev E, Miller G, Ogunnaike B, Gonye G, Kholodenko B, Schwaber J. Multi‐scale modeling of neuronal adaptation mediated by angiotensin II in the central regulation of blood pressure. The FASEB Journal 2008, 22: 756.2-756.2. DOI: 10.1096/fasebj.22.1_supplement.756.2.
Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and SpaceKholodenko B. Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and Space. 2007, 300-318. DOI: 10.1007/978-1-59745-531-2_16.
Ligand‐dependent responses of the ErbB signaling network: experimental and modeling analysesBirtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN. Ligand‐dependent responses of the ErbB signaling network: experimental and modeling analyses. Molecular Systems Biology 2007, 3: 144. PMID: 18004277, PMCID: PMC2132449, DOI: 10.1038/msb4100188.
Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal TransductionBlüthgen N, Legewie S, Herzel H, Kholodenko B. Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction. 2007, 282-299. DOI: 10.1007/978-1-59745-531-2_15.
Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.Yalamanchili N, Zak D, Ogunnaike B, Schwaber J, Kriete A, Kholodenko B. Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach. IET Systems Biology 2006, 153: 236-46. PMID: 16986625, PMCID: PMC2346590, DOI: 10.1049/ip-syb:20050090.
Signaling through Receptors and Scaffolds: Independent Interactions Reduce Combinatorial ComplexityBorisov N, Markevich N, Hoek J, Kholodenko B. Signaling through Receptors and Scaffolds: Independent Interactions Reduce Combinatorial Complexity. Biophysical Journal 2005, 89: 951-966. PMID: 15923229, PMCID: PMC1366644, DOI: 10.1529/biophysj.105.060533.
Mechanistic and modular approaches to modeling and inference of cellular regulatory networksKholodenko B, Bruggeman F, Sauro H. Mechanistic and modular approaches to modeling and inference of cellular regulatory networks. 2005, 13: 143-159. DOI: 10.1007/b136809.
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracyAndrec M, Kholodenko B, Levy R, Sontag E. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. Journal Of Theoretical Biology 2005, 232: 427-441. PMID: 15572066, DOI: 10.1016/j.jtbi.2004.08.022.
The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks.Sakaki Y, Kholodenko B, Hatakeyama M, Kitano H, Kolch W, De Meyts P, Yarden Y, Westerhoff H, Wiley H. The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks. IET Systems Biology 2005, 152: 53-4. PMID: 17044231, DOI: 10.1049/ip-syb:20059002.
Quantitative analysis of signaling networksSauro H, Kholodenko B. Quantitative analysis of signaling networks. Progress In Biophysics And Molecular Biology 2004, 86: 5-43. PMID: 15261524, DOI: 10.1016/j.pbiomolbio.2004.03.002.
Signal processing at the Ras circuit: what shapes Ras activation patterns?Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN. Signal processing at the Ras circuit: what shapes Ras activation patterns? IET Systems Biology 2004, 1: 104-13. PMID: 17052120, DOI: 10.1049/sb:20045003.
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite dataSontag E, Kiyatkin A, Kholodenko BN. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 2004, 20: 1877-1886. PMID: 15037511, DOI: 10.1093/bioinformatics/bth173.
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascadesMarkevich N, Hoek J, Kholodenko B. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. Journal Of Cell Biology 2004, 164: 353-359. PMID: 14744999, PMCID: PMC2172246, DOI: 10.1083/jcb.200308060.
Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation lawPeletier M, Westerhoff H, Kholodenko B. Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. Journal Of Theoretical Biology 2003, 225: 477-487. PMID: 14615206, DOI: 10.1016/s0022-5193(03)00289-3.
Modular Response Analysis of Cellular Regulatory NetworksBRUGGEMAN F, WESTERHOFF H, HOEK J, KHOLODENKO B. Modular Response Analysis of Cellular Regulatory Networks. Journal Of Theoretical Biology 2002, 218: 507-520. PMID: 12384053, DOI: 10.1006/jtbi.2002.3096.
MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?Kholodenko BN. MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience? Trends In Cell Biology 2002, 12: 173-177. PMID: 11978536, DOI: 10.1016/s0962-8924(02)02251-1.
Modular Interaction Strengths in Regulatory Networks; An ExampleBruggeman F, Kholodenko B. Modular Interaction Strengths in Regulatory Networks; An Example. Molecular Biology Reports 2002, 29: 57-61. PMID: 12241075, DOI: 10.1023/a:1020354302260.
Control Analysis for Autonomously Oscillating Biochemical NetworksReijenga K, Westerhoff H, Kholodenko B, Snoep J. Control Analysis for Autonomously Oscillating Biochemical Networks. Biophysical Journal 2002, 82: 99-108. PMID: 11751299, PMCID: PMC1302452, DOI: 10.1016/s0006-3495(02)75377-0.
Temperature Dependence of the Epidermal Growth Factor Receptor Signaling Network Can Be Accounted for by a Kinetic Model †Moehren G, Markevich N, Demin O, Kiyatkin A, Goryanin I, Hoek JB, Kholodenko BN. Temperature Dependence of the Epidermal Growth Factor Receptor Signaling Network Can Be Accounted for by a Kinetic Model †. Biochemistry 2001, 41: 306-320. PMID: 11772030, DOI: 10.1021/bi011506c.
Kinetic Modeling of Energy Metabolism and Superoxide Generation in Hepatocyte MitochondriaDemin O, Goryanin I, Kholodenko B, Westerhoff H. Kinetic Modeling of Energy Metabolism and Superoxide Generation in Hepatocyte Mitochondria. Molecular Biology 2001, 35: 940-949. DOI: 10.1023/a:1013211007465.
Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinaseDE ATAURI P, ACERENZA L, KHOLODENKO B, DE LA IGLESIA N, GUINOVART J, AGIUS L, CASCANTE M. Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase. Biochemical Journal 2001, 355: 787-793. PMID: 11311143, PMCID: PMC1221796, DOI: 10.1042/bj3550787.
Kinetic modeling of energy metabolism and generation of active forms of oxygen in hepatocyte mitochondria.Demin O, Gorianin I, Kholodenko B, Westerhoff H. Kinetic modeling of energy metabolism and generation of active forms of oxygen in hepatocyte mitochondria. Молекулярная Биология 2001, 35: 1095-104. PMID: 11771135.
Diffusion control of protein phosphorylation in signal transduction pathwaysKHOLODENKO B, BROWN G, HOEK J. Diffusion control of protein phosphorylation in signal transduction pathways. Biochemical Journal 2000, 350: 901. DOI: 10.1042/0264-6021:3500901.
Diffusion control of protein phosphorylation in signal transduction pathwaysKHOLODENKO B, BROWN G, HOEK J. Diffusion control of protein phosphorylation in signal transduction pathways. Biochemical Journal 2000, 350: 901-907. PMID: 10970807, PMCID: PMC1221325, DOI: 10.1042/bj3500901.
Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding.Marcinkeviciute A, Mildaziene V, Crumm S, Demin O, Hoek J, Kholodenko B. Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding. Biochemical Journal 2000, 349: 519-26. PMID: 10880351, PMCID: PMC1221175, DOI: 10.1042/0264-6021:3490519.
Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feedingMARCINKEVICIUTE A, MILDAZIENE V, CRUMM S, DEMIN O, HOEK J, KHOLODENKO B. Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding. Biochemical Journal 2000, 349: 519-526. DOI: 10.1042/bj3490519.
Why cytoplasmic signalling proteins should be recruited to cell membranesKholodenko B, Hoek J, Westerhoff H, Kholodenko B, Hoek J, Westerhoff H. Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends In Cell Biology 2000, 10: 173-178. PMID: 10754559, DOI: 10.1016/s0962-8924(00)01741-4.
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen‐activated protein kinase cascadesKholodenko B. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen‐activated protein kinase cascades. The FEBS Journal 2000, 267: 1583-1588. PMID: 10712587, DOI: 10.1046/j.1432-1327.2000.01197.x.
Cellular information transfer regarded from a stoichiometry and control analysis perspectiveSchuster S, Kholodenko B, Westerhoff H. Cellular information transfer regarded from a stoichiometry and control analysis perspective. Biosystems 2000, 55: 73-81. PMID: 10745111, DOI: 10.1016/s0303-2647(99)00085-4.
Engineering a Living Cell to Desired Metabolite Concentrations and Fluxes: Pathways with Multifunctional EnzymesKholodenko B, Westerhoff H, Schwaber J, Cascante M. Engineering a Living Cell to Desired Metabolite Concentrations and Fluxes: Pathways with Multifunctional Enzymes. Metabolic Engineering 2000, 2: 1-13. PMID: 10935931, DOI: 10.1006/mben.1999.0132.
Metabolic Control From The Back Benches: Biochemistry Towards BiocomplexityWesterhoff H, Teusink B, Mensonides F, Reijenga K, Esgalhado E, Kholodenko B, Somsen O, Van Heeswijk W, Boogerd F, Bruggeman F, Snoep J. Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity. 2000, 235-242. DOI: 10.1007/978-94-011-4072-0_26.
Control Analysis of Stationary Forced OscillationsDemin O, Westerhoff H, Kholodenko B. Control Analysis of Stationary Forced Oscillations. The Journal Of Physical Chemistry B 1999, 103: 10695-10710. DOI: 10.1021/jp991597b.
Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor*Kholodenko B, Demin O, Moehren G, Hoek J. Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor*. Journal Of Biological Chemistry 1999, 274: 30169-30181. PMID: 10514507, DOI: 10.1074/jbc.274.42.30169.
Spatial gradients of cellular phospho‐proteinsBrown G, Kholodenko B. Spatial gradients of cellular phospho‐proteins. FEBS Letters 1999, 457: 452-454. PMID: 10471827, DOI: 10.1016/s0014-5793(99)01058-3.
Live Control of the Living Cellvan Heeswijk W, Bakker B, Teusink B, Kholodenko B, Somsen O, Snoep J, Westerhoff H. Live Control of the Living Cell. Biochemical Society Transactions 1999, 27: a18-a18. DOI: 10.1042/bst027a018c.
Live control of the living cellvan Heeswijk W, Bakker B, Teusink B, Kholodenko B, Somsen O, Snoep J, Westerhoff H. Live control of the living cell. Biochemical Society Transactions 1999, 27: 261-264. PMID: 10093744, DOI: 10.1042/bst0270261.
Implications of macromolecular crowding for signal transduction and metabolite channelingRohwer J, Postma P, Kholodenko B, Westerhoff H. 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: 10547-10552. PMID: 9724740, PMCID: PMC27931, DOI: 10.1073/pnas.95.18.10547.
The Intracellular Signaling Network as a Target for EthanolHoek J, Kholodenko B. The Intracellular Signaling Network as a Target for Ethanol. Alcohol Clinical And Experimental Research 1998, 22: 224s-230s. PMID: 9727641, DOI: 10.1111/j.1530-0277.1998.tb04007.x.
Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxesKholodenko B, Cascante M, Hoek J, Westerhoff H, Schwaber J. Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes. Biotechnology And Bioengineering 1998, 59: 239-247. PMID: 10099334, DOI: 10.1002/(sici)1097-0290(19980720)59:2<239::aid-bit11>3.0.co;2-9.
A model of O·2- generation in the complex III of the electron transport chainDemin O, Kholodenko B, Skulachev V. A model of O·2- generation in the complex III of the electron transport chain. Molecular And Cellular Biochemistry 1998, 184: 21-33. PMID: 9746310, DOI: 10.1023/a:1006849920918.
Subtleties in control by metabolic channelling and enzyme organizationKholodenko B, Rohwer J, Cascante M, Westerhoff H. Subtleties in control by metabolic channelling and enzyme organization. Molecular And Cellular Biochemistry 1998, 184: 311-320. PMID: 9746327, DOI: 10.1023/a:1006809028612.
Mathematical modelling of superoxide generation with the bc1 complex of mitochondria Demin O, Westerhoff H, Kholodenko B. Mathematical modelling of superoxide generation with the bc1 complex of mitochondria . Biochemistry (Moscow) 1998, 63: 634-49. PMID: 9668203.
Control analysis of metabolic systems involving quasi-equilibrium reactionsKholodenko B, Schuster S, Garcia J, Westerhoff H, Cascante M. Control analysis of metabolic systems involving quasi-equilibrium reactions. Biochimica Et Biophysica Acta 1998, 1379: 337-352. PMID: 9545597, DOI: 10.1016/s0304-4165(97)00114-1.
Thermodynamics of complexity. The live cellWesterhoff H, Jensen P, Snoep J, Kholodenko B. Thermodynamics of complexity. The live cell. Thermochimica Acta 1998, 309: 111-120. DOI: 10.1016/s0040-6031(97)00353-5.
A model of O·2-generation in the complex III of the electron transport chainDemin O, Kholodenko B, Skulachev V. A model of O·2-generation in the complex III of the electron transport chain. 1998, 21-33. DOI: 10.1007/978-1-4615-5653-4_3.
Subtleties in control by metabolic channelling and enzyme organizationKholodenko B, Rohwer J, Cascante M, Westerhoff H. Subtleties in control by metabolic channelling and enzyme organization. 1998, 311-320. DOI: 10.1007/978-1-4615-5653-4_20.
Hierarchical Control of Electron-TransferWesterhoff H, Jensen P, Egger L, van Heeswijk W, van Spanning R, Kholodenko B, Snoep J. Hierarchical Control of Electron-Transfer. 1998, 99-114. DOI: 10.1007/978-94-011-5133-7_8.
Quantification of information transfer via cellular signal transduction pathwaysKholodenko B, Hoek J, Westerhoff H, Brown G. Quantification of information transfer via cellular signal transduction pathways. FEBS Letters 1997, 414: 430-434. PMID: 9315734, DOI: 10.1016/s0014-5793(97)01018-1.
Why do protein kinase cascades have more than one level?Brown G, Hoek J, Kholodenko B. Why do protein kinase cascades have more than one level? Trends In Biochemical Sciences 1997, 22: 288. PMID: 9270298, DOI: 10.1016/s0968-0004(97)82216-5.
Control Analysis of Periodic Phenomena in Biological SystemsKholodenko B, Demin O, Westerhoff H. Control Analysis of Periodic Phenomena in Biological Systems. The Journal Of Physical Chemistry B 1997, 101: 2070-2081. DOI: 10.1021/jp962336u.
Nonlinear control and self-organizationWesterhoff H, Jensen P, Kahn D, Kholodenko B, Richard P. Nonlinear control and self-organization. 1996, 3245-3254. DOI: 10.1515/9783110883237.3245.
Ca2+ stimulates both the respiratory and phosphorylation subsystems in rat heart mitochondriaMILDAZIENE V, BANIENE R, NAUCIENE Z, MARCINKEVICIUTE A, MORKUNIENE R, BORUTAITE V, KHOLODENKO B, BROWN G. Ca2+ stimulates both the respiratory and phosphorylation subsystems in rat heart mitochondria. Biochemical Journal 1996, 320: 329-334. PMID: 8947505, PMCID: PMC1217935, DOI: 10.1042/bj3200329.
Control analysis of glycolytic oscillationsBier M, Teusink B, Kholodenko B, Westerhoff H. Control analysis of glycolytic oscillations. Biophysical Chemistry 1996, 62: 15-24. PMID: 8962468, DOI: 10.1016/s0301-4622(96)02195-3.
Molecular Control Analysis: Control within Proteins and Molecular ProcessesBrown G, Westerhoff H, Kholodenko B. Molecular Control Analysis: Control within Proteins and Molecular Processes. Journal Of Theoretical Biology 1996, 182: 389-396. PMID: 8944172, DOI: 10.1006/jtbi.1996.0178.
Strong control on the transit time in metabolic channellingKholodenko B, Sakamoto N, Puigjaner J, Westerhoff H, Cascante M. Strong control on the transit time in metabolic channelling. FEBS Letters 1996, 389: 123-125. PMID: 8766813, DOI: 10.1016/0014-5793(96)00532-7.
Paradoxical control properties of enzymes within pathways: can activation cause an enzyme to have increased control?KHOLODENKO B, BROWN G. Paradoxical control properties of enzymes within pathways: can activation cause an enzyme to have increased control? Biochemical Journal 1996, 314: 753-760. PMID: 8615766, PMCID: PMC1217121, DOI: 10.1042/bj3140753.
Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentratedKHOLODENKO B, WESTERHOFF H, CASCANTE C. Effect of channelling on the concentration of bulk-phase intermediates as cytosolic proteins become more concentrated. Biochemical Journal 1996, 313: 921-926. PMID: 8611176, PMCID: PMC1216999, DOI: 10.1042/bj3130921.
Control of Dynamics and Steady State: Applications to Multidrug ResistanceWesterhoff H, Bier M, Molenaar D, Spoelstra E, Lankelma J, Jongsma A, Jensen P, Richard P, Kholodenko B. Control of Dynamics and Steady State: Applications to Multidrug Resistance. 1996, 25-31. DOI: 10.1007/978-3-322-85017-1_3.
Steady-State Characterization of Systems with Moiety-Conservations Made Easy: Matrix Equations of Metabolic Control Analysis and Biochemical System TheoryCascante M, Puigjaner J, Kholodenko B. Steady-State Characterization of Systems with Moiety-Conservations Made Easy: Matrix Equations of Metabolic Control Analysis and Biochemical System Theory. Journal Of Theoretical Biology 1996, 178: 1-6. DOI: 10.1006/jtbi.1996.0001.
Direct Transfer of Control and Multidrug ResistanceWesterhoff H, Rohwer J, Heijn M, Mülder S, Ghauharali R, Wielinga P, Kholodenko B, Spoelstra E, Lankelma J. Direct Transfer of Control and Multidrug Resistance. 1996, 283-292. DOI: 10.1007/978-1-4615-5845-3_29.
Calcium Indirectly Increases the Control Exerted by the Adenine Nucleotide Translocator over 2-Oxoglutarate Oxidation in Rat Heart MitochondriaMildaziene V, Baniene R, Nauciene Z, Bakker B, Brown G, Westerhoff H, Kholodenko B. 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: 130-134. PMID: 7503547, DOI: 10.1006/abbi.1995.9918.
Defining control coefficients in non-ideal metabolic pathwaysKholodenko B, Molenaar D, Schuster S, Heinrich R, Westerhoff H. Defining control coefficients in non-ideal metabolic pathways. Biophysical Chemistry 1995, 56: 215-226. PMID: 17023325, DOI: 10.1016/0301-4622(95)00039-z.
Elusive controlWesterhoff H, Kholodenko B, Cascante M, Van Dam K. Elusive control. Journal Of Bioenergetics And Biomembranes 1995, 27: 491-497. PMID: 8718454, DOI: 10.1007/bf02110189.
Composite control of cell function: metabolic pathways behaving as single control unitsKholodenko B, Schuster S, Rohwer J, Cascante M, Westerhoff H. Composite control of cell function: metabolic pathways behaving as single control units. FEBS Letters 1995, 368: 1-4. PMID: 7615057, DOI: 10.1016/0014-5793(95)00562-n.
Control analysis of transit time for free and enzyme-bound metabolites: physiological and evolutionary significance of metabolic response timesCascante M, Meléndez-Hevia E, Kholodenko B, Sicilia J, Kacser H. Control analysis of transit time for free and enzyme-bound metabolites: physiological and evolutionary significance of metabolic response times. Biochemical Journal 1995, 308: 895-899. PMID: 8948448, PMCID: PMC1136808, DOI: 10.1042/bj3080895.
Energy, control and DNA structure in the living cellWijker J, Jensen P, Snoep J, Gomes A, Guiral M, Jongsma A, de Waal A, Hoving S, van Dooren S, van der Weijden C, van Workum M, van Heeswijk W, Molenaar O, Wielinga P, Richard P, Diderich J, Bakker B, Teusink B, Hemker M, Rohwer J, van der Gugten A, Kholodenko B, Westerhoff H. Energy, control and DNA structure in the living cell. Biophysical Chemistry 1995, 55: 153-165. PMID: 7632875, DOI: 10.1016/0301-4622(94)00148-d.
Molecular biology for flux controlJensen P, Snoep J, Molenaar D, van Heeswijk W, Kholodenko B, van der Gugten A, Westerhoff H. Molecular biology for flux control. Biochemical Society Transactions 1995, 23: 367-370. PMID: 7672396, DOI: 10.1042/bst0230367.
How to reveal various aspects of regulation in group-transfer pathwaysKholodenko B, Westerhoff H. How to reveal various aspects of regulation in group-transfer pathways. Biochimica Et Biophysica Acta (BBA) - Bioenergetics 1995, 1229: 275-289. DOI: 10.1016/0005-2728(95)00013-9.
Control theory of group transfer pathwaysKholodenko B, Westerhoff H. Control theory of group transfer pathways. Biochimica Et Biophysica Acta (BBA) - Bioenergetics 1995, 1229: 256-274. DOI: 10.1016/0005-2728(95)00014-a.
CONTROL THEORY OF CELL METABOLISM: TOWARDS MORE REALISTIC “NON-IDEAL” SYSTEMSKHOLODENKO B, CASCANTE M, MOLENAAR D, DEMIN O, VAN DER GUGTEN A, WESTERHOFF H. CONTROL THEORY OF CELL METABOLISM: TOWARDS MORE REALISTIC “NON-IDEAL” SYSTEMS. Journal Of Biological System 1995, 3: 145-154. DOI: 10.1142/s0218339095000149.
HIERARCHIES IN CONTROLJENSEN P, VAN DER GUGTEN A, BIER M, VAN HEESWIJK W, ROHWER J, MOLENAAR D, VAN WORKUM M, RICHARD P, TEUSINK B, BAKKER B, KHOLODENKO B, WESTERHOFF H. HIERARCHIES IN CONTROL. Journal Of Biological System 1995, 3: 139-144. DOI: 10.1142/s0218339095000137.
Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem.Kholodenko B, Sauro H, Westerhoff H, Cascante M. Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem. IUBMB Life 1995, 35: 615-25. PMID: 7773196.
DYNAMIC ASPECTS OF CASCADE-TYPE METABOLIC REGULATIONMOLENAAR D, KHOLODENKO B, VAN HEESWIJK W, WESTERHOFF H. DYNAMIC ASPECTS OF CASCADE-TYPE METABOLIC REGULATION. Journal Of Biological System 1995, 3: 187-196. DOI: 10.1142/s0218339095000186.
The macroworld versus the microworld of biochemical regulation and controlKholodenko B, Westerhoff H. The macroworld versus the microworld of biochemical regulation and control. Trends In Biochemical Sciences 1995, 20: 52-54. PMID: 7701560, DOI: 10.1016/s0968-0004(00)88955-0.
Control in channelled pathways. A matrix method calculating the enzyme control coefficientsKholodenko B, Westerhoff H, Puigjaner J, Cascante M. Control in channelled pathways. A matrix method calculating the enzyme control coefficients. Biophysical Chemistry 1995, 53: 247-258. PMID: 17020850, DOI: 10.1016/0301-4622(94)00104-r.
Control theory of metabolic channellingKholodenko B, Cascante M, Westerhoff H. Control theory of metabolic channelling. Molecular And Cellular Biochemistry 1995, 143: 151-168. PMID: 7596350, DOI: 10.1007/bf01816949.
Control theory of one enzymeKholodenko B, Westerhoff H. Control theory of one enzyme. Biochimica Et Biophysica Acta 1994, 1208: 294-305. PMID: 7947961, DOI: 10.1016/0167-4838(94)90116-3.
Control by Enzymes, Coenzymes and Conserved MoietiesKholodenko B, Sauro H, Westerhoff H. Control by Enzymes, Coenzymes and Conserved Moieties. The FEBS Journal 1994, 225: 179-186. PMID: 7925436, DOI: 10.1111/j.1432-1033.1994.00179.x.
How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox.Snoep J, Jensen P, Groeneveld P, Molenaar D, Kholodenko B, Westerhoff H. How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox. IUBMB Life 1994, 33: 1023-32. PMID: 7987249.
Rate limitation within a single enzyme is directly related to enzyme intermediate levelsKholodenko B, Westerhoff H, Brown G. Rate limitation within a single enzyme is directly related to enzyme intermediate levels. FEBS Letters 1994, 349: 131-134. PMID: 8045290, DOI: 10.1016/0014-5793(94)00617-2.
Getting to the inside of cells using metabolic control analysisWesterhoff H, Hofmeyr J, Kholodenko B. Getting to the inside of cells using metabolic control analysis. Biophysical Chemistry 1994, 50: 273-283. PMID: 8011948, DOI: 10.1016/0301-4622(93)e0095-m.
Control theory of metabolic channellingKholodenko B, Cascante M, Westerhoff H. Control theory of metabolic channelling. Molecular And Cellular Biochemistry 1994, 133-134: 313-331. PMID: 7808462, DOI: 10.1007/bf01267963.
Control theory of metabolic channellingKholodenko B, Cascante M, Westerhoff H. Control theory of metabolic channelling. 1994, 313-331. DOI: 10.1007/978-1-4615-2612-4_21.
Dramatic changes in control properties that accompany channelling and metabolite sequestrationKholodenko B, Cascante M, Westerhoff H. Dramatic changes in control properties that accompany channelling and metabolite sequestration. FEBS Letters 1993, 336: 381-384. PMID: 8282097, DOI: 10.1016/0014-5793(93)80841-h.
Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both and for ATP synthesis underin vivo conditions using the same enzyme?Kholodenko B. Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both and for ATP synthesis underin vivo conditions using the same enzyme? Journal Of Bioenergetics And Biomembranes 1993, 25: 285-295. PMID: 8394322, DOI: 10.1007/bf00762589.
The function of ATP/ADP translocator in the regulation of mitochondrial respiration during development of heart ischemic injuryBorutaité V, Mildažiene V, Katiliūté Z, Kholodenko B, Toleikis A. The function of ATP/ADP translocator in the regulation of mitochondrial respiration during development of heart ischemic injury. Biochimica Et Biophysica Acta 1993, 1142: 175-180. PMID: 8457582, DOI: 10.1016/0005-2728(93)90099-2.
‘Channelled’ pathways can be more sensitive to specific regulatory signalsKholodenko B, Demin O, Westerhoff H. ‘Channelled’ pathways can be more sensitive to specific regulatory signals. FEBS Letters 1993, 320: 75-78. PMID: 8462681, DOI: 10.1016/0014-5793(93)81661-i.
Metabolic channelling and control of the fluxKholodenko B, Westerhoff H. Metabolic channelling and control of the flux. FEBS Letters 1993, 320: 71-74. PMID: 8462680, DOI: 10.1016/0014-5793(93)81660-r.
The sum of the control coefficients of all enzymes on the flux through a group‐transfer pathway can be as high as twovan DAM K, van der VLAG J, KHOLODENKO B, WESTERHOFF H. The sum of the control coefficients of all enzymes on the flux through a group‐transfer pathway can be as high as two. The FEBS Journal 1993, 212: 791-799. PMID: 8462550, DOI: 10.1111/j.1432-1033.1993.tb17720.x.
Sum of the Flux Control Coefficients: What is it Equal to in Different Systems?Kholodenko B, Westerhoff H. Sum of the Flux Control Coefficients: What is it Equal to in Different Systems? 1993, 205-210. DOI: 10.1007/978-1-4615-2962-0_33.
Control of Respiration in Heart Mitochondria: Comparative Study of Oxidation of Succinate and NAD-Dependent SubstratesMildažienė V, Borutaitė V, Katiliūtė Z, Petroliūnaitė R, Ivanovienė L, Toleikis A, Kholodenko B. Control of Respiration in Heart Mitochondria: Comparative Study of Oxidation of Succinate and NAD-Dependent Substrates. 1993, 347-350. DOI: 10.1007/978-1-4615-2962-0_54.
Multiplicity of ControlWesterhoff H, Jensen P, van der Gugten A, Kahn D, Kholodenko B, Schuster S, Oldenburg N, van Dam K, van Heeswijk W. Multiplicity of Control. 1993, 263-268. DOI: 10.1007/978-1-4615-2962-0_41.
Control of the metabolic flux in a system with high enzyme concentrations and moiety‐conserved cyclesKHOLODENKO B, LYUBAREV A, KURGANOV B. Control of the metabolic flux in a system with high enzyme concentrations and moiety‐conserved cycles. The FEBS Journal 1992, 210: 147-153. PMID: 1446668, DOI: 10.1111/j.1432-1033.1992.tb17402.x.
Regulation of the heart mitochondrial respiration rate. Comparison of oxidation of succinate and NAD-dependent substrates.Kholodenko B, Millazhane V, Borutaĭte V, Ivanovene L, Iuodkaĭte R, Katiliute Z, Toleĭkis A. Regulation of the heart mitochondrial respiration rate. Comparison of oxidation of succinate and NAD-dependent substrates. Биохимия 1991, 56: 1420-8. PMID: 1782265.
The control pattern of respiration in ischemia damaged rabbit heart mitochondriaBorutait≐ V, Katiliüt≐ Z, Mildažien≐ V, Kholodenko B. The control pattern of respiration in ischemia damaged rabbit heart mitochondria. Journal Of Molecular And Cellular Cardiology 1991, 23: s105. DOI: 10.1016/0022-2828(91)90829-b.
The role of long-chain acyl-CoA in the disturbances of oxidative phosphorylation in the myocardium.Borutaĭte V, Mildazhene V, Ivanovene L, Kholodenko B, Toleĭkis A, Prashkiavichius A. The role of long-chain acyl-CoA in the disturbances of oxidative phosphorylation in the myocardium. Биохимия 1989, 54: 1947-51. PMID: 2633800.
The role of long‐chain acyl‐CoA in the damage of oxidative phosphorylation in heart mitochondriaBorutait≐ V, Mildaz̆ien≐ V, Ivanovien≐ L, Kholodenko B, Toleikis A, Pras̆kevic̆ius A. The role of long‐chain acyl‐CoA in the damage of oxidative phosphorylation in heart mitochondria. FEBS Letters 1989, 243: 264-266. PMID: 2917650, DOI: 10.1016/0014-5793(89)80141-3.
Theory of metabolism regulation: a complete system of equations for regulation coefficients.Kholodenko B, Erlikh L. Theory of metabolism regulation: a complete system of equations for regulation coefficients. Биофизика 1989, 34: 802-7. PMID: 2611277.
The role of adenine nucleotide translocator in the regulation of oxidative phosphorylation in heart mitochondria.Kholodenko B, Zhilinskene V, Borutaĭte V, Ivanovene L, Toleĭkis A. The role of adenine nucleotide translocator in the regulation of oxidative phosphorylation in heart mitochondria. Биохимия 1988, 53: 1009-12. PMID: 2846076.
How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic controlKholodenko B. How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control. FEBS Letters 1988, 232: 383-386. PMID: 3378629, DOI: 10.1016/0014-5793(88)80775-0.
The role of adenine nucleotide translocators in regulation of oxidative phosphorylation in heart mitochondriaKholodenko B, Z̆ilinskie·e V, Borutait·e V, Ivanovien·e L, Toleikis A, Pras̆kevic̆ius A. The role of adenine nucleotide translocators in regulation of oxidative phosphorylation in heart mitochondria. FEBS Letters 1987, 223: 247-250. PMID: 2822484, DOI: 10.1016/0014-5793(87)80298-3.
Role of the 2,3-diphosphoglycerate shunt in regulating energy metabolism in human erythrocytes.Kholodenko B, Stepanchikova A, Erlikh L, Ataullakhanov F, Zhabotinskiĭ A. Role of the 2,3-diphosphoglycerate shunt in regulating energy metabolism in human erythrocytes. Bulletin Of The Russian Academy Of Sciences. Biological Series 1985, 196-205. PMID: 3157714.
Control of mitochondrial oxidative phosphorylationKholodenko B. Control of mitochondrial oxidative phosphorylation. Journal Of Theoretical Biology 1984, 107: 179-188. PMID: 6717037, DOI: 10.1016/s0022-5193(84)80020-x.
Dynamic stability of steady states and static stabilization in unbranched metabolic pathwaysDibrov B, Zhabotinsky A, Kholodenko B. Dynamic stability of steady states and static stabilization in unbranched metabolic pathways. Journal Of Mathematical Biology 1982, 15: 51-63. PMID: 7142835, DOI: 10.1007/bf00275788.
Optical tactics of antibacterial therapy for the trigger model of the infection process.Kholodenko B, Geviksman K, Kholodov L. Optical tactics of antibacterial therapy for the trigger model of the infection process. Биофизика 1982, 27: 900-5. PMID: 7138944.
The Regulation of Glycolysis in Human ErythrocytesATAULLAKHANOV F, VITVITSKY V, ZHABOTINSKY A, PICHUGIN A, PLATONOVA O, KHOLODENKO B, EHRLICH L. The Regulation of Glycolysis in Human Erythrocytes. The FEBS Journal 1981, 115: 359-365. PMID: 7238510, DOI: 10.1111/j.1432-1033.1981.tb05246.x.
Regulation of glycolysis in human erythrocytes. The mechanism of ATP concentration stabilization.Ataullakhanov F, Vitvitsky V, Zhabotinsky A, Pichugin A, Kholodenko B, Ehrlich L. Regulation of glycolysis in human erythrocytes. The mechanism of ATP concentration stabilization. Acta Biologica Et Medica Germanica 1981, 40: 991-7. PMID: 7331640.
Dynamic stability and parametric stabilization of steady states of unbranched metabolic pathways.Dibrov B, Zhabotinskiĭ A, Kholodenko B. Dynamic stability and parametric stabilization of steady states of unbranched metabolic pathways. Биофизика 1981, 26: 790-5. PMID: 7317462.
Dynamic stability of a metabolic pathway with single-loop feedback.Dibrov B, Zhabotinskiĭ A, Kholodenko B. Dynamic stability of a metabolic pathway with single-loop feedback. Биофизика 1981, 26: 590-5. PMID: 7284447.
Regulation of erythrocyte energy metabolism. Dependence of glycolysis characteristics on donor individual parameters.Kholodenko B, Dibrov B, Zhabotinskiĭ A. Regulation of erythrocyte energy metabolism. Dependence of glycolysis characteristics on donor individual parameters. Биофизика 1981, 26: 501-6. PMID: 6455164.
Individualization and optimization of dosings of pharmacological preparations; principle of maximum in the analysis of pharmacological responseKholodenko B, Kholodov L. Individualization and optimization of dosings of pharmacological preparations; principle of maximum in the analysis of pharmacological response. Pharmaceutical Chemistry Journal 1980, 14: 287-291. DOI: 10.1007/bf00777393.
Quantitative model of human erythrocyte glycolysis. Relationship between erythrocyte energy metabolism and Na+, K+-ATPase activity.Ataullakhanov F, Vitvitskiĭ V, Zhabotinskiĭ A, Kholodenko B, Erlikh L. Quantitative model of human erythrocyte glycolysis. Relationship between erythrocyte energy metabolism and Na+, K+-ATPase activity. Биофизика 1979, 24: 489-94. PMID: 223657.
Quantitative model of human erythrocyte glycolysis. Region of cell viability determined by ATP concentration.Ataullakhanov F, Vitvitskiĭ V, Zhabotinskiĭ A, Pichugin A, Kholodenko B. Quantitative model of human erythrocyte glycolysis. Region of cell viability determined by ATP concentration. Биофизика 1979, 24: 1048-53. PMID: 159725.
Quantitative model of human erythrocyte glycolysis. I. Relationship between the stationary rate of glycolysis and the ATP concentration.Ataullakhanov F, Vitvitskiĭ V, Zhabotinskiĭ A, Kholodenko B, Erlikh L. Quantitative model of human erythrocyte glycolysis. I. Relationship between the stationary rate of glycolysis and the ATP concentration. Биофизика 1977, 22: 483-8. PMID: 142521.

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