List of works - Boris Kholodenko

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

scientific article

A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network

article

A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network

scientific article published on 6 February 2013

Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies.

scientific article

An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells

scientific article published in January 2012

An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity

scientific article published on 04 July 2019

Bimodal Protein Distributions in Heterogeneous Oscillating Systems

Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements

scientific article published on September 2006

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches

scientific article published on 27 January 2016

Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria.

scientific article published in December 1995

Catching transcriptional regulation by thermostatistical modeling

scientific article published on 7 August 2012

Cell-signalling dynamics in time and space

scientific article

Cellular information transfer regarded from a stoichiometry and control analysis perspective

scientific article

Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device

scientific article

Complexity of receptor tyrosine kinase signal processing

scientific article

Composite control of cell function: metabolic pathways behaving as single control units

scientific article published on 01 July 1995

Computational approaches for analyzing information flow in biological networks

scientific article published on 17 April 2012

Control analysis for autonomously oscillating biochemical networks

scientific article

Control analysis of glycolytic oscillations

scientific article published in November 1996

Control analysis of metabolic systems involving quasi-equilibrium reactions

scientific article published on March 1998

Control by Enzymes, Coenzymes and Conserved Moieties. A Generalisation of the Connectivity Theorem of Metabolic Control Analysis

article

Control in channelled pathways. A matrix method calculating the enzyme control coefficients

scientific article published in February 1995

Control of mitochondrial oxidative phosphorylation

scientific article published in March 1984

Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law

scientific article published on 01 December 2003

Control of the G-protein cascade dynamics by GDP dissociation inhibitors

scientific article published in October 2013

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

scientific article published in November 1992

Control theory of group transfer pathways

Control theory of metabolic channelling.

scientific article published on April 1994

Control theory of metabolic channelling.

scientific article published in February 1995

Control theory of one enzyme

scientific article published in October 1994

Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance.

scientific article published on February 2012

Crosstalk and signaling switches in mitogen-activated protein kinase cascades

scientific article published on 18 September 2012

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks

scientific article published on 29 July 2015

Defining control coefficients in non-ideal metabolic pathways

article

Diffusion control of protein phosphorylation in signal transduction pathways

scientific article

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

scientific article published on 11 July 2018

Domain-oriented reduction of rule-based network models.

scientific article published on September 2008

Dramatic changes in control properties that accompany channelling and metabolite sequestration.

scientific article published in December 1993

Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects

scientific article published on 2 September 2015

Dynamic stability of steady states and static stabilization in unbranched metabolic pathways

scientific article published in January 1982

Effects of sequestration on signal transduction cascades

scientific article published in March 2006

Elusive control

scientific article published on October 1995

Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise ⬇️

scientific article published on August 24, 2012

Endocytosis and signalling: a meeting with mathematics

scientific article published on 16 June 2009

Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes

scientific article published in January 2000

Evaluating strategies to normalise biological replicates of Western blot data

scientific article

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

scientific article published on 24 January 2020

Feedback regulation in cell signalling: Lessons for cancer therapeutics

scientific article

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity

scientific article published on 8 January 2015

Formation of intracellular concentration landscapes by multisite protein modification.

scientific article

Four-dimensional dynamics of MAPK information processing systems.

scientific article published on July 2009

Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors

scientific article

Frequency modulation of ERK activation dynamics rewires cell fate

scientific article

Frequency modulation of ERK activation dynamics rewires cell fate

article

G Protein-Coupled Receptor Signaling Networks from a Systems Perspective

scientific article

Getting to the inside of cells using metabolic control analysis

article

Giving Space to Cell Signaling

HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status

scientific article published on 13 July 2016

How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control

scientific article

How to reveal various aspects of regulation in group-transfer pathways

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction

scientific article published in Scientific Reports

Implications of macromolecular crowding for signal transduction and metabolite channeling

scientific article published on September 1998

Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy

scientific article published in February 2005

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data

scientific article

Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs

scientific article published on 17 December 2020

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology

scientific article

Integrating network reconstruction with mechanistic modeling to predict cancer therapies.

scientific article published on 22 November 2016

It takes two to tango--signalling by dimeric Raf kinases

scientific article published on April 2013

Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both $$\Delta \bar \mu _{H^ + } $$ and $$\Delta \bar \mu _{Na^ + } $$ for ATP synthesis underin vivo conditions using the sam

scientific article published on 01 June 1993

Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding

scientific article published on July 2000

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses

scientific article

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics

scientific article

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

scientific article

MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?

scientific article

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance

scientific article

MST2-RASSF protein-protein interactions through SARAH domains

scientific article published on 5 October 2015

Mammalian protein expression noise: scaling principles and the implications for knockdown experiments

scientific article published on 01 November 2012

Mapping connections in signaling networks with ambiguous modularity

scientific article published on 23 May 2019

Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction

Metabolic channelling and control of the flux

scientific article published on 01 March 1993

Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes

scientific article published on 01 July 1998

Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation

scientific article

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

scientific article published in January 2019

Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols

scientific article

Modular interaction strengths in regulatory networks; an example

scientific article published in January 2002

Modular response analysis of cellular regulatory networks.

scientific article

Molecular Control Analysis: Control within Proteins and Molecular Processes

article

Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor

scientific article published on March 2009

Multistrip Western blotting to increase quantitative data output

scientific article

Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration

scientific article

Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades

scientific article published on 01 March 2000

Network-based identification of feedback modules that control RhoA activity and cell migration

scientific article published on 16 March 2015

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.

scientific article published on 5 March 2018

News

scientific article published on 01 June 2005

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses

scientific article

Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation

article

PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells

scientific article

Performance of objective functions and optimisation procedures for parameter estimation in system biology models

scientific article published on 08 August 2017

Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration

scientific article published on 24 July 2020

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

scientific article published on 8 December 2015

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation

scientific article published on 24 January 2014

Positional information generated by spatially distributed signaling cascades.

scientific article

Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy

scientific article

Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signaling pathway in breast cancer cells

scientific article

Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling

scientific article

Protein–protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose–responses

article

Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2

scientific article

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

scientific article published in Journal of Biological Chemistry

Quantification of information transfer via cellular signal transduction pathways ⬇️

scientific article published on September 8, 1997

Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach

scientific article published on July 2006

Quantitative analysis of signaling networks.

scientific article published in September 2004

Rac1 and RhoA: Networks, loops and bistability

scientific article published on 17 August 2016

Rate limitation within a single enzyme is directly related to enzyme intermediate levels

scientific article published on 01 July 1994

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

scientific article published on 7 October 2016

Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops

scientific article published on 9 May 2006

Signal processing at the Ras circuit: what shapes Ras activation patterns?

scientific article published in June 2004

Signaling cascades as cellular devices for spatial computations

scientific article published on 19 February 2008

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients

scientific article published on 22 December 2015

Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity

scientific article

Signalling ballet in space and time

scientific article

Signalling by protein phosphatases and drug development: a systems-centred view.

scientific article

Signalling mechanisms regulating phenotypic changes in breast cancer cells

scientific article

Signalling over a distance: gradient patterns and phosphorylation waves within single cells

scientific article published on October 2010

Silence on the relevant literature and errors in implementation

scientific article published in April 2015

Spatial gradients of cellular phospho-proteins

scientific article published in September 1999

Spatially distributed cell signalling

scientific article published on December 2009

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate

scientific article published on 20 February 2015

Steady-State Characterization of Systems with Moiety-Conservations Made Easy: Matrix Equations of Metabolic Control Analysis and Biochemical System Theory

article by Marta Cascante Serratosa et al published January 1996 in Journal of Theoretical Biology

Strong control on the transit time in metabolic channelling

scientific article published on 01 July 1996

Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system

scientific article

Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing

scientific article published on 23 October 2020

Systems biology-embedded target validation: improving efficacy in drug discovery.

scientific article

Systems medicine: helping us understand the complexity of disease

scientific article published on 30 July 2013

Systems medicine: opportunities and challenges for systems biology approaches

scientific article published on 30 October 2013

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling.

scientific article published on 07 April 2009

Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model

scientific article published in January 2002

The APC network regulates the removal of mutated cells from colonic crypts

scientific article published on 27 March 2014

The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility

scientific article

The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells

scientific article published on 24 June 2016

The dynamic control of signal transduction networks in cancer cells

scientific article

The function of ATP/ADP translocator in the regulation of mitochondrial respiration during development of heart ischemic injury

article

The macroworld versus the microworld of biochemical regulation and control

scientific article

The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier

scientific article published on 21 December 2010

The regulation of glycolysis in human erythrocytes. The dependence of the glycolytic flux on the ATP concentration

scientific article published in April 1981

The role of adenine nucleotide translocators in regulation of oxidative phosphorylation in heart mitochondria

scientific article published on November 1987

The role of long-chain acyl-CoA in the damage of oxidative phosphorylation in heart mitochondria

scientific article published in January 1989

The topology design principles that determine the spatiotemporal dynamics of G-protein cascades

article

Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle

scientific article published on August 2009

Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains.

scientific article

Transcriptional regulatory mechanisms of fibrosis development in mouse lung tissue exposed to carbon nanotubes

article

Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.

scientific article published on 12 November 2003

Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing

scientific article published on 01 December 2014

Untangling the signalling wires

scientific article published in March 2007

Untangling the wires: a strategy to trace functional interactions in signaling and gene networks

scientific article

Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects

scientific article

When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling ⬇️

scientific article published on July 31, 2013

Why cytoplasmic signalling proteins should be recruited to cell membranes.

scientific article

‘Channelled’ pathways can be more sensitive to specific regulatory signals

scientific article published on 01 March 1993

List of works by Boris Kholodenko

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network

A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network

Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies.

An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells

An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity

Bimodal Protein Distributions in Heterogeneous Oscillating Systems

Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches

Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria.

Catching transcriptional regulation by thermostatistical modeling

Cell-signalling dynamics in time and space

Cellular information transfer regarded from a stoichiometry and control analysis perspective

Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device

Complexity of receptor tyrosine kinase signal processing

Composite control of cell function: metabolic pathways behaving as single control units

Computational approaches for analyzing information flow in biological networks

Control analysis for autonomously oscillating biochemical networks

Control analysis of glycolytic oscillations

Control analysis of metabolic systems involving quasi-equilibrium reactions

Control by Enzymes, Coenzymes and Conserved Moieties. A Generalisation of the Connectivity Theorem of Metabolic Control Analysis

Control in channelled pathways. A matrix method calculating the enzyme control coefficients

Control of mitochondrial oxidative phosphorylation

Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law

Control of the G-protein cascade dynamics by GDP dissociation inhibitors

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

Control theory of group transfer pathways

Control theory of metabolic channelling.

Control theory of metabolic channelling.

Control theory of one enzyme

Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance.

Crosstalk and signaling switches in mitogen-activated protein kinase cascades

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks

Defining control coefficients in non-ideal metabolic pathways

Diffusion control of protein phosphorylation in signal transduction pathways

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Domain-oriented reduction of rule-based network models.

Dramatic changes in control properties that accompany channelling and metabolite sequestration.

Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects

Dynamic stability of steady states and static stabilization in unbranched metabolic pathways

Effects of sequestration on signal transduction cascades

Elusive control

Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise ⬇️

Endocytosis and signalling: a meeting with mathematics

Engineering a living cell to desired metabolite concentrations and fluxes: pathways with multifunctional enzymes

Evaluating strategies to normalise biological replicates of Western blot data

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

Feedback regulation in cell signalling: Lessons for cancer therapeutics

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity

Formation of intracellular concentration landscapes by multisite protein modification.

Four-dimensional dynamics of MAPK information processing systems.

Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors

Frequency modulation of ERK activation dynamics rewires cell fate

Frequency modulation of ERK activation dynamics rewires cell fate

G Protein-Coupled Receptor Signaling Networks from a Systems Perspective

Getting to the inside of cells using metabolic control analysis

Giving Space to Cell Signaling

HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status

How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control

How to reveal various aspects of regulation in group-transfer pathways

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction

Implications of macromolecular crowding for signal transduction and metabolite channeling

Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data

Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology

Integrating network reconstruction with mechanistic modeling to predict cancer therapies.

It takes two to tango--signalling by dimeric Raf kinases

Kinetic models of coupling between H+ and Na+-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: Can a cell utilize both $$\Delta \bar \mu _{H^ + } $$ and $$\Delta \bar \mu _{Na^ + } $$ for ATP synthesis underin vivo conditions using the sam

Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance

MST2-RASSF protein-protein interactions through SARAH domains

Mammalian protein expression noise: scaling principles and the implications for knockdown experiments

Mapping connections in signaling networks with ambiguous modularity

Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction