List of works - Barbara Marleen Bakker

A domino effect in drug action: from metabolic assault towards parasite differentiation

scientific article published on 5 November 2010

A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae during temperature shifts

scientific article published in February 2014

A model reduction method for biochemical reaction networks.

scientific article

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

scientific article published on 12 July 2013

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

scientific article

Acetaldehyde Mediates the Synchronization of Sustained Glycolytic Oscillations in Populations of Yeast Cells

scientific article published on 01 January 1996

Age and Diet Modulate the Insulin-Sensitizing Effects of Exercise: A Tracer-Based Oral Glucose Tolerance Test

scientific article published in 2023

Biochemical competition makes fatty-acid β-oxidation vulnerable to substrate overload

scientific article (publication date: 2013)

Bistability in fatty-acid oxidation resulting from substrate inhibition

scientific article published on 12 August 2021

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

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry

scientific article published on 01 September 2000

Cofactors revisited - Predicting the impact of flavoprotein-related diseases on a genome scale

scientific article published on 29 October 2018

Cofactors revisited − predicting the impact of flavoprotein-related diseases on a genome scale

scientific article published on 11 June 2018

Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes

scholarly article

Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei

scientific article published on 8 November 2007

Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations

scientific article published on 01 July 1996

DNA supercoiling by gyrase is linked to nucleoid compaction

scientific article

Design principles of nuclear receptor signaling: how complex networking improves signal transduction.

scientific article

Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling

scientific article published on 28 June 2013

Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties.

scientific article

Drug target identification through systems biology

scientific article published on 17 July 2015

Drug-efficacy depends on the inhibitor type and the target position in a metabolic network--a systematic study.

scientific article published on 26 September 2007

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism ⬇️

scientific article published on January 19, 2012

Effect of hxk2 deletion and HAP4 overexpression on fermentative capacity in Saccharomyces cerevisiae

scientific article published on 20 December 2007

Emergence of the silicon human and network targeting drugs

article

Energy metabolism and its compartmentation in Trypanosoma brucei

scientific article

Enzyme kinetics for systems biology when, why and how.

scientific article published in January 2011

Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei

scientific article published on 14 June 2005

Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease

scientific article published on 11 March 2020

From genome to phenome—Simple inborn errors of metabolism as complex traits

scientific article published on 03 June 2014

Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes

scientific article published in February 1997

Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.

scientific article

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei

scientific article (publication date: 2013)

Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae.

scientific article

How molecular competition influences fluxes in gene expression networks

scientific article

How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.

scientific article

In or out? On the tightness of glycosomal compartmentalization of metabolites and enzymes in Trypanosoma brucei.

scientific article

In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria

scientific article

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

scientific article published in Nature Communications

Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders.

scientific article

Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity

scientific article published in January 2002

Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction.

scientific article published on 13 June 2016

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

scientific article published on 7 January 2010

Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs.

scientific article

Metabolic regulation rather than de novo enzyme synthesis dominates the osmo-adaptation of yeast

scientific article

Metabolomic systems biology of trypanosomes

scientific article published on 17 February 2010

Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae.

scientific article

Modeling response of glycolysis in S. cerevisiae cells harvested at diauxic shift

scientific article published in January 2002

Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae.

scientific article

Molecular mechanisms of mTOR regulation by stress

scientific article published on 3 December 2014

Naphthoquinone derivatives exert their antitrypanosomal activity via a multi-target mechanism

scientific article

Network-based selectivity of antiparasitic inhibitors

scientific article published on 01 January 2002

News about old histones: A role for histone age in controlling the epigenome

scientific article published on 01 January 2012

Progressive methylation of ageing histones by Dot1 functions as a timer.

scientific article published on September 2011

Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes

scientific article published on 08 May 2012

Protection against the Metabolic Syndrome by Guar Gum-Derived Short-Chain Fatty Acids Depends on Peroxisome Proliferator-Activated Receptor γ and Glucagon-Like Peptide-1

scientific article

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis

scientific article published on 27 April 2020

Quantitative analysis of flux regulation through hierarchical regulation analysis

scientific article published in January 2011

Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.

scientific article published on 18 June 2008

SK2 channels regulate mitochondrial respiration and mitochondrial Ca2+ uptake

scientific article

STRENDA DB: enabling the validation and sharing of enzyme kinetics data

scholarly article by Neil Swainston published in June 2018

Short-Chain Fatty Acids Protect Against High-Fat Diet-Induced Obesity via a PPARγ-Dependent Switch From Lipogenesis to Fat Oxidation

scientific article

Short-term protein restriction at advanced age stimulates FGF21 signalling, energy expenditure and browning of white adipose tissue

scientific article published on 22 October 2020

Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful

article by Keith F. Tipton et al published May 2014 in Perspectives in Science

Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control

scientific article published on October 2010

Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models.

scientific article published in October 2010

Systems biology towards life in silico: mathematics of the control of living cells.

scientific article published on 16 February 2008

TIde: a software for the systematic scanning of drug targets in kinetic network models

scientific article

Targeting pathogen metabolism without collateral damage to the host

scientific article

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics

scientific article

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

scholarly article

The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation.

scientific article

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

scientific article

The short-chain fatty acid uptake fluxes by mice on a guar gum supplemented diet associate with amelioration of major biomarkers of the metabolic syndrome.

scientific article

The silicon trypanosome.

scientific article published on 06 May 2010

The silicon trypanosome: a test case of iterative model extension in systems biology

scientific article published on January 2014

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

scientific article published in September 2006

Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast

article

Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history

scientific article published on 01 March 2010

Training of yeast cell dynamics.

scientific article published in April 2005

Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice

scientific article published on 10 October 2019

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels

scientific article

Translational Targeted Proteomics Profiling of Mitochondrial Energy Metabolic Pathways in Mouse and Human Samples.

scientific article published on 22 July 2016

Two mechanisms for oxidation of cytosolic NADPH by Kluyveromyces lactis mitochondria

scientific article

Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae

scholarly article

Vertical systems biology: from DNA to flux and back

scientific article published in January 2008

What Controls Glycolysis in Bloodstream FormTrypanosoma brucei?

scientific article published in Journal of Biological Chemistry

Whole-Body Vibration Partially Reverses Aging-Induced Increases in Visceral Adiposity and Hepatic Lipid Storage in Mice

scientific article published on 17 February 2016

Yeast cells with a specific cellular make-up and an environment that removes acetaldehyde are prone to sustained glycolytic oscillations

scientific article published on 01 March 1994

Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength.

scientific article published in February 2005

List of works by Barbara Marleen Bakker

A domino effect in drug action: from metabolic assault towards parasite differentiation

A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae during temperature shifts

A model reduction method for biochemical reaction networks.

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

Acetaldehyde Mediates the Synchronization of Sustained Glycolytic Oscillations in Populations of Yeast Cells

Age and Diet Modulate the Insulin-Sensitizing Effects of Exercise: A Tracer-Based Oral Glucose Tolerance Test

Biochemical competition makes fatty-acid β-oxidation vulnerable to substrate overload

Bistability in fatty-acid oxidation resulting from substrate inhibition

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

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry

Cofactors revisited - Predicting the impact of flavoprotein-related diseases on a genome scale

Cofactors revisited − predicting the impact of flavoprotein-related diseases on a genome scale

Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes

Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei

Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations

DNA supercoiling by gyrase is linked to nucleoid compaction

Design principles of nuclear receptor signaling: how complex networking improves signal transduction.

Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling

Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties.

Drug target identification through systems biology

Drug-efficacy depends on the inhibitor type and the target position in a metabolic network--a systematic study.

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism ⬇️

Effect of hxk2 deletion and HAP4 overexpression on fermentative capacity in Saccharomyces cerevisiae

Emergence of the silicon human and network targeting drugs

Energy metabolism and its compartmentation in Trypanosoma brucei

Enzyme kinetics for systems biology when, why and how.

Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei

Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease

From genome to phenome—Simple inborn errors of metabolism as complex traits

Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes

Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei

Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae.

How molecular competition influences fluxes in gene expression networks

How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.

In or out? On the tightness of glycosomal compartmentalization of metabolites and enzymes in Trypanosoma brucei.

In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders.

Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity

Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction.

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs.

Metabolic regulation rather than de novo enzyme synthesis dominates the osmo-adaptation of yeast

Metabolomic systems biology of trypanosomes

Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae.

Modeling response of glycolysis in S. cerevisiae cells harvested at diauxic shift

Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae.

Molecular mechanisms of mTOR regulation by stress

Naphthoquinone derivatives exert their antitrypanosomal activity via a multi-target mechanism

Network-based selectivity of antiparasitic inhibitors

News about old histones: A role for histone age in controlling the epigenome

Progressive methylation of ageing histones by Dot1 functions as a timer.

Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes

Protection against the Metabolic Syndrome by Guar Gum-Derived Short-Chain Fatty Acids Depends on Peroxisome Proliferator-Activated Receptor γ and Glucagon-Like Peptide-1

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis

Quantitative analysis of flux regulation through hierarchical regulation analysis

Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.

SK2 channels regulate mitochondrial respiration and mitochondrial Ca2+ uptake

STRENDA DB: enabling the validation and sharing of enzyme kinetics data

Short-Chain Fatty Acids Protect Against High-Fat Diet-Induced Obesity via a PPARγ-Dependent Switch From Lipogenesis to Fat Oxidation

Short-term protein restriction at advanced age stimulates FGF21 signalling, energy expenditure and browning of white adipose tissue

Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful

Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control

Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models.

Systems biology towards life in silico: mathematics of the control of living cells.

TIde: a software for the systematic scanning of drug targets in kinetic network models

Targeting pathogen metabolism without collateral damage to the host

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation.

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

The short-chain fatty acid uptake fluxes by mice on a guar gum supplemented diet associate with amelioration of major biomarkers of the metabolic syndrome.

The silicon trypanosome.

The silicon trypanosome: a test case of iterative model extension in systems biology

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast

Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history