Lista de obras - Barbara Marleen Bakker - Dominio Público Uruguay

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

artículo científico publicado en 2010

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

artículo científico publicado en 2014

A model reduction method for biochemical reaction networks.

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2002

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

artículo científico publicado en 1996

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

artículo científico publicado en 2023

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

artículo científico publicado en 2013

Bistability in fatty-acid oxidation resulting from substrate inhibition

artículo científico publicado en 2021

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

artículo científico publicado en 1995

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

artículo científico publicado en 2000

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

artículo científico publicado en 2018

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

artículo científico publicado en 2018

Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes

artículo científico publicado en 2008

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

artículo científico publicado en 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

artículo científico publicado en 2002

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Drug target identification through systems biology

artículo científico

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

artículo científico publicado en 2007

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

artículo científico publicado el 19 de enero de 2012

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

artículo científico

Emergence of the silicon human and network targeting drugs

article

Energy metabolism and its compartmentation in Trypanosoma brucei

artículo científico publicado en 2005

Enzyme kinetics for systems biology when, why and how.

artículo científico publicado en 2011

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

artículo científico publicado en 2005

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

artículo científico publicado en 2020

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

artículo científico publicado en 2014

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

artículo científico publicado en 1997

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2005

How molecular competition influences fluxes in gene expression networks

artículo científico publicado en 2011

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

artículo científico publicado en 2000

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

artículo científico publicado en 2014

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

artículo científico publicado en 2000

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2000

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

artículo científico publicado en 2010

Metabolomic systems biology of trypanosomes

artículo científico publicado en 2010

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

artículo científico publicado en 2007

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

artículo científico publicado en 2002

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

artículo científico publicado en 2001

Molecular mechanisms of mTOR regulation by stress

artículo científico publicado en 2014

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

artículo científico publicado en 2013

Network-based selectivity of antiparasitic inhibitors

artículo científico publicado en 2002

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

artículo científico publicado en 2012

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

artículo científico

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

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

artículo científico publicado en 2008

SK2 channels regulate mitochondrial respiration and mitochondrial Ca2+ uptake

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

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

artículo científico publicado en 2008

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

artículo científico publicado en 2009

Targeting pathogen metabolism without collateral damage to the host

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 2007

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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.

artículo científico publicado en 2014

The silicon trypanosome.

scientific article published on 06 May 2010

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

artículo científico publicado en 2014

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

artículo científico publicado en 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

artículo científico publicado en 2010

Training of yeast cell dynamics.

artículo científico publicado en 2005

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

artículo científico publicado en 2019

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

Two mechanisms for oxidation of cytosolic NADPH by Kluyveromyces lactis mitochondria

artículo científico publicado en 2002

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

artículo científico publicado en 2006

Vertical systems biology: from DNA to flux and back

artículo científico publicado en 2008

What Controls Glycolysis in Bloodstream FormTrypanosoma brucei?

artículo científico publicado en 1999

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

artículo científico publicado en 2016

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

artículo científico publicado en 1994

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

artículo científico publicado en 2005

Lista de obras de 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