List of works - Jacky L Snoep

11-Oxygenated androgen precursors are the preferred substrates for aldo-keto reductase 1C3 (AKR1C3): Implications for castration resistant prostate cancer

scientific article published on 21 June 2018

A combined experimental and modelling approach for the Weimberg pathway optimisation

scientific article published on 27 February 2020

A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism

scientific article published on 24 August 2011

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

scientific article

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells

scientific article published on 12 May 2014

An ffh mutant of Streptococcus mutans is viable and able to physiologically adapt to low pH in continuous culture

scientific article

An optical tweezers, epi-fluorescence and microfluidic-setup for synchronization studies of glycolytic oscillations in living yeast cells

Attractive models: how to make the silicon cell relevant and dynamic

scientific article published on January 2003

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

scientific article

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

scientific article

Competition for phosphorus between the nitrogen-fixing cyanobacteria Anabaena and Aphanizomenon

scientific article published on 17 January 2006

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum

scientific article published on 23 March 2015

Control analysis for autonomously oscillating biochemical networks

scientific article

Control analysis of trophic chains

article

DNA supercoiling by gyrase is linked to nucleoid compaction.

scientific article

DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase.

scientific article

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

scientific article published on 01 January 2019

Data and model integration using JWS Online.

scientific article

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

scientific article

Design principles of nuclear receptor signalling: How complex networking improves signal transduction

article

Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy

scientific article

ECA: control in ecosystems

scientific article published in January 2002

Editorial: 12th BTK Meeting: ‘Systems Biology: redefining BioThermoKinetics’

article

Emergence of the silicon human and network targeting drugs

article

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

scientific article

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

scientific article

Fourth-Generation Progestins Inhibit 3β-Hydroxysteroid Dehydrogenase Type 2 and Modulate the Biosynthesis of Endogenous Steroids

scientific article

From Silicon Cellsilicon cell to Silicon Humansilicon human

From isolation to integration, a systems biology approach for building the Silicon Cell

From steady-state to synchronized yeast glycolytic oscillations I: model construction.

scientific article published on 9 July 2012

From steady-state to synchronized yeast glycolytic oscillations II: model validation

scientific article

Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy

scientific article published on 30 April 2013

Glycolysis and Flux Control

scientific article

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells

scientific article

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus

scientific article published on 22 August 2013

JWS online cellular systems modelling and microbiology.

scientific article

Metabolic control in integrated biochemical systems

scientific article

Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis.

scientific article

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article

Modelling the variable incorporation of aromatic amino acids in the tyrocidines and analogous cyclodecapeptides

scientific article published on 10 September 2019

OneStop:JWS Online’s access point to SBML,SBGN and MIRIAM compliant annotation

Phosphofructokinase controls the acetaldehyde-induced phase shift in isolated yeast glycolytic oscillators

scientific article published on 31 January 2019

Phosphoglycerate kinase acts as a futile cycle at high temperature.

scientific article published on 6 October 2017

Physiological implications of class IIa bacteriocin resistance in Listeria monocytogenes strains

scientific article published in February 2004

Putting intentions into cell biochemistry: an artificial intelligence perspective

scientific article published in January 2002

Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients

scientific article

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

scientific article

Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex

scientific article published on 10 December 2009

RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets

RightField: embedding ontology annotation in spreadsheets

scientific article (publication date: 15 July 2011)

Rightfield: Embedding Ontology Term Selection into Spreadsheets for the Annotation of Biological Data

scientific article published in proceedings of the iswc 2010 posters & demonstrations track: collected abstracts

Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae

scientific article

SEEK: a systems biology data and model management platform

scientific article

Selectivity in Overlapping MAP Kinase Cascades

scientific article published on 01 October 2002

Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform

article

Stealthy annotation of experimental biology by spreadsheets

Studying Glycolytic Oscillations in Individual Yeast Cells by Combining Fluorescence Microscopy with Microfluidics and Optical Tweezers

scientific article published on 17 October 2018

Sustained glycolytic oscillations in individual isolated yeast cells

scientific article published on 11 June 2012

Systems biology model databases and resources

scientific article published on January 2008

Systems biology tools for toxicology

scientific article published on 09 May 2012

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

scientific article published on 16 February 2008

Targeting glycolysis in the malaria parasite Plasmodium falciparum

scientific article published on 9 December 2015

Targeting pathogen metabolism without collateral damage to the host

scientific article

The A-ring reduction of 11-ketotestosterone is efficiently catalysed by AKR1D1 and SRD5A2 but not SRD5A1

scientific article published on 03 July 2020

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

scientific article published on 4 February 2016

The JWS online simulation database

scientific article published on 27 January 2017

The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico.

scientific article published on 20 April 2017

The SEEK: a platform for sharing data and models in systems biology

scientific article

The Silicon Cell Initiative

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level

scientific article

The evolution of standards and data management practices in systems biology

scientific article

The extent to which ATP demand controls the glycolytic flux depends strongly on the organism and conditions for growth

scientific article published in January 2002

The glycolytic flux in Escherichia coli is controlled by the demand for ATP.

scientific article published on July 2002

Towards building the silicon cell: a modular approach

scientific article published on 19 October 2005

Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico.

scientific article published on 7 December 2012

Variation in pantothenate kinase type determines the pantothenamide mode of action and impacts on coenzyme A salvage biosynthesis.

scientific article

Web-based kinetic modelling using JWS Online.

scientific article

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

scientific article published on 8 December 2010

Workflows for optimization of enzyme cascades and whole cell catalysis based on enzyme kinetic characterization and pathway modelling

scientific article published on 15 November 2021

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 Jacky L Snoep

11-Oxygenated androgen precursors are the preferred substrates for aldo-keto reductase 1C3 (AKR1C3): Implications for castration resistant prostate cancer

A combined experimental and modelling approach for the Weimberg pathway optimisation

A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism

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

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells

An ffh mutant of Streptococcus mutans is viable and able to physiologically adapt to low pH in continuous culture

An optical tweezers, epi-fluorescence and microfluidic-setup for synchronization studies of glycolytic oscillations in living yeast cells

Attractive models: how to make the silicon cell relevant and dynamic

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Competition for phosphorus between the nitrogen-fixing cyanobacteria Anabaena and Aphanizomenon

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum

Control analysis for autonomously oscillating biochemical networks

Control analysis of trophic chains

DNA supercoiling by gyrase is linked to nucleoid compaction.

DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase.

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Data and model integration using JWS Online.

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

Design principles of nuclear receptor signalling: How complex networking improves signal transduction

Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy

ECA: control in ecosystems

Editorial: 12th BTK Meeting: ‘Systems Biology: redefining BioThermoKinetics’

Emergence of the silicon human and network targeting drugs

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

Erratum: The Systems Biology Graphical Notation

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Fourth-Generation Progestins Inhibit 3β-Hydroxysteroid Dehydrogenase Type 2 and Modulate the Biosynthesis of Endogenous Steroids

From Silicon Cellsilicon cell to Silicon Humansilicon human

From isolation to integration, a systems biology approach for building the Silicon Cell

From steady-state to synchronized yeast glycolytic oscillations I: model construction.

From steady-state to synchronized yeast glycolytic oscillations II: model validation

Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy

Glycolysis and Flux Control

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus

JWS online cellular systems modelling and microbiology.

Metabolic control in integrated biochemical systems

Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis.

Minimum Information About a Simulation Experiment (MIASE)

Minimum information requested in the annotation of biochemical models (MIRIAM)

Modelling the variable incorporation of aromatic amino acids in the tyrocidines and analogous cyclodecapeptides

OneStop:JWS Online’s access point to SBML,SBGN and MIRIAM compliant annotation

OneStop:JWS Online’s access point to SBML,SBGN and MIRIAM compliant annotation

Phosphofructokinase controls the acetaldehyde-induced phase shift in isolated yeast glycolytic oscillators

Phosphoglycerate kinase acts as a futile cycle at high temperature.

Physiological implications of class IIa bacteriocin resistance in Listeria monocytogenes strains

Putting intentions into cell biochemistry: an artificial intelligence perspective

Quantitative analysis of drug effects at the whole-body level: a case study for glucose metabolism in malaria patients

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex

RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets

RightField: embedding ontology annotation in spreadsheets

Rightfield: Embedding Ontology Term Selection into Spreadsheets for the Annotation of Biological Data

Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae

SEEK: a systems biology data and model management platform

Selectivity in Overlapping MAP Kinase Cascades

Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform

Stealthy annotation of experimental biology by spreadsheets

Studying Glycolytic Oscillations in Individual Yeast Cells by Combining Fluorescence Microscopy with Microfluidics and Optical Tweezers

Sustained glycolytic oscillations in individual isolated yeast cells

Systems biology model databases and resources

Systems biology tools for toxicology

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

Targeting glycolysis in the malaria parasite Plasmodium falciparum

Targeting pathogen metabolism without collateral damage to the host

The A-ring reduction of 11-ketotestosterone is efficiently catalysed by AKR1D1 and SRD5A2 but not SRD5A1

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

The JWS online simulation database

The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico.

The SEEK: a platform for sharing data and models in systems biology

The Silicon Cell Initiative

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level

The evolution of standards and data management practices in systems biology

The extent to which ATP demand controls the glycolytic flux depends strongly on the organism and conditions for growth