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Wouter van Winden

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Fredrick O Aboka; Arthur Oudshoorn; Mashego M Reginald; Marco van de Berg; Walter M van Gulik; Wouter A van Winden; Joseph J Heijnen
Identification of informative metabolic responses using a minibioreactor: a small step change in the glucose supply rate creates a large metabolic response in Saccharomyces cerevisiae.
Zheng Zhao; Karel Kuijvenhoven; Walter M van Gulik; Joseph J Heijnen; Wouter A van Winden; Peter Verheijen
Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol.
Alvaro R Lara; Hilal Taymaz-Nikerel; Mlawule R Mashego; Walter M van Gulik; Joseph J Heijnen; Octavio T Ramírez; Wouter A van Winden
Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses.

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All Publications

2012: Fredrick O Aboka; Arthur Oudshoorn; Mashego M Reginald; Marco van de Berg; Walter M van Gulik; Wouter A van Winden; Joseph J Heijnen
Identification of informative metabolic responses using a minibioreactor: a small step change in the glucose supply rate creates a large metabolic response in Saccharomyces cerevisiae.
Yeast (Chichester, England) 2012;29(3-4):95-110.
2011: Zheng Zhao; Karel Kuijvenhoven; Walter M van Gulik; Joseph J Heijnen; Wouter A van Winden; Peter Verheijen
Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol.
Applied microbiology and biotechnology 2011;89(1):63-72.
2009: Alvaro R Lara; Hilal Taymaz-Nikerel; Mlawule R Mashego; Walter M van Gulik; Joseph J Heijnen; Octavio T Ramírez; Wouter A van Winden
Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses.
Biotechnology and bioengineering 2009;104(6):1153-61.
2009: M J L de Groot; R J P van Berlo; Wouter A van Winden; Peter Verheijen; Marcel J T Reinders; D de Ridder
Metabolite and reaction inference based on enzyme specificities.
Bioinformatics (Oxford, England) 2009;25(22):2975-82.
2009: Reza M Seifar; Cor Ras; Jan C van Dam; Walter M van Gulik; Joseph J Heijnen; Wouter A van Winden
Simultaneous quantification of free nucleotides in complex biological samples using ion pair reversed phase liquid chromatography isotope dilution tandem mass spectrometry.
Analytical biochemistry 2009;388(2):213-9.
2009: Fredrick O Aboka; Joseph J Heijnen; Wouter A van Winden
Dynamic 13C-tracer study of storage carbohydrate pools in aerobic glucose-limited Saccharomyces cerevisiae confirms a rapid steady-state turnover and fast mobilization during a modest stepup in the glucose uptake rate.
FEMS yeast research 2009;9(2):191-201.
2009: Emrah Nikerel; Wouter A van Winden; Peter Verheijen; Joseph J Heijnen
Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics.
Metabolic engineering 2009;11(1):20-30.
2008: M T A P Kresnowati; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Energetic and metabolic transient response of Saccharomyces cerevisiae to benzoic acid.
The FEBS journal 2008;275(22):5527-41.
2008: Zheng Zhao; Karel Kuijvenhoven; Cor Ras; Walter M van Gulik; Joseph J Heijnen; Peter Verheijen; Wouter A van Winden
Isotopic non-stationary 13C gluconate tracer method for accurate determination of the pentose phosphate pathway split-ratio in Penicillium chrysogenum.
Metabolic engineering 2008;10(3-4):178-86.
2008: Rintze M Zelle; Erik A F De Hulster; Wouter A van Winden; Pieter de Waard; Cor Dijkema; Ron Winkler; Jan-Maarten A Geertman; Johannes P van Dijken; Jack T. Pronk; Antonius J A van Maris
Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export.
Applied and environmental microbiology 2008;74(9):2766-77.
2008: Reza M Seifar; Zheng Zhao; Jan van Dam; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Quantitative analysis of metabolites in complex biological samples using ion-pair reversed-phase liquid chromatography-isotope dilution tandem mass spectrometry.
Journal of chromatography. A 2008;1187(1-2):103-10.
2008: M T A P Kresnowati; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Dynamic in vivo metabolome response of Saccharomyces cerevisiae to a stepwise perturbation of the ATP requirement for benzoate export.
Biotechnology and bioengineering 2008;99(2):421-41.
2008: M T A P Kresnowati; C M Suarez-Mendez; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulses.
Metabolic engineering 2008;10(1):39-54.
2007: Roeland Costenoble; Dirk Mueller; Timo Barl; Walter M van Gulik; Wouter A van Winden; Matthias Reuss; Joseph J Heijnen
13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae.
FEMS yeast research 2007;7(4):511-26.
2007: M T A P Kresnowati; C Suarez-Mendez; M K Groothuizen; Wouter A van Winden; Joseph J Heijnen
Measurement of fast dynamic intracellular pH in Saccharomyces cerevisiae using benzoic acid pulse.
Biotechnology and bioengineering 2007;97(1):86-98.
2007: Roelco J Kleijn; Jan-Maarten A Geertman; Beckley K Nfor; Cor Ras; Dick Schipper; Jack T. Pronk; Joseph J Heijnen; Antonius J A van Maris; Wouter A van Winden
Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived C-labelling data.
FEMS yeast research 2007;7(2):216-31.
2007: Roelco J Kleijn; Feng Liu; Wouter A van Winden; Walter M van Gulik; Cor Ras; Joseph J Heijnen
Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum.
Metabolic engineering 2007;9(1):112-23.
2006: Fredrick O Aboka; Huiling Yang; Lodewijk P de Jonge; Rob Kerste; Wouter A van Winden; Walter M van Gulik; Rob Hoogendijk; Arthur Oudshoorn; Joseph J Heijnen
Characterization of an experimental miniature bioreactor for cellular perturbation studies.
Biotechnology and bioengineering 2006;95(6):1032-42.
2006: Uly Nasution; Walter M van Gulik; Angela M Proell; Wouter A van Winden; Joseph J Heijnen
Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor.
Metabolic engineering 2006;8(5):395-405.
2006: Roelco J Kleijn; Wouter A van Winden; Cor Ras; Walter M van Gulik; Dick Schipper; Joseph J Heijnen
13C-labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum.
Applied and environmental microbiology 2006;72(7):4743-54.
2006: Uly Nasution; Walter M van Gulik; Roelco J Kleijn; Wouter A van Winden; Angela M Proell; Joseph J Heijnen
Measurement of intracellular metabolites of primary metabolism and adenine nucleotides in chemostat cultivated Penicillium chrysogenum.
Biotechnology and bioengineering 2006;94(1):159-66.
2006: Liang Wu; Jan van Dam; Dick Schipper; M T A P Kresnowati; Angela M Proell; Cor Ras; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse.
Applied and environmental microbiology 2006;72(5):3566-77.
2006: Liang Wu; Mlawule R Mashego; Angela M Proell; Jacobus L Vinke; Cor Ras; Jan van Dam; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
In vivo kinetics of primary metabolism in Saccharomyces cerevisiae studied through prolonged chemostat cultivation.
Metabolic engineering 2006;8(2):160-71.
2006: Emrah Nikerel; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics.
BMC bioinformatics 2006;7():540.
2006: M T A P Kresnowati; Wouter A van Winden; Marinka J H Almering; A ten Pierick; Cor Ras; Theo A Knijnenburg; Pascale Daran-Lapujade; Jack T. Pronk; Joseph J Heijnen; Jean-Marc Daran
When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation.
Molecular systems biology 2006;2():49.
2005: Roelco J Kleijn; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence.
The FEBS journal 2005;272(19):4970-82.
2005: Liang Wu; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Application of metabolome data in functional genomics: a conceptual strategy.
Metabolic engineering 2005;7(4):302-10.
2005: Wouter A van Winden; Jan C van Dam; Cor Ras; Roelco J Kleijn; Jacobus L Vinke; Walter M van Gulik; Joseph J Heijnen
Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites.
FEMS yeast research 2005;5(6-7):559-68.
2005: Christoph Wittmann; Michael Hans; Wouter A van Winden; Cor Ras; Joseph J Heijnen
Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae.
Biotechnology and bioengineering 2005;89(7):839-47.
2005: M T A P Kresnowati; Wouter A van Winden; Joseph J Heijnen
Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics.
Metabolic engineering 2005;7(2):142-53.
2005: Liang Wu; Mlawule R Mashego; Jan C van Dam; Angela M Proell; Jacobus L Vinke; Cor Ras; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards.
Analytical biochemistry 2005;336(2):164-71.
2004: Liang Wu; Weiming Wang; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics.
European journal of biochemistry / FEBS 2004;271(16):3348-59.
2004: Mlawule R Mashego; Liang Wu; Jan C van Dam; Cor Ras; Jacobus L Vinke; Wouter A van Winden; Walter M van Gulik; Joseph J Heijnen
MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites.
Biotechnology and bioengineering 2004;85(6):620-8.
2003: Wouter A van Winden; Walter M van Gulik; Dick Schipper; Peter Verheijen; Preben Krabben; Jacobus L Vinke; Joseph J Heijnen
Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation.
Biotechnology and bioengineering 2003;83(1):75-92.
2002: Wouter A van Winden; Joseph J Heijnen; Peter Verheijen
Cumulative bondomers: a new concept in flux analysis from 2D [13C,1H] COSY NMR data.
Biotechnology and bioengineering 2002;80(7):731-45.
2002: Wouter A van Winden; Christoph Wittmann; Elmar Heinzle; Joseph J Heijnen
Correcting mass isotopomer distributions for naturally occurring isotopes.
Biotechnology and bioengineering 2002;80(4):477-9.
2001: Wouter A van Winden; Dick Schipper; Peter Verheijen; Joseph J Heijnen
Innovations in generation and analysis of 2D [(13)C,(1)H] COSY NMR spectra for metabolic flux analysis purposes.
Metabolic engineering 2001;3(4):322-43.
2001: Wouter A van Winden; Joseph J Heijnen; Peter Verheijen; J Grievink
A priori analysis of metabolic flux identifiability from (13)C-labeling data.
Biotechnology and bioengineering 2001;74(6):505-16.
2001: Wouter A van Winden; Peter Verheijen; S Heijnen
Possible pitfalls of flux calculations based on (13)C-labeling.
Metabolic engineering 2001;3(2):151-62.