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Barbara Bakker

Research Profile

Physiology

Living Beings

Saccharomyces cerevisiae

Chemicals & Drugs

Concepts & Ideas

Occupations

Systems Biology

Phenomena

Oxidation-Reduction

Anatomy

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Publications

TOP 3
Simone Pieretti; Federica Prati; Leonardo Scapozza; Barbara M Bakker; Christian Bergamini; Maria Laura Bolognesi; Reto Brun; Giovanni Capranico; Romana Fato; Jurgen Haanstra; Giorgio Lenaz; Muriel Mazet; Paul A M Michels; Remo Perozzo; Andrea Cavalli
Naphthoquinone derivatives exert their antitrypanosomal activity via a multi-target mechanism.
Alexey Kolodkin; Jeantine Lunshof; Rafael Moreno-Sanchez; Nick Plant; Jacky L Snoep; Barbara M Bakker; Rudi Balling; Fred C Boogerd; Frank J Bruggeman; Valeri Goncharuk; Nilgun Yilmaz; Hans V Westerhoff
Emergence of the silicon human and network targeting drugs.
Jurgen Haanstra; Aloysius G M Tielens; Jan van Dam; Jaap J van Hellemond; Arjen van Tuijl; Wouter van Winden; Barbara M Bakker
Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes.

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All Publications

2013: Simone Pieretti; Federica Prati; Leonardo Scapozza; Barbara M Bakker; Christian Bergamini; Maria Laura Bolognesi; Reto Brun; Giovanni Capranico; Romana Fato; Jurgen Haanstra; Giorgio Lenaz; Muriel Mazet; Paul A M Michels; Remo Perozzo; Andrea Cavalli
Naphthoquinone derivatives exert their antitrypanosomal activity via a multi-target mechanism.
PLoS neglected tropical diseases 2013;7(1):e2012.
2012: Alexey Kolodkin; Jeantine Lunshof; Rafael Moreno-Sanchez; Nick Plant; Jacky L Snoep; Barbara M Bakker; Rudi Balling; Fred C Boogerd; Frank J Bruggeman; Valeri Goncharuk; Nilgun Yilmaz; Hans V Westerhoff
Emergence of the silicon human and network targeting drugs.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2012;46(4):190-7.
2012: Jurgen Haanstra; Aloysius G M Tielens; Jan van Dam; Jaap J van Hellemond; Arjen van Tuijl; Wouter van Winden; Barbara M Bakker
Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes.
International journal for parasitology 2012;42(7):667-73.
2012: Karen van Eunen; Hans V Westerhoff; José A L Kiewiet; Barbara M Bakker
Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics.
PLoS computational biology 2012;8(4):e1002483.
2011: Karen van Eunen; Hans V Westerhoff; Jildau Bouwman; Sergio Rossell; Barbara M Bakker
Quantitative analysis of flux regulation through hierarchical regulation analysis.
Methods in enzymology 2011;500():571-95.
2011: Jurgen Haanstra; Eduard J Kerkhoven; Arjen van Tuijl; Marjolein Blits; Martin Wurst; Rick van Nuland; Marie-Astrid Albert; Paul A M Michels; Jildau Bouwman; Christine Clayton; Hans V Westerhoff; Barbara M Bakker
A domino effect in drug action: from metabolic assault towards parasite differentiation.
Molecular microbiology 2011;79(1):94-108.
2011: Jildau Bouwman; José Kiewiet; Alexander Lindenbergh; Karen van Eunen; Marco Siderius; Barbara M Bakker
Metabolic regulation rather than de novo enzyme synthesis dominates the osmo-adaptation of yeast.
Yeast (Chichester, England) 2011;28(1):43-53.
2010: Alexey N Kolodkin; Frank J Bruggeman; Nick Plant; Martijn J Moné; Barbara M Bakker; Moray J Campbell; Johannes P T M van Leeuwen; Carsten Carlberg; Jacky L Snoep; Hans V Westerhoff
Design principles of nuclear receptor signaling: how complex networking improves signal transduction.
Molecular systems biology 2010;6():446.
2010: Hans V Westerhoff; Malkhey Verma; Maria Nardelli; Malgorzata Adamczyk; Karen van Eunen; Evangelos Simeonidis; Barbara M Bakker
Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control.
Biochemical Society transactions 2010;38(5):1189-96.
2010: Karen van Eunen; Jildau Bouwman; Pascale Daran-Lapujade; Jarne Postmus; André B Canelas; Femke I C Mensonides; Rick Orij; Isil Tuzun; Joost van den Brink; Gertien Smits; Walter M van Gulik; Stanley Brul; Joseph J Heijnen; Johannes H De Winde; M Joost Teixeira de Mattos; Carsten Kettner; Jens Nielsen; Hans V Westerhoff; Barbara M Bakker
Measuring enzyme activities under standardized in vivo-like conditions for systems biology.
The FEBS journal 2010;277(3):749-60.
2009: Karen van Eunen; Jildau Bouwman; Alexander Lindenbergh; Hans V Westerhoff; Barbara M Bakker
Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast.
The FEBS journal 2009;276(19):5521-36.
2009: Hans V Westerhoff; Alexey Kolodkin; Riaan Conradie; Stephen J Wilkinson; Frank J Bruggeman; Klaas Krab; Jan H van Schuppen; Hanna Hardin; Barbara M Bakker; Martijn J Moné; Katja N Rybakova; Marco Eijken; Hans J P van Leeuwen; Jacky L Snoep
Systems biology towards life in silico: mathematics of the control of living cells.
Journal of mathematical biology 2009;58(1-2):7-34.
2008: Jurgen Haanstra; Arjen van Tuijl; Peter Kessler; Willem Reijnders; Paul A M Michels; Hans V Westerhoff; Marilyn Parsons; Barbara M Bakker
Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(46):17718-23.
2008: Jarne Postmus; André B Canelas; Jildau Bouwman; Barbara M Bakker; Walter M van Gulik; M Joost Teixeira de Mattos; Stanley Brul; Gertien Smits
Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.
The Journal of biological chemistry 2008;283(35):23524-32.
2008: Susanne Gerber; Heike Assmus; Barbara M Bakker; Edda Klipp
Drug-efficacy depends on the inhibitor type and the target position in a metabolic network--a systematic study.
Journal of theoretical biology 2008;252(3):442-55.
2008: Jasper Merijn Schuurmans; Sergio Rossell; Arjen van Tuijl; Barbara M Bakker; Klaas J Hellingwerf; M Joost Teixeira de Mattos
Effect of hxk2 deletion and HAP4 overexpression on fermentative capacity in Saccharomyces cerevisiae.
FEMS yeast research 2008;8(2):195-203.
2008: Jurgen Haanstra; Mhairi Stewart; Van-Duc Luu; Arjen van Tuijl; Hans V Westerhoff; Christine Clayton; Barbara M Bakker
Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei.
The Journal of biological chemistry 2008;283(5):2495-507.
2008: Sergio Rossell; Alexander Lindenbergh; Coen C van der Weijden; Arthur L Kruckeberg; Karen van Eunen; Hans V Westerhoff; Barbara M Bakker
Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae.
FEMS yeast research 2008;8(1):155-64.
2008: Annamaria Bevilacqua; Stephen J Wilkinson; Richard Dimelow; Ettore Murabito; Samrina Rehman; Maria Nardelli; Karen van Eunen; Sergio Rossell; Frank J Bruggeman; Nils Blüthgen; Dirk De Vos; Jildau Bouwman; Barbara M Bakker; Hans V Westerhoff
Vertical systems biology: from DNA to flux and back.
SEB experimental biology series 2008;61():65-91.
2007: Pascale Daran-Lapujade; Sergio Rossell; Walter M van Gulik; Marijke A H Luttik; Marco J L de Groot; Monique Slijper; albert heck; Jean-Marc Daran; Johannes H De Winde; Hans V Westerhoff; Jack T. Pronk; Barbara M Bakker
The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(40):15753-8.
2007: Frank J Bruggeman; Sergio Rossell; Karen Van Eunen; Jildau Bouwman; Hans V Westerhoff; Barbara M Bakker
Systems biology and the reconstruction of the cell: from molecular components to integral function.
Sub-cellular biochemistry 2007;43():239-62.
2007: Jorrit J Hornberg; Frank J Bruggeman; Barbara M Bakker; Hans V Westerhoff
Metabolic control analysis to identify optimal drug targets.
Progress in drug research. Fortschritte der Arzneimittelforschung. Progrès des recherches pharmaceutiques 2007;64():171, 173-89.
2006: Daniel G Guerra; Anabelle Decottignies; Barbara M Bakker; Paul A M Michels
The mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase of Trypanosomatidae and the glycosomal redox balance of insect stages of Trypanosoma brucei and Leishmania spp.
Molecular and biochemical parasitology 2006;149(2):155-69.
2006: Frank J Bruggeman; Jurriaan de Haan; H Hardin; Jildau Bouwman; Sergio Rossell; K van Eunen; Barbara M Bakker; Hans V Westerhoff
Time-dependent hierarchical regulation analysis: deciphering cellular adaptation.
Systems biology 2006;153(5):318-22.
2006: Sergio Rossell; Coen C van der Weijden; Alexander Lindenbergh; Arjen van Tuijl; Christof Francke; Barbara M Bakker; Hans V Westerhoff
Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(7):2166-71.
2005: Marie-Astrid Albert; Jurgen Haanstra; Véronique Hannaert; Joris Van Roy; Fred R Opperdoes; Barbara M Bakker; Paul A M Michels
Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei.
The Journal of biological chemistry 2005;280(31):28306-15.
2005: Karin A Reijenga; Barbara M Bakker; Coen C van der Weijden; Hans V Westerhoff
Training of yeast cell dynamics.
The FEBS journal 2005;272(7):1616-24.
2005: Sergio Rossell; Coen C van der Weijden; Arthur L Kruckeberg; Barbara M Bakker; Hans V Westerhoff
Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae.
FEMS yeast research 2005;5(6-7):611-9.
2005: Karin A Reijenga; Yvonne M G A van Megen; Bob W Kooi; Barbara M Bakker; Jacky L Snoep; Henk W van Verseveld; Hans V Westerhoff
Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength.
Journal of theoretical biology 2005;232(3):385-98.
2002: Sarah Koefoed; Marijke Otten; Brian J Koebmann; Frank J Bruggeman; Barbara M Bakker; Jacky L Snoep; Klaas Krab; Rob J M van Spanning; Henk van Verseveld; Peter Jensen; Johanna Koster; Hans V Westerhoff
A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life.
Biochimica et biophysica acta 2002;1555(1-3):75-82.
2002: Karin M Overkamp; Barbara M Bakker; H Yde Steensma; Johannes P van Dijken; Jack T. Pronk
Two mechanisms for oxidation of cytosolic NADPH by Kluyveromyces lactis mitochondria.
Yeast (Chichester, England) 2002;19(10):813-24.
2002: Karin M Overkamp; Barbara M Bakker; Peter Kötter; Marijke A H Luttik; Johannes P van Dijken; Jack T. Pronk
Metabolic engineering of glycerol production in Saccharomyces cerevisiae.
Applied and environmental microbiology 2002;68(6):2814-21.
2002: Rogier Stuger; Conrad L Woldringh; Coen C van der Weijden; Norbert O E Vischer; Barbara M Bakker; Rob J M van Spanning; Jacky L Snoep; Hans V Westerhoff
DNA supercoiling by gyrase is linked to nucleoid compaction.
Molecular biology reports 2002;29(1-2):79-82.
2002: Sergio Rossell; Coen C van der Weijden; Arthur L Kruckeberg; Barbara M Bakker; Hans V Westerhoff
Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity.
Molecular biology reports 2002;29(1-2):255-7.
2002: Barbara M Bakker; Heike Assmus; Frank J Bruggeman; Jurgen Haanstra; Edda Klipp; Hans V Westerhoff
Network-based selectivity of antiparasitic inhibitors.
Molecular biology reports 2002;29(1-2):1-5.
2001: Antonius J A van Maris; Barbara M Bakker; M Brandt; André Boorsma; M J Teixeira de Mattos; Les Grivell; Jack T. Pronk; Jolanda Blom
Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae.
FEMS yeast research 2001;1(2):139-49.
2001: Barbara M Bakker; Karin M Overkamp; Peter Kötter; Marijke A H Luttik; Jack T. Pronk
Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae.
FEMS microbiology reviews 2001;25(1):15-37.
2000: Bas Teusink; Jutta Passarge; C A Reijenga; E Esgalhado; Coen C van der Weijden; M Schepper; Michael C Walsh; Barbara M Bakker; Karel van Dam; Hans V Westerhoff; Jacky L Snoep
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
European journal of biochemistry / FEBS 2000;267(17):5313-29.
2000: Barbara M Bakker; Christoffer Bro; Peter Kötter; Marijke A H Luttik; Johannes P van Dijken; Jack T. Pronk
The mitochondrial alcohol dehydrogenase Adh3p is involved in a redox shuttle in Saccharomyces cerevisiae.
Journal of bacteriology 2000;182(17):4730-7.
2000: Karin M Overkamp; Barbara M Bakker; Peter Kötter; Arjen van Tuijl; Simon de Vries; Johannes P van Dijken; Jack T. Pronk
In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria.
Journal of bacteriology 2000;182(10):2823-30.
2000: Barbara M Bakker; F I Mensonides; Bas Teusink; P van Hoek; Paul A M Michels; Hans V Westerhoff
Compartmentation protects trypanosomes from the dangerous design of glycolysis.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(5):2087-92.
2000: Barbara M Bakker; Hans V Westerhoff; Fred R Opperdoes; Paul A M Michels
Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs.
Molecular and biochemical parasitology 2000;106(1):1-10.
1999: Barbara M Bakker; Michael C Walsh; B H ter Kuile; F I Mensonides; Paul A M Michels; Fred R Opperdoes; Hans V Westerhoff
Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(18):10098-103.
1999: Barbara M Bakker; Paul A M Michels; Fred R Opperdoes; Hans V Westerhoff
What controls glycolysis in bloodstream form Trypanosoma brucei?
The Journal of biological chemistry 1999;274(21):14551-9.
1999: W C van Heeswijk; Barbara M Bakker; Bas Teusink; Boris N Kholodenko; Oscar J G Somsen; Jacky L Snoep; Hans V Westerhoff
Live control of the living cell.
Biochemical Society transactions 1999;27(2):261-4.
1996: D A van Tijn; Barbara M Bakker; Thomas Vulsma
Hypothyroidism: what is the central issue?
The Journal of pediatrics 1996;129(3):480-3.
1996: Bas Teusink; Barbara M Bakker; Hans V Westerhoff
Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations.
Biochimica et biophysica acta 1996;1275(3):204-12.
1996: P Richard; Barbara M Bakker; Bas Teusink; Karel van Dam; Hans V Westerhoff
Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells.
European journal of biochemistry / FEBS 1996;235(1-2):238-41.
1995: V Mildaziene; R Baniene; Z Nauciene; Barbara M Bakker; G C Brown; Hans V Westerhoff; Boris N Kholodenko
Calcium indirectly increases the control exerted by the adenine nucleotide translocator over 2-oxoglutarate oxidation in rat heart mitochondria.
Archives of biochemistry and biophysics 1995;324(1):130-4.
1995: Barbara M Bakker; Hans V Westerhoff; Paul A M Michels
Regulation and control of compartmentalized glycolysis in bloodstream form Trypanosoma brucei.
Journal of bioenergetics and biomembranes 1995;27(5):513-25.
1994: P Richard; Jasper Diderich; Barbara M Bakker; Bas Teusink; Karel van Dam; Hans V Westerhoff
Yeast cells with a specific cellular make-up and an environment that removes acetaldehyde are prone to sustained glycolytic oscillations.
FEBS letters 1994;341(2-3):223-6.