dr. B.M. Bakker

dr.

19982017
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Research Output 1998 2017

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Article
2017

Targeting pathogen metabolism without collateral damage to the host.

Haanstra, J. R., Gerding, A., Dolga, A. M., Sorgdrager, F. J., Buist-Homan, M., du Toit, F., Faber, K. N., Holzhutter, H. G., Szoor, B., Matthews, K. R., Snoep, J. L., Westerhoff, H. V. & Bakker, B. M., 2017, In : Scientific Reports. 7, 40406.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2015

Drug target identification through systems biology.

Haanstra, J. R. & Bakker, B. M., 2015, In : Drug Discovery Today: Technologies. 15, p. 17-22

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
Pharmaceutical Preparations
Neoplasms
2014

A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae druing temperature shift.

Mensonides, F. I. C., Brul, S., Hellingwerf, K. J., Bakker, B. M. & Teixeira de Mattos, M. J., 2014, In : The FEBS Journal. 281, 3, p. 825-841

Research output: Contribution to JournalArticleAcademicpeer-review

Yeast
Saccharomyces cerevisiae
Kinetics
Temperature
Growth

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

Haanstra, J. R., Bakker, B. M. & Michels, P. A. M., 2014, In : Molecular and Biochemical Parasitology. 198, p. 18-28

Research output: Contribution to JournalArticleAcademicpeer-review

Trypanosoma brucei brucei
Microbodies
Peroxisomes
Membranes
Trypanosomiasis

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

Fadda, A., Ryten, M., Droll, D., Rojas, F., Farber, V., Haanstra, J. R., Merce, C., Bakker, B. M., Matthews, K. & Clayton, C., 2014, In : Molecular Microbiology. 94, p. 307-326 12764.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Trypanosomiasis
RNA Stability
Gene Expression Profiling
Messenger RNA
Polyadenylation
2013

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

Mensonides, F. I. C., Bakker, B. M., Cremazy, F., Messiha, H. L., Mendes, P., Boogerd, F. C. & Westerhoff, H. V., 2013, In : FEBS Letters. 587, 17, p. 2860-2867 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biochemistry
Adenine Nucleotides
Yeast
Saccharomyces cerevisiae
Enzymes

Biochemical competition makes fatty-acid beta-oxidation vulnerable to substrate overload.

van Eunen, K., simons, S. M., Gerding, A., Bleeker, A., den Besten, G., Touw, C. M., Houten, S. M., Groen, A. K., Krab, K., Reijngoud, D. J. & Bakker, B. M., 2013, In : PLoS Computational Biology. 9, 8, e1003186.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Palmitoyl Coenzyme A
beta oxidation
Fatty Acids
Overload
Coenzyme A

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

Leroux, A. E., Haanstra, J. R., Bakker, B. M. & Krauth-Siegel, R. L., 2013, In : Journal of Biological Chemistry. 288, p. 23751-23764

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
trypanothione synthetase
Trypanosoma brucei brucei
Kinetics
Spermidine
Kinetic parameters

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

Kerkhoven, E. J., Achcar, R., Alibu, V. P., Burchmore, R. J., Gilbert, I. H., Trybito, M., Driessen, N. N., Gilbert, D., Breitling, R., Bakker, B. M. & Barrett, M. P., 2013, In : PLoS Computational Biology. 9, e1003371.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbodies
Trypanosoma brucei
Pentose Phosphate Pathway
Trypanosoma brucei brucei
pentoses

Naphthoquinone derivates exert their antitrypanosomal activity via a multi-target mechanism.

Pieretti, S., Haanstra, J. R., Mazet, M., Perozzo, R., Bergamini, C., Prati, F., Fato, R., Lenaz, G., Capranico, G., Brun, R., Bakker, B. M., Michels, P. A. M., Scapozza, L., Bolognesi, M. L. & Cavalli, A., 2013, In : PLoS Neglected Tropical Diseases. 7, p. 1-12 e2012.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Naphthoquinones
Lead
1,4-naphthoquinone
2012

Emergence of the silicon human and network targeting drugs.

Kolodkin, A. N., Boogerd, F. C., Plant, N., Bruggeman, F. J., Goncharuk, V., Lunshof, J. E., Moreno-Sanchez, R., Yilmaz, N., Bakker, B. M., Snoep, J. L., Balling, R. & Westerhoff, H. V., 2012, In : European Journal of Pharmaceutical Sciences. 46, p. 190-197

Research output: Contribution to JournalArticleAcademicpeer-review

Silicon
Drug Delivery Systems
Homeostasis
Systems Biology
Human Body

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

Haanstra, J. R., van Tuijl, J. H., van Dam, J., van Winden, W., Tielens, A. G. M., van Hellemond, J. J. & Bakker, B. M., 2012, In : International Journal for Parasitology. 42, p. 667-673

Research output: Contribution to JournalArticleAcademicpeer-review

Trypanosoma brucei brucei
Carbon
Carbon Cycle
Glucose
Trypanosomiasis

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

van Eunen, K., Kiewiet, J. A. L., Westerhoff, H. V. & Bakker, B. M., 2012, In : PLoS Computational Biology. 8, e1002483.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Allosteric Regulation
Enzyme Kinetics
Enzyme kinetics
enzyme kinetics
Biochemistry
2011

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

Haanstra, J. R., Kerkhoven, E. J., van Tuijl, J. H., Blits, M., Wurst, M., van Nuland, R., Albert, M. A., Michels, P. A. M., Bouwman, J., Clayton, C., Westerhoff, H. V. & Bakker, B. M., 2011, In : Molecular Microbiology. 79, 1, p. 94-108

Research output: Contribution to JournalArticleAcademicpeer-review

Parasites
Pharmaceutical Preparations
Trypanosomiasis
Glycolysis
Proteins

How molecular competition influences fluxes in gene expression networks.

de Vos, D. L., Bruggeman, F. J., Westerhoff, H. V. & Bakker, B. M., 2011, In : PLoS ONE. 6, 12, e28494.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Sigma Factor
Gene Regulatory Networks
Protein Biosynthesis
Ribosomes
Gene expression

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

Bouwman, J., Kiewiet, J. A. L., Lindenbergh, A., Van Eunen, K., Siderius, M. H. & Bakker, B. M., 2011, In : Yeast. 28, p. 43-53 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Glycerol
Yeast
Enzymes
Yeasts
Gene expression

Progressive methylation of aging histones by Dot1 acts as a timer.

de Vos, D. L., Frederiks, F., Terweij, M., van Welsem, T., Verzijlbergen, K. F., Iachina, E., de Graaf, E. L., Altelaar, A. F. M., Oudgenoeg, G., Heck, A. J. R., Krijgsveld, J., Bakker, B. M. & van Leeuwen, F., 2011, In : EMBO Reports. 12, p. 956-962

Research output: Contribution to JournalArticleAcademicpeer-review

Methylation
Histones
Aging of materials
Histone Code
Gene expression
2010

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

Kolodkin, A. N., Bruggeman, F. J., Plant, N., Mone, M. J., Bakker, B. M., Campbell, M. J., van Leeuwen, J. P. T. M., Carlberg, C., Snoep, J. L. & Westerhoff, H. V., 2010, In : Molecular Systems Biology. 6, p. 446

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Signal transduction
Signal Transduction
Cytoplasmic and Nuclear Receptors
Networking
Karyopherins

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

Canelas, A. B., Harrison, N., Fazio, A., Zhang, J., Pitkanen, J-P., van der Brink, J., Bakker, B. M., Bogner, L., Bouwman, J., Castrillo, J. I., Cankorur, A., Chumnanpuen, P., Daran-Lapujade, P., Dikicioglu, D., van Eunen, K., Ewald, J. C., Heijnen, J. J., Kirdar, B., Mattila, I., Mensonides, F. I. C. & 15 othersNiebel, A., Pentilla, M., Pronk, J. T., Reuss, M., Salusjarvi, L., Sauer, U., Sherman, D., Siemann-Herzberg, M., Westerhoff, H. V., de Winde, J. H., Petranovi, D., Oliver, S. G., Workman, T., Zamboni, N. & Nielsen, J., 2010, In : Nature Communications. 1, 145.

Research output: Contribution to JournalArticleAcademicpeer-review

protein metabolism
Systems Biology
yeast
biology
Metabolism

Measuring enzyme activities under standardized in vivo-like conditions for Systems Biology

van Eunen, K., Bouwman, J., Daran-Lapujade, P. A. L., Postmus, J., Canelas, A., Mensonides, F. I. C., Orij, R., Tuzun, I., van der Brink, J., Smits, G. J., van Gulik, W. M., Brul, S., Heijnen, J. J., de Winde, J. H., Teixeira de Mattos, M. J., Kettner, C., Nielsen, J., Westerhoff, H. V. & Bakker, B. M., 2010, In : The FEBS Journal. 277, p. 749-760

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
Enzyme activity
Yeast
Kinetic parameters
Yeasts

Systems Biochemistry in practice: experimenting with modeling and understanding with regulation and control.

Westerhoff, H. V., Verma, M., Nardelli, M., Adamczyk, M., van Eunen, K., Simeonidis, E. & Bakker, B. M., 2010, In : Biochemical Society Transactions. 38, p. 1189-1196

Research output: Contribution to JournalArticleAcademicpeer-review

Biochemistry
Genes
Systems Biology
Genomics
Macromolecules

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

Bakker, B. M., van Eunen, K., Jeneson, J. A. L., van Riel, N. A. W., Bruggeman, F. J. & Teusink, B., 2010, In : Biochemical Society Transactions. 38, p. 1294-1301

Research output: Contribution to JournalArticleAcademicpeer-review

The silicon trypanosome

Bakker, B. M., Krauth-Siegel, R. L., Clayton, C., Matthews, K., Girolami, M., Westerhoff, H. V., Michels, P. A. M., Breitling, R. & Barrett, M. P., 2010, In : Parasitology. 137, p. 1333-1341

Research output: Contribution to JournalArticleAcademicpeer-review

Trypanosomiasis
Silicon
silicon
Biological Sciences
metabolomics

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

van Eunen, K., Dool, P., Canelas, A. B., Kiewiet, J. A. L., Bouwman, J., van Gulik, W. M., Westerhoff, H. V. & Bakker, B. M., 2010, In : IET Systems Biology. 4, p. 157-168

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Starvation
Yeast
Nitrogen
Yeasts
2009

A software for the systematic scanning of drug targets in kinetic network models

Schulz, M., Bakker, B. M. & Klipp, E., 2009, In : BMC Bioinformatics. 10, p. 344

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Glycolysis
Kinetic Model
Network Model
Scanning
Drugs

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

Westerhoff, H. V., Kolodkin, A. N., Conradie, R., Wilkinson, S. J., Bruggeman, F. J., Krab, K., Schuppen, J. H., Hardin, H. M., Bakker, B. M., Mone, M. J., Rybakova, E. N., Eijken, M., van Leeuwen, J. P. & Snoep, J. L., 2009, In : Journal of Mathematical Biology. 58, p. 7-34

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Systems Biology
Mathematics
Computer Simulation
Signal Transduction
Cells

Time-dependent regulation analysis dissects shifts between metabolic and gen-expression regulation during differentiation of bloodstream forms.

van Eunen, K., Bouwman, J., Lindenbergh, P. A., Westerhoff, H. V. & Bakker, B. M., 2009, In : The FEBS Journal. 276, p. 5521-5536

Research output: Contribution to JournalArticleAcademicpeer-review

Starvation
Nitrogen
Enzymes
Autophagy
Metabolism
2008

Compartmentation prevents a lether turbo-explosion of glycolysis in trypanosomes.

Haanstra, J. R., van Tuijl, J. H., Kessler, P., Reijnders, W. N. M., Michels, P. A. M., Westerhoff, H. V., Parsons, M. & Bakker, B. M., 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, p. 17718-17723

Research output: Contribution to JournalArticleAcademicpeer-review

Trypanosomiasis
Explosions
Glycolysis
Glycerol
Adenosine Triphosphate

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

Haanstra, J. R., Stewart, M., Luu, V-D., van Tuijl, J. H., Westerhoff, H. V., Clayton, C. & Bakker, B. M., 2008, In : Journal of Biological Chemistry. 283, p. 2495-2507

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Phosphoglycerate Kinase
Trypanosoma brucei brucei
Gene Expression Regulation
Gene expression
RNA Stability

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

Gerber, S., Assmus, H. E., Bakker, B. M. & Klipp, E., 2008, In : Journal of Theoretical Biology. 252, p. 442-455

Research output: Contribution to JournalArticleAcademicpeer-review

Metabolic Network
Metabolic Networks and Pathways
Inhibitor
Efficacy
Drugs

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

Schuurmans, J. M., Rossell, S., van Tuijl, J. H., Bakker, B. M., Hellingwerf, K. J. & Teixeira de Mattos, M. J., 2008, In : FEMS Yeast Research. 8, p. 195-203

Research output: Contribution to JournalArticleAcademicpeer-review

Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathway in response to a HAP4 overexpression in Saccharomyces cerevisiae.

Rossell, S., Lindenbergh, P. A., van der Weijden, C. C., Kruckeberg, A. L., van Eunen, K., Westerhoff, H. V. & Bakker, B. M., 2008, In : FEMS Yeast Research. 8, p. 195-203

Research output: Contribution to JournalArticleAcademicpeer-review

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

Postmus, J., Canelas, A. B., Bouwman, J., Bakker, B. M., van Gulik, W. R., Teixeira de Mattos, M. J., Brul, S. & Smits, G. J., 2008, In : Journal of Biological Chemistry. 283, p. 23524-23532

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Yeast
Saccharomyces cerevisiae
Fluxes
Temperature
Enzymes

Vertical systems biology: from DNA to flux and back.

Bevilacqua, A., Wilkinson, S. J., Dimelow, R., Murabito, E., Rehman, S., Nardelli, M., van Eunen, K., Rossell, S., Bruggeman, F. J., Bluthgen, N., de Vos, D. L., Bouwman, J., Bakker, B. M. & Westerhoff, H. V., 2008, In : SEB Experimental Biology Series. 61, p. 65-91

Research output: Contribution to JournalArticleAcademicpeer-review

2007

Metabolic control analysis to identify optimal drug targets.

Hornberg, J. J., Bruggeman, F. J., Bakker, B. M. & Westerhoff, H. V., 2007, In : Progress in Drug Research. 64, p. 173-189

Research output: Contribution to JournalArticleAcademicpeer-review

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

Daran-Lapujade, P. A. L., Rossell Aragort, S. L., van Gulik, W. M., Luttik, M. A., de Groot, M. J. L., Slijper, M., Heck, A. J., Daran, J. M., de Winde, J. H., Westerhoff, H. V., Pronk, J. T. & Bakker, B. M., 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, p. 15753-15758

Research output: Contribution to JournalArticleAcademicpeer-review

Saccharomyces cerevisiae
Gene Expression
Enzymes
2006

Energy metabolism and its compartmentation in Trypanosoma brucei.

van Hellemond, J. J., Bakker, B. M. & Tielens, A. G. M., 2006, In : Advances in Microbial Physiology. 50, p. 199-226

Research output: Contribution to JournalArticleAcademicpeer-review

The mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase of Trypanosomatidae and the glycocomal redox balance of insect stages of Trypanosoma brucei and Leishmania spp.

Guerra, D. G., Decottignies, A., Bakker, B. M. & Michels, P. A. M., 2006, In : Molecular and Biochemical Parasitology. 149, p. 155-169 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Trypanosomatina
Microbodies
Trypanosoma brucei brucei
Leishmania
Oxidation-Reduction

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

Bruggeman, F. J., de Haan, J., Hardin, H. M., Bouwman, J. G., Rossell Aragort, S. L., van Eunen, K., Bakker, B. M. & Westerhoff, H. V., Sep 2006, In : Systems Biology. 153, 5, p. 318-322 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Enzymes
Enzyme inhibition
Enzyme kinetics
Transcription
Metabolism

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

Rossell, S., van der Weijden, C. C., Lindenbergh, P. A., van Tuijl, J. H., Francke, C., Bakker, B. M. & Westerhoff, H. V., 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, p. 2166-2171 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

starvation
Saccharomyces cerevisiae
enzyme activity
gene expression
nutrients
2005

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

Rossell Aragort, S. L., van der Weijden, C. C., Kruckeberg, A. L., Bakker, B. M. & Westerhoff, H. V., 2005, In : FEMS Yeast Research. 5, p. 611-619 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Starvation
Saccharomyces cerevisiae
Nitrogen
Carbon
Glucose

Training of yeast cell dynamics

Reijenga, C. A., Bakker, B. M., van der Weijden, C. C. & Westerhoff, H. V., 2005, In : The FEBS Journal. 272, p. 1616-1624 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Yeast
Yeasts
Cells
Glucose
NAD

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

Reijenga, K. A., van Megen, Y. M. G. A., Kooi, B. W., Bakker, B. M., Snoep, J. L., van Verseveld, H. W. & Westerhoff, H. V., 2005, In : Journal of Theoretical Biology. 232, p. 385-398

Research output: Contribution to JournalArticleAcademicpeer-review

Yeast
oscillation
Yeasts
Enzymes
Oscillation
2002

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

Koefoed, S., Otten, M. F., Koebmann, B. J., Bruggeman, F. J., Bakker, B. M., Snoep, J. L., Krab, K., van Spanning, R. J. M., van Verseveld, H. W., Jensen, P. R., Koster, J. G. & Westerhoff, H. V., 2002, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1555, p. 75-82

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Energy Metabolism
Engines
Growth
Electrons
Gene expression

DNA supercoiling by gyrase is linked to nucleoid compaction.

Stuger, J. R., Woldringh, C. L., van der Weijden, C. C., Vischer, N. O. E., Bakker, B. M., van Spanning, R. J. M., Snoep, J. L. & Westerhoff, H. V., 2002, In : Molecular Biology Reports. 29, p. 79-82

Research output: Contribution to JournalArticleAcademicpeer-review

DNA Gyrase
DNA
Chloramphenicol
Cellular Structures
Chromosomes

Metabolic engineering of glycerol production in Saccharomyces cerevisiae.

Overkamp, K. M., Bakker, B. M., Kotter, P., Luttik, M. A. H., van Dijken, J. P. & Pronk, J. T., 2002, In : Applied and Environmental Microbiology. 68, p. 2814-2821 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

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

Albers, E., Bakker, B. M. & Gustafsson, L., 2002, In : Molecular Biology Reports. 29, p. 119-123

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Saccharomyces cerevisiae
Glycerol
Ethanol
Glucose

Network-based selectivity of antiparasitic inhibitors.

Bakker, B. M., Assmus, H. E., Bruggeman, F. J., Haanstra, J. R., Klipp, E. & Westerhoff, H. V., 2002, In : Molecular Biology Reports. 29, p. 1-5

Research output: Contribution to JournalArticleAcademicpeer-review

The use of kinetic modeling and differential control analysis for understanding regulation of fermentative capacity in baker's yeast.

Rossell Aragort, S. L., van der Weijden, C. C., Kruckeberg, A. L., Bakker, B. M. & Westerhoff, H. V., 2002, In : Molecular Biology Reports. 29, p. 225-258

Research output: Contribution to JournalArticleAcademicpeer-review

Two mechanisms for oxidation of cytosolic NADPH by Kluyveromyces lactis mitochondria.

Overkamp, K. M., Bakker, B. M., Steensma, H. Y., van Dijken, J. P. & Pronk, J. T., 2002, In : Yeast. 19, p. 813-824 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Kluyveromyces
Mitochondria
NADP
Glucose
Oxidation