dr. B.M. Bakker

dr.

19982017
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Research Output 1998 2017

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
2016

Attacking Blood-Borne Parasites with Mathematics

van Niekerk, D. D., Penkler, G. P., du Toit, F., Snoep, J. L., Bakker, B. M. & Haanstra, J. R., 2016, Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery. Muller, S., Cerdan, R., Radulescu, O. & Selzer, P. (eds.). 1 ed. Wiley-VCH Verlag GmbH & Co. KGaA, Vol. 7. p. 513 541 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

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

Achcar, F., Fadda, A., Haanstra, J. R., Kerkhoven, E. J., Kim, D. H., Leroux, A. E., Papmarkou, T., Rojas, F., Bakker, B. M., Barrett, M. P., Clayton, C., Girolami, M., Krauth-Siegel, R. L., Matthews, K. R. & Breitling, R., 2014, Advance in microbial physiology. Poole, R. K. (ed.). Elsevier Ltd, p. 115-143

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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

Enzyme kinetics for systems biology when, why and how

Adamczyk, M., van Eunen, K., Bakker, B. M. & Westerhoff, H. V., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 233-257 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

From silicon cell to silicon human.

Westerhoff, H. V., Verma, M., Bruggeman, F. J., Kolodkin, A. N., Swat, M., Hayes, N., Nardelli, M., Bakker, B. M. & Snoep, J. L., 2011, BetaSys, Stystems Biology 2. Booss-Bavrbek, B., Klosgen, B., Larsen, J., Pociot, F. & Renstrom, E. (eds.). Springer Science + Business Media., p. 439-460

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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

Quantitative analysis of flux regulation through hierarchical regulation analysis.

van Eunen, K., Rossell, S., Bouwman, J., Westerhoff, H. V. & Bakker, B. M., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 571-595 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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 multifarious and dynamic regulation of the living cell

van Eunen, K., 2010, Enschede: Gildeprint Drukkerijen. 207 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

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

The use of in vivo-like enzyme kinetics in a computational model of yeast glycolysis.

van Eunen, K., Kiewiet, J. A. L., Westerhoff, H. V. & Bakker, B. M., 2010, Experimental standard conditions of enzyme characterizations.. Kettner, C. & Hicks, M. G. (eds.). Rudesheim/Rhein, Germany: Beilstein Institut, p. 165-180 (September 13-16, 2009).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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

The power of network-based drug design and the interplay between metabolism and gene expression in Trypanosoma brucei

Haanstra, J. R., 2009, 271 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

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

A kinetic model as a tool to understand the response of Saccharomyces cerevisiae to heat exposure.

Mensonides, F. I. C., Bakker, B. M., Brul, S., Hellingwerf, K. J. & Teixeira de Mattos, M. J., 2007, Modelling microorganisms in food.. Brul, S., van Gerwen, S. & Zwietering, M. (eds.). Cambridge UK: Woodhead Publishing Limited, p. 228-245

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Standardization and 'In-Vivo'-like enzyme activity measurements in Yeast.

Bouwman, J., van Eunen, K., Tuzun, I., Postmus, J., Canelas, A., van der Brink, J., Lindenbergh, P. A., Teixeira de Mattos, M. J., Smits, G. J., Daran-Lapujade, P. A. L., van Gulik, W. M., van Spanning, R. J. M., Heijnen, J. J., de Winde, J. H., Brul, S., Westerhoff, H. V. & Bakker, B. M., 2007, Experimental standard conditions of enzyme characterization.. Hicks, M. G. & Kettner, C. (eds.). Frankfurt Germany: Beilstein-Institut, p. 11-20 (vol 2).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology and the reconstruction of the Cell: from molecular components to integral function.

Bruggeman, F. J., Rossell Aragort, S. L., van Eunen, K., Bouwman, J., Westerhoff, H. V. & Bakker, B. M., 2007, Subcellular fractionation and proteomics.. Bertrand, E. & Faupel, M. (eds.). Dordrecht The Netherlands: Springer, p. 239-262

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Unravelling the complexity of flux regulation: New insights through the quantitative description of regulatory processes

Rossell Aragort, S. L., 2007, 128 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File
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

Exploiting metabolic and gene-expression networks for drug design.

Haanstra, J. R., van Tuijl, J. H., van Nuland, R., Bouwman, J., Albert, M. A., Michels, P. A. M., Holzhutter, H. G., Westerhoff, H. V. & Bakker, B. M., 2006, Proceedings of the 11 th international congress of parasitology. Medimond, p. 91-96

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review