prof. dr. F.J. Bruggeman

prof. dr.

20002019
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Research Output 2000 2019

2019

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
strength (mechanics)
glucose
mutation
chemostat
fitness

Physical biology of GPCR signalling dynamics inferred from fluorescence spectroscopy and imaging

Chavez-Abiega, S., Goedhart, J. & Bruggeman, F. J., 1 Apr 2019, In : Current Opinion in Structural Biology. 55, p. 204-211 8 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Optical Imaging
Fluorescence Spectrometry
G-Protein-Coupled Receptors
GTP-Binding Proteins
Carrier Proteins

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

de Groot, D. H., van Boxtel, C., Planque, R., Bruggeman, F. J. & Teusink, B., 11 Mar 2019, In : PLoS Computational Biology. 15, 3, p. 1-24 24 p., e1006858.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
biochemical pathways
Pathway
enzyme
Fluxes
2018

Balance on many scales: growth and gene expression in Bacillus subtilis

Nordholt, N., 2018, 118 p.

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

Open Access
File

Constraint-based models of microbial physiology: Surprisingly versatile

Teusink, B., Planqué, B., Molenaar, D. & Bruggeman, F., 1 Jan 2018, 10th International Conference on Simulation and Modelling in the Food and Bio-Industry 2018, FOODSIM 2018. Eurosis, p. 5-10 6 p.

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

microbial physiology
Physiology
Fluxes
Microbiological Phenomena
Growth

Editorial overview: Special Section: Single cell systems biology

Bruggeman, F. J. & Swain, P., Apr 2018, In : Current Opinion in Systems Biology. 8, p. vi-vi 1 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

Maintaining maximal metabolic flux by gene expression control

Planqué, R., Hulshof, J., Teusink, B., Hendriks, J. C. & Bruggeman, F. J., 20 Sep 2018, In : PLoS Computational Biology. 14, 9, p. 1-20 20 p., e1006412.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolites
Metabolic Networks and Pathways
Gene expression
Gene Expression
gene expression

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Wortel, M. T., Noor, E., Ferris, M., Bruggeman, F. J. & Liebermeister, W., 16 Feb 2018, In : PLoS Computational Biology. 14, 2, e1006010.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
variable costs
microbial growth
Enzymes
Trade-offs
enzyme

Understanding start-up problems in yeast glycolysis

Overal, G. B., Teusink, B., Bruggeman, F. J., Hulshof, J. & Planqué, R., May 2018, In : Mathematical Biosciences. 299, May, p. 117-126 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Start-up
glycolysis
Yeast
Yeasts
2017

Effects of growth rate and promoter activity on single-cell protein expression

Nordholt, N., Van Heerden, J., Kort, R. & Bruggeman, F. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 6299.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Noise
Growth
Proteins
Biochemical Phenomena
Synthetic Genes

Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest

Bisschops, M. M. M., Luttik, M. A. H., Doerr, A., Verheijen, P. J. T., Bruggeman, F., Pronk, J. T. & Daran-Lapujade, P., 1 Jan 2017, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1864, 1, p. 231-242 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Yeasts
Growth
Batch Cell Culture Techniques
G1 Phase
Eukaryotic Cells

Maintaining maximal metabolic rates by gene expression control

Planque, R., Hulshof, J., Teusink, B., Hendriks, J. C. & Bruggeman, F. J., 9 Mar 2017, In : bioRxiv.

Research output: Contribution to JournalArticleAcademicpeer-review

Model-based quantification of metabolic interactions from dynamic microbial-community data

Hanemaaijer, M., Olivier, B. G., Röling, W. F. M., Bruggeman, F. J. & Teusink, B., 1 Mar 2017, In : PLoS ONE. 12, 3, e0173183.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbial Interactions
Coculture Techniques
microbial communities
Hydrogen
Wolinella

Statistics and simulation of growth of single bacterial cells: Illustrations with B. subtilis and E. coli

Van Heerden, J. H., Kempe, H., Doerr, A., Maarleveld, T., Nordholt, N. & Bruggeman, F. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 16094.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
statistics
cells
simulation
proteins
Bacillus
Open Access
Genetic Selection
Growth
Population
2016

Constraint-based stochiometric modelling from single organisms to microbial communities.

Gottstein, W. G., Olivier, B. G., Bruggeman, F. J. & Teusink, B., 2016, In : Journal of the Royal Society Interface. 13, 124, 20160627.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Evolutionary pressures on microbial metabolic strategies in the chemostat.

Wortel, M. T., Bosdriesz, E., Teusink, B. & Bruggeman, F. J., 2016, In : Scientific Reports. 6, 29503.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Hoe je van een bacterie chocola kunt maken

Bruggeman, F. J., 2016, Amsterdam: Vrije Universiteit Amsterdam. 59 p.

Research output: Book / ReportInaugural speechProfessional

Open Access
File

Photonfluxostat: A method for light-limited batch cultivation of cyanobacteria at different, yet constant, growth rates.

Du, W., Jongbloets, J. A., Pineda Hernandez, H., Bruggeman, F. J., Hellingwerf, K. J. & Branco dos Santos, F., 2016, In : Algal research. 20, p. 118-125

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Public goods and metabolic strategies

Bachmann, H., Bruggeman, F. J., Molenaar, D., Santos, F. & Teusink, B., Jun 2016, In : Current Opinion in Microbiology. 31, p. 109-115

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Where is the bias?

Roth, S., 2016, 161 p.

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

Open Access
File
2015

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

Bosdriesz, E., Magnúsdóttir, S., Bruggeman, F. J., Teusink, B. & Molenaar, D., 2015, In : The FEBS Journal. 282, p. 2394-2407 12.

Research output: Contribution to JournalArticleAcademicpeer-review

Carrier Proteins
Substrates
Nutrients
Food
Active Biological Transport

Darwin s invisible hand

Bosdriesz, E., 2015

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

Open Access
File

Fast flux module detection using matroid theory.

Reimers, A. C., Bruggeman, F. J., Olivier, B. G. & Stougie, L., 2015, In : Journal of Computational Biology. 22, p. 414-424 5.

Research output: Contribution to JournalArticleAcademicpeer-review

Matroid
Fluxes
Metabolic Networks and Pathways
Module
Genome

Fluxes and fluctuations in biochemical models

Maarleveld, T. R., 2015

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

Open Access
File

G Protein–Coupled Receptor Signaling Networks from a Systems Perspective.

Roth, S., Kholodenko, B. N., Smit, M. J. & Bruggeman, F. J., 2015, In : Molecular Pharmacology. 88, 3, p. 604-616

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
G-Protein-Coupled Receptors
Biophysical Phenomena
Proteins
Biochemical Phenomena

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization.

Bosdriesz, E., Molenaar, D., Teusink, B. & Bruggeman, F. J., 2015, In : The FEBS Journal. 282, p. 2029-2044 10.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ribosomes
Bacteria
Escherichia coli
Growth
Ribosomal Proteins

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models.

Maarleveld, T. R., Wortel, M. T., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2015, In : PLoS Computational Biology. 7, 11, 4.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
Optimality
Genome
genome
Genes

Metabolism at Evolutionary Optimal States.

Rabbers, I., van Heerden, J. H., Nordholt, N., Bachmann, H., Teusink, B. & Bruggeman, F. J., 2015, In : Metabolites. 5, 2, p. 311-343

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

Rybakova, E. N., Bruggeman, F. J., Tomaszewska, A., Mone, M. J., Carlberg, C. & Westerhoff, H. V., 2015, In : PLoS Computational Biology. 11, 4

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ratchet
Bursting
Chromatin
Cycling
Transcription

Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic.

van Heerden, J. H., Bruggeman, F. J. & Teusink, B., 2015, In : BioEssays. 37, p. 34-45 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Multitasking
Glycolysis
Metabolic Networks and Pathways
Biosynthesis
Free energy

Silence on the relevant literature and errors in implementation.

Bastiaens, P., Birtwistle, M. R., Blüthgen, N., Bruggeman, F. J., Cho, K. H., Cosentino, C., de la Fuente, A., Hoek, J. B., Kiyatkin, A., Klamt, S., Kolch, W., Legewie, S., Mendes, P., Naka, T., Santra, T., Sontag, E., Westerhoff, H. V. & Kholodenko, B. N., 2015, In : Nature Biotechnology. 33, 4, p. 336-339

Research output: Contribution to JournalArticleAcademicpeer-review

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Hanemaaijer, M. J., Roling, W. F. M., Olivier, B. G., Khandelwal, R. A., Teusink, B. & Bruggeman, F. J., 2015, In : Frontiers in Microbiology. 6, 213.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metagenomics
Genome
Ecosystem
Theoretical Models
Occupational Health

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise.

Kempe, H., Schwabe, A., Crémazy, F., Verschure, P. J. & Bruggeman, F. J., 2015, In : Molecular Biology of the Cell. 26, p. 797-804 4.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Noise
Homeostasis
Cell Count
Cell Size
Messenger RNA

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model.

Rybakova, E. N., Tomaszewska, A., van Mourik, A., Blom, J., Westerhoff, H. V., Carlberg, C. & Bruggeman, F. J., 2015, In : Nucleic Acids Research. 43, p. 153-161 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Theoretical Models
RNA Stability
Messenger RNA
Transcription Factors
Peroxisome Proliferator-Activated Receptors
2014

A conformation-equilibrium model captures ligand-ligand interactions and ligand-baised signaling by G-protein coupled receptors.

Roth, S. & Bruggeman, F. J., 2014, In : The FEBS Journal. 281, 20, p. 4659-4671

Research output: Contribution to JournalArticleAcademicpeer-review

G-Protein-Coupled Receptors
Conformations
Ligands
Intracellular Signaling Peptides and Proteins
Cell Surface Receptors

A data integration and visualization resource for the metabolic network of synechocystis sp. PCC6803.

Maarleveld, T. R., Boele, J., Bruggeman, F. J. & Teusink, B., 2014, In : Plant Physiology. 164, p. 1111-1121

Research output: Contribution to JournalArticleAcademicpeer-review

Synechocystis sp. PCC 6803
Synechocystis
Metabolic Networks and Pathways
Systems Biology
Boidae

Contributions of cell growth and biochemical reactions to nongenetic variability of cells.

Schwabe, A. & Bruggeman, F. J., 2014, In : Biophysical Journal. 107, 2, p. 301-313

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Growth
DNA Replication
Cell Division
Noise
Cell Cycle

Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose.

van Heerden, J. H., Wortel, M. T., Bruggeman, F. J., Heijnen, J. J., Bollen, Y. J. M., Planque, R., Hulshof, J., O'Toole, T. G., Wahl, A. & Teusink, B., 2014, In : Microbial Cell. 1, 3, p. 103-106

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells.

van Heerden, J. H., Wortel, M. T., Bruggeman, F. J., Heijnen, J. J., Bollen, Y. J. M., Planque, R., Hulshof, J., O'Toole, T. G., Wahl, S. A. & Teusink, B., 2014, In : Science. 343, 6174, 1245114.

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Substrate Cycling
Energy Metabolism
Hydrolysis
Adenosine Triphosphate

Mechanistic stochastic model of histone modification pattern formation.

Annink-Groenen, L. C. M., Maarleveld, T. R., Verschure, P. J. & Bruggeman, F. J., 2014, In : Epigenetics & Chromatin. 7, p. 30

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Histone Code
Chromatin
Gene Expression Regulation
Genes
Nucleosomes

Metabolic states with maximal specific rate carry flux through an elementary flux mode.

Wortel, M. T., Peters, H., Hulshof, J., Teusink, B. & Bruggeman, F. J., 2014, In : The FEBS Journal. 28, p. 1547-1555

Research output: Contribution to JournalArticleAcademicpeer-review

Genes
Metabolic Networks and Pathways
Fluxes
Genome
Enzyme kinetics

Non-genetic cell-to-cell variability: theory and experiments

Schwabe, A., 2014

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

Open Access
File

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network.

Kolodkin, A., Sahin, N., Phillips, A., Hood, S. R., Bruggeman, F. J., Westerhoff, H. V. & Plant, N., 2014, In : Nature Communications. 4

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cytoplasmic and Nuclear Receptors
Hydrocortisone
optimization
Biological Adaptation
affinity

Stochastic simulation of prokaryotic two component signaling indicates stochasticity-induced active-locking and growth rate dependent bistability.

Wei, K., Moinat, M., Maarleveld, T. R. & Bruggeman, F. J., 2014, In : Molecular BioSystems. 10, 9, p. 2338-2346

Research output: Contribution to JournalArticleAcademicpeer-review

Growth
Cell Division
Signal Transduction
Gene Expression
Population

Understanding bistability in yeast glycolysis using general properties of metabolic pathways.

Planque, R., Bruggeman, F. J., Teusink, B. & Hulshof, J., 2014, In : Mathematical Biosciences. 7492, p. 33-42

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Bistability
glycolysis
Metabolic Networks and Pathways
Yeast
2013

Basic concepts and principles of stoichiometric modeling of metabolic networks.

Maarleveld, T. R., Khandelwal, R. A., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2013, In : Biotechnology Journal. 8, 9, p. 997-1008

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
Maintenance
Growth

Community flux balance analysis for microbial consortia at balanced growth

Khandelwal, R. A., Olivier, B. G., Roling, W. F. M., Teusink, B. & Bruggeman, F. J., 2013, In : PLoS ONE. 8, 5

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbial Consortia
microbial communities
Fluxes
microorganisms
Growth

Design Principles of The Regulation of Biological Networks

Berkhout, J., 2013, 157 p.

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

Open Access
File

Exploration of the spontaneous fluctuating activity of single enzyme molecules

Schwabe, A., Maarleveld, T. R. & Bruggeman, F. J., 2013, In : FEBS Letters. 587, 17, p. 2744-2752

Research output: Contribution to JournalArticleAcademicpeer-review

Molecules
Enzymes
Enzyme activity
Enzyme kinetics
Transcription