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

Price CE, Branco Dos Santos F, Hesseling A, Uusitalo JJ, Bachmann H, Benavente V, Goel A, Berkhout J, Bruggeman FJ, Marrink SJ, Montalban-Lopez M, de Jong A, Kok J, Molenaar D, Poolman B, Teusink B, Kuipers OP.

BMC Evol Biol. 2019 Jan 10;19(1):15. doi: 10.1186/s12862-018-1331-x.


Maintaining maximal metabolic flux by gene expression control.

Planqué R, Hulshof J, Teusink B, Hendriks JC, Bruggeman FJ.

PLoS Comput Biol. 2018 Sep 20;14(9):e1006412. doi: 10.1371/journal.pcbi.1006412. eCollection 2018 Sep.


Understanding start-up problems in yeast glycolysis.

Overal GB, Teusink B, Bruggeman FJ, Hulshof J, Planqué R.

Math Biosci. 2018 May;299:117-126. doi: 10.1016/j.mbs.2018.03.007. Epub 2018 Mar 15.


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

Wortel MT, Noor E, Ferris M, Bruggeman FJ, Liebermeister W.

PLoS Comput Biol. 2018 Feb 16;14(2):e1006010. doi: 10.1371/journal.pcbi.1006010. eCollection 2018 Feb.


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

van Heerden JH, Kempe H, Doerr A, Maarleveld T, Nordholt N, Bruggeman FJ.

Sci Rep. 2017 Nov 23;7(1):16094. doi: 10.1038/s41598-017-15895-4.


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

Nordholt N, van Heerden J, Kort R, Bruggeman FJ.

Sci Rep. 2017 Jul 24;7(1):6299. doi: 10.1038/s41598-017-05871-3.


Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments.

van Boxtel C, van Heerden JH, Nordholt N, Schmidt P, Bruggeman FJ.

J R Soc Interface. 2017 Jul;14(132). pii: 20170141. doi: 10.1098/rsif.2017.0141. Review.


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

Hanemaaijer M, Olivier BG, Röling WF, Bruggeman FJ, Teusink B.

PLoS One. 2017 Mar 9;12(3):e0173183. doi: 10.1371/journal.pone.0173183. eCollection 2017.


Evolutionary pressures on microbial metabolic strategies in the chemostat.

Wortel MT, Bosdriesz E, Teusink B, Bruggeman FJ.

Sci Rep. 2016 Jul 6;6:29503. doi: 10.1038/srep29503.


Public goods and metabolic strategies.

Bachmann H, Bruggeman FJ, Molenaar D, Branco Dos Santos F, Teusink B.

Curr Opin Microbiol. 2016 Jun;31:109-115. doi: 10.1016/j.mib.2016.03.007. Epub 2016 Apr 4. Review.


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

Gottstein W, Olivier BG, Bruggeman FJ, Teusink B.

J R Soc Interface. 2016 Nov;13(124). pii: 20160627. doi: 10.1098/rsif.2016.0627. Review.


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

Roth S, Kholodenko BN, Smit MJ, Bruggeman FJ.

Mol Pharmacol. 2015 Sep;88(3):604-16. doi: 10.1124/mol.115.100057. Epub 2015 Jul 10. Review.


Metabolism at evolutionary optimal States.

Rabbers I, van Heerden JH, Nordholt N, Bachmann H, Teusink B, Bruggeman FJ.

Metabolites. 2015 Jun 2;5(2):311-43. doi: 10.3390/metabo5020311. Review.


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

Rybakova KN, Bruggeman FJ, Tomaszewska A, Moné MJ, Carlberg C, Westerhoff HV.

PLoS Comput Biol. 2015 Apr 24;11(4):e1004236. doi: 10.1371/journal.pcbi.1004236. eCollection 2015 Apr.


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

Hanemaaijer M, Röling WF, Olivier BG, Khandelwal RA, Teusink B, Bruggeman FJ.

Front Microbiol. 2015 Mar 19;6:213. doi: 10.3389/fmicb.2015.00213. eCollection 2015.


Silence on the relevant literature and errors in implementation.

Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN.

Nat Biotechnol. 2015 Apr;33(4):336-9. doi: 10.1038/nbt.3185. No abstract available.


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

Maarleveld TR, Wortel MT, Olivier BG, Teusink B, Bruggeman FJ.

PLoS Comput Biol. 2015 Apr 7;11(4):e1004166. doi: 10.1371/journal.pcbi.1004166. eCollection 2015 Apr.


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

Bosdriesz E, Magnúsdóttir S, Bruggeman FJ, Teusink B, Molenaar D.

FEBS J. 2015 Jun;282(12):2394-407. doi: 10.1111/febs.13289. Epub 2015 Apr 24.


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

Bosdriesz E, Molenaar D, Teusink B, Bruggeman FJ.

FEBS J. 2015 May;282(10):2029-44. doi: 10.1111/febs.13258. Epub 2015 Mar 26.


Fast flux module detection using matroid theory.

Reimers AC, Bruggeman FJ, Olivier BG, Stougie L.

J Comput Biol. 2015 May;22(5):414-24. doi: 10.1089/cmb.2014.0141. Epub 2015 Jan 7.


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

Kempe H, Schwabe A, Crémazy F, Verschure PJ, Bruggeman FJ.

Mol Biol Cell. 2015 Feb 15;26(4):797-804. doi: 10.1091/mbc.E14-08-1296. Epub 2014 Dec 17.


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

Rybakova KN, Tomaszewska A, van Mourik S, Blom J, Westerhoff HV, Carlberg C, Bruggeman FJ.

Nucleic Acids Res. 2015 Jan;43(1):153-61. doi: 10.1093/nar/gku1272. Epub 2014 Dec 3.


Mechanistic stochastic model of histone modification pattern formation.

Anink-Groenen LC, Maarleveld TR, Verschure PJ, Bruggeman FJ.

Epigenetics Chromatin. 2014 Oct 27;7(1):30. doi: 10.1186/1756-8935-7-30. eCollection 2014.


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

van Heerden JH, Bruggeman FJ, Teusink B.

Bioessays. 2015 Jan;37(1):34-45. doi: 10.1002/bies.201400108. Epub 2014 Oct 28. Review.


Single yeast cells vary in transcription activity not in delay time after a metabolic shift.

Schwabe A, Bruggeman FJ.

Nat Commun. 2014 Sep 2;5:4798. doi: 10.1038/ncomms5798.


A conformation-equilibrium model captures ligand-ligand interactions and ligand-biased signalling by G-protein coupled receptors.

Roth S, Bruggeman FJ.

FEBS J. 2014 Oct;281(20):4659-71. doi: 10.1111/febs.12970. Epub 2014 Sep 17.


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

Schwabe A, Bruggeman FJ.

Biophys J. 2014 Jul 15;107(2):301-313. doi: 10.1016/j.bpj.2014.05.004.


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

Planqué R, Bruggeman FJ, Teusink B, Hulshof J.

Math Biosci. 2014 Sep;255:33-42. doi: 10.1016/j.mbs.2014.06.006. Epub 2014 Jun 21.


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

Wei K, Moinat M, Maarleveld TR, Bruggeman FJ.

Mol Biosyst. 2014 Jul 29;10(9):2338-46. doi: 10.1039/c4mb00264d.


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

Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJ, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B.

Microb Cell. 2014 Feb 20;1(3):103-106. doi: 10.15698/mic2014.01.133.


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

Wortel MT, Peters H, Hulshof J, Teusink B, Bruggeman FJ.

FEBS J. 2014 Mar;281(6):1547-55. doi: 10.1111/febs.12722. Epub 2014 Feb 12.


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

van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJ, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B.

Science. 2014 Feb 28;343(6174):1245114. doi: 10.1126/science.1245114. Epub 2014 Jan 16.


A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.

Maarleveld TR, Boele J, Bruggeman FJ, Teusink B.

Plant Physiol. 2014 Mar;164(3):1111-21. doi: 10.1104/pp.113.224394. Epub 2014 Jan 8.


StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes.

Maarleveld TR, Olivier BG, Bruggeman FJ.

PLoS One. 2013 Nov 18;8(11):e79345. doi: 10.1371/journal.pone.0079345. eCollection 2013.


Basic concepts and principles of stoichiometric modeling of metabolic networks.

Maarleveld TR, Khandelwal RA, Olivier BG, Teusink B, Bruggeman FJ.

Biotechnol J. 2013 Sep;8(9):997-1008. doi: 10.1002/biot.201200291. Epub 2013 Jul 29. Review.


Exploration of the spontaneous fluctuating activity of single enzyme molecules.

Schwabe A, Maarleveld TR, Bruggeman FJ.

FEBS Lett. 2013 Sep 2;587(17):2744-52. doi: 10.1016/j.febslet.2013.07.005. Epub 2013 Jul 12.


Community flux balance analysis for microbial consortia at balanced growth.

Khandelwal RA, Olivier BG, Röling WF, Teusink B, Bruggeman FJ.

PLoS One. 2013 May 31;8(5):e64567. doi: 10.1371/journal.pone.0064567. Print 2013.


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

Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N.

Nat Commun. 2013;4:1792. doi: 10.1038/ncomms2799.


How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

Berkhout J, Bosdriesz E, Nikerel E, Molenaar D, de Ridder D, Teusink B, Bruggeman FJ.

Genetics. 2013 Jun;194(2):505-12. doi: 10.1534/genetics.113.150631. Epub 2013 Mar 27.


Gene network requirements for regulation of metabolic gene expression to a desired state.

Berkhout J, Teusink B, Bruggeman FJ.

Sci Rep. 2013;3:1417. doi: 10.1038/srep01417.


Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico.

Quinton-Tulloch MJ, Bruggeman FJ, Snoep JL, Westerhoff HV.

FEBS J. 2013 Jan;280(1):160-73. doi: 10.1111/febs.12057. Epub 2012 Dec 7.


Transcription stochasticity of complex gene regulation models.

Schwabe A, Rybakova KN, Bruggeman FJ.

Biophys J. 2012 Sep 19;103(6):1152-61. doi: 10.1016/j.bpj.2012.07.011.


Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks.

Kelk SM, Olivier BG, Stougie L, Bruggeman FJ.

Sci Rep. 2012;2:580. doi: 10.1038/srep00580. Epub 2012 Aug 15.


What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.

Swat M, Kiełbasa SM, Polak S, Olivier B, Bruggeman FJ, Tulloch MQ, Snoep JL, Verhoeven AJ, Westerhoff HV.

Interface Focus. 2011 Feb 6;1(1):16-23. doi: 10.1098/rsfs.2010.0011. Epub 2010 Dec 8.


Optimality principles in the regulation of metabolic networks.

Berkhout J, Bruggeman FJ, Teusink B.

Metabolites. 2012 Aug 29;2(3):529-52. doi: 10.3390/metabo2030529.


How molecular competition influences fluxes in gene expression networks.

De Vos D, Bruggeman FJ, Westerhoff HV, Bakker BM.

PLoS One. 2011;6(12):e28494. doi: 10.1371/journal.pone.0028494. Epub 2011 Dec 5.


Origins of stochastic intracellular processes and consequences for cell-to-cell variability and cellular survival strategies.

Schwabe A, Dobrzyński M, Rybakova K, Verschure P, Bruggeman FJ.

Methods Enzymol. 2011;500:597-625. doi: 10.1016/B978-0-12-385118-5.00028-1.


Emergence of the silicon human and network targeting drugs.

Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno-Sanchez R, Yilmaz N, Bakker BM, Snoep JL, Balling R, Westerhoff HV.

Eur J Pharm Sci. 2012 Jul 16;46(4):190-7. doi: 10.1016/j.ejps.2011.06.006. Epub 2011 Jun 16.


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

Kolodkin AN, Bruggeman FJ, Plant N, Moné MJ, Bakker BM, Campbell MJ, van Leeuwen JP, Carlberg C, Snoep JL, Westerhoff HV.

Mol Syst Biol. 2010 Dec 21;6:446. doi: 10.1038/msb.2010.102.


AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

Boogerd FC, Ma H, Bruggeman FJ, van Heeswijk WC, García-Contreras R, Molenaar D, Krab K, Westerhoff HV.

FEBS Lett. 2011 Jan 3;585(1):23-8. doi: 10.1016/j.febslet.2010.11.055. Epub 2010 Dec 8.

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