Publications

2017

  1. van Boxtel, C, van Heerden, JH, Nordholt, N, Schmidt, P, Bruggeman, FJ. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J R Soc Interface. 2017;14 (132):. doi: 10.1098/rsif.2017.0141. PubMed PMID:28701503 .
  2. Bachmann, H, Molenaar, D, Branco Dos Santos, F, Teusink, B. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol. Rev. 2017; :. doi: 10.1093/femsre/fux024. PubMed PMID:28633473 .
  3. Brown, DM, Okoro, S, van Gils, J, van Spanning, R, Bonte, M, Hutchings, T et al.. Comparison of landfarming amendments to improve bioremediation of petroleum hydrocarbons in Niger Delta soils. Sci. Total Environ. 2017;596-597 :284-292. doi: 10.1016/j.scitotenv.2017.04.072. PubMed PMID:28437647 .
  4. Hanemaaijer, M, Olivier, BG, Röling, WF, Bruggeman, FJ, Teusink, B. Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS ONE. 2017;12 (3):e0173183. doi: 10.1371/journal.pone.0173183. PubMed PMID:28278266 PubMed Central PMC5344373.
  5. Haanstra, JR, Gerding, A, Dolga, AM, Sorgdrager, FJH, Buist-Homan, M, du Toit, F et al.. Targeting pathogen metabolism without collateral damage to the host. Sci Rep. 2017;7 :40406. doi: 10.1038/srep40406. PubMed PMID:28084422 PubMed Central PMC5234033.
  6. Bisschops, MM, Luttik, MA, Doerr, A, Verheijen, PJ, Bruggeman, F, Pronk, JT et al.. Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest. Biochim. Biophys. Acta. 2017;1864 (1):231-242. doi: 10.1016/j.bbamcr.2016.11.002. PubMed PMID:27818273 .
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2016

  1. Cvijovic, M, Höfer, T, Aćimović, J, Alberghina, L, Almaas, E, Besozzi, D et al.. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective. NPJ Syst Biol Appl. 2016;2 :16011. doi: 10.1038/npjsba.2016.11. PubMed PMID:28725471 PubMed Central PMC5516850.
  2. Artaza, H, Chue Hong, N, Corpas, M, Corpuz, A, Hooft, R, Jimenez, RC et al.. Top 10 metrics for life science software good practices. F1000Res. 2016;5 :. doi: 10.12688/f1000research.9206.1. PubMed PMID:27635232 PubMed Central PMC5007752.
  3. Wortel, MT, Bosdriesz, E, Teusink, B, Bruggeman, FJ. Evolutionary pressures on microbial metabolic strategies in the chemostat. Sci Rep. 2016;6 :29503. doi: 10.1038/srep29503. PubMed PMID:27381431 PubMed Central PMC4933952.
  4. Antwi, EB, Haanstra, JR, Ramasamy, G, Jensen, B, Droll, D, Rojas, F et al.. Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression. BMC Genomics. 2016;17 :306. doi: 10.1186/s12864-016-2624-3. PubMed PMID:27118143 PubMed Central PMC4845500.
  5. Bachmann, H, Bruggeman, FJ, Molenaar, D, Branco Dos Santos, F, Teusink, B. Public goods and metabolic strategies. Curr. Opin. Microbiol. 2016;31 :109-15. doi: 10.1016/j.mib.2016.03.007. PubMed PMID:27054480 .
  6. Levering, J, Fiedler, T, Sieg, A, van Grinsven, KW, Hering, S, Veith, N et al.. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets. J. Biotechnol. 2016;232 :25-37. doi: 10.1016/j.jbiotec.2016.01.035. PubMed PMID:26970054 .
  7. Gottstein, W, Olivier, BG, Bruggeman, FJ, Teusink, B. Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface. 2016;13 (124):. doi: 10.1098/rsif.2016.0627. PubMed PMID:28334697 PubMed Central PMC5134014.
  8. Olivier, BG, Swat, MJ, Moné, MJ. Modeling and Simulation Tools: From Systems Biology to Systems Medicine. Methods Mol. Biol. 2016;1386 :441-63. doi: 10.1007/978-1-4939-3283-2_19. PubMed PMID:26677194 .
  9. Mania, D, Heylen, K, van Spanning, RJ, Frostegård, Å. Regulation of nitrogen metabolism in the nitrate-ammonifying soil bacterium Bacillus vireti and evidence for its ability to grow using N2 O as electron acceptor. Environ. Microbiol. 2016;18 (9):2937-50. doi: 10.1111/1462-2920.13124. PubMed PMID:26548448 .
  10. Haanstra, JR, González-Marcano, EB, Gualdrón-López, M, Michels, PA. Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites. Biochim. Biophys. Acta. 2016;1863 (5):1038-48. doi: 10.1016/j.bbamcr.2015.09.015. PubMed PMID:26384872 .
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2015

  1. Kort, R, Westerik, N, Mariela Serrano, L, Douillard, FP, Gottstein, W, Mukisa, IM et al.. A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods. Microb. Cell Fact. 2015;14 :195. doi: 10.1186/s12934-015-0370-x. PubMed PMID:26643044 PubMed Central PMC4672519.
  2. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform. 2015;12 (2):271. doi: 10.2390/biecoll-jib-2015-271. PubMed PMID:26528569 PubMed Central PMC5457286.
  3. Olivier, BG, Bergmann, FT. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J Integr Bioinform. 2015;12 (2):269. doi: 10.2390/biecoll-jib-2015-269. PubMed PMID:26528567 .
  4. Haanstra, JR, Bakker, BM. Drug target identification through systems biology. Drug Discov Today Technol. 2015;15 :17-22. doi: 10.1016/j.ddtec.2015.06.002. PubMed PMID:26464086 .
  5. Haanstra, JR, González-Marcano, EB, Gualdrón-López, M, Michels, PA. Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites. Biochim. Biophys. Acta. 2016;1863 (5):1038-48. doi: 10.1016/j.bbamcr.2015.09.015. PubMed PMID:26384872 .
  6. Roth, S, Kholodenko, BN, Smit, MJ, Bruggeman, FJ. G Protein-Coupled Receptor Signaling Networks from a Systems Perspective. Mol. Pharmacol. 2015;88 (3):604-16. doi: 10.1124/mol.115.100057. PubMed PMID:26162865 .
  7. Rabbers, I, van Heerden, JH, Nordholt, N, Bachmann, H, Teusink, B, Bruggeman, FJ et al.. Metabolism at evolutionary optimal States. Metabolites. 2015;5 (2):311-43. doi: 10.3390/metabo5020311. PubMed PMID:26042723 PubMed Central PMC4495375.
  8. Lu, P, Heineke, MH, Koul, A, Andries, K, Cook, GM, Lill, H et al.. The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress. Sci Rep. 2015;5 :10333. doi: 10.1038/srep10333. PubMed PMID:26015371 PubMed Central PMC4450806.
  9. Rybakova, KN, Bruggeman, FJ, Tomaszewska, A, Moné, MJ, Carlberg, C, Westerhoff, HV et al.. Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Comput. Biol. 2015;11 (4):e1004236. doi: 10.1371/journal.pcbi.1004236. PubMed PMID:25909187 PubMed Central PMC4409292.
  10. Hanemaaijer, M, Röling, WF, Olivier, BG, Khandelwal, RA, Teusink, B, Bruggeman, FJ et al.. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol. 2015;6 :213. doi: 10.3389/fmicb.2015.00213. PubMed PMID:25852671 PubMed Central PMC4365725.
  11. Bastiaens, P, Birtwistle, MR, Blüthgen, N, Bruggeman, FJ, Cho, KH, Cosentino, C et al.. Silence on the relevant literature and errors in implementation. Nat. Biotechnol. 2015;33 (4):336-9. doi: 10.1038/nbt.3185. PubMed PMID:25850052 .
  12. Maarleveld, TR, Wortel, MT, Olivier, BG, Teusink, B, Bruggeman, FJ. Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models. PLoS Comput. Biol. 2015;11 (4):e1004166. doi: 10.1371/journal.pcbi.1004166. PubMed PMID:25849486 PubMed Central PMC4388735.
  13. Bosdriesz, E, Magnúsdóttir, S, Bruggeman, FJ, Teusink, B, Molenaar, D. Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate. FEBS J. 2015;282 (12):2394-407. doi: 10.1111/febs.13289. PubMed PMID:25846030 .
  14. Goel, A, Eckhardt, TH, Puri, P, de Jong, A, Branco Dos Santos, F, Giera, M et al.. Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?. Mol. Microbiol. 2015;97 (1):77-92. doi: 10.1111/mmi.13012. PubMed PMID:25828364 .
  15. Alemdehy, MF, Haanstra, JR, de Looper, HW, van Strien, PM, Verhagen-Oldenampsen, J, Caljouw, Y et al.. ICL-induced miR139-3p and miR199a-3p have opposite roles in hematopoietic cell expansion and leukemic transformation. Blood. 2015;125 (25):3937-48. doi: 10.1182/blood-2014-11-612507. PubMed PMID:25778535 .
  16. Bosdriesz, E, Molenaar, D, Teusink, B, Bruggeman, FJ. How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization. FEBS J. 2015;282 (10):2029-44. doi: 10.1111/febs.13258. PubMed PMID:25754869 PubMed Central PMC4672707.
  17. Reimers, AC, Bruggeman, FJ, Olivier, BG, Stougie, L. Fast flux module detection using matroid theory. J. Comput. Biol. 2015;22 (5):414-24. doi: 10.1089/cmb.2014.0141. PubMed PMID:25565150 .
  18. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  19. Kempe, H, Schwabe, A, Crémazy, F, Verschure, PJ, Bruggeman, FJ. The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Mol. Biol. Cell. 2015;26 (4):797-804. doi: 10.1091/mbc.E14-08-1296. PubMed PMID:25518937 PubMed Central PMC4325848.
  20. Rybakova, KN, Tomaszewska, A, van Mourik, S, Blom, J, Westerhoff, HV, Carlberg, C et al.. Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Res. 2015;43 (1):153-61. doi: 10.1093/nar/gku1272. PubMed PMID:25477385 PubMed Central PMC4288170.
  21. van Heerden, JH, Bruggeman, FJ, Teusink, B. Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. Bioessays. 2015;37 (1):34-45. doi: 10.1002/bies.201400108. PubMed PMID:25350875 .
  22. Willemsen, AM, Hendrickx, DM, Hoefsloot, HC, Hendriks, MM, Wahl, SA, Teusink, B et al.. MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst. 2015;11 (1):137-45. doi: 10.1039/c4mb00510d. PubMed PMID:25315283 .
  23. Bachmann, H, Pronk, JT, Kleerebezem, M, Teusink, B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr. Opin. Biotechnol. 2015;32 :1-7. doi: 10.1016/j.copbio.2014.09.003. PubMed PMID:25269887 .
Search PubMed


2014

  1. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  2. Kempe, H, Schwabe, A, Crémazy, F, Verschure, PJ, Bruggeman, FJ. The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Mol. Biol. Cell. 2015;26 (4):797-804. doi: 10.1091/mbc.E14-08-1296. PubMed PMID:25518937 PubMed Central PMC4325848.
  3. Bergmann, FT, Adams, R, Moodie, S, Cooper, J, Glont, M, Golebiewski, M et al.. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15 :369. doi: 10.1186/s12859-014-0369-z. PubMed PMID:25494900 PubMed Central PMC4272562.
  4. Rybakova, KN, Tomaszewska, A, van Mourik, S, Blom, J, Westerhoff, HV, Carlberg, C et al.. Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Res. 2015;43 (1):153-61. doi: 10.1093/nar/gku1272. PubMed PMID:25477385 PubMed Central PMC4288170.
  5. Anink-Groenen, LC, Maarleveld, TR, Verschure, PJ, Bruggeman, FJ. Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin. 2014;7 (1):30. doi: 10.1186/1756-8935-7-30. PubMed PMID:25408711 PubMed Central PMC4234852.
  6. van Heerden, JH, Bruggeman, FJ, Teusink, B. Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. Bioessays. 2015;37 (1):34-45. doi: 10.1002/bies.201400108. PubMed PMID:25350875 .
  7. Willemsen, AM, Hendrickx, DM, Hoefsloot, HC, Hendriks, MM, Wahl, SA, Teusink, B et al.. MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst. 2015;11 (1):137-45. doi: 10.1039/c4mb00510d. PubMed PMID:25315283 .
  8. Bachmann, H, Pronk, JT, Kleerebezem, M, Teusink, B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr. Opin. Biotechnol. 2015;32 :1-7. doi: 10.1016/j.copbio.2014.09.003. PubMed PMID:25269887 .
  9. Murabito, E, Verma, M, Bekker, M, Bellomo, D, Westerhoff, HV, Teusink, B et al.. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS ONE. 2014;9 (9):e106453. doi: 10.1371/journal.pone.0106453. PubMed PMID:25268481 PubMed Central PMC4182131.
  10. Kok, J, Johansen, E, Kleerebezem, M, Teusink, B. Lactic Acid Bacteria: embarking on 30 more years of research. Microb. Cell Fact. 2014;13 Suppl 1 :I1. doi: 10.1186/1475-2859-13-S1-I1. PubMed PMID:25187380 PubMed Central PMC4155817.
  11. Schwabe, A, Bruggeman, FJ. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Nat Commun. 2014;5 :4798. doi: 10.1038/ncomms5798. PubMed PMID:25178355 .
  12. Roth, S, Bruggeman, FJ. A conformation-equilibrium model captures ligand-ligand interactions and ligand-biased signalling by G-protein coupled receptors. FEBS J. 2014;281 (20):4659-71. doi: 10.1111/febs.12970. PubMed PMID:25145284 .
  13. Boele, J, Persson, H, Shin, JW, Ishizu, Y, Newie, IS, Søkilde, R et al.. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (31):11467-72. doi: 10.1073/pnas.1317751111. PubMed PMID:25049417 PubMed Central PMC4128123.
  14. Schwabe, A, Bruggeman, FJ. Contributions of cell growth and biochemical reactions to nongenetic variability of cells. Biophys. J. 2014;107 (2):301-13. doi: 10.1016/j.bpj.2014.05.004. PubMed PMID:25028872 PubMed Central PMC4104058.
  15. Planqué, R, Bruggeman, FJ, Teusink, B, Hulshof, J. Understanding bistability in yeast glycolysis using general properties of metabolic pathways. Math Biosci. 2014;255 :33-42. doi: 10.1016/j.mbs.2014.06.006. PubMed PMID:24956444 .
  16. Wei, K, Moinat, M, Maarleveld, TR, Bruggeman, FJ. Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability. Mol Biosyst. 2014;10 (9):2338-46. doi: 10.1039/c4mb00264d. PubMed PMID:24955938 .
  17. Solopova, A, van Gestel, J, Weissing, FJ, Bachmann, H, Teusink, B, Kok, J et al.. Bet-hedging during bacterial diauxic shift. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (20):7427-32. doi: 10.1073/pnas.1320063111. PubMed PMID:24799698 PubMed Central PMC4034238.
  18. Mania, D, Heylen, K, van Spanning, RJ, Frostegård, A. The nitrate-ammonifying and nosZ-carrying bacterium Bacillus vireti is a potent source and sink for nitric and nitrous oxide under high nitrate conditions. Environ. Microbiol. 2014;16 (10):3196-210. doi: 10.1111/1462-2920.12478. PubMed PMID:24708037 .
  19. Heerden, JH, Wortel, MT, Bruggeman, FJ, Heijnen, JJ, Bollen, YJ, Planqué, R et al.. Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose. Microb Cell. 2014;1 (3):103-106. doi: 10.15698/mic2014.01.133. PubMed PMID:28357229 PubMed Central PMC5349229.
  20. Wortel, MT, Peters, H, Hulshof, J, Teusink, B, Bruggeman, FJ. Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS J. 2014;281 (6):1547-55. doi: 10.1111/febs.12722. PubMed PMID:24460934 .
  21. van Heerden, JH, Wortel, MT, Bruggeman, FJ, Heijnen, JJ, Bollen, YJ, Planqué, R et al.. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science. 2014;343 (6174):1245114. doi: 10.1126/science.1245114. PubMed PMID:24436182 .
  22. Maarleveld, TR, Boele, J, Bruggeman, FJ, Teusink, B. A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. Plant Physiol. 2014;164 (3):1111-21. doi: 10.1104/pp.113.224394. PubMed PMID:24402049 PubMed Central PMC3938606.
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2013

  1. Maarleveld, TR, Olivier, BG, Bruggeman, FJ. StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS ONE. 2013;8 (11):e79345. doi: 10.1371/journal.pone.0079345. PubMed PMID:24260203 PubMed Central PMC3832486.
  2. Bachmann, H, Fischlechner, M, Rabbers, I, Barfa, N, Branco dos Santos, F, Molenaar, D et al.. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl. Acad. Sci. U.S.A. 2013;110 (35):14302-7. doi: 10.1073/pnas.1308523110. PubMed PMID:23940318 PubMed Central PMC3761572.
  3. Maarleveld, TR, Khandelwal, RA, Olivier, BG, Teusink, B, Bruggeman, FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J. 2013;8 (9):997-1008. doi: 10.1002/biot.201200291. PubMed PMID:23893965 PubMed Central PMC4671265.
  4. Schwabe, A, Maarleveld, TR, Bruggeman, FJ. Exploration of the spontaneous fluctuating activity of single enzyme molecules. FEBS Lett. 2013;587 (17):2744-52. doi: 10.1016/j.febslet.2013.07.005. PubMed PMID:23850890 .
  5. Khandelwal, RA, Olivier, BG, Röling, WF, Teusink, B, Bruggeman, FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS ONE. 2013;8 (5):e64567. doi: 10.1371/journal.pone.0064567. PubMed PMID:23741341 PubMed Central PMC3669319.
  6. Kolodkin, A, Sahin, N, Phillips, A, Hood, SR, Bruggeman, FJ, Westerhoff, HV et al.. Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nat Commun. 2013;4 :1792. doi: 10.1038/ncomms2799. PubMed PMID:23653204 PubMed Central PMC3644104.
  7. Abeln, S, Molenaar, D, Feenstra, KA, Hoefsloot, HC, Teusink, B, Heringa, J et al.. Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds. Brief. Bioinformatics. 2013;14 (5):589-98. doi: 10.1093/bib/bbt023. PubMed PMID:23603092 .
  8. Berkhout, J, Bosdriesz, E, Nikerel, E, Molenaar, D, de Ridder, D, Teusink, B et al.. How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. Genetics. 2013;194 (2):505-12. doi: 10.1534/genetics.113.150631. PubMed PMID:23535382 PubMed Central PMC3664859.
  9. Berkhout, J, Teusink, B, Bruggeman, FJ. Gene network requirements for regulation of metabolic gene expression to a desired state. Sci Rep. 2013;3 :1417. doi: 10.1038/srep01417. PubMed PMID:23475326 PubMed Central PMC3593220.
  10. Branco dos Santos, F, de Vos, WM, Teusink, B. Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr. Opin. Biotechnol. 2013;24 (2):200-6. doi: 10.1016/j.copbio.2012.11.003. PubMed PMID:23200025 .
  11. Quinton-Tulloch, MJ, Bruggeman, FJ, Snoep, JL, Westerhoff, HV. Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J. 2013;280 (1):160-73. doi: 10.1111/febs.12057. PubMed PMID:23121761 .
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2012

  1. Branco dos Santos, F, de Vos, WM, Teusink, B. Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr. Opin. Biotechnol. 2013;24 (2):200-6. doi: 10.1016/j.copbio.2012.11.003. PubMed PMID:23200025 .
  2. Quinton-Tulloch, MJ, Bruggeman, FJ, Snoep, JL, Westerhoff, HV. Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J. 2013;280 (1):160-73. doi: 10.1111/febs.12057. PubMed PMID:23121761 .
  3. Schwabe, A, Rybakova, KN, Bruggeman, FJ. Transcription stochasticity of complex gene regulation models. Biophys. J. 2012;103 (6):1152-61. doi: 10.1016/j.bpj.2012.07.011. PubMed PMID:22995487 PubMed Central PMC3446772.
  4. Goel, A, Wortel, MT, Molenaar, D, Teusink, B. Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol. Lett. 2012;34 (12):2147-60. doi: 10.1007/s10529-012-1038-9. PubMed PMID:22936303 PubMed Central PMC3487007.
  5. Kelk, SM, Olivier, BG, Stougie, L, Bruggeman, FJ. Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep. 2012;2 :580. doi: 10.1038/srep00580. PubMed PMID:22896812 PubMed Central PMC3419370.
  6. Nikerel, E, Berkhout, J, Hu, F, Teusink, B, Reinders, MJ, de Ridder, D et al.. Understanding regulation of metabolism through feasibility analysis. PLoS ONE. 2012;7 (7):e39396. doi: 10.1371/journal.pone.0039396. PubMed PMID:22808034 PubMed Central PMC3392259.
  7. Hendrickx, DM, Hoefsloot, HC, Hendriks, MM, Vis, DJ, Canelas, AB, Teusink, B et al.. Inferring differences in the distribution of reaction rates across conditions. Mol Biosyst. 2012;8 (9):2415-23. doi: 10.1039/c2mb25015b. PubMed PMID:22782002 .
  8. Solopova, A, Bachmann, H, Teusink, B, Kok, J, Neves, AR, Kuipers, OP et al.. A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl. Environ. Microbiol. 2012;78 (16):5612-21. doi: 10.1128/AEM.00455-12. PubMed PMID:22660716 PubMed Central PMC3406120.
  9. Levering, J, Musters, MW, Bekker, M, Bellomo, D, Fiedler, T, de Vos, WM et al.. Role of phosphate in the central metabolism of two lactic acid bacteria--a comparative systems biology approach. FEBS J. 2012;279 (7):1274-90. doi: 10.1111/j.1742-4658.2012.08523.x. PubMed PMID:22325620 .
  10. Boele, J, Olivier, BG, Teusink, B. FAME, the Flux Analysis and Modeling Environment. BMC Syst Biol. 2012;6 :8. doi: 10.1186/1752-0509-6-8. PubMed PMID:22289213 PubMed Central PMC3317868.
  11. Berkhout, J, Bruggeman, FJ, Teusink, B. Optimality principles in the regulation of metabolic networks. Metabolites. 2012;2 (3):529-52. doi: 10.3390/metabo2030529. PubMed PMID:24957646 PubMed Central PMC3901211.
  12. Bergaust, L, van Spanning, RJ, Frostegård, A, Bakken, LR. Expression of nitrous oxide reductase in Paracoccus denitrificans is regulated by oxygen and nitric oxide through FnrP and NNR. Microbiology (Reading, Engl.). 2012;158 (Pt 3):826-34. doi: 10.1099/mic.0.054148-0. PubMed PMID:22174385 PubMed Central PMC3541799.
  13. Goel, A, Santos, F, Vos, WM, Teusink, B, Molenaar, D. Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl. Environ. Microbiol. 2012;78 (1):134-43. doi: 10.1128/AEM.05276-11. PubMed PMID:22020503 PubMed Central PMC3255609.
  14. Kolodkin, A, Boogerd, FC, Plant, N, Bruggeman, FJ, Goncharuk, V, Lunshof, J et al.. Emergence of the silicon human and network targeting drugs. Eur J Pharm Sci. 2012;46 (4):190-7. doi: 10.1016/j.ejps.2011.06.006. PubMed PMID:21704158 .
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2011

  1. Swat, M, Kiełbasa, SM, Polak, S, Olivier, B, Bruggeman, FJ, Tulloch, MQ et al.. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform. Interface Focus. 2011;1 (1):16-23. doi: 10.1098/rsfs.2010.0011. PubMed PMID:22419971 PubMed Central PMC3262244.
  2. Bergaust, L, van Spanning, RJ, Frostegård, A, Bakken, LR. Expression of nitrous oxide reductase in Paracoccus denitrificans is regulated by oxygen and nitric oxide through FnrP and NNR. Microbiology (Reading, Engl.). 2012;158 (Pt 3):826-34. doi: 10.1099/mic.0.054148-0. PubMed PMID:22174385 PubMed Central PMC3541799.
  3. De Vos, D, Bruggeman, FJ, Westerhoff, HV, Bakker, BM. How molecular competition influences fluxes in gene expression networks. PLoS ONE. 2011;6 (12):e28494. doi: 10.1371/journal.pone.0028494. PubMed PMID:22163025 PubMed Central PMC3230629.
  4. Teusink, B, Bachmann, H, Molenaar, D. Systems biology of lactic acid bacteria: a critical review. Microb. Cell Fact. 2011;10 Suppl 1 :S11. doi: 10.1186/1475-2859-10-S1-S11. PubMed PMID:21995498 PubMed Central PMC3231918.
  5. Goel, A, Santos, F, Vos, WM, Teusink, B, Molenaar, D. Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl. Environ. Microbiol. 2012;78 (1):134-43. doi: 10.1128/AEM.05276-11. PubMed PMID:22020503 PubMed Central PMC3255609.
  6. Schwabe, A, Dobrzyński, M, Rybakova, K, Verschure, P, Bruggeman, FJ. Origins of stochastic intracellular processes and consequences for cell-to-cell variability and cellular survival strategies. Meth. Enzymol. 2011;500 :597-625. doi: 10.1016/B978-0-12-385118-5.00028-1. PubMed PMID:21943916 .
  7. Santos, F, Boele, J, Teusink, B. A practical guide to genome-scale metabolic models and their analysis. Meth. Enzymol. 2011;500 :509-32. doi: 10.1016/B978-0-12-385118-5.00024-4. PubMed PMID:21943912 .
  8. Santos, F, Spinler, JK, Saulnier, DM, Molenaar, D, Teusink, B, de Vos, WM et al.. Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis. Microb. Cell Fact. 2011;10 :55. doi: 10.1186/1475-2859-10-55. PubMed PMID:21777454 PubMed Central PMC3162504.
  9. Kolodkin, A, Boogerd, FC, Plant, N, Bruggeman, FJ, Goncharuk, V, Lunshof, J et al.. Emergence of the silicon human and network targeting drugs. Eur J Pharm Sci. 2012;46 (4):190-7. doi: 10.1016/j.ejps.2011.06.006. PubMed PMID:21704158 .
  10. Saulnier, DM, Santos, F, Roos, S, Mistretta, TA, Spinler, JK, Molenaar, D et al.. Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS ONE. 2011;6 (4):e18783. doi: 10.1371/journal.pone.0018783. PubMed PMID:21559529 PubMed Central PMC3084715.
  11. Boogerd, FC, Ma, H, Bruggeman, FJ, van Heeswijk, WC, García-Contreras, R, Molenaar, D et al.. 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. FEBS Lett. 2011;585 (1):23-8. doi: 10.1016/j.febslet.2010.11.055. PubMed PMID:21134373 .
  12. van Berlo, RJ, de Ridder, D, Daran, JM, Daran-Lapujade, PA, Teusink, B, Reinders, MJ et al.. Predicting metabolic fluxes using gene expression differences as constraints. IEEE/ACM Trans Comput Biol Bioinform. ;8 (1):206-16. doi: 10.1109/TCBB.2009.55. PubMed PMID:21071808 .
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