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Items: 1 to 50 of 109

1.

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.

2.

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.

3.

Further Elucidation of Galactose Utilization in Lactococcus lactis MG1363.

Solopova A, Bachmann H, Teusink B, Kok J, Kuipers OP.

Front Microbiol. 2018 Aug 3;9:1803. doi: 10.3389/fmicb.2018.01803. eCollection 2018.

4.

Training for translation between disciplines: a philosophy for life and data sciences curricula.

Anton Feenstra K, Abeln S, Westerhuis JA, Brancos Dos Santos F, Molenaar D, Teusink B, Hoefsloot HCJ, Heringa J.

Bioinformatics. 2018 Jul 1;34(13):i4-i12. doi: 10.1093/bioinformatics/bty233.

5.

Dynamic elementary mode modelling of non-steady state flux data.

Folch-Fortuny A, Teusink B, Hoefsloot HCJ, Smilde AK, Ferrer A.

BMC Syst Biol. 2018 Jun 18;12(1):71. doi: 10.1186/s12918-018-0589-3.

6.

Metabolite Depletion Affects Flux Profiling of Cell Lines.

Nilsson A, Haanstra JR, Teusink B, Nielsen J.

Trends Biochem Sci. 2018 Jun;43(6):395-397. doi: 10.1016/j.tibs.2018.03.009. Epub 2018 Apr 12. Review.

PMID:
29656822
7.

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux.

Bosdriesz E, Wortel MT, Haanstra JR, Wagner MJ, de la Torre Cortés P, Teusink B.

Sci Rep. 2018 Apr 3;8(1):5576. doi: 10.1038/s41598-018-23528-7.

8.

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.

PMID:
29550298
9.

Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough.

Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P.

Appl Environ Microbiol. 2017 Aug 25. pii: AEM.01528-17. doi: 10.1128/AEM.01528-17. [Epub ahead of print]

10.

Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria.

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

FEMS Microbiol Rev. 2017 Aug 1;41(Supp_1):S201-S219. doi: 10.1093/femsre/fux024. Review.

PMID:
28633473
11.

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.

12.

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.

13.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S.

NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016.

14.

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.

15.

Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets.

Levering J, Fiedler T, Sieg A, van Grinsven KW, Hering S, Veith N, Olivier BG, Klett L, Hugenholtz J, Teusink B, Kreikemeyer B, Kummer U.

J Biotechnol. 2016 Aug 20;232:25-37. doi: 10.1016/j.jbiotec.2016.01.035. Epub 2016 Mar 10.

PMID:
26970054
16.

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.

17.

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods.

Kort R, Westerik N, Mariela Serrano L, Douillard FP, Gottstein W, Mukisa IM, Tuijn CJ, Basten L, Hafkamp B, Meijer WC, Teusink B, de Vos WM, Reid G, Sybesma W.

Microb Cell Fact. 2015 Dec 8;14:195. doi: 10.1186/s12934-015-0370-x.

18.

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.

19.

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.

20.

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.

21.

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.

22.

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Goel A, Eckhardt TH, Puri P, de Jong A, Branco Dos Santos F, Giera M, Fusetti F, de Vos WM, Kok J, Poolman B, Molenaar D, Kuipers OP, Teusink B.

Mol Microbiol. 2015 Jul;97(1):77-92. doi: 10.1111/mmi.13012. Epub 2015 May 9.

23.

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.

24.

Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism.

Veith N, Solheim M, van Grinsven KW, Olivier BG, Levering J, Grosseholz R, Hugenholtz J, Holo H, Nes I, Teusink B, Kummer U.

Appl Environ Microbiol. 2015 Mar;81(5):1622-33. doi: 10.1128/AEM.03279-14. Epub 2014 Dec 19.

25.

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.

PMID:
25350875
26.

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis.

Willemsen AM, Hendrickx DM, Hoefsloot HC, Hendriks MM, Wahl SA, Teusink B, Smilde AK, van Kampen AH.

Mol Biosyst. 2015 Jan;11(1):137-45. doi: 10.1039/c4mb00510d. Epub 2014 Oct 15.

PMID:
25315283
27.

Evolutionary engineering to enhance starter culture performance in food fermentations.

Bachmann H, Pronk JT, Kleerebezem M, Teusink B.

Curr Opin Biotechnol. 2015 Apr;32:1-7. doi: 10.1016/j.copbio.2014.09.003. Epub 2014 Sep 29. Review.

PMID:
25269887
28.

Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation.

Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R.

PLoS One. 2014 Sep 30;9(9):e106453. doi: 10.1371/journal.pone.0106453. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e116129. PLoS One. 2014;9(10):e112204.

29.

Lactic Acid Bacteria: embarking on 30 more years of research.

Kok J, Johansen E, Kleerebezem M, Teusink B.

Microb Cell Fact. 2014 Aug 29;13 Suppl 1:I1. doi: 10.1186/1475-2859-13-S1-I1. Epub 2014 Aug 29. No abstract available.

30.

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11467-72. doi: 10.1073/pnas.1317751111. Epub 2014 Jul 21.

31.

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.

PMID:
24956444
32.

Bet-hedging during bacterial diauxic shift.

Solopova A, van Gestel J, Weissing FJ, Bachmann H, Teusink B, Kok J, Kuipers OP.

Proc Natl Acad Sci U S A. 2014 May 20;111(20):7427-32. doi: 10.1073/pnas.1320063111. Epub 2014 May 5.

33.

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.

34.

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.

35.

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.

PMID:
24436182
36.

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.

37.

Availability of public goods shapes the evolution of competing metabolic strategies.

Bachmann H, Fischlechner M, Rabbers I, Barfa N, Branco dos Santos F, Molenaar D, Teusink B.

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14302-7. doi: 10.1073/pnas.1308523110. Epub 2013 Aug 12.

38.

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.

39.

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.

40.

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds.

Abeln S, Molenaar D, Feenstra KA, Hoefsloot HC, Teusink B, Heringa J.

Brief Bioinform. 2013 Sep;14(5):589-98. doi: 10.1093/bib/bbt023. Epub 2013 Apr 19.

PMID:
23603092
41.

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.

42.

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.

43.

Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria.

Branco dos Santos F, de Vos WM, Teusink B.

Curr Opin Biotechnol. 2013 Apr;24(2):200-6. doi: 10.1016/j.copbio.2012.11.003. Epub 2012 Nov 28. Review.

PMID:
23200025
44.

Metabolic shifts: a fitness perspective for microbial cell factories.

Goel A, Wortel MT, Molenaar D, Teusink B.

Biotechnol Lett. 2012 Dec;34(12):2147-60. doi: 10.1007/s10529-012-1038-9. Epub 2012 Aug 31. Review.

45.

Understanding regulation of metabolism through feasibility analysis.

Nikerel E, Berkhout J, Hu F, Teusink B, Reinders MJ, de Ridder D.

PLoS One. 2012;7(7):e39396. doi: 10.1371/journal.pone.0039396. Epub 2012 Jul 9.

46.

Inferring differences in the distribution of reaction rates across conditions.

Hendrickx DM, Hoefsloot HC, Hendriks MM, Vis DJ, Canelas AB, Teusink B, Smilde AK.

Mol Biosyst. 2012 Sep;8(9):2415-23. Epub 2012 Jul 11.

PMID:
22782002
47.

A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363.

Solopova A, Bachmann H, Teusink B, Kok J, Neves AR, Kuipers OP.

Appl Environ Microbiol. 2012 Aug;78(16):5612-21. doi: 10.1128/AEM.00455-12. Epub 2012 Jun 1.

48.

Role of phosphate in the central metabolism of two lactic acid bacteria--a comparative systems biology approach.

Levering J, Musters MW, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B.

FEBS J. 2012 Apr;279(7):1274-90. doi: 10.1111/j.1742-4658.2012.08523.x. Epub 2012 Mar 12.

49.

FAME, the Flux Analysis and Modeling Environment.

Boele J, Olivier BG, Teusink B.

BMC Syst Biol. 2012 Jan 30;6:8. doi: 10.1186/1752-0509-6-8.

50.

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.

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