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• Conference contribution

  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 proceeding › Conference contribution › Academic › peer-review

  • microbial physiology
  • Physiology
  • Fluxes
  • Microbiological Phenomena
  • Growth
• Article

  A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

  Atashgahi, S., Hornung, B., Van Der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., Van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 14 Mar 2018, In : Scientific Reports. 8, 1, p. 1-12 12 p., 4490.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  • benzene
  • nitrates
  • degradation
  • anaerobes
  • oxygen production

• 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, F. C., Ma, H., Bruggeman, F. J., van Heeswijk, W. C., Garcia-Contreras, R., Molenaar, D., Krab, K. & Westerhoff, H. V., 3 Jan 2011, In : FEBS Letters. 585, 1, p. 23-28

  Research output: Contribution to Journal › Article › Academic › peer-review

• Characterization of cellular composition of evolved strains of Lactococcus lactis

  Price, C. J., Santos, F., Molenaar, D., Teusink, B., Poolman, B. & Kuipers, O. P., Jun 2010, In : The FEBS Journal. 277, p. 114-114

  Research output: Contribution to Journal › Article › Academic › peer-review

• Complete genome sequence of Lactococcus lactis subsp. Lactis KF147, a plant-associated lactic acid bacterium.

  Siezen, R. J., Bayjanov, J., Renckens, B., Wels, M., van Hijum, S. A. F. T., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Journal of Bacteriology. 192, p. 2649-2650

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File
  178 Downloads (Pure)

• Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

  Marco, M. L., de Vries, M. C., Wels, M., Molenaar, D., Mangell, P., Ahrne, S., de Vos, W. M., Vaughan, E. E. & Kleerebezem, M., 2010, In : ISME Journal. 4, p. 1481-1484

  Research output: Contribution to Journal › Article › Academic › peer-review

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

  Bachmann, H., Molenaar, D., Branco dos Santos, F. & Teusink, B., 1 Aug 2017, In : FEMS Microbiology Reviews. 41, Supp_1, p. S201-S219

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  • Lactobacillales
  • Resource Allocation
  • Population Dynamics
  • Research Design
  • Genome

• Explorin metabolic pathway reconstruction and genome-wide expression profiling in lactobacillus reuteri to define functional probiotic features.

  Saulnier, D. M. A., Santos, F., Roos, S., Mistretta, T-A., Spinler, J. K., Molenaar, D., Teusink, B. & Versalovic, J., 2011, In : PLoS ONE. 6, p. e18783

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File

  • Lactobacillus reuteri
  • probiotics
  • biochemical pathways
  • genome
  • breast milk
  94 Downloads (Pure)

• Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis

  Rud, I., Naterstad, K., Bongers, R. S., Molenaar, D., Kleerebezem, M. & Axelsson, L., 2011, In : Microbial Biotechnology. 4, p. 345-356

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

• Functional Identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis.

  Santos, F., Spinler, J. K., Saulnier, D. M. A., Molenaar, D., Teusink, B., de Vos, D. L., Versalovic, J. & Hugenholtz, J., 2011, In : Microbial Cell Factories. 10, p. 55

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File

  • Lactobacillus reuteri
  • Vitamins
  • Transcription factors
  • Vitamin B Complex
  • Glycerol
  145 Downloads (Pure)

• Gene expression analysis reveals a gene set discriminatory to different metals in soil.

  Nota, B., Verweij, R. A., Molenaar, D., Ylstra, B., van Straalen, N. M. & Roelofs, D., 2010, In : Toxicological Sciences. 115, 1, p. 34-40

  Research output: Contribution to Journal › Article › Academic › peer-review

  • Gene expression
  • Soil
  • Genes
  • Metals
  • Soils

• Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

  Siezen, R. J., Bayjanov, J. R., Felis, G. E., van der Sijde, M. R., Starrenburg, M., Molenaar, D., Wels, M., Hijum, S. A. & van Hylckama Vlieg, J. E. T., 2011, In : Microbial Biotechnology. 4, p. 383-402

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  • Lactococcus lactis
  • Comparative Genomic Hybridization
  • Genes
  • Genome
  • Biosynthesis

• High local substrate availability stabilizes a cooperative trait.

  Bachmann, H., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2011, In : ISME Journal. 5, p. 929-932

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  • milk
  • peptide
  • cooperatives
  • Peptide Hydrolases
  • cooperative behavior

• Identification of lactobacillus plantarum genes modulating, the cytokine response of human peripheral blood mononuclear cells.

  van Hemert, S., Meijerink, M., Molenaar, D., Bron, P. A., de Vos, D. L., Kleerebezem, M., Wells, J. M. & Marco, M. L., 2011, In : BMC Microbiology. 10, p. 293

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File

  • Lactobacillus plantarum
  • Blood Cells
  • Cytokines
  • Interleukin-12
  • Genes
  128 Downloads (Pure)

• Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide-stress tolerance.

  Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Applied and Environmental Microbiology. 76, p. 3748-3752

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File

  • RNA Polymerase Sigma 54
  • Lactobacillus plantarum
  • sigma factors
  • Peroxides
  • gene deletion
  172 Downloads (Pure)

• Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in Streptococcus thermophilus and Lactobacillus bulgaricus

  Sieuwerts, S., Molenaar, D., van Hijum, S. A. F. T., Beerthuyzen, M., Stevens, M. J. A., Janssen, P. W. M., Ingham, C. J., de Bok, F. A. M., de Vos, W. M. & Vlieg, J. E. T. V. H., Dec 2010, In : Applied and Environmental Microbiology. 76, 23, p. 7775-7784

  Research output: Contribution to Journal › Article › Academic › peer-review

• Naturally fermented milk from northern Senegal: Bacterial community composition and probiotic enrichment with Lactobacillus rhamnosus

  Parker, M., Zobrist, S., Donahue, C., Edick, C., Mansen, K., Nadjari, M. H. Z., Heerikhuisen, M., Sybesma, W., Molenaar, D., Diallo, A. M., Milani, P. & Kort, R., 21 Sep 2018, In : Frontiers in Microbiology. 9, September, p. 1-12 12 p., 2218.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

• Phenotypic and genomic diversity of Lactobacillues plantarum strains isolated from various environmental niches.

  Siezen, R. J., Tzeneva, V. A., Castioni, A., Wels, M., Phan, H. T. K., Rademaker, J. L. W., Starrenburg, M. J. C., Kleerebezem, M., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Environmental Microbiology. 12, 3, p. 758-773

  Research output: Contribution to Journal › Article › Academic › peer-review

• Physiological responses to folate overproduction in lactobacillys plantarum WCFS1.

  Wegkamp, H. B. A., Mars, A. E., Faijes, M., Molenaar, D., de Vos, R. C. H., Klaus, S. M. J., Hanson, A. D., Vos, W. M. & Smid, E. J., 2010, In : Microbial Cell Factories. 9, p. 100 14 p.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File
  88 Downloads (Pure)

• Sigma 54 mediated control of the mannose PTS in Lactobacillus plantarum impacts on carbohydrate metabolism.

  Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Microbiology. 156, p. 695-707

  Research output: Contribution to Journal › Article › Academic › peer-review

  • Bacterial RNA
  • Lactobacillus plantarum
  • Sigma Factor
  • Mannose
  • Carbohydrate Metabolism

• Systems biology of lactic acid bacteria: For food and thought

  Teusink, B. & Molenaar, D., 1 Dec 2017, In : Current Opinion in Systems Biology. 6, p. 7-13 7 p.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  • Lactic acid
  • Systems Biology
  • Lactobacillales
  • Bacteria
  • Lactic Acid

• Systems Biology of lactic acid bacteria: a critical review.

  Teusink, B., Bachmann, H. & Molenaar, D., 2011, In : Microbial Cell Factories. 10, A11, 17 p.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File

  • Lactic acid
  • Systems Biology
  • Lactobacillales
  • Systems Analysis
  • Bacteria
  179 Downloads (Pure)

• The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis.

  van der Veen, S. ., van Schalkwijk, S., Molenaar, D., de Vos, W. M., Abee, T. & Wells-Bennik, M. H. J., 2010, In : Microbiology. 156, p. 374-384

  Research output: Contribution to Journal › Article › Academic › peer-review

• Training for translation between disciplines: A philosophy for life and data sciences curricula

  Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J. & Heringa, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i4-i12 9 p.

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

• Volatile compound fingerprinting of mixed-culture fermentations.

  de Bok, F. A. M., Janssen, P. W. M., Bayjanov, J. R., Sieuwerts, S., Lommen, A., van Hylckama Vlieg, J. E. T. & Molenaar, D., 2011, In : Applied and Environmental Microbiology. 77, p. 6233-6239

  Research output: Contribution to Journal › Article › Academic › peer-review

  Open Access

  File
  145 Downloads (Pure)