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  • D Molenaar
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 JournalArticleAcademicpeer-review

Open Access

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

Amino acid analysis using chromatography–mass spectrometry: An inter platform comparison study

Krumpochova, P., Bruyneel, B., Molenaar, D., Koukou, A., Wuhrer, M., Niessen, W. M. A. & Giera, M. A., 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 114, p. 398-407

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, S. N., Olivier, B. G., Molenaar, D. & Teusink, B., 7 Aug 2019, In : Genome Biology. 20, 1, 158.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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., 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, p. 14302-14307

Research output: Contribution to JournalArticleAcademicpeer-review

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

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

Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C., Teusink, B. & Heringa, J., Sep 2013, In : Briefings in bioinformatics. 14, 5, p. 589-98 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

Van Der Veer, C., Hertzberger, R. Y., Bruisten, S. M., Tytgat, H. L. P., Swanenburg, J., De Kat Angelino-Bart, A., Schuren, F., Molenaar, D., Reid, G., De Vries, H. & Kort, R., 29 Mar 2019, In : Microbiome. 7, 1, p. 1-14 14 p., 49.

Research output: Contribution to JournalArticleAcademicpeer-review

File
193 Downloads (Pure)

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 JournalArticleAcademicpeer-review

Open Access
File
86 Downloads (Pure)

Finding functional differences between species in a microbial community: Case studies in wine fermentation and Kefir culture

Melkonian, C., Gottstein, W., Blasche, S., Kim, Y., Abel-Kistrup, M., Swiegers, H., Saerens, S., Edwards, N., Patil, K. R., Teusink, B. & Molenaar, D., 25 Jun 2019, In : Frontiers in Microbiology. 10, JUNE, p. 1-14 14 p., 01347.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-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 JournalArticleAcademicpeer-review

Open Access
File
139 Downloads (Pure)

Genome instability in Lactobacillus rhamnosus GG

Sybesma, W., Molenaar, D., Ijcken, W., Venema, K. & Kort, R., 2013, In : Applied and Environmental Microbiology. 79, p. 2233-2239

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

Weerdenburg, E. M., Abdallah, A., Rangkuti, F., Abd El Ghany, M., Otto, T. D., Adroub, S. A., Molenaar, D., Ummels, R., Ter Veen, K., van Stempvoort, G., van der Sar, A. M., Ali, S., Langridge, G. C., Thomson, N. R., Pain, A. & Bitter, W., 2015, In : Infection and Immunity. 83, p. 1778-1788 5.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access

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, F. J., 2013, In : Genetics. 194, 2, p. 505-512

Research output: Contribution to JournalArticleAcademicpeer-review

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

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 JournalArticleAcademicpeer-review

Open Access
File
123 Downloads (Pure)

Microbial communities in sediments from four mildly acidic ephemeral salt lakes in the Yilgarn craton (Australia) – terrestrial analogs to ancient Mars

Aerts, J. W., van Spanning, R. J. M., Flahaut, J., Molenaar, D., Bland, P. A., Genge, M. J., Ehrenfreund, P. & Martins, Z., 6 May 2019, In : Frontiers in Microbiology. 10, MAY, p. 1-19 19 p., 779.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Molecular analysis of the vaginal microbiome: an alternative for the diagnosis of bacterial vaginosis?

Dols, J. A. M., Molenaar, D., Helm, J., Caspers, M. P. M., de Kat-Angelino, A., Speksnijder, A. G. C. L., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de vries, H. J. C. & Kort, R., 2015, In : BMC Infectious Diseases.

Research output: Contribution to JournalArticleAcademicpeer-review

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

Dols, J. A. M., Molenaar, D., van der Helm, J. J., Caspers, M. P., de Kat Angelino-Bart, A., Schuren, F. H., Speksnijder, A. G., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de Vries, H. J. & Kort, R., 2016, In : BMC Infectious Diseases. 16, 180.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-review

Open Access

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni

Collombel, I., Melkonian, C., Molenaar, D., Campos, F. M. & Hogg, T., 8 Nov 2019, In : Frontiers in Microbiology. 10, p. 1-14 14 p., 2597.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Non-hierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp PCC6803.

Du, W., Angermayr, S. A., Jongbloets, J. A., Molenaar, D., Bachmann, H., Hellingwerf, K. J. & Santos, F., 2016, In : ACS synthetic biology. 2016/12/12

Research output: Contribution to JournalArticleAcademicpeer-review

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, T. H., Puri, P., de Jong, A., Santos, F., Giera, M. A., Fusetti, F., Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P. & Teusink, B., 2015, In : Molecular Microbiology. 97, p. 77-92 1.

Research output: Contribution to JournalArticleAcademicpeer-review

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

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 JournalArticleAcademicpeer-review

Open Access
File
170 Downloads (Pure)

Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must

Sirén, K., Mak, S. S. T., Melkonian, C., Carøe, C., Swiegers, J. H., Molenaar, D., Fischer, U. & Thomas P Gilbert, M., 1 Jan 2019, In : Frontiers in Microbiology. 10, APR, 697.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-review

Open Access

Vesicle trafficking via the Spitzenkoerper during hyphal tip growth in Rhizoctonia solani

Dijksterhuis, J. & Molenaar, D., 2013, In : Antonie van Leeuwenhoek. 103, p. 921-931

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access
File
136 Downloads (Pure)
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 proceedingConference contributionAcademicpeer-review