Molecular Cell Biology

Research Output

Adaptations in the glucose metabolism of procyclic Trypanosoma brucei isolates from Tsetse flies and during differentiation of bloodstream forms.

van Grinsven, K. W. A., van den Abbeele, J., van den Bossche, P., van Hellemond, J. J. & Tielens, A. G. M., 2009, In : Eukaryotic Cell. 8, p. 1307-1311

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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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

Adaptogenic effect of the vitamin D3 containing supplement "videchol" on the activity of glucose-6-phosphate dehydrogenase in irradiated rats erithrone.

Becerill Aragon, G. A., Starikovich, L. S., Kolodkin, A. N., Gorot, I. V. & Veliky, M. M., 2007, In : Ukrainian Biochemical Journal. 79, p. 70-78 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Adapt or disperse: understanding species persistence in a changing world.

Berg, M. P., Kiers, E. T., Driessen, G. J. J., van der Heijden, M. G. A., Kooi, B. W., Kuenen, F. J. A., Liefting, M., Verhoef, H. A. & Ellers, J., 2010, In : Global Change Biology. 16, p. 587-598

Research output: Contribution to JournalArticleAcademicpeer-review

A data integration and visualization resource for the metabolic network of synechocystis sp. PCC6803.

Maarleveld, T. R., Boele, J., Bruggeman, F. J. & Teusink, B., 2014, In : Plant Physiology. 164, p. 1111-1121

Research output: Contribution to JournalArticleAcademicpeer-review

Adding value to ecological risk assessment with population modeling.

Forbes, V. E., Calow, P., Grimm, V., Hayashi, T. I., Jager, T., Katholm, A., Palmqvist, A., Pastorok, R., Salvito, D., Sibly, R., Spromberg, J., Stark, J. & Stillman, R. A., 2011, In : Human and Ecological Risk Assessment. 17, p. 287-299

Research output: Contribution to JournalArticleAcademicpeer-review

A dictionary of programs for sequence analysis (Appendix 2)

Konopka, A. K. & Heringa, J., 2004, Compact handbook of computational biology.. Konopka, A. K. & Crabbe, M. J. C. (eds.). New York (NY - USA): Marcel Dekker, p. 503-536

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

A domino effect in drug action: from metabolic assault towards parasite differentiation.

Haanstra, J. R., Kerkhoven, E. J., van Tuijl, J. H., Blits, M., Wurst, M., van Nuland, R., Albert, M. A., Michels, P. A. M., Bouwman, J., Clayton, C., Westerhoff, H. V. & Bakker, B. M., 2011, In : Molecular Microbiology. 79, 1, p. 94-108

Research output: Contribution to JournalArticleAcademicpeer-review

Adsorption of bovine alpha-lactalbumin on suspended solid nanospheres and its subsequent displacement studied by NMR spectroscopy.

Engel, M. F. M., Visser, A. J. W. G. & Van Mierlo, C. P. M., 2004, In : Langmuir. 20, p. 5530-5538 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Advances and strategies in discovery of new antibacterials for combating metabolically resting bacteria

Bald, D. & Koul, A., 2013, In : Drug Discovery Today. 18, p. 250-255

Research output: Contribution to JournalArticleAcademicpeer-review

Advantages of storage in a fluctuating environment.

Kooi, B. W. & Troost, T. A., 2006, In : Theoretical Population Biology. 70, p. 527-541

Research output: Contribution to JournalArticleAcademicpeer-review

A dynamic energy budget for the whole life-cycle of holometabolous insects.

Llandres, A. L., Marques, G. M., Maino, J. L., Kooijman, S. A. L. M., Kearney, M. R. & Casas, J., 2015, In : Ecological Monographs.

Research output: Contribution to JournalArticleAcademicpeer-review

A dynamic energy budget model for small yellow croaker Larimichthys polyactis: Parameterisation and application in its main geographic distribution waters

Ren, J. S., Jin, X., Yang, T., Kooijman, S. A. L. M. & Shan, X., 29 Apr 2020, In : Ecological Modelling. 427, p. 1-8 8 p., 109051.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A dynamics whole-plant model of integrated metabolism of nitrogen and carbon. 1. Comparative ecological implications of ammonium-nitrate interactions.

Bijlsma, R. J., Lambers, H. & Kooijman, S. A. L. M., 2000, In : Plant and Soil. 220, p. 49-69

Research output: Contribution to JournalArticleAcademicpeer-review

Aerobe en anaerobe bacterien: Ademhalen zonder zuurstof.

van Spanning, R. J. M., 2011, Microcanon; wat je beslist moet weten over microbiologie.. De wetenschappelijke Bibliotheek, Natuurwetenschap en Techniek. (ed.). Diemen: Veen Magazines, p. 61-64

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

Aerobic and anaerobic bacteria – Respiration without oxygen

van Spanning, R., van der Oost, J. & Richardson, D., 2017, Mighty Microbes: The amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H. & Willemsen, P. (eds.). Microcanon Foundation / Stichting Microcanon, p. 56-58

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

Aflatoxins: Occurrence, exposure, and binding to lactobacillus species from the gut microbiota of rural ugandan children

Wacoo, A. P., Atukunda, P., Muhoozi, G., Braster, M., Wagner, M., van den Broek, T. J., Sybesma, W., Westerberg, A. C., Iversen, P. O. & Kort, R., Mar 2020, In : Microorganisms. 8, 3, p. 1-15 15 p., 347.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A fluorescence-based reporter for monitoring expression of mycobacterial cytochrome bd in response to antibacterials and during infection.

Boot, M., JIm, K. K., Liu, T., Commandeur, S., Lu, P., Verboom, T., Lill, H., Bitter, W. & Bald, D., 2017, In : Scientific Reports. 7, 1, 10665.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A frequency domain approach to some results on fractional brownian motion.

Dzhaparidze, K. & Ferreira, J. A., 2002, In : Statistics and Probability Letters. 60, p. 155-168

Research output: Contribution to JournalArticleAcademicpeer-review

Afterthoughts as foundations for systems biology.

Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J. H. S. & Westerhoff, H. V., 2007, Systems Biology - Philosophical Foundations. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J-HS. & Westerhoff, H. V. (eds.). Amsterdam The Netherlands: Elsevier, p. 321-336 342 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

A full lifecycle bioenergetic model for bluefin tuna.

Jusup, M., Klanjscek, T., Matsuda, H. & Kooijman, S. A. L. M., 2011, In : PLoS ONE. p. 6:e21903

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Age and geochemistry of Silurian gabbroic rocks in the Tongbai orogen, central China: implications for the geodynamic evolution of the North Qinling arc–back-arc system

Wang, H., Wu, Y. B., Qin, Z. W., Zhu, L. Q., Liu, Q., Liu, X. C., Gao, J., Wijbrans, J. R., Gong, H. J. & Yuan, H. L., 2013, In : Lithos. 179, p. 1-15

Research output: Contribution to JournalArticleAcademicpeer-review

A general approach to detect folding intermediates from steady-state and time-resolved fluorescence of single tryptophan-containing proteins

Laptenok, S., Visser, N. V., Engel, R., Westphal, A. H., van Hoek, A., van Mierlo, C. P. M., van Stokkum, I. H. M., van Amerongen, H. & Visser, A. J. W. G., 2011, In : Biochemistry. 50, 17, p. 3441-3450 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A general model for multiple substrate biodegradation, application to co-metabolisms of non structurally analogous compounds.

Brandt, B. W., van Leeuwen, I. M. M. & Kooijman, S. A. L. M., 2003, In : Water Research. 37, p. 4843-4854

Research output: Contribution to JournalArticleAcademicpeer-review

A general secretion signal for the mycobacterial type VII secretion pathway

Daleke, M. H., Ummels, R., Bawono, P., Heringa, J., Vandenbroucke-Grauls, C. M. J. E., Luirink, S. & Bitter, W., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 28, p. 11342-11347

Research output: Contribution to JournalArticleAcademicpeer-review

A generic view of classic microbial growth models.

van den Berg, H. A., 1998, In : Acta Biotheoretica. 46, p. 117-130 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

Özcan, E., Selvi, S. S., Nikerel, E., Teusink, B., Toksoy Öner, E. & Çakır, T., 1 Jan 2019, In : Applied Microbiology and Biotechnology. 103, 7, p. 3153-3165 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Aggregation Methods in Food Chains.

Kooi, B. W., Poggiale, J. C. & Auger, P., 1998, In : Mathematical and Computer Modelling. 27, 4, p. 109-120

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Aggregation methods in food chains with nutrient recycling.

Kooi, B. W., Poggiale, J. C., Auger, P. & Kooijman, S. A. L. M., 2002, In : Ecological Modelling. 157, p. 69-86

Research output: Contribution to JournalArticleAcademicpeer-review

Aglycon specificity of the cyanogenic beta-glucosidases of leaves of Trifolium species and Cassava (Manihot esculenta).

Kakes, P. & Hakvoort, H. W. J., 1999, In : Thaiszia Journal of Botany. 9, p. 73-80

Research output: Contribution to JournalArticleAcademicpeer-review

Agricultural aspects of sulfur.

Ernst, W. H. O., 2000, Environmental Technologies to Treat Sulfur Pollution. Principles and Engineering.. Lens, P. N. L. & Hulshoff Pol, L. (eds.). London: IWA Publishers, p. 355-376

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Agriculture-induced changes in mycorrhizal fungal assemblages: Implications for ecological risk assessment of transgenic crops

Verbruggen, E., 2012, Enschede: Ipskamp B.V.. 194 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
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A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA

van der Rest, ME., Lange, C. & Molenaar, D., Oct 1999, In : Applied Microbiology and Biotechnology. 52, 4, p. 541-545

Research output: Contribution to JournalArticleAcademicpeer-review

A high-throughput cheese manufacturing model for effective cheese starter screening.

Bachmann, H., Kruijswijk, Z., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2009, In : Journal of Dairy Science. 92, p. 5868-5882

Research output: Contribution to JournalArticleAcademicpeer-review

Air pollution and global change: Significance and prospectives.

prof.dr. Posthumus, A. C., 1998, Responses of plant metabolism to air pollution and global change.. De Kok, L. J. & Stulen, I. (eds.). Leiden: Backhuys Publishers, p. 3-14 12 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

A kinetic inhibition mechanism for the maintenance process.

Tolla, C., Kooijman, S. A. L. M. & Poggiale, J. C., 2007, In : Journal of Theoretical Biology. 244, p. 576-587

Research output: Contribution to JournalArticleAcademicpeer-review

A kinetic model as a tool to understand the response of Saccharomyces cerevisiae to heat exposure.

Mensonides, F. I. C., Bakker, B. M., Brul, S., Hellingwerf, K. J. & Teixeira de Mattos, M. J., 2007, Modelling microorganisms in food.. Brul, S., van Gerwen, S. & Zwietering, M. (eds.). Cambridge UK: Woodhead Publishing Limited, p. 228-245

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae druing temperature shift.

Mensonides, F. I. C., Brul, S., Hellingwerf, K. J., Bakker, B. M. & Teixeira de Mattos, M. J., 2014, In : The FEBS Journal. 281, 3, p. 825-841

Research output: Contribution to JournalArticleAcademicpeer-review

A kinetic model of glucose catabolism in Plasmodium falciparum

Penkler, G. P., 2013, 143 p.

Research output: PhD ThesisPhD Thesis - Research external, graduation VU

Open Access
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Algal defenses, population stability and the risk of herbivore extinctions: A chemostat model and experiment.

v.d. Stap, I., Vos, M., Kooi, B. W., Mulling, B. T., van Donk, E. & Mooij, W. M., 2009, In : Ecological Research. 24, p. 1145-1153

Research output: Contribution to JournalArticleAcademicpeer-review

Alignment of microbial fitness with engineered product formation: Obligatory coupling between acetate production and photoautotrophic growth

Du, W., Jongbloets, J. A., van Boxtel, C., Hernández, H. P., Lips, D., Olivier, B. G., Hellingwerf, K. J. & dos Santos, F. B., 13 Feb 2018, In : Biotechnology for Biofuels. 11, 38, p. 1-13 13 p., 38.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A lipoprotein lipase mutation (Asn291Ser) is associated with reduced HDL cholesterol levels in premature atherosclerosis

Reymer, P. W. A., Gagné, S. E., Groenemeyer, B. E., Zhang, H., Forsyth, I., Jansen, H., Seidell, J. C., Kromhout, D., Lie, K. E. & Kastelein, J. J., 1995, In : Nature Genetics. 10, 1, p. 28-34 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Alkalispirillum mobile gen. nov., spec. nov., an alkaliphilic non-phototrophic member of the Ectothiorhodospiraceae

Rijkenberg, M. J., Kort, R. & Hellingwerf, K. J., May 2001, In : Archives of Microbiology. 175, 5, p. 369-75 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Allocation patterns of zinc and cadmium in heavy metal tolerant and sensitive Silene vulgaris.

Chardonnens, A. N., ten Bookum, W. M., Vellinga, S., Schat, H., Verkley, J. A. C. & Ernst, W. H. O., 1999, In : Journal of Plant Physiology. 155, p. 778-787

Research output: Contribution to JournalArticleAcademicpeer-review

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells.

Gustavsson, A-K., van Niekerk, D. D., Adiels, C. B., Kooi, B. W., Goksor, M. & Snoep, J. L., 2014, In : The FEBS Journal. 281, 12, p. 2784-2793 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A longelivety assurance gene homolog of tomato mediates resistance to Alernaria Alternata f.sp.Lycopersici toxins and fumonisin B1

Brandwagt, B. F., Mesbah, L. A., Takken, F. L. W., Laurent, P. L., Kneppers, T. J. A., Hille, J. & Nijkamp, H. J. J., 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 9, p. 4961-4966

Research output: Contribution to JournalArticleAcademic

A longevity assurance gene homolog of tomato mediates resistance to Alternaria alternata f. sp. Lycopersici toxins and fumonisin B1.

Brandwagt, B. F., Mesbah, L. A., Takken, F. L. W., Laurent, P. L., Kneppers, T. J. A., Hille, J. & Nijkamp, H. J. J., 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 9, p. 4961-4966 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Altering textural properties of fermented milk by using surface-engineered Lactococcus lactis

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., Jul 2018, In : Microbial Biotechnology. 11, 4, p. 770-780 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access