Molecular Cell Biology

Research Output

Attacking Blood-Borne Parasites with Mathematics

van Niekerk, D. D., Penkler, G. P., du Toit, F., Snoep, J. L., Bakker, B. M. & Haanstra, J. R., 2016, Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery. Muller, S., Cerdan, R., Radulescu, O. & Selzer, P. (eds.). 1 ed. Wiley-VCH Verlag GmbH & Co. KGaA, Vol. 7. p. 513 541 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Attractive models; how to make the silicon cell relevant and dynamic.

Westerhoff, H. V., Bruggeman, F. J., Hofmeyr, J. H. S. & Snoep, J. L., 2003, In : Comparative and Functional Genomics. 4, p. 155-158 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life.

Koefoed, S., Otten, M. F., Koebmann, B. J., Bruggeman, F. J., Bakker, B. M., Snoep, J. L., Krab, K., van Spanning, R. J. M., van Verseveld, H. W., Jensen, P. R., Koster, J. G. & Westerhoff, H. V., 2002, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1555, p. 75-82

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Aubergene - a sensitive genome alignment tool.

Szklarczyk, R. & Heringa, J., 2006, In : Bioinformatics. 22, p. 1431-1436 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Autoamplification of a two component regulatory system results in "learning" behavior.

Hoffer, S. M., Westerhoff, H. V., Hellingwerf, K. J., Postma, P. W. & Tommassen, J., 2001, In : Journal of Bacteriology. 183, p. 4914-4917

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Autotransporter-based antigen display in bacterial ghosts.

Hjelm, A., Söderström, B., Vikström, D., Jong, W. S. P., Luirink, S. & de Gier, J. W., Jan 2015, In : Applied and Environmental Microbiology. 81, 2, p. 726-735 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Autotransporter beta-domains have a specific function in protein secretion beyond outer-membrane targeting

Sauri, A., Oreshkova, N., Soprova, Z., Jong, W. S. P., Sani, M., Peters, P. J., Luirink, J. & van Ulsen, P., 2011, In : Journal of Molecular Biology. 412, p. 553-67

Research output: Contribution to JournalArticleAcademicpeer-review

Autotransporters

Otto, B. R., 2003, Protein Secretion Pathways in Bacteria. Boston/Dordrecht/London: Kluwer Academic Publishers, p. 191-206 16 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Auxin effects on ion transport in Chara corallina

Zhang, S., de Boer, A. H. & van Duijn, B., 2016, In : Journal of Plant Physiology. 193, p. 37-44

Research output: Contribution to JournalArticleAcademicpeer-review

Availability of polycyclic aromatic hydrocarbons to earthworms (Eisenia andrei, Oligochaeta) in field-polluted soils and soil-sediment mixtures.

Jager, D. T., Baerselman, R., Dijkman, E., de Groot, A. C., Hogendoorn, E. A., de Jong, A., Kruitbosch, J. A. W. & Peijnenburg, W. J. G. M., 2003, In : Environmental Toxicology and Chemistry. 22, p. 767-775

Research output: Contribution to JournalArticleAcademicpeer-review

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

A wave of reactive oxygen species (ROS)-induced ROS release in a sea of excitable mitochondria.

Brady, N., Hamacher-Brady, A., Westerhoff, H. V. & Gottlieb, R. A., 2006, In : Antioxidants and Redox Signaling. 8, p. 1651-1665 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station.

Oliveira Lebre Direito, M. S., Ehrenfreund, P., Marees, A., Staats, M. & Roling, W. F. M., 2011, In : International Journal of Astrobiology. 10, 10, p. 191-207 16 p., 3.

Research output: Contribution to JournalArticleAcademicpeer-review

Background reduction in a young interferometer biosensor

Mulder, H. K. P., Subramaniam, V. & Kanger, J. S., 21 Jul 2014, Optical Sensors, 2014. Optical Society of America (OSA)

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Bacterial cell wall synthesis: new insights from localization studies

Scheffers, D. J. & Pinho, M. G., 2005, In : Microbiology and Molecular Biology Reviews. 69, p. 585-607 23 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Bacterial community dynamics and hydorcarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with burried oil.

Roling, W. F. M., Milner, M. G., Jones, D. M., Fratepietro, F., Swannell, R. P. J., Daniel, F. & Head, I. M., 2004, In : Applied and Environmental Microbiology. 70, p. 2603-2613 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Groenenboom, A. E., Parker, M. E., De Vries, A., De Groot, S., Zobrist, S., Mansen, K., Milani, P., Kort, R., Smid, E. J. & Schoustra, S. E., 10 May 2019, In : PLoS ONE. 14, 5, e0215658.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Bacterial community structure and metabolic profiles in a forest soil exhibiting spatially variable net nitrate production.

Laverman, A. M., Braster, M., Roling, W. F. M. & van Verseveld, H. W., 2005, In : Soil Biology and Biochemistry. 37, p. 1581-1588 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Bacterial degradation of disscolved organic carbon in the water column An experimental and modelling approach

Eichinger, M., 2008, Marseille, France. 165 p.

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

Open Access
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Bacterial inclusion bodies function as vehicles for dendritic cell-mediated T cell responses

Schetters, S. T. T., Jong, W., Kruijssen, L. J. W., van den Berg van Saparoea, B., Engels, S., Unger, W. W. J., Houben, D., den Haan, J. M. M., Luirink, J. & van Kooyk, Y., 8 Oct 2019, In : cellular & molecular immunology. 17, 4, p. 415-417 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Bacterial secretion chaperones: The mycobacterial type VII case

Phan, T. H. & Houben, E. N. G., 1 Sep 2018, In : FEMS Microbiology Letters. 365, 18, p. 1-8 8 p., fny197.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access

Bactericidal mode of action of bedaquiline.

Hards, K., Robson, J. R., Berney, M., Shaw, L., Bald, D., Koul, A., Andries, K. & Cook, G. M., 2015, In : Journal of Antimicrobial Chemotherapy. 70, 7, p. 2028-2037

Research output: Contribution to JournalArticleAcademicpeer-review

Bad habits die hard; the NOEC's persistence reflects poorly on ecotoxicology.

Jager, T., 2012, In : Environmental Toxicology and Chemistry. 31, p. 228-229

Research output: Contribution to JournalArticleAcademicpeer-review

Balance on many scales: growth and gene expression in Bacillus subtilis

Nordholt, N., 2018, 118 p.

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

Open Access
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Balancing nutrients, water and heat in the face of environmental change: a thermodynamic niche framework.

Kearney, M., Simpson, S., Raubenheimer, D. & Kooijman, S. A. L. M., 2012, In : Functional Ecology.

Research output: Contribution to JournalArticleAcademicpeer-review

Barley 14-3-3 Biology

Schoonheim, P. J., 2007, Zutphen: Wohrmann print service. 128 p.

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

Open Access
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Basic concepts and principles of stoichiometric modeling of metabolic networks.

Maarleveld, T. R., Khandelwal, R. A., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2013, In : Biotechnology Journal. 8, 9, p. 997-1008

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

BDI-modelling of complex intracellular dynamics.

Jonker, C. M., Snoep, J. L., Treur, J., Westerhoff, H. V. & Wijngaards, W. C. A., 2008, In : Journal of Theoretical Biology. 251, p. 1-23

Research output: Contribution to JournalArticleAcademicpeer-review

BDI-Modelling of Intracellular Dynamics

Jonker, C. M., Snoep, J. L., Treur, J., Westerhoff, H. V. & Wijngaards, W. C. A., 2002, Proceedings of the First International Workshop on Bioinformatics and Multi-Agent Systems, BIXMAS'02. Williams, A. B. & Decker, K. (eds.). p. 15-23

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition

van der Waals, M. J., Atashgahi, S., da Rocha, U. N., van der Zaan, B. M., Smidt, H. & Gerritse, J., 1 Jun 2017, In : Applied Microbiology and Biotechnology. 101, 12, p. 5175-5188 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Bethedging during bacterial diauxic shift.

Solopova, A., van Gestel, J., Weissing, F. J., Bachmann, H., Teusink, B., Kok, J. & Kuipers, O. P., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. p. 7427-7432

Research output: Contribution to JournalArticleAcademicpeer-review

Bias in behaviour genetics: an ecological perspective.

vd Steen, W. J., 1999, In : Acta Biotheoretica. 46, p. 369-377

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcation analysis can unify ecological and evolutionary aspects of ecosystems.

Troost, T. A., Kooi, B. W. & Kooijman, S. A. L. M., 2007, In : Ecological Modelling. 204, p. 253-268

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcation analysis of a family of multi-strain epidemiology models.

Kooi, B. W., Aguiar, M. & Stollenwerk, N., 2013, In : Journal of computational and applied mathematics. 252, p. 148-158

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcation analysis of a predator-prey model with predators using hawk dove tactics.

Auger, P., Kooi, B. W., Bravo de la Parra, R. & Poggiale, J. C., 2006, In : Journal of Theoretical Biology. 238, p. 597-607

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcations in ecosystem models and their biological interpretation.

Kooi, B. W. & Boer, M. P., 2001, In : Applicable Analysis. 77, p. 29-59

Research output: Contribution to JournalArticleAcademicpeer-review

Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein

van der Horst, M. A., Arents, J. C., Kort, R. & Hellingwerf, K. J., May 2007, In : Photochemical and Photobiological Sciences. 6, 5, p. 571-9 9 p.

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

Bioaccumulation of organic chemicals in contaminated soils, evaluation of bioassays with earthworms.

Jager, D. T., van der Wal, L., Fleuren, R. H. L. J., Barendregt, A. & Hermens, J. L. M., 2005, In : Environmental Science and Technology. 39, p. 293-298

Research output: Contribution to JournalArticleAcademicpeer-review

Biochemical and genetic characterization of the membrane-associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum

Molenaar, D., van der Rest, ME. & Petrovic, S., 1 Jun 1998, In : European Journal of Biochemistry. 254, 2, p. 395-403

Research output: Contribution to JournalArticleAcademicpeer-review

Biochemical competition makes fatty-acid beta-oxidation vulnerable to substrate overload.

van Eunen, K., simons, S. M., Gerding, A., Bleeker, A., den Besten, G., Touw, C. M., Houten, S. M., Groen, A. K., Krab, K., Reijngoud, D. J. & Bakker, B. M., 2013, In : PLoS Computational Biology. 9, 8, e1003186.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Biochemistry and molecular biology of nitrification.

Ferguson, S. J., Richards, D. J. & van Spanning, R. J. M., 2007, Biology of the nitrogen cycle.. Bothe, H., Ferguson, S. J. & Newton, W. E. (eds.). Elsevier Science, p. 209-222

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Biocomplexity and the essence of the living state.

Somsen, O. J. G., van Grondelle, R. & Westerhoff, H. V., 1997, Complexity 2. p. 3-4

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Biodegradation

Lynch, J. M. & van Verseveld, H. W., 2002, Dordrecht, The Netherlands: Kluwer Academic Press.

Research output: Book / ReportBook

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 30 Oct 2019, In : Ecotoxicology and Environmental Safety. 182, p. 1-10 10 p., 109414.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum

Pretzer, G., Snel, J., Molenaar, D., Wiersma, A., Bron, P. A., Lambert, J., Vos, W. M., van der Meer, R., Smits, MA. & Kleerebezem, M., Sep 2005, In : Journal of Bacteriology. 187, 17, p. 6128-6136

Research output: Contribution to JournalArticleAcademicpeer-review

Bioenergetic modelling of the growth, development and reproduction of a small pelagic fish: the Bay of Biscay anchovy

Pecquerie, L., 2008, 272 p.

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

Open Access
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Biofumigation using a wild Brassica oleracea accession with high glucosinolate content affects beneficial soil invertebrates

Zuluaga, D. L., van Ommen Kloeke, A. E. E., Verkerk, R., Roling, W. F. M., Ellers, J., Roelofs, D. & Aarts, M. G. M., 2015, In : Plant and Soil. 394, 1, p. 155-163

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access