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11-Oxygenated androgen precursors are the preferred substrates for aldo-keto reductase 1C3 (AKR1C3): Implications for castration resistant prostate cancer

Barnard, M., Quanson, J. L., Mostaghel, E., Pretorius, E., Snoep, J. L. & Storbeck, K. H., Oct 2018, In : Journal of Steroid Biochemistry and Molecular Biology. 183, p. 192-201 10 p.

Research output: Contribution to JournalArticle

16S rDNA-based characterization of the BTX-catabolizing microbial associations isolated from a South African sandy oil.

Ralebitso, T. K., Roling, W. F. M., Braster, M., Senior, E. & van Verseveld, H. W., 2001, In : Biodegradation. 11, p. 351-357

Research output: Contribution to JournalArticle

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.

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Abiotic and microbiotic factors controlling biofilm formation of thermophilic spore formers.

Zhao, Y., Caspers, M. P., Metselaar, K. I., de Boer, W. P. H., Roeselers, G., Moezelaar, R., Nierop Groot, M. N., Montijn, R., Abee, T. & Kort, R., 2013, In : Applied and Environmental Microbiology. 79, 18, p. 5652-5660

Research output: Contribution to JournalArticle

Accurate confidence aware clustering of array CGH tumor profiles.

van Houte, B. P. P. & Heringa, J., 2010, In : Bioinformatics. 26, p. 6-14

Research output: Contribution to JournalArticle

Acetate formation int he energy metabolism of parasitic helminths and protists.

Tielens, A. G. M., van Grinsven, K. W. A., Henze, K., van Hellemond, J. J. & Martin, W. ., 2010, In : International Journal for Parasitology. 40, p. 387-384

Research output: Contribution to JournalArticleAcademicpeer-review

Acidophilic microbial communities associated with a natural, biodegradated hydrocarbon seepage.

Roling, W. F. M., Ortega-Lucach, O. S., Larter, S. R. & Head, I. M., 2006, In : Journal of Applied Microbiology. 101, p. 290-299 10 p.

Research output: Contribution to JournalArticle

A combined experimental and modelling approach for the Weimberg pathway optimisation

Shen, L., Kohlhaas, M., Enoki, J., Meier, R., Schönenberger, B., Wohlgemuth, R., Kourist, R., Niemeyer, F., van Niekerk, D., Bräsen, C., Niemeyer, J., Snoep, J. & Siebers, B., 27 Feb 2020, In : Nature Communications. 11, 1, p. 1-13 13 p., 1098.

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A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., Hucka, M. & 26 others, Hull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nokaew, I., Le Novère, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E., Sigurdsson, M. I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J. H. G. M., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H. V., Kell, D. B., Mendes, P. & Palsson, B. O., 2013, In : Nature Biotechnology. 31, 5, p. 419-425

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A comparative analysis of kinetic models of erythrocyte glycolysis.

du Preez, F. B., Conradie, R., Penkler, G. P., Holm, K., van dooren, F. L. J. & Snoep, J. L., 2008, In : Journal of Theoretical Biology. 252, p. 488-496

Research output: Contribution to JournalArticle

A comparison of respiratory pathways in fully habituated and a normal non-organogenic sugerbeet callus.

Bisbis, B., Wagner, A. M., Kevers, C. & Gaspar, T., 2000, In : Journal of Plant Physiology. 156, p. 312-318 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A consensus yeast metabolic network obtained from a community approach to systems biology.

Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, E. R., Heinemann, M., Hucka, M., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonides, E., Smallbone, K., Spasi, I. & 14 others, Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Paton, N., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B., 2008, In : Nature Biotechnology. 26, p. 1155-1160

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A contamination assessment of the CI carbonaceous meteorite Orgueil using a DNA-directed approach

Aerts, J. W., Elsaesser, A., Röling, W. F. M. & Ehrenfreund, P., 1 May 2016, In : Meteoritics and Planetary Science. p. 920-931 12 p.

Research output: Contribution to JournalArticle

A critical view of metabolic network adaptations.

Papp, B., Teusink, B. & Notebaart, R. A., 2009, In : HFSP journal. 3, p. 24-35

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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

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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.

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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 JournalArticle

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 JournalArticle

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 JournalArticle

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.

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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 JournalArticle

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 JournalArticle

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 JournalArticle

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 JournalArticle

A mathematical modeling approach to assessing the reliabilty of biomarkers of glutathione metabolism.

Geenen, S., du Preez, F. B., Reed, M., Nijhout, H. F., Kenna, J. G., Wilson, I. D., Westerhoff, H. V. & Snoep, J. L., 16 Jul 2012, In : European Journal of Pharmaceutical Sciences. 46, 4, p. 233-243 11 p.

Research output: Contribution to JournalArticle

A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage

Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D. M., Barberis, M. & Helikar, T., 2 Aug 2018, In : Frontiers in Physiology. 9, AUGUST, p. 1-18 18 p., 878.

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A metabolic control analysis of kinetic controls in ATP free energy metabolism in contracting skeletal muscle.

Jeneson, J. A. L., Westerhoff, H. V. & Kushmerick, M. J., 2000, In : American Journal of Physiology. 279, p. C813-C832

Research output: Contribution to JournalArticle

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Damiani, C., Colombo, R., Gaglio, D., Mastroianni, F., Pescini, D., Westerhoff, H. V., Mauri, G., Vanoni, M. & Alberghina, L., 1 Sep 2017, In : PLoS Computational Biology. 13, 9, e1005758.

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A method for introduction of unmarked mutations in the genome of Paracoccus denitrificans: construction of strains with multiple mutations in the genes encoding periplasmic cytochromes c550, c551i, and c553i

Van Spanning, R. J., Wansell, C. W., Reijnders, W. N., Harms, N., van Ras, N. J. P., Oltmann, L. F. & Stouthamer, A. H., Nov 1991, In : Journal of Bacteriology. 173, 21, p. 6962-70 9 p.

Research output: Contribution to JournalArticle

A method for studying plasma membrane transport with intact cells using computerized fluorometry.

Wielinga, P. W., Heijn, M., Westerhoff, H. V. & Lankelma, J., 1998, In : Analytical Biochemistry. 263, p. 221-231 11 p.

Research output: Contribution to JournalArticle

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 JournalArticle

A mixed-species microarray for identification of food spoilage bacilli

Caspers, M. P. M., Schuren, F. H. J., van Zuijlen, A. C. M., Brul, S., Montijn, R. C., Abee, T. & Kort, R., Apr 2011, In : Food microbiology. 28, 2, p. 245-51 7 p.

Research output: Contribution to JournalArticle

A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P., Simeonidis, E., Spasic, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., Gaskell, S. J. & 5 others, McCarthy, J. E. G., Paton, N. W., Westerhoff, H. V., Kell, D. B. & Mendes, P., 2013, In : The FEBS Journal. 587, p. 2832-2841

Research output: Contribution to JournalArticle

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A molecular movie at 1.8 A resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds

Ren, Z., Perman, B., Srajer, V., Teng, T. Y., Pradervand, C., Bourgeois, D., Schotte, F., Ursby, T., Kort, R., Wulff, M. & Moffat, K., 20 Nov 2001, In : Biochemistry. 40, 46, p. 13788-801 14 p.

Research output: Contribution to JournalArticle

Ample arsenite bio-oxidation activity in Bangladesh drinking water wells: A bonanza for bioremediation?

Hassan, Z., Sultana, M., Khan, S. I., Braster, M., Röling, W. F. M. & Westerhoff, H. V., Aug 2019, In : Microorganisms. 7, 8, p. 1-22 22 p., 246.

Research output: Contribution to JournalArticle

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Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores.

de Boer, P., Caspers, M., Sanders, J. W., Kemperman, R., Wijman, J., Lommerse, G., Roeselers, G., Montijn, R., Abee, T. & Kort, R., 2015, In : Microbiome. 27, p. 30 3.

Research output: Contribution to JournalArticle

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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 JournalArticle

A multivariate geostatistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles.

Mouser, P. J., Rizzo, D. M., Roling, W. F. M. & van Breukelen, B. M., 2005, In : Environmental Science and Technology. 39, p. 7551-7559 9 p.

Research output: Contribution to JournalArticle

Anaerobic biodegradation of crude oil under sulphate-reducing conditions leads to only modest enrichment of recognized sulphate-reducing taxa

Sherry, A., Gray, N. D., Ditchfield, A. K., Aitken, C. M., Jones, D. M., Roling, W. F. M., Hallmann, C., Larter, S. R., Bowler, B. F. J. & Head, I. M., 2013, In : International Biodeterioration & Biodegradation. 81, p. 105-113

Research output: Contribution to JournalArticle

An alternative model for haem ligation in nitrate reductase and analogues respiratory cytochrome b complexes.

van der Oost, J., Nederkoorn, P. H. J., Stouthamer, A. H., Westerhoff, H. V. & van Spanning, R. J. M., 1996, In : Molecular Microbiology. 22, 1, p. 193-196

Research output: Contribution to JournalArticle

An alternative P-II protein in the regulation of glutamine synthetase in Escherichia coli

vanHeeswijk, WC., Hoving, S., Molenaar, D., Stegeman, B., Kahn, D. & Westerhoff, HV., Jul 1996, In : Molecular Microbiology. 21, 1, p. 133-146

Research output: Contribution to JournalArticle

Analysis of concentration response curves to describe and compare tha antimicrobial activity anof model cationic alpha-helical peptides.

Rautenbach, M., Gerstner, G. D., Vlok, N. M., Kulenkampff, J. & Westerhoff, H. V., 2006, In : Analytical Biochemistry. 350, p. 81-90 10 p.

Research output: Contribution to JournalArticle

Analysis of effects of 2,2',5,5'-tetracholorobiphenyl on the flux control in oxidative phosphorylation system in rat liver mitochondria.

Mildaziene, V., Nauciene, Z., Baniene, R., Demin, O. V. & Krab, K., 2002, In : Molecular Biology Reports. 29, p. 35-40

Research output: Contribution to JournalArticle

Analysis of microbial communities in a landfill leachate polluted aquifer using a new method for anaerobic physiological profiling and 16S rDNA Fingerprinting.

Roling, W. F. M., van Breukelen, B. M., Braster, M., Goeltom, M. T., Groen, J. & van Verseveld, H. W., 2000, In : Microbial Ecology. 40, p. 177-188

Research output: Contribution to JournalArticle

Analysis of multiple gene expression array experiments after repetitive hybridisations on nylon membranes.

Hornberg, J. J., de Haas, R. R., Dekker, H. & Lankelma, J., 2002, In : BioTechniques. 33, p. 108-117 10 p.

Research output: Contribution to JournalArticle

Analysis of single quantum-dot mobility inside 1D nanochannel devices

Hoang, T. H., Segers-Nolten, I. M. J., Tas, N. R., van Honschoten, J. W., Subramaniam, V. & Elwenspoek, M. C., 8 Jul 2011, In : Nanotechnology. 22, 27, p. 275201

Research output: Contribution to JournalArticle

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach

Hettling, H., Heringa, J. & van Beek, J. H. G. M., 2010, In : BMC Bioinformatics. 11, Suppl. 10, p. O9

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Ancestry in translational genomic medicine: handle with care

Gurwitz, D. & Lunshof, J., 2009, In : Genome Medicine. 1, p. 24:1-24:3

Research output: Contribution to JournalArticle

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