Molecular Cell Physiology

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2009

Changes in nitrification and bacterial community structure upon cross-inoculation of Scots pine forest soils with different initial nitrification rates.

Nugroho, R. A., Röling, W. F. M., van Straalen, N. M. & Verhoef, H. A., Feb 2009, In : Soil Biology and Biochemistry. 41, 2, p. 243-250 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Characterization of the quinine reductase activity of the ferrice reductase B protein from Paracoccus denitrificans.

Sedlacek, V., van Spanning, R. J. M. & Kucera, I., 2009, In : Archives of Biochemistry and Biophysics. 483, p. 29-36

Research output: Contribution to JournalArticleAcademicpeer-review

Children and populations biobanks.

Gurwitz, D., Fortier, I., Lunshof, J. E. & Knoppers, B. M., 2009, In : Science. 325, p. 818-819

Research output: Contribution to JournalArticleAcademicpeer-review

Crystall Ball - Anchoring (environmental micro)biology in physics-based theory.

Teusink, B., Bruggeman, F. J. & Molenaar, D., 2009, In : Environmental Microbiology Reports. 1, p. 19-20

Research output: Contribution to JournalArticleAcademicpeer-review

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

Rajilic-Stojanovic, M., Heilig, H. G. H. J., Molenaar, D., Kajander, K., Surakka, A., Smidt, H. & de Vos, W. M., Jul 2009, In : Environmental Microbiology. 11, 7, p. 1736-1751

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri.

Santos, F., Teusink, B., Molenaar, D., van Heck, M., Sieuwerts, S., de Vos, W. M. & Hugenholtz, J., 2009, In : Applied and Environmental Microbiology. 75, p. 3930-3936

Research output: Contribution to JournalArticleAcademicpeer-review

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Effects of probiotic Lactobacillus salivarius on the compositional stability of oral microbial communities.

Pham, C. I., van Spanning, R. J. M., Roling, W. F. M., Prosperi, A. C., Terefework, Z., ten Cate, J. M., Crielaard, W. & Zaura, E., 2009, In : Archives of Oral Biology. 54, p. 132-137

Research output: Contribution to JournalArticleAcademicpeer-review

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

Pillay, C. S., Hofmeyr, J. H. S., Olivier, B. G., Snoep, J. L. & Rohwer, J. M., 1 Jan 2009, In : Biochemical Journal. 417, 1, p. 269-275 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development

Bonzanni, N., Krepska, E., Feenstra, K. A., Fokkink, W. J., Kielmann, T., Bal, H. E. & Heringa, J., 15 Aug 2009, In : Bioinformatics. 25, 16, p. 2049-56 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Ferric reductase A is essential for effective iron acquisition in Paracoccus denitrificans.

Sedlacek, V., van Spanning, R. J. M. & Kucera, I., 2009, In : Microbiology. 155, p. 1294-1301

Research output: Contribution to JournalArticleAcademicpeer-review

Folate overproduction in Lactobacillus plantarum WCFS1 causes methotrexate resistance.

Wegkamp, H. B. A., Vos, W. M. & Smid, E. J., 2009, In : FEMS Microbiology Letters. 297, p. 261-265

Research output: Contribution to JournalArticleAcademicpeer-review

Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison.

Pastink, M. I., Teusink, B., Hols, P., Visser, S., Vos, W. M. & Hugenholtz, J., 2009, In : Applied and Environmental Microbiology. 75, p. 3627-3633

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slog-growth habitat-simulating retentostats.

Lin, B., Westerhoff, H. V. & Roling, W. F. M., 2009, In : Environmental Microbiology. 11, p. 2425-2433

Research output: Contribution to JournalArticleAcademicpeer-review

Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome.

Wels, M., Bongers, R. S., Boekhorst, J., Molenaar, D., Sturme, M., de Vos, W. M., Siezen, R. J. & Kleerebezem, M., 2009, In : Journal of Bacteriology. 191, p. 3420-3424

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Lifestyle of Lactobacillus plantarum in the mouse caecum.

Marco, M. L., Peter, T. H. F., Bongers, R. S., Molenaar, D., van Hemert, S., Sonnenburg, J. L., Gordon, J. I. & Kleerebezem, M., 2009, In : Environmental Microbiology. 11, p. 2747-2757

Research output: Contribution to JournalArticleAcademicpeer-review

Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration.

Ma, H., Boogerd, F. C. & Goryanin, I., 2009, In : Journal of Biotechnology. 144, p. 175-183

Research output: Contribution to JournalArticleAcademicpeer-review

Modular kinetic analysis reveals differences in Cd2+ and Cu2+ ion-induced impairment of oxidative phosphorylation in liver.

Ciapaite, J., Nauciene, Z., Baniene, R., Wagner, M. J., Krab, K. & Mildaziene, V., 2009, In : The FEBS Journal. 276, p. 3656-3668

Research output: Contribution to JournalArticleAcademicpeer-review

Noise management by molecular networks.

Bruggeman, F. J., Bluthgen, N. & Westerhoff, H. V., 2009, In : PLoS Computational Biology. 5, 9, p. e1000506 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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PanCGH: a genotype-calling algorithm for pangenome CGH data

Bayjanov, J. R., Wels, M., Starrenburg, M. J. C., van Hylckama Vlieg, J. E. T., Siezen, R. J. & Molenaar, D., 2009, In : Bioinformatics. 25, p. 309-314

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

PhyloPars: estimation of missing parameter values using phylogeny.

Bruggeman, J., Heringa, J. & Brandt, B. W., 2009, In : Nucleic Acids Research. 37, p. W179-W184

Research output: Contribution to JournalArticleAcademicpeer-review

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Population-level transcription cycles derive from stochastic timing of single-cell transcription.

Degenhardt, T., Rybakova, E. N., Tomaszewska, A., Mone, M. J., Westerhoff, H. V., Bruggeman, F. J. & Carlberg, C., 2009, In : Cell. 138, p. 489-501

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Regulatory phenotyping reveals important diversity within the species Lactococcus lactis.

Bachmann, H., Starrenburg, M. J. C., Dijkstra, A., Molenaar, D., Kleerebezem, M., Rademaker, J. L. W. & van Hylckama Vlieg, J. E. T., 2009, In : Applied and Environmental Microbiology. 75, p. 5687-5694

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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RNA structure prediction from evolutionary patterns of nucleotide composition.

Smit, S., Knight, R. & Heringa, J., 2009, In : Nucleic Acids Research. 37, p. 1378-1386

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Seasonal dynamics in leachate hydrochemistry and natural attentuation in surface run-off waste from a tropical landfill

Mangimbulude, J. C., van Breukelen, B. M., Krave, A. S., van Straalen, N. M. & Roling, W. F. M., 2009, In : Waste Management & Research. 29, p. 829-838

Research output: Contribution to JournalArticleAcademicpeer-review

Selectivity of TMC207 towards mycobacterial ATP synthase compared with that towards the eukaryotic homologue

Haagsma, A. C., Ibrahim, R. A., Wagner, M. J., Krab, K., Vergauwen, K., Guillemont, J., Andries, K., Lill, H., Koul, A. & Bald, D., Mar 2009, In : Antimicrobial Agents and Chemotherapy. 53, 3, p. 1290-1292 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Shifts in growth strategies reflect tradeoffs in cellular economics.

Molenaar, D., van Berlo, R., de Ridder, D. & Teusink, B., 2009, In : Molecular Systems Biology. 5, e-323, p. 1-10

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Simplified yet highly accurate enzyme kinetics for cases of low substrate concentrations.

Hardin, H. M., Zagaris, A., Krab, K. & Westerhoff, H. V., 2009, In : The FEBS Journal. 276, p. 5491-5506

Research output: Contribution to JournalArticleAcademicpeer-review

Spatial And Temporal Analysis Of Intestinal Microbiota In Conventionalized Germ Free Mice In Correlation With The Host Responses, Using A High-Throughput Phylogenetic Microarray.

Derrien, M., El Aidy, S., Rajilic-Stojanovic, M., Molenaar, D., Levenez, F., Zoetendal, E. G., Dore, A. J. & Kleerebezem, M., Apr 2009, In : Microbial Ecology. 57, 3, p. 566-567

Research output: Contribution to JournalArticleAcademicpeer-review

Structure and function analysis of flexible alignment regions in proteins.

Pirovano, W. A., van der Reijden, A., Feenstra, K. A. & Heringa, J., 2009, In : BMC Bioinformatics. 10, 13, p. P6

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Sulfosys (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation.

Albers, S. V., Birkeland, N. K., Driessen, A. J., Gertig, S., Haferkamp, P., Klenk, H. P., Kouril, T., Manica, A., Pham, T. K., Ruoff, P., Schleper, C., Schomburg, D., Sharkey, K. J., Siebers, B., Sierocinski, P., Steuer, R., van der Oost, J., Westerhoff, H. V., Wieloch, P., Wright, P. C. & 1 others, Zaparty, M., 2009, In : Biochemical Society Transactions. 37, p. 58-64

Research output: Contribution to JournalArticleAcademicpeer-review

Super Life: how and why 'cell selection' leads to the fastest growing eukaryote.

Groeneveld, P., Stouthamer, A. H. & Westerhoff, H. V., 2009, In : The FEBS Journal. 276, p. 254-270

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology: the elements and principles of life.

Westerhoff, H. V., Winder, C., Messiha, H., Simeonidis, E., Adamczyk, M., Verma, M., Bruggeman, F. J. & Dunn, W., 2009, In : FEBS Letters. 583, p. 3882-3890

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology towards life in silico: mathematics of the control of living cells.

Westerhoff, H. V., Kolodkin, A. N., Conradie, R., Wilkinson, S. J., Bruggeman, F. J., Krab, K., Schuppen, J. H., Hardin, H. M., Bakker, B. M., Mone, M. J., Rybakova, E. N., Eijken, M., van Leeuwen, J. P. & Snoep, J. L., 2009, In : Journal of Mathematical Biology. 58, p. 7-34

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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The contribution of CHEK2 to the TP53-negative Li-Fraumeni phenotype

Ruijs, M. W. G., Broeks, A., Menko, F. H., Ausems, M. G., Wagner, A. M., Oldenburg, R., Heijboer-Meijers, J. E., van 't Veer, L. J. & Verhoef, S. C., 2009, In : Hereditary Cancer in Clinical Practice. 7

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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The evidence that pseudovitamin B12 is biologically active in mammals is still lacking.

Santos, F., Teusink, B., de Vos, W. M. & Hugenholtz, J., 2009, In : Journal of Applied Microbiology. 107, p. 1763-1763

Research output: Contribution to JournalArticleAcademicpeer-review

The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context dependent control.

van Heeswijk, W. C., Molenaar, D., Hoving, S. & Westerhoff, H. V., 2009, In : The FEBS Journal. 276, p. 3324-3340

Research output: Contribution to JournalArticleAcademicpeer-review

The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and x chromosome specific allelic properties.

Monkhorst, K., de Hoon, B., Jonkers, I., Achame, E. M., Monkhorst, W., Hoogerbrugge, J., Rentmeester, E., Westerhoff, H. V., Grosveld, F., Grootegoed, A. & Gribnau, J., 2009, In : PLoS ONE. 4, 5, p. e-5616 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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Time-dependent regulation analysis dissects shifts between metabolic and gen-expression regulation during differentiation of bloodstream forms.

van Eunen, K., Bouwman, J., Lindenbergh, P. A., Westerhoff, H. V. & Bakker, B. M., 2009, In : The FEBS Journal. 276, p. 5521-5536

Research output: Contribution to JournalArticleAcademicpeer-review

Understanding the adaptive growth strategy of lactobacillus plantarum by in silico optimization.

Teusink, B., Wiersma, A., Jacobs, L., Notebaart, R. A. & Smid, E. J., 2009, In : PLoS Computational Biology. 5, 6, p. e1000410 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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webPRC: the profile comparer for alignment-based searching of public domain databases.

Brandt, B. W. & Heringa, J., 2009, In : Nucleic Acids Research. 37, p. W48-W52

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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2008

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 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

Research output: Contribution to JournalArticleAcademic

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

Changes at the KinA PAS-A dimerization interface influence histidine kinase function

Lee, J., Tomchick, D. R., Brautigam, C. A., Machius, M., Kort, R., Hellingwerf, K. J. & Gardner, K. H., 1 Apr 2008, In : Biochemistry. 47, 13, p. 4051-64 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Compartmentation prevents a lether turbo-explosion of glycolysis in trypanosomes.

Haanstra, J. R., van Tuijl, J. H., Kessler, P., Reijnders, W. N. M., Michels, P. A. M., Westerhoff, H. V., Parsons, M. & Bakker, B. M., 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, p. 17718-17723

Research output: Contribution to JournalArticleAcademicpeer-review

Control, responses and modularity of cellular regulatory networks: a contol analysis perspective.

Bruggeman, F. J., Snoep, J. L. & Westerhoff, H. V., 2008, In : IET Systems Biology. 2, p. 397-410

Research output: Contribution to JournalArticleAcademicpeer-review

Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei.

Haanstra, J. R., Stewart, M., Luu, V-D., van Tuijl, J. H., Westerhoff, H. V., Clayton, C. & Bakker, B. M., 2008, In : Journal of Biological Chemistry. 283, p. 2495-2507

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Design Issues for Qualitative Modelling of Biological Cells with Petri Nets

Krepska, E., Bonzanni, N., Feenstra, K. A., Fokkink, W. J., Kielmann, T., Bal, H. E. & Heringa, J., 2008, In : Lecture Notes in Computer Science. 5054, p. 48-62

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Drug-efficacy depends on the inhibitor type and the target positionin a metabolic network - a systematic study.

Gerber, S., Assmus, H. E., Bakker, B. M. & Klipp, E., 2008, In : Journal of Theoretical Biology. 252, p. 442-455

Research output: Contribution to JournalArticleAcademicpeer-review

Effect of hxk2 deletion and HAP4 overexpression on fermentative capacity in Saccharomyces cerevisiae.

Schuurmans, J. M., Rossell, S., van Tuijl, J. H., Bakker, B. M., Hellingwerf, K. J. & Teixeira de Mattos, M. J., 2008, In : FEMS Yeast Research. 8, p. 195-203

Research output: Contribution to JournalArticleAcademicpeer-review