Molecular Cell Physiology

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2008

Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate

Brad, T., Braster, M., van Breukelen, B. M., van Straalen, N. M. & Roling, W. F. M., 2008, In : Applied and Environmental Microbiology. 74, 13, p. 3959-3968

Research output: Contribution to JournalArticle

Open Access
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From genetic privacy to open consent.

Lunshof, J., Chadwick, R., Vorhaus, D. B. & Church, G. M., 2008, In : Nature Reviews Genetics. 9, p. 406-411

Research output: Contribution to JournalArticle

Hippocrates revisited? Old ideals and new realities.

Lunshof, J., Chadwick, R. & Church, G. M., 2008, In : Genomic Medicine. 2, p. 1-3

Research output: Contribution to JournalArticle

Open Access
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Increased glucose metabolism and atp level in brain tissue of Huntington's disease transgenic mice.

Olah, J., Kliveny, P., Gardian, G., Vecsey, L., Orosz, F., Kovacs, G. G., Westerhoff, H. V. & Ovadi, J., 2008, In : The FEBS Journal. 275, p. 4740-4755

Research output: Contribution to JournalArticle

Integrating systems approaches into pharmaceutical sciences.

Westerhoff, H. V., Mosekilde, E., Noe, C. & Clemensen, A. M., 2008, In : European Journal of Pharmaceutical Sciences. 35, p. 1-4

Research output: Contribution to JournalArticle

Microarray analysis reveals a mechanism of phenolic polybrominated diphenylether toxicity in zebrafish

van Boxtel, A. L., Kamstra, J. H., Cenijn, P. H., Pieterse, B., Wagner, M. J., Antink, M., Krab, K., van der Burg, B., Marsh, G., Brouwer, A. & Legler, J., 2008, In : Environmental Science and Technology. 42, 5, p. 1773-1779 7 p.

Research output: Contribution to JournalArticle

Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathway in response to a HAP4 overexpression in Saccharomyces cerevisiae.

Rossell, S., Lindenbergh, P. A., van der Weijden, C. C., Kruckeberg, A. L., van Eunen, K., Westerhoff, H. V. & Bakker, B. M., 2008, In : FEMS Yeast Research. 8, p. 195-203

Research output: Contribution to JournalArticle

MLPA diagnostics of complex microbial communities. Relative quantification of bacterial species in oral biofilms.

Terefework, Z., Pham, C. I., Prosperi, A. C., Entius, M. M., Errami, A., van Spanning, R. J. M., Zaura, E., ten Cate, J. M. & Crielaard, W., 2008, In : Journal of Microbiological Methods. 75, p. 558-565

Research output: Contribution to JournalArticle

Modelling the effect of sub(lethal) heat treatment of Bacillus subtilis spores on germination rate and outgrowth to exponentially growing vegetative cells

Smelt, J. P. P. M., Bos, A. P., Kort, R. & Brul, S., 30 Nov 2008, In : International Journal of Food Microbiology. 128, 1, p. 34-40 7 p.

Research output: Contribution to JournalArticle

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

Ye, K., Feenstra, K. A., Heringa, J., Ijzerman, A. P. & Marchiori, E., 1 Jan 2008, In : Bioinformatics. 24, 1, p. 18-25 8 p.

Research output: Contribution to JournalArticle

On defining the dynamics of hydrophobic patches on protein surfaces

Lijnzaad, P., Feenstra, K. A., Heringa, J. & Holstege, F. C. P., Jul 2008, In : Proteins. 72, 1, p. 105-14 10 p.

Research output: Contribution to JournalArticle

Personal-genome tests a blurring the boundary between experts and lay people.

Prainsack, B., Reardon, J., Hindmarsh, R., Gottweis, H., Naue, U. & Lunshof, J., 2008, In : Nature. 456, p. 34-35

Research output: Contribution to JournalArticleAcademicpeer-review

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

Pirovano, W., Feenstra, K. A. & Heringa, J., 15 Feb 2008, In : Bioinformatics. 24, 4, p. 492-7 6 p.

Research output: Contribution to JournalArticle

Predicting protein interactions from functional specificity.

Feenstra, K. A., Bastianelli, G. & Heringa, J., 2008, In : NIC Series. 40, p. 89-92

Research output: Contribution to JournalArticle

Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation.

Postmus, J., Canelas, A. B., Bouwman, J., Bakker, B. M., van Gulik, W. R., Teixeira de Mattos, M. J., Brul, S. & Smits, G. J., 2008, In : Journal of Biological Chemistry. 283, p. 23524-23532

Research output: Contribution to JournalArticle

Open Access
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Regulation of the thermogenesis in flowering Araceae: the role of the alternative oxidase.

Wagner, A. M., Krab, K., Wagner, M. J. & Moore, A. L., 2008, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1777, p. 993-1000

Research output: Contribution to JournalArticle

Open Access

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

Brandt, B. W., Heringa, J. & Leunissen, J. A. M., 2008, In : Nucleic Acids Research. 36, p. W255-W259

Research output: Contribution to JournalArticle

Open Access
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Signalling control strength.

Westerhoff, H. V., 2008, In : Journal of Theoretical Biology. 252, p. 555-567

Research output: Contribution to JournalArticle

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer

Brad, T., van Breukelen, B. M., Braster, M., van Straalen, N. M. & Roling, W. F. M., 2008, In : FEMS Microbiology Ecology. 65, 3, p. 534-543

Research output: Contribution to JournalArticle

Systems biology - The grand challenge for european biology.

Westerhoff, H. V., 2008, In : Screening. 9, p. 34-37

Research output: Contribution to JournalArticle

Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability

Kort, R., Keijser, B. J., Caspers, M. P. M., Schuren, F. H. J. & Montijn, R. C., 6 Dec 2008, In : BMC Genomics. 9, p. 590

Research output: Contribution to JournalArticle

Open Access

Two Homologous Agr-Like Quorum-Sensing Systems Cooperatively Control Adherence, Cell Morphology, and Cell Viability Properties in Lactobacillus plantarum WCFS1

Fujii, T., Ingham, C., Nakayama, J., Beerthuyzen, M., Kunuki, R., Molenaar, D., Sturme, M., Vaughan, E., Kleerebezem, M. & de Vos, W., Dec 2008, In : Journal of Bacteriology. 190, 23, p. 7655-7665

Research output: Contribution to JournalArticle

Vertical systems biology: from DNA to flux and back.

Bevilacqua, A., Wilkinson, S. J., Dimelow, R., Murabito, E., Rehman, S., Nardelli, M., van Eunen, K., Rossell, S., Bruggeman, F. J., Bluthgen, N., de Vos, D. L., Bouwman, J., Bakker, B. M. & Westerhoff, H. V., 2008, In : SEB Experimental Biology Series. 61, p. 65-91

Research output: Contribution to JournalArticle

2007

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

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 JournalArticle

Dominance of Geobacteraceae in BTX-grading enrichments from an iron-reducing aquifer.

Botton, S., van Harmelen, M., Braster, M., Parsons, J. & Roling, W. F. M., 2007, In : FEMS Microbiology Ecology. 62, p. 118-130 13 p.

Research output: Contribution to JournalArticle

FluxSimulator: An R package to simulate isotopomer distributions in metabolic networks

Binsl, T. W., Mullen, K. M., van Stokkum, I. H. M., Heringa, J. & van Beek, J. H. G. M., 2007, In : Journal of Statistical Software. 18, 7

Research output: Contribution to JournalArticle

Open Access
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Functioning phosphorylation in liver mitochondria of high-fat diet fed rats.

Ciapaite, J., Bakker, S. J. L., van Eikenhorst, G., Wagner, M. J., Schalkwijk, C. G., Teerlink, T., Fodor, M., Ouwens, D. M., Diamant, M., Heine, R. J., Westerhoff, H. V. & Krab, K., 2007, In : Biochimica et Biophysica Acta. Molecular Basis of Disease. 1772, p. 307-316

Research output: Contribution to JournalArticle

Open Access

Influence of El Niña climate events and litter removal on inorganic nitrogen dynamics in pine forest soils on Central Java, Indonesia.

Krave, A. S., van Straalen, N. M., van Verseveld, H. W. & Roling, W. F. M., 2007, In : European Journal of Soil Biology. 43, p. 39-47

Research output: Contribution to JournalArticle

Iron-reducing microorganisms in a landfill leachate-polluted aquifer: complementing culture-independent information with enrichments and isolations

Lin, B., Braster, M., Roling, W. F. M. & van Breukelen, B. M., 2007, In : Geomicrobiology Journal. 24, p. 283-294

Research output: Contribution to JournalArticle

Low nitrification rates in acid Scots pine forest soils are due to pH-related factors.

Nugroho, R. A., Roling, W. F. M., Laverman, A. M. & Verhoef, H. A., 2007, In : Microbial Ecology. 53, p. 89-97

Research output: Contribution to JournalArticle

Open Access
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Metabolic control analysis to identify optimal drug targets.

Hornberg, J. J., Bruggeman, F. J., Bakker, B. M. & Westerhoff, H. V., 2007, In : Progress in Drug Research. 64, p. 173-189

Research output: Contribution to JournalArticle

Modeling the effects of binary mixtures on survival in time.

Baas, J., van Houte, B. P. P., van Gestel, C. A. M. & Kooijman, S. A. L. M., 2007, In : Environmental Toxicology and Chemistry. 26, p. 1320-1327

Research output: Contribution to JournalArticle

Observers for linear positive systems.

Hardin, H. M. & Schuppen, J. H., 2007, In : Linear Algebra and its Applications. 425, p. 571-607

Research output: Contribution to JournalArticle

Open Access

Palmitate and oleate have distinct effects on the inflammatory phenotype of human endothelial cells.

Ciapaite, J., van Bezu, J., van Eikenhorst, G., Bakker, S. J. L., Teerlink, T., Diamant, M., Heine, R. J., Krab, K., Westerhoff, H. V. & Schalkwijk, C. G., 2007, In : Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 1771, p. 147-154

Research output: Contribution to JournalArticle

Phylogenetic and physiological diversity of dissimilatory ferric iron reducers in sediments of the polluted Scheldt estuary, Northwest Europe.

Lin, B., Hyacinthe, C., Bonneville, S., Braster, M., van Cappellen, P. & Roling, W. F. M., 2007, In : Environmental Microbiology. 9, p. 1956-1968

Research output: Contribution to JournalArticle

Right-ventricular failure is associated with increased mitochondrial complex II activity and production of reactive oxygen species.

Redout, E. M., Wagner, M. J., Zuidwijk, M. J., Boer, C., Musters, R. J. P., van Hardeveld, C., Paulus, W. J. S. & Simonides, W. S., 2007, In : Cardiovascular Research. 74, p. 770-781

Research output: Contribution to JournalArticle

Sequence harmony: detecting functional specificity from alignments

Feenstra, K. A., Pirovano, W., Krab, K. & Heringa, J., Jul 2007, In : Nucleic Acids Research. 35, Web Server issue, p. W495-8

Research output: Contribution to JournalArticle

Open Access
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Systems Biology - Is Europe taking up the Grand Challenge?

Westerhoff, H. V., 2007, In : BIOforum Europe. 12, p. 2-3

Research output: Contribution to JournalArticle

Temperature compensation through Systems Biology.

Ruoff, P., Zakhartsev, M. & Westerhoff, H. V., 2007, In : The FEBS Journal. 274, p. 940-950

Research output: Contribution to JournalArticle

The domains carrying the oposing activities in adenylyltransferase are separated by a central regulatory domain.

Clancy, P., Xu, Y., van Heeswijk, W. C., Vasudevan, S. G. & Ollis, D. L., 2007, In : The FEBS Journal. 274, p. 2865-2877

Research output: Contribution to JournalArticle

The flux through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

Daran-Lapujade, P. A. L., Rossell Aragort, S. L., van Gulik, W. M., Luttik, M. A., de Groot, M. J. L., Slijper, M., Heck, A. J., Daran, J. M., de Winde, J. H., Westerhoff, H. V., Pronk, J. T. & Bakker, B. M., 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, p. 15753-15758

Research output: Contribution to JournalArticle

The nature of systems biology

Bruggeman, F. J. & Westerhoff, H. V., 2007, In : Trends In Microbiology. 15, p. 45-50 6 p.

Research output: Contribution to JournalArticle

2006

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

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

Approaches to biosimulation of cellular processes.

Bruggeman, F. J. & Westerhoff, H. V., 2006, In : Journal of Biological Physics. 32, p. 273-288 16 p.

Research output: Contribution to JournalArticle

Aubergene - a sensitive genome alignment tool.

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

Research output: Contribution to JournalArticle

Open Access
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