Molecular Cell Physiology

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2006

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 JournalArticle

Blue light activates the sigmaB-dependent stress response of Bacillus subtilis via YtvA

Avila-Pérez, M., Hellingwerf, K. J. & Kort, R., Sep 2006, In : Journal of Bacteriology. 188, 17, p. 6411-4 4 p.

Research output: Contribution to JournalArticle

Cancer: A systems biology disease.

Hornberg, J. J., Bruggeman, F. J., Westerhoff, H. V. & Lankelma, J., 2006, In : BioSystems. 83, p. 81-90 10 p.

Research output: Contribution to JournalArticle

Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms

Olivier, B. G., Rohwer, J. M., Snoep, J. L. & Hofmeyr, J. H. S., Sep 2006, In : Systems Biology. 153, 5, p. 335-337 3 p.

Research output: Contribution to JournalArticle

Effects of phosphorelay perturbations on architecture, sporulation, and spore resistance in biofilms of Bacillus subtilis

Veening, J-W., Kuipers, O. P., Brul, S., Hellingwerf, K. J. & Kort, R., Apr 2006, In : Journal of Bacteriology. 188, 8, p. 3099-109 11 p.

Research output: Contribution to JournalArticle

Effects of sequestration on signal transduction cascades.

Bluthgen, N., Bruggeman, F. J., Legewie, S., Herzel, H., Westerhoff, H. V. & Kholodenko, B. N., 2006, In : The FEBS Journal. 273, p. 895-906 12 p.

Research output: Contribution to JournalArticle

Energy metabolism and its compartmentation in Trypanosoma brucei.

van Hellemond, J. J., Bakker, B. M. & Tielens, A. G. M., 2006, In : Advances in Microbial Physiology. 50, p. 199-226

Research output: Contribution to JournalArticle

Epidermal growth factor receptor-induced activato protein 1 activity controls density-dependent growht inhibition in normal rat kidney fibroblasts.

Hornberg, J. J., Dekker, H., Peters, P. H. J., Langerak, P., Westerhoff, H. V., Lankelma, J. & Zoelen, E. J. J., 2006, In : Molecular Biotechnology. 34, p. 101-108 8 p.

Research output: Contribution to JournalArticle

Global multiple sequence alignment with repeats.

Sammeth, M. & Heringa, J., 2006, In : Proteins. 64, p. 263-274 12 p.

Research output: Contribution to JournalArticle

Marine microbes make a meal of oil.

Head, I. M., Jones, D. M. & Roling, W. F. M., 2006, In : Nature Reviews Microbiology. 4, p. 173-182 10 p.

Research output: Contribution to JournalArticle

Metabolic control of mitochondrial properties by adenine nucleotide translocator determines palmitoyl-CoA effects.

Ciapaite, J., Bakker, S. J., Diamant, M., van Eikenhorst, G., Heine, R. J., Westerhoff, H. V. & Krab, K., 2006, In : The FEBS Journal. 273, p. 5288-5302 15 p.

Research output: Contribution to JournalArticle

Microbial communities in the world's largest acid volcanic lake, Kawah Ijen in Indonesia, and inthe Banyupahit river originating from it.

Lohr, A. J., Laverman, A. M., Braster, M., van Straalen, N. M. & Roling, W. F. M., 2006, In : Microbial Ecology. 52, p. 609-618 10 p.

Research output: Contribution to JournalArticle

Net nitrification rate and presence of Nitrosospira cluster 2 in acid coniferous forest soils appear to be tree species specific.

Nugroho, R. A., Roling, W. F. M., Laverman, A. M. & Verhoef, H. A., 2006, In : Soil Biology and Biochemistry. 38, p. 1166-1171

Research output: Contribution to JournalArticle

Oncogenes are to lose control on signaling following mutation. Should we aim off target.

Hornberg, J. J. & Westerhoff, H. V., 2006, In : Molecular Biotechnology. 34, p. 109-116 8 p.

Research output: Contribution to JournalArticle

Reduction of Fe(III) colloids by Shewanella putrefaciens: a kinetic model.

Bonneville, S., Behrends, T., van Cappellen, P., Hyacinthe, C. & Roling, W. F. M., 2006, In : Geochimica et Cosmochimica Acta. 70, p. 5842-5854 13 p.

Research output: Contribution to JournalArticle

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Specificity of FNR-type regulators in Paracoccus denitrificans.

Veldman, R., Reijnders, W. N. M. & van Spanning, R. J. M., 2006, In : Biochemical Society Transactions. 34, p. 94-96 3 p.

Research output: Contribution to JournalArticle

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

Bruggeman, F. J., de Haan, J., Hardin, H. M., Bouwman, J. G., Rossell Aragort, S. L., van Eunen, K., Bakker, B. M. & Westerhoff, H. V., Sep 2006, In : Systems Biology. 153, 5, p. 318-322 5 p.

Research output: Contribution to JournalArticle

Towards building the silicon cell: A modular approach

Snoep, J. L., Bruggeman, F., Olivier, B. G. & Westerhoff, H. V., Feb 2006, In : BioSystems. 83, 2-3 SPEC. ISS., p. 207-216 10 p.

Research output: Contribution to JournalArticle

Unraveling the complexity of flux regulation; a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae.

Rossell, S., van der Weijden, C. C., Lindenbergh, P. A., van Tuijl, J. H., Francke, C., Bakker, B. M. & Westerhoff, H. V., 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, p. 2166-2171 6 p.

Research output: Contribution to JournalArticle

2005

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

Assessment of heat resistance of bacterial spores from food product isolates by fluorescence monitoring of dipicolinic acid release

Kort, R., O'Brien, A. C., van Stokkum, I. H. M., Oomes, S. J. C. M., Crielaard, W., Hellingwerf, K. J. & Brul, S., Jul 2005, In : Applied and Environmental Microbiology. 71, 7, p. 3556-64 9 p.

Research output: Contribution to JournalArticle

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 JournalArticle

Control of MAPK signalling: from complexity to what really matters.

Hornberg, J. J., Binder, B., Bruggeman, F. J., Schoeberl, B., Heinrich, R. & Westerhoff, H. V., 2005, In : Oncogene. 24, p. 5533-5542 10 p.

Research output: Contribution to JournalArticle

Emergence and its place in nature; a case study of biochemical networks

Boogerd, F. C., Bruggeman, F. J., Richardson, R. C., Stephan, A. & Westerhoff, H. V., 2005, In : Synthese. 145, p. 131-164 34 p.

Research output: Contribution to JournalArticle

Evolutie, het enige intelligent design

van den Bergh, J. C. J. M., Berkhout, F. G. H., Eiben, G., Smit, G., van Straalen, N. M. & Westerhoff, H. V., 18 Jun 2005, In : de Volkskrant katern "Het Betoog". p. 3-3 1 p.

Research output: Contribution to JournalArticle

Evolutietheorie is een verbluffend goed werkende theorie

van den Bergh, J. C. J. M., Berkhout, F. G. H., Eiben, G., Smit, G., van Straalen, N. M. & Westerhoff, H. V., 30 Jun 2005, In : Ad Valvas. p. 10-10 1 p.

Research output: Contribution to JournalArticle

Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill.

Lin, B., Braster, M., van Breukelen, B. M., van Verseveld, H. W., Westerhoff, H. V. & Roling, W. F. M., 2005, In : Applied and Environmental Microbiology. 71, p. 5983-5991 9 p.

Research output: Contribution to JournalArticle

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Geobacteraceae community composition is related to hydrochemistry and biodegradetion in an iron-reducing aquifer polluted by a neigbour landfill

Lin, B., van Breukelen, B. M., van Verseveld, H. W., Westerhoff, H. V. & Roling, W. F. M., 2005, In : Applied and Environmental Microbiology. 10, 71, p. 5983-5991

Research output: Contribution to JournalArticle

Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae.

Rossell Aragort, S. L., van der Weijden, C. C., Kruckeberg, A. L., Bakker, B. M. & Westerhoff, H. V., 2005, In : FEMS Yeast Research. 5, p. 611-619 9 p.

Research output: Contribution to JournalArticle

Loss of periplasmic NosX locks the nitrous oxide reductase of Paracoccus denitrificans in a catalytically incompetent state in vivo.

Wunsch, P., Kroner, H., van Spanning, R. J. M., Kroneck, P. & Zumft, W. G., 2005, In : FEBS Letters. 579, p. 4605-4609

Research output: Contribution to JournalArticle

Modular kinetic analysis of the adenine nucleotide translocator-mediated effects of palmitoyl-CoA on the oxidative phosphorylation in isolated rat liver mitochondria

Ciapaite, J., van Eikenhorst, G., Bakker, S. J. L., Diamant, M., Heine, R. J., Wagner, M. J., Westerhoff, H. V. & Krab, K., 2005, In : Diabetes. 54, 4, p. 944-951

Research output: Contribution to JournalArticle

Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite

Beaumont, H. J. E., Lens, S. I., Westerhoff, H. V. & van Spanning, R. J. M., Oct 2005, In : Journal of Bacteriology. 187, 19, p. 6849-51 3 p.

Research output: Contribution to JournalArticle

Presence of Nitrosospiral cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils.

Nugroho, R. A., Roling, W. F. M., Laverman, A. M., Zoomer, R. & Verhoef, H. A., 2005, In : FEMS Microbiology Ecology. 53, p. 473-481 9 p.

Research output: Contribution to JournalArticle

Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control

Hornberg, J. J., Bruggeman, F. J., Binder, B., Geest, C. R., de Vaate, A. J., Lankelma, J., Heinrich, R. & Westerhoff, H. V., 2005, In : The FEBS Journal. 272, 1, p. 244-258

Research output: Contribution to JournalArticle

Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control.

Hornberg, J. J., Bruggeman, F. J., Binder, B., Geest, C. R., bij de Vaate, M. J., Lankelma, J., Heinrich, R. & Westerhoff, H. V., 2005, In : The FEBS Journal. 272, p. 244-258 15 p.

Research output: Contribution to JournalArticle

Systems Biology ... in action.

Westerhoff, H. V., 2005, In : Current Opinion in Biotechnology. 16, p. 326-328

Research output: Contribution to JournalArticle

Systems Biology in Europe ...... a fermenting paradox.

Westerhoff, H. V., 2005, In : BIOforum Europe. 02, p. 25-27

Research output: Contribution to JournalArticle

Training of yeast cell dynamics

Reijenga, C. A., Bakker, B. M., van der Weijden, C. C. & Westerhoff, H. V., 2005, In : The FEBS Journal. 272, p. 1616-1624 9 p.

Research output: Contribution to JournalArticle

Yeast glycolytic oscillations that are not controlled by a single oscillophore: A new definition of oscillophore strength.

Reijenga, K. A., van Megen, Y. M. G. A., Kooi, B. W., Bakker, B. M., Snoep, J. L., van Verseveld, H. W. & Westerhoff, H. V., 2005, In : Journal of Theoretical Biology. 232, p. 385-398

Research output: Contribution to JournalArticle

2004

A tool for gene expression based PubMed search through combining data sources.

Korotkiy, M., Middelburg, R. A., Dekker, H., van Harmelen, F. A. H. & Lankelma, J., 2004, In : Bioinformatics. 20, 12, p. 1980-1982 3 p.

Research output: Contribution to JournalArticle

Open Access
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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 JournalArticle

Open Access
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Contact-based sequence alignment.

Kleinjung, J., Romein, J. W., Lin, K. & Heringa, J., 2004, In : Nucleic Acids Research. 32, 8, p. 2464-2473 10 p.

Research output: Contribution to JournalArticle

Open Access
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Coordinated behavior of mitochondria in both space and time: a reactive species-activated wave of mitochondrial depolarization.

Brady, N., Elmore, S. P., van Beek, J. H. G. M., Krab, K., Courtoy, P. J., Hue, L. & Westerhoff, H. V., 2004, In : Biophysical Journal. 87, p. 2022-2034 13 p.

Research output: Contribution to JournalArticle

Open Access
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Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type and NirK- and NorB-deficient mutants.

Schmidt, I., van Spanning, R. J. M. & Jetten, M., 2004, In : Microbiology. 150, p. 4107-4114 8 p.

Research output: Contribution to JournalArticle

DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction

Kort, R., Komori, H., Adachi, S., Miki, K. & Eker, A., Jul 2004, In : Acta Crystallographica Section D. Biological Crystallography. 60, Pt 7, p. 1205-13 9 p.

Research output: Contribution to JournalArticle

Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor

Beaumont, H. J. E., Lens, S. I., Reijnders, W. N. M., Westerhoff, H. V. & van Spanning, R. J. M., Oct 2004, In : Molecular Microbiology. 54, 1, p. 148-58 11 p.

Research output: Contribution to JournalArticle

Initial events in the photocycle of photoactive yellow protein

Kort, R., Hellingwerf, K. J. & Ravelli, R. B. G., 18 Jun 2004, In : Journal of Biological Chemistry. 279, 25, p. 26417-24 8 p.

Research output: Contribution to JournalArticle