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  • Hans Victor Westerhoff
2011

Absorption spectroscopy.

Nilapwar, S. M., Nardelli, M., Westerhoff, H. V. & Verma, M., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 59-75 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

A probabilistic approach to identify putative drug targets in biochemical networks.

Murabito, E., Smalbone, K., Swinton, J., Westerhoff, H. V. & Steuer, R., 2011, In : Journal of the Royal Society Interface. 8, p. 880-895

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Dupuytren's: a systems biology disease.

Rehman, S., Goodacre, R., Day, P. J., Bayat, A. & Westerhoff, H. V., 2011, In : Arthritis Research & Therapy. 13, 328, p. 1-12

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Enzyme kinetics for systems biology when, why and how

Adamczyk, M., van Eunen, K., Bakker, B. M. & Westerhoff, H. V., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 233-257 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

From silicon cell to silicon human.

Westerhoff, H. V., Verma, M., Bruggeman, F. J., Kolodkin, A. N., Swat, M., Hayes, N., Nardelli, M., Bakker, B. M. & Snoep, J. L., 2011, BetaSys, Stystems Biology 2. Booss-Bavrbek, B., Klosgen, B., Larsen, J., Pociot, F. & Renstrom, E. (eds.). Springer Science + Business Media., p. 439-460

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Health technology assessment in the era of personalized health care.

Becla, L., Lunshof, J. E., Gurwitz, D., Schulte in de Baumen, T., Westerhoff, H. V., Lange, B. & Brand, A., 2011, In : International Journal of Technology Assessessment in Health Care. 27, p. 118-126

Research output: Contribution to JournalArticleAcademicpeer-review

How molecular competition influences fluxes in gene expression networks.

de Vos, D. L., Bruggeman, F. J., Westerhoff, H. V. & Bakker, B. M., 2011, In : PLoS ONE. 6, 12, e28494.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

HPLC-MS/MS methods for the quantitative analysis of 5-oxoproline (pyroglutamate) in rat plasma and hepatic cell line culture medium.

Geenen, A., Guallar-Hoays, C., Michopoulos, F., Kenna, J. G., Kolaja, K. L., Westerhoff, H. V., Thomas, P. & Wilson, I., 2011, In : Journal of Pharmaceutical and Biomedical Analysis. 56, p. 655-663

Research output: Contribution to JournalArticleAcademicpeer-review

HPLC-MS/MS methods for the quantitative analysis of ophthalmic acid in rodent plasma and hepatic cell line culture medium

Geenen, S., Michopoulos, F., Kenna, J. G., Kolaja, K. L., Westerhoff, H. V. & Wilson, I., 2011, In : Journal of Pharmaceutical and Biomedical Analysis. 54, p. 1128-1135

Research output: Contribution to JournalArticleAcademicpeer-review

ITFoM - The IT Future of Medicine

Lehrach, H., Subrak, R., Boyle, P., Pasterk, M., Zatloukal, K., Muller, H., Hubbard, T., Brand, A., Girolami, M., Jameson, D., Bruggeman, F. J. & Westerhoff, H. V., 2011, In : Procedia Computer Science. 7, p. 26-29

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Metabolite profiling of recombinant CHO cells: Designing tailored feeding regimes that enhance recombinant antibody production.

Sellick, C. A., Croxford, A. S., Maqsood, A. R., Stephens, G., Westerhoff, H. V., Goodacre, R. & Dickson, A. J., 2011, In : Biotechnology and Bioengineering. 108, 12, p. 3025-3031

Research output: Contribution to JournalArticleAcademicpeer-review

Methods in Enzymology

Jameson, D. (ed.), Verma, M. (ed.) & Westerhoff, H. V. (ed.), 2011, Burlington: Academic Press. (Methods in System Biology; no. 500)

Research output: Book / ReportBook editingAcademic

Modelling approaches in systems biology, including Silicon Cell models.

Kolodkin, A. N., Boogerd, F. C., Bruggeman, F. J. & Westerhoff, H. V., 2011, Systems Biology and Livestock Science. te Pas, M. F. W., Woelders, H. & Bannink, A. (eds.). Wiley-Blackwell, p. 31-51

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Quantitative analysis of flux regulation through hierarchical regulation analysis.

van Eunen, K., Rossell, S., Bouwman, J., Westerhoff, H. V. & Bakker, B. M., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 571-595 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Recommendations for terminology and databases for biochemical thermodynamics.

Alberty, R. A., Cornish-Bowden, A., Goldberg, R. N., Hammes, G. G., Tipton, K. & Westerhoff, H. V., 2011, In : Biophysical Chemistry. 155, p. 89-103

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology has reached adulthood ..... in some places.

Westerhoff, H. V., 2011, Systems Biology in Baden_Wurttemberg. BIOPRO Baden-Wurttemberg (ed.). Stuttgart, Germany: BIOPRO Baden-Wurttemberg GmbH, p. 6-12 (BIOPRO; no. 07).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology left and right .

Westerhoff, H. V., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 3-11 (Methods in Systems Biology; no. 500).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.

Swat, M., Kielbasa, S. M., Polak, S., Olivier, B. G., Bruggeman, F. J., Quinton Tulloch, M., Snoep, J. L., Verhoeven, A. J. & Westerhoff, H. V., 2011, In : Interfaces. 1, p. 16-23

Research output: Contribution to JournalArticleAcademicpeer-review

2012

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 JournalArticleAcademicpeer-review

A systems biology approach to deciphering the etiology of steatosis employing patient-derived dermal fibroblasts and iPS cells.

Jozefczuk, J., Kashofer, K., Ummani, R., Henjes, F., Rehman, S., Geenen, S., Wruck, W., Regenbrecht, C., Daskalaki, A., Wierling, C., Turano, P., Bertini, I., Korf, U., Zatloukal, K., Westerhoff, H. V., Lehrach, H. & Adjaye, J., 2012, In : Frontiers in Physiology. 3, 339, p. 1-4 UNSP 339.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Dupuytren's disease metabolite analyses reveals alterations following initial short-term fibroblast culturing.

Rehman, S., Xu, Y., Dunn, W. B., Day, P. J., Westerhoff, H. V., Goodacre, R. & Bayat, A., 2012, In : Molecular BioSystems. 8, p. 2274-2288

Research output: Contribution to JournalArticleAcademicpeer-review

Emergence of the silicon human and network targeting drugs.

Kolodkin, A. N., Boogerd, F. C., Plant, N., Bruggeman, F. J., Goncharuk, V., Lunshof, J. E., Moreno-Sanchez, R., Yilmaz, N., Bakker, B. M., Snoep, J. L., Balling, R. & Westerhoff, H. V., 2012, In : European Journal of Pharmaceutical Sciences. 46, p. 190-197

Research output: Contribution to JournalArticleAcademicpeer-review

Systems biology tools for toxicology.

Geenen, S., Taylor, P. N., Snoep, J. L., Wilson, I. D., Kenna, J. G. & Westerhoff, H. V., 2012, In : Archives of Toxicology. 86, 8, p. 1251-1271

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Testing biochemistry revisited: how in viov metabolism can be understood from in vitro enzyme kinetics.

van Eunen, K., Kiewiet, J. A. L., Westerhoff, H. V. & Bakker, B. M., 2012, In : PLoS Computational Biology. 8, e1002483.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Understanding complexityin neurodegenerative diseases: in silico reconstructionof emergence

Kolodkin, A. N., Simeonides, E., Balling, R. & Westerhoff, H. V., 2012, In : Frontiers in Physiology. UNSP 291.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism

Rehman, S., Day, P. J. R., Bayat, A. & Westerhoff, H. V., 2012, In : Frontiers in Physiology. 3, UNSP 316.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Why in vivo may not equal in vitro-new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions

Garcia Contreras, R., Vos, P., Westerhoff, H. V. & Boogerd, F. C., 2012, In : The FEBS Journal. 279, 22, p. 4145-4159

Research output: Contribution to JournalArticleAcademicpeer-review

2013
Open Access

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

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-review

Open Access

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

Mensonides, F. I. C., Bakker, B. M., Cremazy, F., Messiha, H. L., Mendes, P., Boogerd, F. C. & Westerhoff, H. V., 2013, In : FEBS Letters. 587, 17, p. 2860-2867 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Computing life: add Logos to Biology and Bios to Physics

Kolodkin, A. N., Simeonidis, E. & Westerhoff, H. V., 2013, In : Progress in Biophysics and Molecular Biology. 111, p. 69-74

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Glutathione metabolism modelling: a mechanism for liver drug-robustness and a new biomarker strategy

Geenen, S., du Preez, F. B., Snoep, J. L., Foster, A. J., Sarda, S., Kenna, J. G., Wilson, I. D. & Westerhoff, H. V., 2013, In : Biochimica et Biophysica Acta (BBA) - General Subjects. 1830, p. 4943-4959

Research output: Contribution to JournalArticleAcademicpeer-review

Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus

Kouril, J., Kort, J., Siebers, B., Westerhoff, H. V. & Snoep, J. L., 2013, In : The FEBS Journal. 280, p. 4660-4680

Research output: Contribution to JournalArticleAcademicpeer-review

Mathematical modelling of miRNA medidated BCR.ABL protein regulation in chronic myeloid leukaemia vis-à-vis therapeutic strategies

Verma, M., Karimiani, E. G., Byers, R. J., Rehman, S., Westerhoff, H. V. & Day, P. J. R., 2013, In : Integrative Biology. 5, p. 543-554

Research output: Contribution to JournalArticleAcademicpeer-review

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

van Heeswijk, W. C., Westerhoff, H. V. & Boogerd, F. C., 2013, In : Microbiology and Molecular Biology Reviews. 77, p. 628-695

Research output: Contribution to JournalArticleAcademicpeer-review

Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico

Quinton-Tulloch, M. J., Bruggeman, F. J., Snoep, J. L. & Westerhoff, H. V., 2013, In : The FEBS Journal. 280, p. 160-173

Research output: Contribution to JournalArticleAcademicpeer-review

‘Domino’ systems biology and the ‘A’ of ATP

Westerhoff, H. V., Verma, M., Zakhartsev, M. & Reuss, M., 2013, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1827, p. 19-29

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2014

An in vivo control map for the eukaryotic mRNA translation machinery

Firczuk, H., Kannambath, S., Pahle, J., Claydon, A., Beynon, R., Duncan, J., Westerhoff, H. V., Mendes, P. & McCarthy, J. E. G., 2014, In : Molecular Systems Biology. 6

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Clusters of reaction rates and concentrations in protein networks such as phosphotransferase system

Hardin, H. M., Zagaris, A., Willms, A. R. & Westerhoff, H. V., 2014, In : The FEBS Journal. 281, p. 531-548

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Effects of cadmium and mercury on theupper part of skeletal muscle glycolysis in mice.

Ramirez-Bajo, M. J., de Atauri, P., Ortega, F., Westerhoff, H. V., Gelpi, J. L., Centelles, J. J. & Cascante, M., 2014, In : PLoS ONE. 9, 1, e80018.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Macromolecular networks and intelligence in microorganisms.

Westerhoff, H. V., Brooks, A., Simeonidis, E., Garcia-Contreras, R., He, F., Boogerd, F. C., Jackson, V. J., Goncharuk, V. & Kolodkin, A. N., 2014, In : Frontiers in Microbiology. 5, p. 1-17 379.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: Insigths into metabolic regulation.

Murabito, E., Verma, M., Bekker, M., Bellomo, D., Westerhoff, H. V., Teusink, B. & Steuer, R., 2014, In : PLoS ONE. 9, 9, e106453.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Multiscale modelling approach combining a kinetic model of glutathione metabolism with PBPK models of paracetamol and the potential glutathione-depletion biomarkes ophthalmic acid and 5-oxoproline in humans and rats

Geenen, S., Yates, J. W. T., Kenna, J. G., Bois, F. Y., Wilson, I. D. & Westerhoff, H. V., 2014, In : Integrative Biology. 5, p. 877-888

Research output: Contribution to JournalArticleAcademicpeer-review

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network.

Kolodkin, A., Sahin, N., Phillips, A., Hood, S. R., Bruggeman, F. J., Westerhoff, H. V. & Plant, N., 2014, In : Nature Communications. 4

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria

Feldman-Salit, A., Hering, S., Messiha, H., Veith, N., Cojocaru, V., Sieg, A., Westerhoff, H. V., Kreikemeyer, B., Wade, R. & Fiedler, T., 2014, In : Journal of Biological Chemistry. 288, p. 21295-21306

Research output: Contribution to JournalArticleAcademicpeer-review

The control analysis of signal transduction.

Westerhoff, H. V., Rehman, S., Boogerd, F. C., Yilmaz, N. & Verma, M., 2014, Systems biology of metabolic and signaling networks. Aon, M. (ed.). Berlin - Germany: Springer Verlag, p. 39-62

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review