Molecular Cell Physiology

Research Output 1978 2020

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2007

Systems Biology: new paradigms for cell biology and drug design.

Westerhoff, H. V., 2007, System Biology. Springer, p. 45-67 (Schering Workshop; no. 61).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems biology and food microbiology

Brul, S. & Westerhoff, H. V., 2007, Modelling microorganisms in food. Brul, S., van Gerwen, S. & Zwietering, M. (eds.). Cambridge UK: Woodhead Publishing Limited, p. 250-288

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology and the reconstruction of the Cell: from molecular components to integral function.

Bruggeman, F. J., Rossell Aragort, S. L., van Eunen, K., Bouwman, J., Westerhoff, H. V. & Bakker, B. M., 2007, Subcellular fractionation and proteomics.. Bertrand, E. & Faupel, M. (eds.). Dordrecht The Netherlands: Springer, p. 239-262

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

The methodologies of systems biologies

Westerhoff, H. V. & Kell, D. B., 2007, Systems Biology - Philosophical Foundations. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J-HS. & Westerhoff, H. V. (eds.). Amsterdam The Netherlands: Elsevier, p. 23-70

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

The prokaryotic nitrate reductases.

Richardson, D. J., van Spanning, R. J. M. & Ferguson, S. J., 2007, Biology of the nitrogen cycle.. Bothe, H., Ferguson, S. J. & Newton, W. E. (eds.). Elsevier Science, p. 21-36

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Towards philosophical foundations of Systems Biology: introduction.

Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J. H. S. & Westerhoff, H. V., 2007, Systems Biology - Philosophical Foundations. Boogerd, F. C., Bruggeman, F. J., Hofmeyr, J-HS. & Westerhoff, H. V. (eds.). Amsterdam The Netherlands: Elsevier, p. 3-20 342 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

2005

From isolation to integration, a systems biology approach for building the Silicon Cell.

Snoep, J. L. & Westerhoff, H. V., 2005, Systems Biology: Definitions and Perspectives.. Alberghina, L. & Westerhoff, H. V. (eds.). Heidelberg: Springer Verlag, p. 13-30 402 p. (Topics in Current Genetics; no. 13).

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

Interaktion von Biologie und Wissenschaftsphilosophie: Erklarungen emergenten Verhaltens von Zellen

Bruggeman, F. J., Boogerd, F. C., Westerhoff, H. V., Richardson, R. C. & Stephan, A., 2005, Einfuhrung in die Philosophie der Biologie.. Krohs, U. & Toepher, G. (eds.). p. 379-400

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Introduction to computational models of biochemical reaction networks.

Bruggeman, F. J., Bakker, B. M., Hornberg, J. J. & Westerhoff, H. V., 2005, Computational Systems Biology. Kriete, A. & Eils, R. (eds.). London: Elsevier Academic Press, p. 127-148

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

Prokaryotic systematics: PCR and sequence analysis of amplified 16S rRNA genes.

Roling, W. F. M. & Head, I. M., 2005, Molecular Microbial Ecology. Osborn, A. M. & Smith, C. J. (eds.). p. 25-64

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

Systems Biology; did we know it all along

Westerhoff, H. V. & Alberghina, L., 2005, Systems Biology: Definitions and Perspectives. Alberghina, L. & Westerhoff, H. V. (eds.). Heidelberg: Springer Verlag, p. 3-9 408 p. (Topics in Current Genetics; no. 13).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology: necessary developments and trends.

Alberghina, L., Hohmann, S. & Westerhoff, H. V., 2005, Systems Biology: Definitions and Perspectives. Alberghine, L. & Westerhoff, H. V. (eds.). Heidelberg: Springer Verlag, p. 389-402 (Topics in Current Genetics; no. 13).

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

The genus Paracoccus.

van Spanning, R. J. M., Stouthamer, A. H., Baker, S. C. & van Verseveld, H. W., 2005, Bergey's manual of systematic bacteriology, 2nd edition. p. 197-204

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

The nitrogen cycle: denitrification and relationship to N2 fixation.

van Spanning, R. J. M., Delgado, M. J. & Richardson, D. J., 2005, Nitrogen Fixation 1888-2001. Newton, W. (ed.). Dordrecht: Kluwer Academic Publishers, p. 277-342

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

What is systems biology? From genes to function and back.

Westerhoff, H. V. & Hofmeyr, J. H. S., 2005, Systems Biology: Definitions and Perspectives. Alberghina, L. & Westerhoff, H. V. (eds.). Heidelberg: Springer Verlag, p. 119-141 408 p. (Topics in Current Genetics; no. 13).

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

2004

'28 entries in an Encyclopedia'

Heringa, J., 2004, Dictionary of bioinformatics and computational biology. Hancock, J. & Zvelebil, M. (eds.). Hoboken NJ - USA: John Wiley & Sons Inc, 636 p.

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

A dictionary of programs for sequence analysis (Appendix 2)

Konopka, A. K. & Heringa, J., 2004, Compact handbook of computational biology.. Konopka, A. K. & Crabbe, M. J. C. (eds.). New York (NY - USA): Marcel Dekker, p. 503-536

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

Cluster analysis and statistical comparison of molecular community profile data.

van Verseveld, H. W. & Roling, W. F. M., 2004, Molecular Microbiological Ecology Manual. Dordrecht (The Netherlands): Kluwer Academic Publishers, p. 1-24

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

Computational Biology: annotated glossary of terms (appendix 1).

Konopka, A. K., Bucher, P., Crabbe, M. J. C., Crochemore, M., Heringa, J., Lisacek, F., Makalowska, I., Makalowska, W., Pesole, G., Saccone, C., Sagot, M-F., Sarai, A., Stadler, P. & Taylor, W. R., 2004, Compact handbook of computational biology. Konopka, A. K. & Crabbe, M. J. C. (eds.). New York (NY - USA): Marcel Dekker, p. 451-501

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

Metabolic engineering, what it was and what it is.

Westerhoff, H. V. & Kholodenko, B. N., 2004, Metabolic engineering in the post genomic era.. Kholodenko, B. N. & Westerhoff, H. V. (eds.). Norfolk (UK): Horizon Scientific Press, p. 1-35 456 p.

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

Metabolic engineering in the post genomic era: what it should become.

Westerhoff, H. V. & Kholodenko, B. N., 2004, Metabolic engineering in the post genomic era.. Kholodenko, B. N. & Westerhoff, H. V. (eds.). Norfolk (UK): Horizon Scientific Press, p. 435-442

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

Metabolic engineering of branched systems: redirecting the main pathway flux.

Snoep, J. L., Hoefnagel, M. H. N. & Westerhoff, H. V., 2004, Metabolic engineering in the post genomic era.. Kholodenko, B. N. & Westerhoff, H. V. (eds.). Norfolk (UK): Horizon Scientific Press, p. 357-375 456 p.

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

Protein sequence analysis and prediction of secondary structural features.

Heringa, J., 2004, Compact handbook of computational Biology. Konopka, A. K. & Crabbe, M. J. C. (eds.). New York (NY - USA): Marcel Dekker, p. 99-185

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

2003

On the mathematical modelling of metabolic pathways and its use in the identification of the most suitable drug target.

Michels, P. A. M., Bakker, B. M., Opperdoes, F. R. & Westerhoff, H. V., 2003, Tropical disease guidelines and issues: discoveries and drug development.. Fairlamb, A. H., Ridley, R. G. & Vial, H. J. (eds.). Geneva: World Health Organization, p. 135-144

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

2001

Gevaar van water, water in gevaar

de Vries, J. J., Roling, W. F. M. & van Verseveld, H. W., 2001, Grondwater: Van levensbron tot afvalverwerkingsysteem.. Everdingen, J. E. E. & Goudsmit (eds), J. (eds.). Overveen/Alphen a/d Rijn: Belvedere/Medidact, p. 141-154

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

Grondwater - Van levensbron tot afvalverwerkingsysteem.

de Vries, J. J., Roling, W. F. M. & van Verseveld, H. W., 2001, Gevaar van water, water in gevaar.. van Everdingen, J. J. E. & Goudsmit, J. (eds.). Overveen/Alphen aan de Rijn: Belvedere/Medidact, p. 141-154

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

2000

A new millenium: functional genomics, cellular bioinformatics, regulation analysis.

Westerhoff, H. V., Reijenga, C. A., Snoep, J. L., Kholodenko, B. N. & ter Kuile, B., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 1-8

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

An in vivo assay for metabolic regulation? Control by a metabolic variable.

Somsen, O. J. G. & Westerhoff, H. V., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 93-98

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Can metabolic control analysis be applied to hierarchical regulated metabolism?

de la Fuente van Benthem, A., Mendes, P., Westerhoff, H. V. & Snoep, J. L., 2000, Animating tbe cellular map. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 191-198

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

Control and metabolic dynamics: How the frequency of glycolytic oscillations in Saccharomyces cerevisiae is controlled by glucose transport.

Reijenga, C. A., Snoep, J. L. & Westerhoff, H. V., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 49-54

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Hierarchical control of DNA supercoiling in Escherichia coli: How to study homeostatically controlled systems using control analysis.

Snoep, J. L., van der Weijden, C. C., Andersen, H. W., Westerhoff, H. V. & Jensen, P. R., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 181-187

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Is the signal transduction network emanating from the EGP receptor bistable in vivo

Bruggeman, F. J., Boogerd, F. C., Hornberg, J. J., Lankelma, J., Somsen, O. J. G. & Westerhoff, H. V., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). STellenbosch - South Africa: Stellenbosch University Press, p. 159-163

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

Metabolic control from the back benches: Biochemistry towards Biocomplexity

Westerhoff, H. V., Teusink, B., Mensonides, F. I. C., Reijenga, C. A., Esgalhado, M. E. L. M., Kholodenko, B. N., Somsen, O. J. G., van Heeswijk, W. C., Boogerd, F. C. & Snoep, J. L., 2000, Technological and medical implications of Metabolic Control Analysis. Cornish-Bowden, A. C. & Cardenas, M. L. (eds.). Dordrecht - The Netherlands: Kluwer Academic Press, p. 235-242

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Modelling pyruvate distribution in Lactococcus lactis: a kinetic model to support metabolic engineering strategies.

Hoefnagel, M. H. N., Hugenholtz, J., Westerhoff, H. V. & Snoep, J. L., 2000, Animating the cellular map. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 243-247

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

Modular control analysis: are membranes or cytosol more important for growth fo the industrial yeast Kluyweromyces marxianus?

Groeneveld, P. & Westerhoff, H. V., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 277-284

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

Using metabolic control analysis to improve the selectivity and effectiviness of drugs against parasitic diseases.

Bakker, B. M., Michels, P. A. M., Walsh, M. C., Opperdoes, F. R. & Westerhoff, H. V., 2000, Technological and medical implications of metabolic control analysis.. Cornish-Bowden, A. C. & Cardenas, M. L. (eds.). Dordrecht - The Netherlands: Kluwer Academic Publishers, p. 157-164

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

What controls the growth rate of Escherichia coli? Is it transport after all?

Boogerd, F. C., Ibiyemi, D., Michelsen, O. & Jensen, P. R., 2000, Animating the cellular map.. Hofmeyr, J-HS., Rohwer, J. M. & Snoep, J. L. (eds.). Stellenbosch - South Africa: Stellenbosch University Press, p. 19-24

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

1999

In-situ bioremediation at old Dutch landfills; Plume delineation, intrinsic degradation capacity and determination of microbial community structure.

van Verseveld, H. W., van Breukelen, B. M., Roling, W. F. M., Braster, M., Soeteman, A. & Groen, J., 1999, Proceedings of the "1999 contaminated site remediation conference", Fremantle, Western Australia.. Fremantle Western Australia, p. 415-423

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

1998

A modular kinetic approach to determine which step in electron transfer from external NAD(P)H to oxygen in potato callus mitochondria is stimulated by high salt conditions

Krab, K., Wagner, A. M., Wagner, M. J. & Moller, I. M., 1998, Plant Mitochondria: From gene to function. Moller, I. M., Gardestrom, P., Glimenius, K. & Glaser, E. (eds.). Leiden - The Netherlands: Backhuys Publishers, p. 537-541 603 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

BTK traditions and perspectives: Complex biothermokinetics and control analysis.

Westerhoff, H. V., van Rotterdam, B. J., van Heeswijk, W. C., Somsen, O. J. G. & Kholodenko, B. N., 1998, BioThermoKinetics in the post Genomic Era.. Larsson, C., Pahlmann, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 1-6 402 p.

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

Cancer chemotherapy in terms of metabolic control analysis

Lankelma, J., van der Wel, H. & Westerhoff, H. V., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 163-166 402 p.

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

Control Analysis of Cellular Signal Transduction Pathways

Kholodenko, B. N., Hoek, J. B., Brown, G. C. & Westerhoff, H. V., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 102-107 402 p.

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

Control of the F1F0ATP synthetase on cell metabolism and growth in Saccharomyces cerevisiae.

Raamsdonk, L. M., Berden, J. A., Westerhoff, H. V. & van Dam, K., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 167-170 402 p.

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

Correlation of glucose catabolism and the frequency of glycolytic oscillations in Saccharomyces cerevisiae.

Reijenga, C. A., Teusink, B., van Verseveld, H. W., Snoep, J. L. & Westerhoff, H. V., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 246-249 402 p.

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

Growth of Escherichia coli on C4-dicarboxylates is significantly controlled by the C4-dicarboxylate transporter

Boogerd, F. C., Boe, L., Michelsen, O. & Ruhdal Jensen, P., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg, Sweden: Chalmers, p. 117-122 402 p.

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

Hierarchical control of DNA supercoiling

Snoep, J. L., van der Weijden, C. C., Andersen, H. W., Ruhdal Jensen, P. & Westerhoff, H. V., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 157-162 402 p.

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

Hierarchical control of electron-transfer

Westerhoff, H. V., Jensen, P. R., Egger, L., van Heeswijk, W. C., van Spanning, R. J. M., Kholodenko, B. N. & Snoep, J. L., 1998, Biological electron-transfer chains: Genetics, composition and mode of operation.. Canters, G. W. & Vijgenboom, E. (eds.). Dordrecht - The Netherlands: Kluwer Academic Publishers, (NATO ASI SERIES C).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Hierarchical control of the H+-ATPase on cytochrome expression in Escherichia coli.

Koefoed, S., Ruhdal Jensen, P., Egger, L., Westerhoff, H. V. & Snoep, J. L., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 171-174 402 p.

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

How do mitochondrial enzymes control the respiration and superoxide production rates

Demin, O. V., Westerhoff, H. V., Hoek, J. & Kholodenko, B. N., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg, Sweden: Chalmers, p. 365-369 402 p.

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

Kinetics, thermodynamics and control analysis of ATP homeostasis in contracting skeletal muscle.

Jeneson, J. A. L., Wiseman, R. W., Kushmerick, M. J. & Westerhoff, H. V., 1998, BioThermoKinetics in the post Genomic Era. Larsson, C., Pahlman, I-L. & Gustafsson, L. (eds.). Goteborg - Sweden: Chalmers, p. 179-182 402 p.

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