Molecular Cell Physiology

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12 The family Geobacteraceae

Roling, W. F. M., 2014, The Prokaryotes - Deltaproteobacteria and Epsilonproteobacteria. Rosenberg, E., Delong, E. F., Lory, S., Stackebrand, E. & Thompson, F. (eds.). p. 157-172

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'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.

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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).

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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

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Aerobe en anaerobe bacterien: Ademhalen zonder zuurstof.

van Spanning, R. J. M., 2011, Microcanon; wat je beslist moet weten over microbiologie.. De wetenschappelijke Bibliotheek, Natuurwetenschap en Techniek. (ed.). Diemen: Veen Magazines, p. 61-64

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Afterthoughts as foundations for systems biology.

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. 321-336 342 p.

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A kinetic model as a tool to understand the response of Saccharomyces cerevisiae to heat exposure.

Mensonides, F. I. C., Bakker, B. M., Brul, S., Hellingwerf, K. J. & Teixeira de Mattos, M. J., 2007, Modelling microorganisms in food.. Brul, S., van Gerwen, S. & Zwietering, M. (eds.). Cambridge UK: Woodhead Publishing Limited, p. 228-245

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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.

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Analysis of the hierarchical and metabolic regulation of flux through metabolic pathways.

Roling, W. F. M., Fillinger, L. & Nunes da Rocha, U., 2014, (Accepted/In press) Hydrocarbon and lipid microbiology protocols.. Timmis, K. N. (ed.). Berlin-Heidelberg: Springer Verlag

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Analysis of the regulation of the rate of hydrocarbon and nutrient flow through microbial communities.

Roling, W. F. M., Fillinger, L. & Nunes da Rocha, U., 2014, Hydrocarbon and Lipid Microbiology Protocols.. Timmis, K.N. (ed.). Humana Press

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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

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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

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A practical guide to genome-scale metabolic models and their analysis.

Santos, F., Boele, J. & Teusink, B., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 509-532 (Methods in Systems Biology; no. 500).

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A systems biology perspective on obesity and type 2 diabetes.

Ciapaite, J., Bakker, S. J. L., Heine, R. J., Krab, K. & Westerhoff, H. V., 2007, Molecular System Bioenergetics. Saks, V. (ed.). Weinheim Germany: Wiley-VCH Verlag GmbH & Co. KGaA, p. 571-592

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Attacking Blood-Borne Parasites with Mathematics

van Niekerk, D. D., Penkler, G. P., du Toit, F., Snoep, J. L., Bakker, B. M. & Haanstra, J. R., 2016, Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery. Muller, S., Cerdan, R., Radulescu, O. & Selzer, P. (eds.). 1 ed. Wiley-VCH Verlag GmbH & Co. KGaA, Vol. 7. p. 513 541 p.

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Biochemistry and molecular biology of nitrification.

Ferguson, S. J., Richards, D. J. & van Spanning, R. J. M., 2007, Biology of the nitrogen cycle.. Bothe, H., Ferguson, S. J. & Newton, W. E. (eds.). Elsevier Science, p. 209-222

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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.

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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.

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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

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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

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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

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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.

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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

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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.

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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.

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De eerste microbe. Van speculaties tot hypothesen.

Boogerd, F. C., 2011, Microcanon; wat je beslist moet weten over microbiologie.. Natuurwetenschap en Techniek (ed.). Diemen: Veen Magazines, p. 3-5 (Wetenschappelijke Bibliotheek).

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

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).

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Flux-related metabolic network descriptions.

Roling, W. F. M., 2010, Handbook of hydrocarbon and lipid microbiology.. Timmis, K. N. (ed.). Germany: Springer Verlag Berlin Heidelberg, p. 4340-4346

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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).

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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

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Genomics, inconvenient truths, and accountability

Lunshof, J. E. & Chadwick, R., 2014, The right to know and the right not to know: genetic privacy and responsibility. Chadwick , Levitt, Shickle (ed.). Cambridge, UK: Cambridge University Press

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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

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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

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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.

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Het kleinste leven als bron van grote ontwikkelingen in de biologie: Naar een wiskundig model voor de cel.

Krab, K., 2011, Microcanon; wat je beslist moet weten over microbiologie.. De Wetenschappelijke Biobliotheek, Natuurwetenschap en Techniek. (ed.). Diemen: Veen Magazines, p. 213-214

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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.

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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

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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).

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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.

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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.

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How specific microbial commnities benefit the oil industry: Dynamics of Alcanivorax spp. In oil contaminated intertidal beach sediments undergoing bioremediation.

Singh, A., Sherry, A., Gray, N. D., Jones, D. M., Roling, W. F. M. & Head, I. M., 2011, Applied Microbiology in Oil Field Systems. Whithby, C. & Lund Skovhus, T. (eds.). Springer Verlag Berlin, p. 199-209

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Hydrocarbon-degradation by acidophilic microorganisms

Roling, W. F. M., 2010, Handbook of hydrocarbon and lipid microbiology.. Timmins, K. N. (ed.). Germany: Springer Verlag Berling Heidelberg, p. 1924-1929

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Hydrocarbon degradation in petroleum reservoirs.

Head, I. M., Larter, S. R., Gray, N. D., Sherry, A., Adams, J. J., Jones, D. M., Rowan, A. K., Huang, H. & Roling, W. F. M., 2010, Handbook of hydrocarbon and lipid microbiology.. Timmis, K. N. (ed.). Springer Verlag Berlin Heidelberg, p. 3098-3107

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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

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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

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Introduction computer-assisted analysis in hydrocarbon and lipid microbiology.

Roling, W. F. M., 2015, Hydrocarbon and Lipid Microbiology Protocols. McGenity, T. J., Timmis, K. N. & Nogales, B. (eds.). Humana Press, (Springer Protocols Handbooks).

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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

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Introduction to Systems Biology.

Bruggeman, F. J., Hornberg, J. J., Boogerd, F. C. & Westerhoff, H. V., 2007, Plant Systems Biology. Baginsky, S. & Fernie, A. R. (eds.). Experientia Supplementum, p. 1-19

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Introduction to the biochemistry and molecular biology of denitrification.

van Spanning, R. J. M., Richardson, D. J. & Ferguson, S. J., 2007, Biology of the nitrogen cycle. Bothe, H., Ferguson, S. J. & Newton, W. E. (eds.). Elsevier Science, p. 3-20

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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

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