Molecular Cell Physiology

Research Output 1978 2020

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2018

Mens en bacterie

Kort, R., 1 Nov 2018, Ontwikkelingen in de Geneeskunde 2018 . Rotterdam: Erasmus MC, p. 70-76 7 p.

Research output: Chapter in Book / Report / Conference proceedingChapterProfessional

File

Remote sensing of homochirality: A proxy for the detection of extraterrestrial life

Patty, C. H. L., Ten Kate, I. L., Sparks, W. B. & Snik, F., 2018, Chiral Analysis: Advances in Spectroscopy, Chromatography and Emerging Methods: Second Edition. Polavarapu, P. L. (ed.). 2nd ed. Elsevier Inc., p. 29-69 41 p.

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

Remote sensing
Sugar Acids
Polarimeters
Earth (planet)
Polarization
2017

The first Microbe

Boogerd, F. C. & Koonin, E. V., 2017, Mighty Microbes: The amazing world of microorganisms. Microcanon Foundation, p. 8-11 4 p.

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

2016

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.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology in the broad sense

Boogerd, F. C., 2016, Philosophy of Systems Biology: Perspectives form Scientists and Philosophers. Springer, p. 49-58 10 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

2015

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).

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

2014

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

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

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

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

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

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

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

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

The silicon trypanosome: a test case of iterative model extension in systems biology.

Achcar, F., Fadda, A., Haanstra, J. R., Kerkhoven, E. J., Kim, D. H., Leroux, A. E., Papmarkou, T., Rojas, F., Bakker, B. M., Barrett, M. P., Clayton, C., Girolami, M., Krauth-Siegel, R. L., Matthews, K. R. & Breitling, R., 2014, Advance in microbial physiology. Poole, R. K. (ed.). Elsevier Ltd, p. 115-143

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

2013

The bioenergetics of periplasmic electron transport systems in bacteria

Richardson, D. J., Sawers, G. & van Spanning, R. J. M., 2013, Encyclopedia of Biological Chemistry. Lennarz, W. J. & Lane, M. D. (eds.). Academic Press, Elsevier, p. 400-406 7 p.

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

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

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

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

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).

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

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).

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

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

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

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

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

Melkzuurbacterien: Het spel tussen profiteurs en sukkels.

Teusink, B., 2011, Microcanon; wat je beslist moet weten over microbiologie.. De Wetenschappelijke Bibliotheek, natuurwetenschap en techniek (ed.). Diemen: Veen Magazines, p. 68-71

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

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

Modular kinetic analysis

Krab, K., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 555-570 (Methods in Systems Biology; no. 500).

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

Origins of stochastic intracellular processes and consequences for cell-to-cell variability and cellular survival strategies

Schwabe, A., Dobrzynski, M., Rybakova, E. N., Verschure, P. & Bruggeman, F. J., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 597-625 (Methods in Systems Biology; no. 50).

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

Structure, function, regulation and evolution of the nitrite and nitrous oxide reductases: denintrification enzymes with a beta-propeller fold.

van Spanning, R. J. M., 2011, Nitrogen cycling in bacteria: Molecular Analysis.. Moir, J. W. B. (ed.). Caister Academic Press, p. Ch 7

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

The SEEK A platform for sharingdata and models in Systems Biology.

Wolstencroft, K. J., Owen, S., du Preez, F. B., Krebs, O., Mueller, W., Gable, C. & Snoep, J. L., 2011, Methods in Enzymology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). Burlington: Academic Press, p. 629-655 (Methods in Systems Biology; no. 500).

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

2010

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

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

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

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

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

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

Multiple alignment of transmembrane protein sequences

Pirovano, W. A., Abeln, S., Feenstra, K. A. & Heringa, J., 2010, Structural Bioinformatics of Membrane Proteins. Frishman, D. (ed.). Vienna: Springer-Verlag, p. 103-122 400 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Systems Biology: towards realistic and useful models of molecular networks.

Bruggeman, F. J., Kolodkin, A. N., Rybakova, E. N., Mone, M. J. & Westerhoff, H. V., 2010, Nuclear receptors. Current concepts and future challenges.. Bunce, C. M. & Campbell, M. J. (eds.). Springer Science+Bunsiness Media BV, p. 439-453 (Proteins and Cell Regulation).

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

The living cell as a multiagent organisation: a compositional organisation model of intracellular dynamic.

Jonker, C. M., Snoep, J. L., Treur, J., Westerhoff, H. V. & Wijngaards, W. C. A., 2010, Transactions on computational collective intelligence.. Nguyen, N. T. & Kowalczyk, R. (eds.). Germany: Springer-Verlag Berlin-Heidelberg, p. 160-206

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

The use of in vivo-like enzyme kinetics in a computational model of yeast glycolysis.

van Eunen, K., Kiewiet, J. A. L., Westerhoff, H. V. & Bakker, B. M., 2010, Experimental standard conditions of enzyme characterizations.. Kettner, C. & Hicks, M. G. (eds.). Rudesheim/Rhein, Germany: Beilstein Institut, p. 165-180 (September 13-16, 2009).

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

2008

JWS online: a web accesible model database, simulator and research tool.

Snoep, J. L., van Gend, C., Conradie, R., du Preez, F. B., Penkler, G. P. & Stoof, C., 2008, Proceedings of the 3rd ESCEC Symposium. Sept23-26, 2007. Kettner, C. & Hicks, M. G. (eds.). Ruedesheim, Germany: Beilstein Institute, p. 149-162

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

Multiple sequence alignment.

Pirovano, W. & Heringa, J., 2008, Methods in molecular biology, bioinformatics data, sequence analysis and evolution. Keith, J. M. (ed.). p. 143-161

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

Silicon cell models: construction, analysis, and reduction.

Bruggeman, F. J., Hardin, H. M., Schuppen, J. H. & Westerhoff, H. V., 2008, Biosimulation in Drug Development.. Bertau, M., Mosekilde, E. & Westerhoff, H. V. (eds.). Weinheim, Germany: Wiley-VCH Verlag GmbH, KGaA, p. 403-423

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

The new genomics and personal genome information ethical issues.

Lunshof, J., 2008, Next generation genome sequencing: towards personalized medicine.. Janitz, M. (ed.). Weinheim, Germany: Wiley-VCH GmbH & Co, KGaA

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

2007

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.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

JWS online: a web-based tool for curation, review, sotrage and analysis of kinetic models.

Snoep, J. L., van Gend, C., Stoof, C., Oliver, B. G., Conradie, R., du Preez, F. B., Schaboret, D. T. W. P., Penkler, G. P. & Holm, K., 2007, Experimental standard conditions of enzyme characterizations.. Hicks, M. G. & Kettner, C. (eds.). Frankfurt Germany: Beilstein Institut, p. 227-236

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Sequence similarity searches.

Heringa, J. & Pirovano, W., 2007, Bioinformatics. Dear, P. (ed.). Oxfordshire UK: Scion Publishing Limited, p. 39-67 (Methods Express Series).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Standardization and 'In-Vivo'-like enzyme activity measurements in Yeast.

Bouwman, J., van Eunen, K., Tuzun, I., Postmus, J., Canelas, A., van der Brink, J., Lindenbergh, P. A., Teixeira de Mattos, M. J., Smits, G. J., Daran-Lapujade, P. A. L., van Gulik, W. M., van Spanning, R. J. M., Heijnen, J. J., de Winde, J. H., Brul, S., Westerhoff, H. V. & Bakker, B. M., 2007, Experimental standard conditions of enzyme characterization.. Hicks, M. G. & Kettner, C. (eds.). Frankfurt Germany: Beilstein-Institut, p. 11-20 (vol 2).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic