Molecular Cell Biology

Research Output 1978 2020

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2020

Sensing Extracellular Calcium – An Insight into the Structure and Function of the Calcium-Sensing Receptor (CaSR)

Chavez-Abiega, S., Mos, I., Centeno, P. P., Elajnaf, T., Schlattl, W., Ward, D. T., Goedhart, J. & Kallay, E., 2020, Calcium Signaling. Islam, S. (ed.). 2nd ed. Cham: Springer Nature Switzerland AG, p. 1031-1063 33 p. (Advances in Experimental Medicine and Biology; vol. 1131).

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

Calcium-Sensing Receptors
Calcium
Tissue
Secondary Hyperparathyroidism
Parathyroid Glands
2018

Biomass conversion at population level

Kooijman, S. A. L. M., 2018, Individual-Based Models and Approaches in Ecology: Populations, Communities and Ecosystems. CRC Press, p. 338-358 21 p.

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

Biomass
Predator
Prey
Harvesting
Energy

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

Single-molecule imaging of Escherichia coli transmembrane proteins

Varadajan, A., Oswald, F. & Bollen, Y. J. M., 2018, Methods in Molecular Biology. Peterman, E. (ed.). Humana Press Inc, Vol. 1665. p. 135-144 10 p. (Methods in Molecular Biology; vol. 1665).

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

Escherichia coli Proteins
Biological Phenomena
Cell Fusion
Gram-Negative Bacteria
Fluorescence Microscopy
2017

Aerobic and anaerobic bacteria – Respiration without oxygen

van Spanning, R., van der Oost, J. & Richardson, D., 2017, Mighty Microbes: The amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H. & Willemsen, P. (eds.). Microcanon Foundation / Stichting Microcanon, p. 56-58

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

Aerobic Bacteria
Anaerobic Bacteria
cell respiration
Bacteria
Respiration

Optimizing E. coli-based membrane protein production using Lemo21(DE3) or pReX and GFP-Fusions

Kuipers, G., Peschke, M., Ismail, N. B., Hjelm, A., Schlegel, S., Vikström, D., Luirink, J. & de Gier, J. W., 2017, Methods in Molecular Biology. Humana Press Inc, Vol. 1586. p. 109-126 18 p. (Methods in Molecular Biology; vol. 1586).

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Green Fluorescent Proteins
Membrane Proteins
Escherichia coli
Gene Expression Regulation
Protein C

The first Microbe

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

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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).

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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

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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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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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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

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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

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2013

Flow of energy and matter in marine benthic animal populations.

van der Meer, J., Brey, T., Heip, C. H. & Herman, P. J. M., 2013, Methods in marine benthos studies.. Eleftheriou, F. (ed.). Oxford: Blackwell, p. 329-207

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Gedachten Uitpluizen

van der Gaag, M., Staring, T., van den Berg, D. P. G. & Baas, J., 2013, Cognitief Gedragstherapeutische Protocollen Bij Psychotische Klachten. 3rd edition ed.. Oegstgeest: Stichting Cognitie en Psychose.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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

2012

Energy budgets.

Kooijman, S. A. L. M., 2012, Sourcebook in Theoretical Ecology. Hastings, A., Gross, L. & eds. (eds.). California: University of California Press

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).

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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

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).

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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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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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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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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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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

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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

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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).

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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).

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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).

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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

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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).

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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).

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Toxicokinetics and toxicodynamics.

Svendsen, C., Jager, T., Haddad, S., Yang, R. S. H., Dorne, J. L. C. M., Broerse, M. & Kramarz, P., 2011, Mixture Toxicity. Linking approaches from ecological and human toxicology.. van Gestel, C. A. M. (ed.). Boca Raton, Florida, USA: CRC Press, p. 47-93-Chapter 2

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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

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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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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).

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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

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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).

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2009

Development of the petunia inflorescence. In Petunia: Evolutionary, Developmental and Physiological Genetics.

Koes, R. E., Bliek, M., Castel, R., Kusters, E., Rebocho, A. B., Procissi, A. & Roobeek, I., 2009, Petunia: Evolutionary, Developmental and Physiological Genetics.. T. Gerats, J. S. (ed.). Springer, p. 179-198 20 p.

Research output: Chapter in Book / Report / Conference proceedingChapterProfessional

Ecotoxicological applications of Dynamic Energy Budget theory.

Kooijman, S. A. L. M., Baas, J., Bontje, D. M., Broerse, M., van Gestel, C. A. M. & Jager, T., 2009, Ecotoxicology Modeling. Devillers, J. (ed.). Springer, p. 237-259

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

The genetics of flower color.

Tornielli, G. B., Koes, R. E. & Quattrocchio, F. M., 2009, Petunia: Evolutionary, Developmental and Physiological Genetics. Gerats, T. & Strommer, J. (eds.). Heidelberg: Springer, p. 269-300

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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

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