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6 th AQUAdeb meeting. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam [email protected] http://www.bio.vu.nl/thb /. Nantes, 2009/11/05. Graduations 2009. Publications 2009.

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6 th aquadeb meeting
6thAQUAdeb meeting

Bas Kooijman

Dept theoretical biology

Vrije Universiteit Amsterdam

[email protected]


Nantes, 2009/11/05

Publications 2009
Publications 2009

  • M. Aguiar, N. Stollenwerk and B. W. Kooi. Torus bifurcations, isolas and chaotic attractors in a simple dengue fever model with ade and temporary cross immunity. International Journal of Computer Mathematics, 86:1867-1877

  • M. Alunno-Bruscia, H. v. d. Veer and S. A. L. M. Kooijman. The aquadeb project (phase i): Analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using dynamic energy budgets. J. Sea Res., 62:43-48

  • J. Baas, H. Hoogenboorn and S. A. L. M. Kooijman. Sterfte van Daphnia in beheersgebied Delfland verklaard. H2O., 16/17:35-37

  • J. Baas, T. Jager and S. A. L. M. Kooijman. Estimation of no effect concentrations from exposure experiments when values scatter among individuals. Ecotoxicological Modelling, 220:411-418, 2009b.

  • J. Baas, T. Jager and S. A. L. M. Kooijman. A model to analyze effects of complex mixtures on survival. Ecotox. Eviron. Saf., 72:669-676

  • J. Baas, J. Willems, T. Jager, M. H. S. Kraak, T. Vandenbrouck and S. A. L. M. Kooijman. Prediction of daphnid survival after in situ exposure to complex mixtures. Environ. Sci. Technol., 43:6064-6069

  • D. Bontje, B. W. Kooi, M. Liebig and S. A. L. M. Kooijman. Modelling long-term ecotoxicological effects on an algal population under dynamic nutrient stress. Water Research, 43:3292-3300

  • Bourles, M. Alunno-Bruscia, S. Pouvreau, G. Tollu, D. Leguay, C. Arnaud, P. Goulletquer and S. A. L. M. Kooijman. Modelling growth and reproduction of the pacific oyster Crassostrea gigas: application of the oyster-DEB model in a coastal pond. J. Sea Res., 62:62-71

  • J. Bruggeman. Succession in plankton communities: A trait-based perspective. Ph.D. thesis, Vrije Universiteit, Amsterdam

  • J. Bruggeman, J. Heringa and B. W. Brandt. Phylopars: estimation of missing parameters values using phylogeny. Nucleic Acids Research, 37:W179-W184

  • J. Campos. The eco-geography of the brown shrimp in Europe. Ph.D. thesis, Vrije Universiteit, Amsterdam

  • J. Campos, H. v. d. Veer, V. Freitas and S. A. L. M. Kooijman. Contribution of different generations of the brown shrimp Crangon crangon (l.) in the dutch wadden sea to commercial fisheries: a dynamic energy budgets approach. J. Sea Res., 62:106-113

  • E. J. Doedel, B. W. Kooi, G. A. K. v. Voorn and Y. A. Kuznetzov. Continuation of connecting orbits in 3d-ODEs" (ii): cycle-to-cycle connenctions. Internat. J. of Bifurcation and Chaos, 19:159-169

  • M. Eichinger, S. A. L. M. Kooijman, R. Sempéré and J.-C. Poggiale. Consumption and release of dissolved organic carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling. Aquatic Microbial Ecology, 56:41-54

  • H. Eijsackers, J. Bruggeman, J. Harmsen, T. d. Kort and A. H. Schakel. Colonization of PAH-contaminated dredged sediment by earthworms. Applied Soil Ecology, 43:216-225,

  • Flye Sainte Marie, F. Jean, C. Paillard and S. Kooijman. A quantitative estimation of the energtic cost of brown ring disease in the Manila clam using Dynamic Energy Budget theory. J. Sea Res., 62:114-123

  • V. Freitas, J. F. M. F. Cardoso, S. Santos, J. Campos, J. Drent, J. I. Witte, S. A. L. M. Kooijman and H. v. d. Veer. Reconstruction of food conditions for Northeast Atlantic bivalve species based on Dynamic Energy Budget theory. J. Sea Res., 62:75-82

  • D. J. Gerla, M. Vos, B. W. Kooi and W. M. Mooij. Effects of resources and predation on the predictability of community composition. Oikos, 22:771-799

  • T. Jager and S. A. L. M. Kooijman. A biology-based approach for quantitative structure-activity relationships (QSARs) in ecotoxicity. Ecotoxicol., 18:187-196

  • S. A. L. M. Kooijman. Social interactions can affect feeding behaviour of fish in tanks. J. Sea Res., 62:175-178

  • S. A. L. M. Kooijman. What the egg can tell about its hen: embryo development on the basis of dynamic energy budgets. J. Math. Biol., 58:377-394

  • S. A. L. M. Kooijman, J. Baas, D. Bontje, M. Broerse, C. A. M. v. Gestel and T. Jager. Ecotoxicological applications of dynamic energy budget theory. In J. Devillers, ed., Ecotoxicology Modeling, pp. 237-259. Springer

  • C. Kraan, J. Van der Meer, A. Dekinga and T. Piersma. Patchiness of macrobenthic invertebrates in homogenized intertidal habitats: hidden spatial structure at a landscape scale. Marine Ecology Progress Series, 383:211-224

  • J. Van der Meer and I. M. Smallegange. A stochastic version of the Beddington-DeAngelis functional response: Modelling interference for a finite number of predators. Journal of Animal Ecology, 78:134-142

  • E. B. Muller, S. A. L. M. Kooijman, P. J. Edmunds, F. J. Doyle and R. M. Nisbet. Dynamic energy budgets in syntrophic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts. J. theor. Biol., 259:44-57

  • A. W. Omta. Eddies and algal stoichiometry: Physical and biological influences on the organic carbon pump. Ph.D. thesis, Vrije Universiteit, Amsterdam

  • A. W. Omta, J. Bruggeman, S. A. L. M. Kooijman and H. A. Dijkstra. The physics of the biological carbon pump. J. Sea Res., 62:179-187

  • A. W. Omta, J. Llido, S. A. L. M. Kooijman, V. Gar\ccon and H. A. Dijkstra. How to interpret satellite chlorophyll observations: a case study about the mozambique channel. J. Deep Sea Res., 56:974-988

  • L. Pecquerie, P. Petitgas and S. A. L. M. Kooijman. Modelling fish growth and reproduction in the context of the dynamic energy budget theory to predict environmental impact on anchovy spawning duration. J. Sea Res., 62:93-105

  • F. Peterse, S. Schouten, M. T. Van der Meer, J. Van der Meer and J. S. Sinninghe Damsté. Distribution of branched tetraether lipids in geothermally heated soils: Implications for the MBT/CBT temperature proxy. Organic Geochemistry, 40:201-205

  • S. Schouten, E. Hopmans, J. Van der Meer and A. Mets. An interlaboratory study of TEX86 and BIT analysis using high-performance liquid chromatography-mass spectrometry. Geochemistry Geophysics Geosystems, 10:Q03012, doi:10.1029/2008GC002221

  • I. M. Smallegange and J. Van der Meer. The distribution of unequal predators across food patches is not necessarily (semi)truncated. Behavioral Ecology, p. doi:10.1093/beheco/arp027

  • I. v. d. Stap, M. Vos, B. W. Kooi, B. T. Mulling, D. E. van and W. M. Mooij. Algal defenses, population stability and the risk of herbivore extinctions: A chemostat model and experiment. Ecological Research, 24:1145-1153

  • D. Stiefs. Relating generalized and specific modeling in population dynamical systems. Ph.D. thesis, Oldenburg University & Vrije Universiteit, Amsterdam

  • H. v. d. Veer, J. F. M. F. Cardoso, M. A. Peck and S. A. L. M. Kooijman. Physiological performance of plaice Pleuronectes platessa (L.): from Static to Dynamic Energy Budgets. J. Sea Res., 62:83-92

Publications 2009 to appear
Publications 2009 to appear

  • G. A. K. v. Voorn. Ecological implications of global bifurcations. Ph.D. thesis, Vrije Universiteit, Amsterdam

  • J. Baas, T. Jager and S. A. L. M. Kooijman. Understanding (mixture) toxicity as processes in time. Sci. Total Environm

  • J. Baas, T. Jager and S. A. L. M. Kooijman. A review of DEB-theory in assessing effects of mixtures. Sci. Total Environm.

  • J. Baas, A. M. Stefanowicz, B. Klimek, R. Laskowski and S. A. L. M. Kooijman. Model-based experimental design for assessing effects of mixtures of chemicals. Environmental Pollution

  • J. Campos, V. Freitas, C. Pedrosa, R. G. Guillot and H. v. d. Veer. Latitudinal variation in growth of Crangon crangon (L.): Does counter-gradient growth compensation occur?. J. Sea Res

  • J. Campos, C. Pedrosa, J. Rodrigues, S. Santos, J. I. Witte, P. Santos and H. v. d. Veer. Population zoogeopgraphy of brown shrimp Crangon crangon along its distributional range based on morphometric characters. J. Mar. Biol. Assoc. U.K

  • T. Jager, T. Vandenbrouck, J. Baas, W. M. D. Coen and S. A. L. M. Kooijman. A biology-based approach for mixture toxicity of multiple endpoints over the life cycle. Ecotoxicology.

  • A. Merico, J. Bruggeman and K. W. Wirtz. A trait-based approach for downscaling complexity in plankton ecosystem models. Ecological Modelling, x:doi:10.1016/j