1. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thbhttp://www.bio.vu.nl/thb/ 6 th AQUAdeb meeting Nantes, 2009/11/05

2. Graduations 2009 2010/01/18Baas, J. Effects of mixtures explained: From laboratory tests to effects in the environment 2009/12/?? 2009/11/26 Bourles, Y. Kooijman, S. A. L. M. Metabolic organisation has a formal basis 2009/11/19Bruggeman, J.Succession in plankton communities: A trait-based perspective 2009/09/30Voorn, G. A. K. vanEcological implications of global bifurcations. 2009/09/30Stiefs, D.Relating generalized and specific modeling in population dynamical systems 2009/09/10Campos, Mrs J.The eco-geography of the brown shrimp Crangon crangon L. in Europe.. 2009/03/06Omta, A. W.Eddies and algal stoichiometry: Physical and biological influences on the organic carbon pump.

3. 1.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 2.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 3.J. Baas, H. Hoogenboorn and S. A. L. M. Kooijman. Sterfte van Daphnia in beheersgebied Delfland verklaard. H2O., 16/17:35-37 4.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. 5.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 6.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 7.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 8.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 9. J. Bruggeman. Succession in plankton communities: A trait-based perspective. Ph.D. thesis, Vrije Universiteit, Amsterdam 10.J. Bruggeman, J. Heringa and B. W. Brandt. Phylopars: estimation of missing parameters values using phylogeny. Nucleic Acids Research, 37:W179-W184 11.J. Campos. The eco-geography of the brown shrimp in Europe. Ph.D. thesis, Vrije Universiteit, Amsterdam 12.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 13.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 14.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 15.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, 16.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 17.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 18.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 19.T. Jager and S. A. L. M. Kooijman. A biology-based approach for quantitative structure-activity relationships (QSARs) in ecotoxicity. Ecotoxicol., 18:187-196 20.S. A. L. M. Kooijman. Social interactions can affect feeding behaviour of fish in tanks. J. Sea Res., 62:175-178 21.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 22.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 23. 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 24.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 25.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 26.A. W. Omta. Eddies and algal stoichiometry: Physical and biological influences on the organic carbon pump. Ph.D. thesis, Vrije Universiteit, Amsterdam 27.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 28.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 29.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 30.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 31.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 32.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 33.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 34.D. Stiefs. Relating generalized and specific modeling in population dynamical systems. Ph.D. thesis, Oldenburg University & Vrije Universiteit, Amsterdam 35.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

4. 1.G. A. K. v. Voorn. Ecological implications of global bifurcations. Ph.D. thesis, Vrije Universiteit, Amsterdam 2.J. Baas, T. Jager and S. A. L. M. Kooijman. Understanding (mixture) toxicity as processes in time. Sci. Total Environm 3.J. Baas, T. Jager and S. A. L. M. Kooijman. A review of DEB-theory in assessing effects of mixtures. Sci. Total Environm. 4.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 5.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 6. 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 7.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. 8.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 Publications 2009 to appear

5. Primary DEB parameters