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Curriculum vitae
Bote Willem Kooi

March 18, 2012

Dept. Theoretical Biology, Faculty of Earth and Life Sciences, Vrije Universiteit,
De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
Privat: Galvanistraat 14, 1433 MA Kudelstaart, The Netherlands.

+31 20 5987129; Secretary: +31 20 5987003; Privat: +31 297 343137

+31 20 5987123



Sex: male. Status: married with Petra van Egmond and we have one son called Derk. Nationality: Dutch. Hobbies: Archery.

20 febr '50
Date of birth in Uithuizermeeden, Prov. Groningen, The Netherlands.

Aug '73- March '79
Study Mathematics at University of Groningen
Specialization: Applied Mechanics, Computer Science and Numerical Analysis.
March '79 Masters degree (ingenieurs examen Technische Mechanica).

March '79- March '83
PhD student employed by the Netherlands Organization for Pure Scientific Research (ZWO) at the Mathematical Institute, University of Groningen.
March '83 Ph-Degree, promotor prof. dr. J.A. Sparenberg (Applied Mathematics, University of Groningen), referees prof. ir. M. Kuipers (Applied Mechanics, University of Groningen) and prof. dr. ir. J.G. Lekkerkerker (Applied Mechanics, Technical University Delft).

Aug '83-May '88
Research worker at Fokker, Space & Systems Amsterdam, cq. Division of Structural Analysis (now Dutch Space). Main field of activity: Structural Analysis of satellites and appendices such as solar arrays. Thermal-Structural interactions, Fluid-Structural interactions, Test-Analysis Correlation, Modal Survey Analysis.
Adviser in mathematical problems in the Department of Structural Analysis.
Cooperation with: National Aerospace Laboratory (NLR), University of Groningen (Prof. R.F. Curtain) and Technical University of Twente (Prof. H. Tijdeman).

May '88-present
Assistant-Professor Dept. Theoretical Biology, Vrije Universiteit, Amsterdam, The Netherlands;

Jan '99- May '99
Visiting-Professor Dept. Ecology & Evolutionary Biology and Dept. Mathematics, University of Tennessee, Knoxville TN 37996 USA; My host was Prof. Dr. T.G. Hallam.

Side activities
(list is not exhaustive)
'94-'01 Editor of the Newsletter of the National Program on Non-linear Dynamics, sub-program Population Dynamics (NWO).
'96-'01 Coordinator of the National Program on Massive Parallel Processing, cluster Biological Application (NWO).
'01-'05 President of the NVTB (Nederlandse Vereniging voor Theoretische Biologie) Dutch Society of Theoretical Biology

Publications by B.W. Kooi after 2000
Updated till Jan. 2012

Hanegraaf, P.P.F., Kooi, B.W. & Kooijman, S.A.L.M. 2000. The role of intracellular components in food chain dynamics Comptes rendus de l'Academie des science, series III, Sciences de la vie, 323:99-111.

Kooi B.W. & Kooijman S.A.L.M., 2000. Invading species can stabilize simple trophic systems Ecological Modelling, 133(1-2):57-72.

Kelpin, F.D.L., Kirkilionis, M.A. & Kooi, B.W. 2000. Numerical methods and parameter estimation of a structured population model with discrete events in the life history Journal of Theoretical Biology, 207(2):217-230.

Boer, M.P., Kooi, B.W. & Kooijman, S.A.L.M. 2001. Multiple attractors and boundary crises in a tri-trophic food chain, Mathematical Biosciences, 169(2):109-128.

Kooi, B.W. & Hanegraaf, P.P.F. 2001. Bi-trophic food chain dynamics with multiple component populations. Bulletin of Mathematical Biology, 63(2):271-299.

Kooi, B.W. & Boer, M.P. 2001. Bifurcations in ecosystem models and their biological interpretation. Applicable Analysis, 77(1-2):29-59.

Kooi, B.W. 2001. Plato's Plant, Feike Schieving. Plant Ecology, 152(2):203-204.

Kooi, B.W., Hallam T.G., Kelpin F.D.L., Krohn C.M. & Kooijman S.A.L.M. 2001. Iteroparous Reproduction Strategies and Population Dynamics. Bulletin of Mathematical Biology, 63(4):769-794.

Kooijman, S.A.L.M., Dijkstra, H. A. & Kooi, B.W. 2002. Light-induced mass turnover in a mono-species community of mixotrophs. Journal of Theoretical Biology, 214(2):233-254.

Kooi, B.W., Kuijper, L.D.J., Boer, M.P. & Kooijman, S.A.L.M. 2002. Numerical bifurcation analysis of a tri-trophic food web with omnivory, Mathematical Biosciences, 177-178:201-228.

Hanegraaf, P.P.F. & Kooi, B.W. 2002. The dynamics of a tri-trophic food chain with two-component populations from a biochemical perspective. Ecological Modelling, 152(1):47-64.

Kooi, B.W., Poggiale, J.C., Auger, P. & Kooijman, S.A.L.M. 2002. Aggregation methods in food chains with nutrient recycling. Ecological Modelling, 157(1):69-86.

Kooi, B.W., & Boer, M.P. 2003. Chaotic behaviour of a predator-prey system. Dynamics of Continuous, Discrete and Impulsive Systems, Series B: Applications and Algorithms, 10:259-272.

Kooi, B.W., & Kelpin, F.D.L. 2003. Structured population dynamics, a modeling perspective. Comments on Theoretical Biology, 8:125-168.

Kuijper, L.D.J., Kooi, B.W., Zonneveld, C.& Kooijman, S.A.L.M. 2003. Omnivory and food web dynamics. Ecological Modelling, 163:19-32.

Kooijman, S.A.L.M., Auger, P., Poggiale, J.C. & Kooi, B.W. 2003. Quantitative steps in symbiogenesis and the evolution of homeostasis. Biol. Rev., 78:435-463.

Kooi, B.W. 2003. Numerical bifurcation analysis of ecosystems in a spatially homogeneous environment. Acta Biotheoretica, 51:189-222.

Kooi, B.W., Kuijper, L.D.J. & Kooijman, S.A.L.M. 2004. Consequences of symbiosis for food web dynamics, Journal of Mathematical Biology, 49(3):227-271.

Kooijman, S.A.L.M., Andersen, T. & Kooi, B.W. 2004. Dynamic energy budget representations of stoichiometric constraints on population dynamics. Ecology, 85(5):1230-1243

Vos, M., Kooi, B.W., Mooij, W.M. & DeAngelis, D.L. 2004. Inducible defences and the paradox of enrichment, OIKOS, 105(3): 471-480.

Vos, M., Verschoor, A.M., Kooi, B.W., Wäckers, F.L., DeAngelis, D.L. & Mooij, W.M. 2004. Inducible defenses and trophic structure. Ecology, 85(10):2783-2794

S.A.L.M. Kooijman, Jager, T.& B.W. Kooi. 2004 The relationship between elimination rates and partition coefficients of chemical compounds. Chemosphere, 57:745-753.

Kuijper, L.D.J., Kooi, B.W., Anderson, T.R. & Kooijman, S.A.L.M. 2004. Stoichiometry and food chain dynamics. Theoretical Population Biology 66:323-339.

Reijenga, K.A., Megen, Y.M.G.A. van, Kooi, B.W., Bakker, B.M., Snoep, J.L., Verseveld, H.W. van & Westerhoff, H.V. 2005. Yeast glycolytic oscillations that are not controlled by a single oscillophore: A new definition of oscillophore strength. Journal of Theoretical Biology, 232:385-398.

Troost, T.A., Kooi, B.W. & Kooijman, S.A.L.M. 2005. When do mixotrophs specialize? Adaptive dynamics theory applied to a dynamic energy budget model. Math. Biosci., 193(2): 159-182.

Kuijper, L.D., Berg, M.P., E. Morriën, E., Kooi B.W., Verhoef, H.A. 2005. Global change effects on a mechanistic decomposer food web model. Global Change Biology, 11:249-265.

Vos, M., Kooi, B.W., DeAngelis, D.L.& Mooij, W.M. 2005. Inducible defences in food webs, In: P.C. de Ruiter, V. Wolters and J. C. Moore editors Dynamic Food Webs: Multispecies assemblages, ecosystem development, and environmental change - A volume of Theoretical Biology, pages 114-127, Elsevier Inc.

Troost, T.A., Kooi, B.W. & Kooijman, S.A.L.M. 2005. Ecological specializaton of mixotrophic plankton in a mixed water column. The American Naturalist,166(3): E45-E61.

Auger, P., Kooi, B.W., Bravo de la Parra, R. & Poggiale, J.C. 2006. Bifurcation analysis of a predator-prey model with predators using hawk-dove tactics. Journal of Theoretical Biology, 238:597-607.

Baer, S.M., Kooi, B.W., Kuznetzov, Yu.A. & Thieme H.R. 2006. Multidimensional bifurcation analysis of a basic two-stage population model. SIAM Applied Mathematics, 66(4):1339-1365.

Kooi, B.W. & Troost, T. 2006. Advantages of storage in a fluctuating environment. Theoretical Population Biology, 70(4):527-541.

Bruggeman, J., Burchard, H., Kooi, B.W. & Sommeijer, B. 2007. A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems, Applied Numerical Mathematics 57(1):36-58.

Troost, T.A., Kooi, B.W. & Kooijman, S.A.L.M. 2007. Bifurcation analysis of ecological and evolutionary processes in ecosystems.
Ecological Modelling, 204:253-268.

Voorn, v. G.A.K., Hemerik, L., Boer, M.P. & Kooi, B.W. 2007. Heteroclinic orbits indicate overexploitation in predator-prey systems with a strong Allee effect.
Mathematical Biosciences, 209:451-469.

Abdllaoui, A.El., Auger, P., Kooi, B.W., Bravo de la Parra, R.& Mchich, R. 2007. Effects of density-dependent migrations on stability of a two-patch predator-prey model. Mathematical Biosciences, 210:335-354

Kooijman, S.A.L.M., Grasman, J. & Kooi, B.W. 2007. A new class of non-linear stochastic population models with mass conservation. Mathematical Biosciences, 210: 378-394.

Kooi, B.W., Bontje, D., Voorn, van G.A.K.& Kooijman, S.A.L.M. 2008. Sublethal toxic effects in a simple aquatic food chain. Ecological Modelling, 212: 304-318.

Troost, T.A., Kooi, B.W.& Dieckmann, U. 2008. Joint evolution of predator body size and prey-size preference. Evolutionary Ecology, 22:771-799.

Doedel, E.J., Kooi, B.W., Voorn, van G.A.K. & Kuznetsov, YU.A. 2008. Continuation of connecting orbits in 3D-ODEs: (I) Point-to-cycle connections. International Journal of Bifurcation and Chaos, 18(7):1889-1903.

Kooi, B.W., Bontje, D., & Liebig, M. 2008. Model analysis of a simple aquatic ecosystems with sublethal toxic effects. Mathematical Biosciences and Engineering, 5(4):771-787.

Liebig, M., Schmidt, G., Bontje, D., Kooi, B.W., Streck, G., Traunspurger, W., & Knacker T. 2008.
Direct and indirect effects of pollutants on algae and algivorous ciliates in an aquatic indoor microcosm. Aquatic Toxicology, 88:102-110.

Voorn, van. G.A.K., Stiefs, D. , Gross,T., Kooi, B.W., Feudel, U., & Kooijman, S.A.L.M. 2008. Stabilization due to predator interference: Comparison of different analysis approaches. Mathematical Biosciences and Engineering, 5(3):567-583.

Aguiar, M., Kooi, B.W., & Stollenwerk, N. 2008. Epidemiology of dengue fever: A model with temporary cross-immunity and possible secondary infection shows bifurcations and chaotic behaviour in wide parameter regions. Mathematical Modelling of Natural Phenomena, 3(4):48-70.

Bontje, D., Kooi,B.W., Liebig, M., & Kooijman, S.A.L.M. 2009. Modelling long-term ecotoxicological effects on an algal population under dynamic nutrient stress, Water Research, 16:587-598.

Doedel, E.J., Kooi, B.W., Voorn, van G.A.K. & Kuznetsov, YU.A. 2009. Continuation of connecting orbits in 3D-ODEs: (II) Cycle-to-cycle connections. International Journal of Bifurcation and Chaos, 19(1):159-169.

Gerla, D., Vos, M., Kooi, B.W., & Mooij, W. 2009. Effects of resources and predation on the predictability of community composition. OIKOS, 118:1044-1052.

Stap, I. van der, Vos, M, Kooi, B.W., Mulling, B.T. Donk E. van, & Mooij, W.M. 2009, Algal defenses, population stability and the risk of herbivore extinctions: A chemostat model and experiment. Ecological Research, 24: 1145-1153.

Aguiar, M., Stollenwerk, N., & Kooi, B.W. 2009. Torus bifurcations, isolas and chaotic attractors in a simple dengue fever model with ADE and temporary cross immunity. International Journal of Computer Mathematics, 86(10/11): 1867-1877.

Troost, T.A., Dam, J.A. van, Kooi, B.W., & Tuenter, E. 2009. Seasonality, climate cycles and body size evolution Mathematical Modelling of Natural Phenomena, 4(6): 137-157.

Bontje, D., Kooi, B.W., Voorn G.A.K. van, & Kooijman, S.A.L.M. 2009. Feeding threshold and the paradox of enrichment, Mathematical Modelling of Natural Phenomena, 4(6): 92-110.

Berg, M.P., Kiers, E.T., Driessen G., Heijden, M. van der, Kooi B.W., Kuenen F., Liefting M., Verhoef H.A., & Ellers J. 2010. Adapt or disperse: understanding species persistence in a changing world
Global Change Biology, 43:3292-3300.

Auger, P., Mchich, R., Raïssi, N., & Kooi, B.W. 2010. Effects of market price on the dynamics of a spatial fishery model: Over-exploited fishery/traditional fishery. Ecological Complexity, 7:13-20.

Voorn, v. G.A.K., Kooi, B.W. & Boer, M.P. 2010. Ecological consequences of global bifurcations in some food chain models
Mathematical Biosciences, 226:120-133.

Kooi, B.W.& J. van der Meer 2010. Bifurcation theory, adaptive dynamics and DEB-structured populations of iteroparous species. Philosophical Transactions of the Royal Society, 365:3579-3590.

Stiefs, D., Voorn, van. G.A.K., Kooi, B.W., Feudel, U., & Gross, T. 2010. Food quality in producer-grazer models: A generalized analysis, The American Naturalist, 176:367-380.

Kooi, B.W., Voorn, v. G.A.K. & pada Das, K. 2011. Stabilization and complex dynamics in a predator-prey model with predator suffering from an infectious disease. Ecological Complexity, 8:113-122.

Bontje, D., Kooi, B.W. & Hattum, v. B. 2011. Sublethal toxic effects in a generic aquatic ecosystem. Ecotoxicology and Environmental Safety, 74:929-939.

Aguiar, M., Ballesteros, S., Kooi, B.W., & Stollenwerk, N 2011. The role of seasonality and import in a minimalistic multi-strain dengue model capturing differences between primary and secondary infections: complex dynamics and its implications for data analysis. Journal of Theoretical Biology, 289:181-196.

Gerla, D., Gsell, A. S., Kooi, B.W., Ibelings, B.W., Van Donk, E.& Mooij, W. 2012. Effects of resources and predation on the predictability of community composition. Freshwater Biology,

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Bob Kooi
Sun Mar 18 08:44:31 MET 2012