Curriculum vitae
Bote Willem Kooi
May 15, 2012

Adress

Dept. Theoretical Biology, Faculty of Earth and Life Sciences, Vrije Universiteit,
De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.

Phone

+31 20 5987129; Secretary: +31 20 4447003

Telefax

+31 20 5987123

E-mail

kooi@bio.vu.nl

General

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

20 febr 1950

Date of birth in Uithuizermeeden, Prov. Groningen, The Netherlands.

Aug 1973- March 1979

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

March 1979- March 1983

PhD student employed by the Netherlands Organization for Pure Scientific Research (ZWO) at the Mathematical Institute, University of Groningen.
March 1983 Ph-Degree, title thesis: "On the Mechanics of the Bow and Arrow", 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 1983-May 1988

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.

May 1988-June 2009

Assistant-Professor Dept. Theoretical Biology, Vrije Universiteit, Amsterdam, The Netherlands;

Jan 1999- May 1999

Visiting-Professor Dept. Ecology & Evolutionary Biology and Dept. Mathematics, University of Tennessee, Knoxville TN 37996 USA; My host was Prof. Dr. T.G. Hallam.

June 2009-present

Associate-Professor Dept. Theoretical Biology, Vrije Universiteit, Amsterdam, The Netherlands;

side activities

(list is not exhaustive)
1996-2001 Coordinator of the National Program on Massive Parallel Processing, cluster Biological Application (NWO).
2001-2005 President of the NVTB (Nederlandse Vereniging voor Theoretische Biologie) Dutch Society of Theoretical Biology http://www.bio.vu.nl/nvtb/.
1991-present Founding member of European Society for Mathematical and Theoretical Biology (ESMTB)

co-promotor

C.H. Ratsak. Grazer induced sludge reduction in wastewater treatment, 1994
M.P. Boer. The dynamics of tri-trophic food chains, 2000
L.D.J. Kuijper. The role of trophic flows in food web dynamics, 2004
T. Troost. Evolution of community metabolism, 2006
G.A.K. van Voorn. Ecological implications of global bifurcations, 2009
D. Stiefs. (Oldenburg Germany) Relating generalized and specific modeling in population dynamical systems, 2009
J. Bruggeman. Succession in plankton communities: A trait-based perspective, 2009
D. Bontje. Analysis of toxic effects and nutrient stress in aquatic ecosystems, 2010
Maira Aguiar Freire dos Santos. Rich dynamics in multi-strain models: non-linear dynamics and deterministic chaos in dengue fever epidemiology, 2012
Daniël Jakob Gerla. Positive feedback in species communities

interests

My main research interests are the use of mathematical models to help solve problems in Ecology and Epidemiology. Research emphasis is on application of bifurcation theory for the analysis mathematical models based on processes and mechanisms at lower levels of organization, such as the individual, to solve problems at higher levels, such as populations and ecosystems. Topics of special interest are the role of interactions between populations, such as predator-prey interaction, disease transmission, inducible defence mechanisms and competition on ecosystem structure and functioning.

Publications by B.W. Kooi
2004-2012
see website for a complete list.

=2pc =1 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.

=2pc =1 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

=2pc =1 Vos, M., Kooi, B.W., Mooij, W.M. & DeAngelis, D.L. 2004 Inducible defences and the paradox of enrichment, OIKOS, 105(3): 471-480.

=2pc =1 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

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 Kooi, B.W. & Troost, T. 2006. Advantages of storage in a fluctuating environment. Theoretical Population Biology, 70(4):527-541.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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

=2pc =1 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.

=2pc =1 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.

=2pc =1 Troost, T.A., Kooi, B.W. & Dieckmann, U. 2008. Joint evolution of predator body size and prey-size preference. Evolutionary Ecology, 22:771-799.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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

=2pc =1 Aguiar, M., Stollenwerk, N. & Kooi, B.W. 2008. Torus bifurcations, isolas and chaotic attractors in a simple dengue fever model with ADE and temporary cross immunity. International Journal of Computer Mathematics, Accepted.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 Gerla, D., Vos, M., Kooi, B.W. & Mooij, W. 2009. Bottom-up and top-down effects on the predictability of community composition. OIKOS, 118:1044-1052.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 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.

=2pc =1 Kooi, B.W., Voorn, v. G.A.K. & Das, K. 2011. Stabilization and complex dynamics in a predator-prey model with predator suffering from an infectious disease. Ecological Complexity, 8:113-122.

=2pc =1 Bontje, D., Kooi, B.W. & Hattum, v. B. 2011. Sublethal toxic effects in a generic aquatic ecosystem. Ecotoxicology and Environmental Safety, 74:929-939.

=2pc =1 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.

=2pc =1 N. Stollenwerk, M. Aguiar, S. Ballesteros, J. Boto, B. Kooi, and L. Mateus 2012.
Dynamic noise, chaos and parameter estimation in population biology Interface Focus, 2(2): 156-169.