**
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.

Tue May 15 09:14:02 MEST 2012