Curriculum vitae
Bote Willem Kooi
March 18, 2012
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,