19982019
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Research Output 1998 2019

2009

Seasonality, climate cycles and body size evolution.

Troost, T. A., van Dam, J., Kooi, B. W. & Tuenter, E., 2009, In : Mathematical Modelling of Natural Phenomena. 4, p. 137-157

Research output: Contribution to JournalArticleAcademicpeer-review

Seasonality
Climate
Cycle
Time Scales
Forcing

Succession in plankton communities: A trait-based perspective

Bruggeman, J., 2009, Amsterdam: Gildeprint Drukkerijen. 158 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Torus bifurcations, isolas and chaotic attractors in a simple dengue fever model with ade and temporary cross immunity.

Agular, M., Stollenwerk, N. & Kooi, B. W., 2009, In : International Journal of Computer Mathematics. 86, p. 1867-1877

Research output: Contribution to JournalArticleAcademicpeer-review

Chaotic Attractor
Immunity
Torus
Bifurcation
Deterministic Chaos
2008

Continuation of connecting orbits in 3d-ODEs' (i) point-to-cycle connections.

Doedel, E. J., Kooi, B. W., van Voorn, G. A. K. & Kuznetzov, Y. A., 2008, In : International Journal of Bifurcation and Chaos. 18, p. 1889-1903

Research output: Contribution to JournalArticleAcademicpeer-review

Connecting Orbits
Eigenvalues and eigenfunctions
Continuation
Eigenfunctions
Orbits
Epidemiology
Immunity
Chaotic Behavior
Infection
Bifurcation

Model analysis of a simple aquatic ecosystem with sublethal toxic effects.

Kooi, B. W., Bontje, D. M. & Liebig, M., 2008, In : Mathematical Bioscience and Engineering. 5, p. 771-787

Research output: Contribution to JournalArticleAcademicpeer-review

Toxicants
Aquatic ecosystems
Poisons
Model Analysis
toxic substances

Stabilization due to predator interference: Comparison of different analysis approaches.

van Voorn, G. A. K., Stiefs, D., Gross, T., Kooi, B. W., Feudel, U. & Kooijman, S. A. L. M., 2008, In : Mathematical Bioscience and Engineering. 5, p. 567-583

Research output: Contribution to JournalArticleAcademicpeer-review

Sublethal contaminants effects in a simple aquatic food chain.

Kooi, B. W., Bontje, D. M., van Voorn, G. A. K. & Kooijman, S. A. L. M., 2008, In : Ecological Modelling. 112, p. 304-318

Research output: Contribution to JournalArticleAcademicpeer-review

food chain
predator
pollutant
nutrient
bifurcation
2007

A new class of non-linear stochastic population models with mass conservation.

Kooijman, S. A. L. M., Graman, J. & Kooi, B. W., 2007, In : Mathematical Biosciences. 210, p. 378-394

Research output: Contribution to JournalArticleAcademicpeer-review

Mass Conservation
Bifurcation Point
Population Model
Nutrients
Stochastic Model

A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems.

Bruggeman, J., Burchard, H., Kooi, B. W. & Sommeijer, B., 2007, In : Applied Numerical Mathematics. 57, p. 36-58

Research output: Contribution to JournalArticleAcademicpeer-review

Conservation
Chemical compounds
Positivity
High Order Accuracy
Conserve

Bifurcation analysis can unify ecological and evolutionary aspects of ecosystems.

Troost, T. A., Kooi, B. W. & Kooijman, S. A. L. M., 2007, In : Ecological Modelling. 204, p. 253-268

Research output: Contribution to JournalArticleAcademicpeer-review

bifurcation
ecosystem
timescale
invasibility
resident population

Effects of density-dependent migrations on stability of a two-patch predator-prey model.

Abdllaoui, A. E., Auger, P., Kooi, B. W., Bravo de la Parra, R. & Mchich, R., 2007, In : Mathematical Biosciences. 210, p. 335-354

Research output: Contribution to JournalArticleAcademicpeer-review

Predator-prey Model
Migration
Patch
predators
Predator

Heteroclinic orbits indicate overwxploitation in predator prey systems with a strong allee effect.

van Voorn, G. A. K., Hemerik, L., Boer, M. & Kooi, B. W., 2007, In : Mathematical Biosciences. 209, p. 451-469

Research output: Contribution to JournalArticleAcademicpeer-review

Predator prey systems
Allee Effect
Heteroclinic Orbit
orbits
Predator-prey System

Joint evolution of predator body size and prey-size preference

Troost, T., Kooi, B. & Dieckmann, U., 2007, In : Evolutionary Ecology.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
prey size
body size
predator
predators
filter feeder

Joint evolution of predator body size and prey-size preference.

Troost, T. A., Kooi, B. W. & Dieckmann, U., 2007, In : Evolutionary Ecology. 22, p. 771-799

Research output: Contribution to JournalArticleAcademicpeer-review

prey size
body size
predator
predators
filter feeder
2006

Advantages of storage in a fluctuating environment.

Kooi, B. W. & Troost, T. A., 2006, In : Theoretical Population Biology. 70, p. 527-541

Research output: Contribution to JournalArticleAcademicpeer-review

energy
bifurcation
chemostat
multipliers
timescale

Bifurcation analysis of a predator-prey model with predators using hawk dove tactics.

Auger, P., Kooi, B. W., Bravo de la Parra, R. & Poggiale, J. C., 2006, In : Journal of Theoretical Biology. 238, p. 597-607

Research output: Contribution to JournalArticleAcademicpeer-review

Hawks
doves
hawks
Predator-prey Model
Bifurcation Analysis

Evolution of Community Metabolism

Troost, T. A., 2006, Gildeprint Drukkerijen. 167 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Inducible defences in food webs.

Vos, M., Kooi, B. W., DeAngelis, D. L. & Mooij, W. M., 2006, Dynamic Food Webs: Multispecies assemblages, ecosystem development, and environmental change A volume of Theoretical Biology.. P.C. de Ruiter, V. Wolters and C.J. Moore (ed.). p. 114-127

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Multiparametric bifurcation analysis of a basic two stage population model.

Baer, S. M., Kooi, B. W., Kuznetsov, Y. A. & Thieme, H. R., 2006, In : SIAM journal on applied mathematics. 66, p. 1339-1365

Research output: Contribution to JournalArticleAcademic

Two-stage Model
Bifurcation Analysis
Population Model
Unfolding
Bogdanov-Takens Bifurcation
2005

Ecological specialization of mixotrophic plankton in a mixed water column.

Troost, T. A., Kooi, B. W. & Kooijman, S. A. L. M., 2005, In : The American Naturalist. 166, p. E45-E61

Research output: Contribution to JournalArticleAcademicpeer-review

Global change effects on a mechanistic decomposer food web model

Kuijper, L. D. J., Berg, M. P., Morrien, E., Kooi, B. W. & Verhoef, H. A., 2005, In : Global Change Biology. 11, p. 249-265

Research output: Contribution to JournalArticleAcademicpeer-review

Carbon Monoxide
Fungi
Refractory materials
global change
Ecosystems

When do mixotrophs specialize? Adaptive dynamics theory applied to a dynamic energy budget model.

Troost, T. A., Kooi, B. W. & Kooijman, S. A. L. M., 2005, In : Mathematical Biosciences. 193, p. 159-182

Research output: Contribution to JournalArticleAcademicpeer-review

Dynamics (theory)
Adaptive Dynamics
Budgets
Cost functions
Nutrients

Yeast glycolytic oscillations that are not controlled by a single oscillophore: A new definition of oscillophore strength.

Reijenga, K. A., van Megen, Y. M. G. A., Kooi, B. W., Bakker, B. M., Snoep, J. L., van Verseveld, H. W. & Westerhoff, H. V., 2005, In : Journal of Theoretical Biology. 232, p. 385-398

Research output: Contribution to JournalArticleAcademicpeer-review

Yeast
oscillation
Yeasts
Enzymes
Oscillation
2004

Consequences of symbiosis for food web dynamics.

Kooi, B. W., Kuijper, L. D. J. & Kooijman, S. A. L. M., 2004, In : Journal of Physical Chemistry A. 3, p. 227-271

Research output: Contribution to JournalArticleAcademicpeer-review

Dynamic energy budget representations of stoichiometric constraints to population models.

Kooijman, S. A. L. M., Andersen, T. R. & Kooi, B. W., 2004, In : Ecology. 85, p. 1230-1243

Research output: Contribution to JournalArticleAcademicpeer-review

Inducible defences and the paradox of enrichment.

Vos, M., Kooi, B. W., Mooij, W. M. & DeAngelis, D. L., 2004, In : Oikos. 105, p. 471-480

Research output: Contribution to JournalArticleAcademicpeer-review

food chain
polymorphism
persistence
primary productivity
extinction

Inducible defences and trophic structure.

Vos, M., Verschoor, A. M., Kooi, B. W., Wackers, F. L., DeAngelis, D. L. & Mooij, W. M., 2004, In : Ecology. 85, 10, p. 2783-2794

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
trophic structure
trophic level
bottom-up control
top-down control
ecological theory

Stoichiometry and food chain dynamics.

Kuijper, L. D. J., Kooi, B. W., Anderson, T. R. & Kooijman, S. A. L. M., 2004, In : Theoretical Population Biology. 66, p. 323-339

Research output: Contribution to JournalArticleAcademicpeer-review

stoichiometry
food chain
chemostat
nitrogen
carbon

The relationship between elimination rates and partition coefficients of chemical compounds.

Kooijman, S. A. L. M., Jager, D. T. & Kooi, B. W., 2004, In : Chemosphere. 57, p. 745-753

Research output: Contribution to JournalArticleAcademicpeer-review

Chemical compounds
chemical compound
partition coefficient
Daphnia
Octanols

The role of trophic flows in food web dynamics.

Kuijper, L. D. J., 2004, 125 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

2003

Chaotic behaviour of a predator-prey system.

Kooi, B. W. & Boer, M. P., 2003, In : Dynamics of Continuous, Discrete and Impulsive Systems Series B. Applications and Algorithms.. 10, p. 259-272

Research output: Contribution to JournalArticleAcademicpeer-review

Numerical bifurcation analysis of ecosystems in a spatially homogeneous environment.

Kooi, B. W., 2003, In : Acta Biotheoretica. 51, p. 189-222

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcation Analysis
bifurcation
Ecosystem
Ecosystems
Numerical Analysis

Omnivory and food web dynamics

Kuijper, L. D. J., Kooi, B. W., Zonneveld, C. & Kooijman, S. A. L. M., 2003, In : Ecological Modelling. 163, p. 19-32

Research output: Contribution to JournalArticleAcademicpeer-review

omnivory
intraguild predation
food web
nutrient enrichment
predator

Quantitative steps in symbiogenesis and the evolution of homeostasis.

Kooijman, S. A. L. M., Auger, P., Poggiale, J. C. & Kooi, B. W., 2003, In : Biological Reviews. 78, p. 435-463

Research output: Contribution to JournalArticleAcademicpeer-review

homeostasis
Homeostasis
Budgets
Substrates
symbionts

Structured population dynamics, a modeling perspective.

Kooi, B. W. & Kelpin, F. L. D., 2003, In : Comments on Theoretical Biology. 8, p. 125-168

Research output: Contribution to JournalArticleAcademicpeer-review

2002

Aggregation methods in food chains with nutrient recycling.

Kooi, B. W., Poggiale, J. C., Auger, P. & Kooijman, S. A. L. M., 2002, In : Ecological Modelling. 157, p. 69-86

Research output: Contribution to JournalArticleAcademicpeer-review

food chain
recycling
chemostat
nutrient
trophic level

Light-induced mass turnover in a mono-species community of mixotrophs.

Kooijman, S. A. L. M., Dijkstra, H. A. & Kooi, B. W., 2002, In : Journal of Theoretical Biology. 214, p. 233-254

Research output: Contribution to JournalArticleAcademicpeer-review

Nitrogen
Carbon
Light
autotrophs
carbon

Numerical bifurcation analysis of a tri-trophic food web with omnivory.

Kooi, B. W., Kuijper, L. D. J., Boer, M. P. & Kooijman, S. A. L. M., 2002, In : Mathematical Biosciences. 177-178, p. 201-228

Research output: Contribution to JournalArticleAcademicpeer-review

Food Web
Food Chain
omnivores
Bifurcation Analysis
Prey

The dynamics of a tri-trophic food chain with two-component populations from a biochemical perspective.

Hanegraaf, P. P. F. & Kooi, B. W., 2002, In : Ecological Modelling. 152, p. 47-64

Research output: Contribution to JournalArticleAcademicpeer-review

food chain
bifurcation
chemostat
predator-prey interaction
nutrient enrichment
2001

Bifurcations in ecosystem models and their biological interpretation.

Kooi, B. W. & Boer, M. P., 2001, In : Applicable Analysis. 77, p. 29-59

Research output: Contribution to JournalArticleAcademicpeer-review

Bi-trophic food chain dynamics with multiple component populations.

Kooi, B. W. & Hanegraaf, P. P. F., 2001, In : Bulletin of Mathematical Biology. 63, p. 271-299

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain
food chain
Population
Food Web
Maintenance

Iterparous reproduction strategies and population dynamics.

Kooi, B. W., Hallam, T. G., Kelpin, F. L. D., Krohn, C. M. & Kooijman, S. A. L. M., 2001, In : Bulletin of Mathematical Biology. 63, p. 769-794

Research output: Contribution to JournalArticleAcademicpeer-review

Population dynamics
Population Dynamics
Population Model
Reproduction
population dynamics

Multiple attractors and boundary crises in a tri-trophic food chain.

Boer, M. P., Kooi, B. W. & Kooijman, S. A. L. M., 2001, In : Mathematical Biosciences. 169, 2, p. 109-128

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain
food chain
saddles
Limit Cycle
orbits
2000

Invading species can stabilize simple trophic systems.

Kooi, B. W. & Kooijman, S. A. L. M., 2000, In : Ecological Modelling. 133, p. 57-72

Research output: Contribution to JournalArticleAcademicpeer-review

predator
bifurcation
nutrient
food web
invasibility

Numerical analysis and parameter estimation of a structured population model with discrete events in the life history.

Kelpin, F. L. D., Kirkilionis, M. & Kooi, B. W., 2000, In : Journal of Theoretical Biology. 207, p. 217-230

Research output: Contribution to JournalArticleAcademicpeer-review

Structured Populations
Discrete Event
Population Model
Parameter estimation
Parameter Estimation

The dynamic of tritrophic food chains.

Boer, M. P., 2000, Amsterdam. 97 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

The role of intracellular components in food chain dynamics.

Hanegraaf, P. P. F., Kooi, B. W. & Kooijman, S. A. L. M., 2000, In : Life Sciences. 323, p. 99-111

Research output: Contribution to JournalArticleAcademicpeer-review

1999

Diffusion barriers limit the effect of mobile calcium buffers on exocytosis of large dense cored vesicles

Kits, K. S., de Vlieger, T. A., Kooi, B. W. & Mansvelder, H. D., 1999, In : Biophysical Journal. 76, 3, p. 1693-1705 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access