19982019
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Research Output 1998 2019

Article

Adapt or disperse: understanding species persistence in a changing world.

Berg, M. P., Kiers, E. T., Driessen, G. J. J., van der Heijden, M. G. A., Kooi, B. W., Kuenen, F. J. A., Liefting, M., Verhoef, H. A. & Ellers, J., 2010, In : Global Change Biology. 16, p. 587-598

Research output: Contribution to JournalArticleAcademicpeer-review

Global warming
persistence
life history trait
Ecology
Climate change

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

Aggregation Methods in Food Chains.

Kooi, B. W., Poggiale, J. C. & Auger, P., 1998, In : Mathematical and Computer Modelling. 27, 4, p. 109-120

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Food Chain
Aggregation
Agglomeration
Chemostats
Chemostat

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

Algal defenses, population stability and the risk of herbivore extinctions: A chemostat model and experiment.

v.d. Stap, I., Vos, M., Kooi, B. W., Mulling, B. T., van Donk, E. & Mooij, W. M., 2009, In : Ecological Research. 24, p. 1145-1153

Research output: Contribution to JournalArticleAcademicpeer-review

algae
chemostat
Rotifera
herbivore
herbivores

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells.

Gustavsson, A-K., van Niekerk, D. D., Adiels, C. B., Kooi, B. W., Goksor, M. & Snoep, J. L., 2014, In : The FEBS Journal. 281, 12, p. 2784-2793 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Allosteric Regulation
Phosphofructokinases
Yeast
Yeasts
Cells

Alternative states and population crashes in a resource-susceptible-infected model for planktonic parasites and hosts.

Gerla, D. J., Gsell, A., Kooi, B. W., Ibelings, W., van der Donk, E. & Mooij, W. M., 2013, In : Functional Ecology. 58, p. 538-551

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of an asymmetric two-strain dengue model.

Kooi, B. W., Aguiar, M. & Stollenwerk, N., 2014, In : Mathematical Biosciences. 248, p. 128-139

Research output: Contribution to JournalArticleAcademicpeer-review

dengue
Dengue
Coinfection
Immunity
Infection

Analysis of a predator–prey model with specific time scales: a geometrical approach proving the occurrence of canard solutions

Poggiale, J. C., Aldebert, C., Girardot, B. & Kooi, B. W., 20 Feb 2019, In : Journal of Mathematical Biology. p. 1-22 22 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Canard
Predator-prey Model
Time Scales
Predator
Prey

An ecoepidemic model with prey herd behavior and predator feeding saturation response on both healthy and diseased prey

Banerjee, M., Kooi, B. W. & Venturino, E., 21 Apr 2017, In : Mathematical Modelling of Natural Phenomena. 12, 2, p. 133-161

Research output: Contribution to JournalArticleAcademicpeer-review

Predator prey systems
Predator
Prey
Saturation
Functional Response

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 new mathematical pharmacodynamic model of clonogenic cancer cell death by doxorubicin

Lankelma, J., Fernandez Luque, R., Dekker, H., van den Berg, J. & Kooi, B. W., 2013, In : Journal of Pharmacokinetics and Pharmacodynamics. 40, 4, p. 513-525

Research output: Contribution to JournalArticleAcademicpeer-review

Doxorubicin
Cell Death
Theoretical Models
Neoplasms
Cell Count

A reason for intermittent fasting to suppress the awakening of dormant breast tumors.

Lankelma, J., Kooi, B. W., Krab, K., Dorsman, J. C., Joenje, H. & Westerhoff, H. V., 2015, In : BioSystems. 127, p. 1-6

Research output: Contribution to JournalArticleAcademicpeer-review

Tumors
Tumor
Fasting
Glucose
Breast Neoplasms

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

Bifurcation analysis of a family of multi-strain epidemiology models.

Kooi, B. W., Aguiar, M. & Stollenwerk, N., 2013, In : Journal of computational and applied mathematics. 252, p. 148-158

Research output: Contribution to JournalArticleAcademicpeer-review

Epidemiology
Bifurcation Analysis
Immunity
Infection
Antibody

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

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

Reproduction
spawning
Population
Food storage
Chemostats

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

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

Combining bifurcation and sensitivity analysis for ecological models: Model analysis, and the allegory of the cave

van Voorn, GAK. & Kooi, B. W., 2017, In : European Physical Journal. Special Topics. 226, p. 2101-2118

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
caves
Caves
Bifurcation (mathematics)
sensitivity analysis
Sensitivity analysis

Competition for Light and Nutrients in Layered Communities of Aquatic Plants

van Gerven, L. P. A., Klein, J. J. M., Gerla, D. J., Kooi, B. W., Kuiper, J. J. & Mooij, W. M., 2015, In : The American Naturalist. 186, p. 72-83

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
aquatic plant
aquatic plants
nutrient
nutrients
submerged aquatic plants

Consequences of population models on the dynamics of food chains.

Kooi, B. W., Boer, M. P. & Kooijman, S. A. L. M., 1998, In : Mathematical Biosciences. 153, p. 99-124 25 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain
Population Model
food chain
Bifurcation Diagram
Population

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

Continuation of connecting orbits in 3d-ODEs. (ii) cycle-to-cycle connections.

Doedel, E. J., Kooi, B. W., van Voorn, G. A. K. & Kuznetzov, Y. A., 2009, In : International Journal of Bifurcation and Chaos. 19, p. 159-169

Research output: Contribution to JournalArticleAcademicpeer-review

Connecting Orbits
Continuation
Orbits
Numerical Continuation
Cycle

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

Detecting tipping points in ecological models with sensitivity analysis

ten Broeke, G. A., van Voorn, G. A. K., Kooi, B. W. & Molenaar, J., 2016, In : Mathematical Modelling of Natural Phenomena. 11, 4, p. 47-72

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Ecological Model
Sensitivity analysis
Sensitivity Analysis
Simulation Model
Bifurcation Analysis

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

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, p. 1693-1705

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Discrete event versus continuous approach to reproduction in structured population dynamics.

Kooi, B. W. & Kooijman, S. A. L. M., 1999, In : Theoretical Population Biology. 56, p. 91-105

Research output: Contribution to JournalArticleAcademicpeer-review

population dynamics
chemostat
Rotifera
dilution
egg

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

Dynamic noise, chaos and parameter estimation in population biology

Stollenwerk, N., Aguiar, M., Ballesteros, S., Boto, J., Kooi, B. W. & Mateus, L., 2012, In : Interface Focus. 2, p. 156-168

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Ecoepidemic models with prey group defense and feeding saturation

Gimmelli, G., Kooi, B. W. & Venturino, E., 2015, In : Ecological Complexity. 22, p. 50-58

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
bifurcation
saturation
predators
saddles
satiety

Ecoepidemic predator-prey model with feeding satiation, prey herd behavior and abandoned infected prey

Kooi, B. W. & Venturino, E., 2016, In : Mathematical Biosciences. 2016, p. 58-72

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Satiation
Predator-prey Model
Prey
satiety
herds

Ecological consequences of global bifurcations in some food chain models.

van Voorn, G. A. K., Kooi, B. W. & Boer, M. P., 2010, In : Mathematical Biosciences. 226, p. 120-133

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain Model
Food Chain
Global Bifurcation
food chain
environmental impact

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

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

Effects of market price on the dynamics of a spatial fishery model: Over-exploited fishery/traditional fishery.

Auger, P., Mchich, R., Raissi, N. & Kooi, B. W., 2010, In : Ecology. 17, p. 13-20

Research output: Contribution to JournalArticleAcademicpeer-review

Effects of resources and predation on the predictability of community composition.

Gerla, D. J., Vos, M., Kooi, B. W. & Mooij, W. M., 2009, In : Oikos. 22, p. 771-799

Research output: Contribution to JournalArticleAcademicpeer-review

community composition
predation
resource
predators
predator
Epidemiology
Immunity
Chaotic Behavior
Infection
Bifurcation

Feeding threshold for predators stabilises predator-prey systems.

Bontje, D. M., Kooi, B. W., van Voorn, G. A. K. & Kooijman, S. A. L. M., 2009, In : Mathematical Modelling of Natural Phenomena. 4, p. 92-110

Research output: Contribution to JournalArticleAcademicpeer-review

Food chain dynamics in the chemostat.

Boer, M. P., Kooi, B. W. & Kooijman, S. A. L. M., 1998, In : Mathematical Biosciences. 150, p. 43-62 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Chemostats
Food Chain
Chemostat
food chain
Food Chain Model

Food quality in producer-grazer models 0 a generalized analysis.

Stiefs, D., van Voorn, G. A. K., Kooi, B. W., Gross, T. & Feudel, U., 2010, In : The American Naturalist. 176, p. 367-380

Research output: Contribution to JournalArticleAcademicpeer-review

food quality
intraspecific competition
stoichiometry
bifurcation
modeling

From steady-state to synchronized yeast glycolytic oscillations I: model construction.

du Preez, F. B., van Niekerk, D. D., Kooi, B. W., Rohwer, J. M. & Snoep, J. L., 2012, In : The FEBS Journal. 279, p. 2810-2822

Research output: Contribution to JournalArticleAcademicpeer-review

Yeast
Yeasts
Phosphofructokinases
Glycolysis
Silicon

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

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

Homoclinic and heteroclinic orbits to a cycle in a tri-trophic food chain.

Boer, M. P., Kooi, B. W. & Kooijman, S. A. L. M., 1999, In : Journal of Mathematical Biology. 39, p. 19-38

Research output: Contribution to JournalArticleAcademicpeer-review

Hopf and torus bifurcations, torus destruction and chaos in population biology

Stollenwerk, N., Sommer, PF., Kooi, B. W., Mateus, L., Ghaffari, P. & Aguiar, M., 2017, In : Ecological Complexity. 30, June, p. 91-99

Research output: Contribution to JournalArticleAcademicpeer-review

chaotic dynamics
bifurcation
Biological Sciences
stochasticity
food handling

How much complexity is needed to describe the fluctuations observed in dengue hemorrhagic fever incidence data?

Aguiar, M., Kooi, B. W., Rocha, F., Ghaffari, P. & Stollenwerk, N., 2013, In : Ecological Complexity. 16, p. 31-40

Research output: Contribution to JournalArticleAcademicpeer-review

dengue fever
incidence
dengue
chaotic dynamics
dengue hemorrhagic fever