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Research Output 1998 2019

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2019

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

On the role of vector modeling in a minimalistic epidemic model

Rashkov, P., Venturino, E., Aguiar, M., Stollenwerk, N. & Kooi, B. W., 1 Jan 2019, In : Mathematical Biosciences and Engineering. 16, 5, p. 4314-4338 25 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Epidemic Model
Virus Diseases
Infection
Ecology
Modeling

Three-dimensional bifurcation analysis of a predator-prey model with uncertain formulation

Aldebert, C., Kooi, B. W., Nerini, D., Gauduchon, M. & Poggiale, J. C., Feb 2019, In : SIAM journal on applied mathematics. 79, 1, p. 377-395 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Dimensional Analysis
Predator-prey Model
Bifurcation Analysis
Three-dimensional
Formulation
2018

Is structural sensitivity a problem of oversimplified biological models? Insights from nested Dynamic Energy Budget models

Aldebert, C., Kooi, B. W., Nerini, D. & Poggiale, J-C., 7 Jul 2018, In : Journal of Theoretical Biology. 448, p. 1-8 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biological Models
Budgets
Theoretical Models
Prediction Model
Sensitivity Analysis

Modelling, singular perturbation and bifurcation analyses of bitrophic food chains

Kooi, B. W. & Poggiale, J. C., 1 Jul 2018, In : Mathematical Biosciences. 301, p. 93-110 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain
Explosions
Singular Perturbation
food chain
Bifurcation
2017

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

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

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

The impact of a predator on the outcome of competition in the three-trophic food web

Dutta, PS., Kooi, B. W. & Feudel, U., 21 Mar 2017, In : Journal of Theoretical Biology. 417, p. 28-42

Research output: Contribution to JournalArticleAcademicpeer-review

Food Web
Food Chain
Predator
food webs
predators

The practice of prediction: What can ecologists learn from applied, ecology-related fields?

Pennekamp, F., Adamson, M. W., Petchey, O. L., Poggiale, J-C., Aguiar, M., Kooi, B. W., Botkin, D. B. & DeAngelis, D. L., 5 Dec 2017, In : Ecological Complexity. 32, Part B, December, p. 156-167

Research output: Contribution to JournalArticleAcademicpeer-review

ecologists
ecology
prediction
global change
epidemiology
2016

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

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

Inherent characteristics of sawtooth cycles can explain different glacial periodicities

Omta, A. W., Kooi, B. W., van Voorn, G. A. K., Rickaby, R. E. M. & Follows, M. J., 2016, In : Climate Dynamics. 46, p. 557-569

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
periodicity
glacial-interglacial cycle
prediction
orbital forcing
interglacial

Over-shading is critical for inducing a regime shift from heathland to grassland under nitrogen enrichment

van Voorn, GAK., Kooi, B. W. & Bregt, A. K., 2016, In : Ecological Complexity. 27, p. 74-83

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
heathland
heathlands
shading
shade
grasslands
2015

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

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

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

Modelling the dynamics of traits involved in fighting-predators–prey system

Kooi, B. W., 2015, In : Journal of Mathematical Biology. 71, 6, p. 1575-1605

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Prey
Hawks
Modeling
Predator
Population

Revealing the role of predator interference in a predator–prey system with disease in prey population

Chakraborty, S., Kooi, B. W., Biswas, A. & Chattopadhyay, P., 2015, In : Ecological Complexity. 21, p. 100-110

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
predator
predators
disease control
predation
infectious disease
2014

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

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

Multiple resource limitation: Non-equilibrium coexistence of species in a competition model using a synthesizing unit.

Dutta, P. S., Kooi, B. W. & Feudel, U., 2014, In : Theoretical Ecology. 7, p. 407-421

Research output: Contribution to JournalArticleAcademicpeer-review

coexistence
resource
supersaturation
chaotic dynamics
bifurcation

Serving many at once: How a database approach can create unity in dynamical ecosystem modelling

Mooij, W. M., Brederveld, R. J., de Klein, J. M., DeAngelis, D. L., Downing, A. S., Faber, M., Gerla, D. J., Hipsey, M. R., 't Hoen, J., Janse, J. H., Janssen, A. B. G., Jeuken, M., Kooi, B. W., Lischke, B., Petzoldt, T., Postma, L., Schep, S. A., Scholten, H., Teurlincx, S., Thiange, C. & 5 othersTrolle, D., van Dam, A. A., van Gerven, L. P. A., van Nes, E. H. & Kuiper, J. J., 2014, In : Environmental Modelling & Software. 61, p. 266-273

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
ecosystem modeling
Ecosystems
Lotka-Volterra model
OSIRIS
Ecology
2013

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

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

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

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

Resource competition: a bifurcation theory approach.

Kooi, B. W., Dutta, P. S. & Feudel, U., 2013, In : Mathematical Modelling of Natural Phenomena. 8, p. 165-185

Research output: Contribution to JournalArticleAcademicpeer-review

Bifurcation Theory
Resources
Chemostats
Ecosystems
Chemical analysis

Smoking epidemic eradication in a eco-epidemiological dynamic model.

van Voorn, G. A. K. & Kooi, B. W., 2013, In : Ecological Complexity. 14, p. 180-189

Research output: Contribution to JournalArticleAcademicpeer-review

smoking
dynamic models
bifurcation
population dynamics
modeling
2012

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

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

Scaling of stochasticity in dengue hemorrhagic fever epidemics

Aguiar, M., Kooi, B. W., Martins, J. & Stollenwerk, N., 2012, In : Mathematical Modelling of Natural Phenomena. 7, p. 1-11

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Epidemiology
Stochasticity
Stochastic systems
Skeleton
Parameter estimation
2011

Stabilization and complex dynamics in a predator-prey model with predator suffering from an infectious disease.

Kooi, B. W., van Voorn, G. A. K. & Pada Das, K., 2011, In : Ecological Complexity. 8, p. 113-122

Research output: Contribution to JournalArticleAcademicpeer-review

infectious disease
infectious diseases
stabilization
bifurcation
predator

Sublethal toxic effects in a generic aquatic system

Bontje, D. M., Kooi, B. W. & van Hattum, A. G. M., 2011, In : Ecotoxicology and Environmental Safety. 74, 4, p. 929-939 11 p., 52.

Research output: Contribution to JournalArticleAcademicpeer-review

Poisons
Ecosystems
Nutrients
Ecosystem
Food
Seasonality
dengue
Dengue
Complex Dynamics
Coinfection
2010

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
Reproduction
spawning
Population
Food storage
Chemostats

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

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

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
2009

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

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

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

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

Modelling long-term ecotoxicological effect on an algal population under dynamic nutrient stress.

Bontje, D. M., Kooi, B. W., Liebig, M. & Kooijman, S. A. L. M., 2009, In : Water Research. 43, p. 3292-3300

Research output: Contribution to JournalArticleAcademicpeer-review

nutrient dynamics
Algae
Nutrients
alga
microcosm

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

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