DEB papers

This page presents a selection of papers on DEB theory and its applications, sorted by topic. See DEB library on Zotero for a full list. The papers include summaries of particular aspects of the theory, formal (axiom-based) and less formal (biology-based), introductions, sub- and supra-organismic levels and applications. Becoming a Zotero member is easy (and has no costs), which gives access to all PDFs.

A systematic account of the theory is given in the book DEB3 (Cambridge Univ Press, 3rd edition 2010). The notation document contains the rules for notation that are used, as well as the notation itself. The Comments to DEB3 is a collection of developments since 2010 and explanations of parts of the book. It is a document which changes frequently. The summary of concepts presents the meaning of the various concepts and their function in the theory. It has no formulae or biological observations and follows the section-structure of DEB3.

See also the DEB video collection.

Journal issues on DEB theory

• Ecological Modelling, 488 (2023)
• Conservation Physiology (2021)
• Ecological Modelling, 428 (2020)
• Journal of Sea Research 143 (2019)
• Journal of Sea Research 94 (2014)
• Journal of Sea Research 65 (2011) issue 1
• Philosophical Transactions of the Royal Society 365 (2010) issue 1557
• Journal of Sea Research 62 (2009) issue 2 3
• Journal of Sea Research 56 (2006) issue 2

Editorials of DEB special issues

• Lavaud et al 2023: Metabolic organization across scales of space and time
• Lavaud et al 2021: The role of Dynamic Energy Budgets in conservation physiology
• Augustine and Kooijman 2019: A new phase in DEB research
• van der Meer et al 2014: 35 years of DEB research
• Alunno-Bruscia et al 2011: The AquaDEB project: Physiological flexibility of aquatic animals analysed with a generic Dynamic energy Budget model (phase II)
• Sousa et al 2010: Dynamic Energy Budget theory restores coherence in biology
• Alunno-Bruscia et al 2009: The AquaDEB project (phase I): Analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using Dynamic Energy Budgets
• van der Veer & Alunno-Bruscia 2006: The DEBBIB project: Dynamic Energy Budgets in bivalves

DEB model introductions

• Lika et al 2024: The metabolic interpretation of the von Bertalanffy growth rate
• Kearney 2020: What is the status of metabolic theory one century after Pütter invented the von Bertalanffy growth curve?
• Kooijman 2020: The standard Dynamic Energy Budget model has no plausible alternatives
• Jager 2020: Revisiting simplified DEBtox models for analysing ecotoxicity data
• Muller et al 2019: Regulation of reproductive processes with dynamic energy budgets
• Jusup et al 2017: Physics of metabolic organization
• Sara et al 2014: Thinking beyond organism energy use: a trait-based bioenergetic mechanistic approach for predictions of life history traits in marine organisms
• Kearney et al 2015: Dynamic Energy Budget Theory: An Efficient and General Theory for Ecology
• Ledder 2014: The basic Dynamic Energy Budget model and some implications
• Kooijman 2012: Energy budgets
• Lika and Kooijman 2011: The comparative topology of energy allocation in budget models
• Lorena 2010: Stylized facts in microalgal growth - interpretation in a DEB context.
• van der Meer 2006: Metabolic theories in ecology
• Sousa et al 2006: The thermodynamics of organisms in the context of Dynamic Energy Budget theory
• Kooijman 2001: Quantitative aspects of metabolic organization; a discussion of concepts
• Kooijman 1998: The Dynamic Energy Budget (DEB) model

DEB in evolutionary context

• Troost et al 2009: Seasonality, climate cycles and body size evolution
• Kooijman and Troost 2007: Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory
• Kooijman and Hengeveld 2005: The symbiontic nature of metabolic evolution
• Troost et al 2005: When do mixotrophs specialize? Adaptive Dynamics theory applied to a Dynamic Energy Budget model
• Kooijman 2004: On the coevolution of life and its environment
• Kooijman et al 2003: Quantitative steps in symbiogenesis and the evolution of homeostasis

Parameter estimation & methodology

• Kooijman et al 2024:From formulae, via models to theories: Dynamic Energy Budget theory illustrates requirements
• Lika et al 2024: The relationship between confidence intervals and distributions of estimators for parameters of deterministic models SI
• Matyja 2023: Standard dynamic energy budget model parameter sensitivity
• Lika et al 2020: The use of augmented loss functions for estimating Dynamic Energy Budget parameters SI
• Augustine et al 2020: Comparing loss functions and interval estimates for survival data
• Marques et al 2019: Fitting Multiple Models to Multiple Data Sets
• Kooijman 2018: Models in stress research
• Marques et al 2018: The AmP project: Comparing Species on the Basis of Dynamic Energy Budget Parameters
• Morais et al 2018: Calibration of parameters in Dynamic Energy Budget models using Direct-Search methods
• Lika et al 2011: The `covariation method' for estimating the parameters of the standard Dynamic Energy Budget model II: Properties of the estimation method and some patterns
• Lika et al 2011: The `covariation method' for estimating the parameters of the standard Dynamic Energy Budget model I: philosophy and approach
• Kooijman et al 2008: From food-dependent statistics to metabolic parameters, a practical guide to the use of Dynamic Energy Budget theory
• Sousa et al 2008: From empirical patterns to theory: A formal metabolic theory of life
• van der Meer 2006: An introduction to Dynamic Energy Budget (DEB) models with special emphasis on parameter estimation

Species accounts

mammals

• Desforges et al 2020: Quantifying energetic and fitness consequences of seasonal heterothermy in an Arctic ungulate
• Silva et al 2020: Life cycle bioenergetics of the gray seal (Halichoerus grypus) in the Baltic Sea: Population response to environmental stress
• Desforges et al 2019: Quantification of the full lifecycle bioenergetics of a large mammal in the high Arctic
• Goedegebuure et al 2019: Modelling southern elephant seals in East Antarctica using an individual-based model with a dynamic energy budget
• Monar et al 2010: Predicting survival, reproduction and abundance of polar bears under climate change

reptiles

• Skorczewski and Andersen 2021: A Dynamic Energy Budget Model of Ornate Box Turtle Shell Growth
• Stubbs et al 2020: Simulated growth and reproduction of green turtles (Chelonia mydas) under climate change and marine heatwave scenarios
• Arnall et al 2019: Life in the slow lane? A dynamic energy budget model for the western swamp turtle, Pseudemydura umbrina
• Stubbs et al 2019: A full life cycle Dynamic Energy Budget (DEB) model for the green sea turtle (Chelonia mydas) fitted to data on embryonic development
• Marn et al 2019: Comparative physiological energetics of Mediterranean and North Atlantic loggerhead turtles
• Marn et al 2017: Inferring physiological energetics of loggerhead turtle (Caretta caretta) from existing data using a general metabolic theory
• Marn et al 2017: Environmental effects on growth, reproduction, and life-history traits of loggerhead turtles
• Arnall et al 2014: A thermal profile of metabolic performance in the rare Australian chelid, Pseudemydura umbrina

fish

• Zhang et al 2024: A mechanistic model approach to characterize suitable regions for Salmo salar aquaculture in the Yellow Sea under global warming
• He et al 2024: Dynamic energy budget model for the complete life cycle of chub mackerel in the Northwest Pacific
• Wang et al 2023: A dynamic energy budget model for black rockfish Sebastes schlegelii: Parameterization and application in marine ranching areas, Yellow Sea, China
• Hatzonikolakis et al 2021: Investigating growth and reproduction of the Mediterranean swordfish Xiphias gladius through a full life cycle bioenergetics model
• Nepal et al 2021: Effects of food limitation on growth, body condition and metabolic rates of non-native blue catfish
• Dortel et al 2020: A Dynamic Energy Budget simulation approach to investigate the ecophysiological factors behind the two-stanza growth of yellowfin tuna (Thunnus albacares)
• Ren et al 2020: A dynamic energy budget model for small yellow croaker Larimichthys polyactis: Parameterisation and application in its main geographic distribution waters
• Dambrine et al 2020: Contribution of a bioenergetics model to investigate the growth and survival of European seabass in the Bay of Biscay - English Channel area
• Stavrakidis-Zachou et al 2019: A DEB model for European sea bass (Dicentrarchus labrax): Parameterisation and application in aquaculture
• Lavaud et al 2019: Modeling the impact of hypoxia on the energy budget of Atlantic cod in two populations of the Gulf of Saint-Lawrence, Canada
• Strople et al 2018: The effect of environmental conditions on Atlantic salmon smolts' (Salmo salar) bioenergetic requirements and migration through an inland sea
• MacDonald et al 2018: Exploring the Influence of Food and Temperature on North Sea Sandeels Using a New Dynamic Energy Budget Model
• Augustine et al 2017: Comment on the ecophysiology of the Greenland shark, Somniosus microcephalus
• Leloutre et al 2016: A bioenergetics model of the entire life cycle of the three-spined stickleback, Gasterosteus aculeatus
• Jusup and Matsuda 2015: Mathematical modelling of bluefin tuna growth, and reproduction based on physiological energetics
• Jusup et al 2014: Simple measurements reveal the feeding history, the onset of reproduction, and energy conversion efficiencies in captive bluefin tuna
• Rinaldi et al 2014: Estimation of dynamic energy budget parameters for the Mediterranean toothcarp (Aphanius fasciatus)
• Serpa et al 2013: Modelling the growth of white seabream (Diplodus sargus) and gilthead seabream (Sparus aurata) in semi-intensive earth production ponds using the Dynamic Energy Budget approach
• Saraiva et al 2012: Modelling the skipjack tuna dynamics in the Indian Ocean with APECOSM-E - Part 2: Parameter estimation and sensitivity analysis
• Jusup et al 2011: A full lifecycle bioenergetic model for bluefin tuna
• Freitas et al 2011: Food conditions of the sand goby Pomatoschistus minutus in shallow waters: an analysis in the context of Dynamic Energy Budget theory
• Einarsson et al 2011: A dynamic energy budget (DEB) model for the energy usage and reproduction of the Icelandic capelin (Mallotus villosus)
• Pecquerie et al 2011: Analyzing variations in life-history traits of Pacific salmon in the context of Dynamic Energy Budget (DEB) theory
• Augustine et al 2011: Developmental energetics of zebrafish, Danio rerio
• van der Veer 2009: Physiological performance of plaice Pleuronectes platessa (L.): from Static to Dynamic Energy Budgets
• Pecqerie et al 2009: Modeling fish growth and reproduction in the context of the Dynamic Energy Budget theory to predict environmental impact on anchovy spawning duration

echinoderms

• Agüera et al 2021: Bioenergetics of the common seastar Asterias rubens: a keystone predator and pest for European bivalve culture
• Chary et al 2020: Integrated multi-trophic aquaculture of red drum (Sciaenops ocellatus) and sea cucumber (Holothuria scabra): Assessing bioremediation and life-cycle impacts
• Ren et al 2017: Parameterisation and application of dynamic energy budget model to sea cucumber Apostichopus japonicus
• Agüera et al 2015: Parameter Estimations of Dynamic Energy Budget (DEB) Model over the Life History of a Key Antarctic Species: The Antarctic Sea Star Odontaster validus Koehler, 1906
• Monaco et al 2014: Thermal ecology and physiology of an intertidal predator-prey system: Pisaster ochraceus and Mytilus californianus
• Monaco et al 2014: A Dynamic Energy Budget (DEB) Model for the Keystone Predator Pisaster ochraceus

molluscs

• Lavaud et al 2024: redicting restoration and aquaculture potential of eastern oysters through an eco-physiological mechanistic model
• Bruggeman et al 2022: The paralarval stage as key to predicting squid catch (Loligo reynaudii): Hints from a process-based model
• Krupandan et al 2022: Exploring South African Pacific oyster mariculture potential through combined Earth observation and bioenergetics modelling
• Pousse et al 2022: Dynamic energy budget modeling of Atlantic surfclam, Spisula solidissima, under future ocean acidification and warming
• Nan et al 2021: Spatial difference in net growth rate of Yesso scallop Patinopecten yessoensis revealed by an aquaculture ecosystem model
• Gaudron et al 2021: Inferring functional traits in a deep-sea wood-boring bivalve using dynamic energy budget theory
• Duan et al 2021: A dynamic energy budget model for abalone, Haliotis discus hannai Ino
• Monaco et al 2021: Dynamic Energy Budget model suggests feeding constraints and physiological stress in black-lip pearl oysters, 5 years post mass-mortality event
• Bertolini et al 2021: Testing a Model of Pacific Oysters' (Crassostrea gigas) Growth in the Adriatic Sea: Implications for Aquaculture Spatial Planning
• Lavaud et al 2021: Dynamic energy budget modeling to predict eastern oyster growth, reproduction, and mortality under river management and climate change scenarios
• Sangare et al 2020: Impact of environmental variability on Pinctada margaritifera life-history traits: A full life cycle deb modeling approach
• Dong et al 2020: Simulation and validation of Manila clam Ruditapes philippinarum growth with a DEB-based individual growth model in Jiaozhou Bay
• Maynou et al 2020: Impact of temperature increase and acidification on growth and the reproductive potential of the clam Ruditapes philippinarum using DEB
• Duan et al 2020: The measurement of parameters for the dynamic energy budget (DEB) model in Haliotis discus hannai (disk abalone)
• Haberle et al 2020: Dynamic energy budget of endemic and critically endangered bivalve Pinna nobilis: A mechanistic model for informed conservation
• Guillaumot et al 2020: Can DEB models infer metabolic differences between intertidal and subtidal morphotypes of the Antarctic limpet Nacella concinna (Strebel, 1908)?
• Ren et al 2020: Ocean acidification and dynamic energy budget models: Parameterisation and simulations for the green-lipped mussel
• Stechele et al 2020: Modeling native oyster metabolism for aquaculture and restoration purposes; Modelling the metabolism of European flat oyster larvae
• Palmer et al 2020: Remote Sensing-Driven Pacific Oyster (Crassostrea gigas) Growth Modeling to Inform Offshore Aquaculture Site Selection
• Chowdhury et al 2019: Growth potential of rock oyster (Sacosstrea cucullata) exposed to dynamic environmental conditions simulated by a Dynamic Energy Budget model
• Wijsman 2019: Dynamic Energy Budget (DEB) model Blue mussels (Mytilus edulis)
• Jiang et al 2019: Simulation of Yesso scallop, Patinopecten yessoensis, growth with a dynamic energy budget (DEB) model in the mariculture area of Zhangzidao Island
• Aguirre-Velarde et al 2019: Predicting the energy budget of the scallop Argopecten purpuratus in an oxygen-limiting environment
• Gourault et al 2019: New insights into the reproductive cycle of two Great Scallop populations in Brittany (France) using a DEB modelling approach
• Ballesta-Artero et al 2019: Energetics of the extremely long-living bivalve Arctica islandica based on a Dynamic Energy Budget model
• Mariño et al 2019: Dynamic Energy Budget theory predicts smaller energy reserves in thyasirid bivalves that harbour symbionts
• Chowdhury et al 2018: DEB parameter estimation for Saccostrea cucullata (Born), an intertidal rock oyster in the Northern Bay of Bengal
• Cheng et al 2018: Predicting effective aquaculture in subtropical waters: A dynamic energy budget model for the green lipped mussel, Perna viridis
• Aguirre-Velarde et al 2018: Feeding behaviour and growth of the Peruvian scallop (Argopecten purpuratus) under daily cyclic hypoxia conditions
• Hatzonikolakis et al 2017: Simulation of mussel Mytilus galloprovincialis growth with a dynamic energy budget model in Maliakos and Thermaikos Gulfs (Eastern Mediterranean)
• Agüera et al 2017: A Dynamic Energy Budget (DEB) model to describe Laternula elliptica (King, 1832) seasonal feeding and metabolism
• Agüera and Birne 2018: A dynamic energy budget model to describe the reproduction and growth of invasive starfish Asterias amurensis in southeast Australia
• Wijsman 2017: Relating a DEB model for mussels (Mytilus edulis) to growth data from the Oosterschelde; Trace-back analysis of food conditions
• Lavaud et al 2017: Integrating the effects of salinity on the physiology of the eastern oyster, Crassostrea virginica, in the northern Gulf of Mexico through a Dynamic Energy Budget model
• Thomas et al 2016: Global change and climate-driven invasion of the Pacific oyster (Crassostrea gigas) along European coasts: a bioenergetics modelling approach
• Zhang et al 2016: The estimation of dynamic energy budget (DEB) model parameters for scallop Patinopecten yessoensis
• Zimmer et al 2014: Metabolic acceleration in the pond snail Lymnaea stagnalis?
• Montalto et al 2014: Dynamic Energy Budget parameterisation of Brachidontes pharaonis, a lessepsian bivalve in the Mediterranean Sea
• Petter et al 2014: Consequences of altered temperature and food conditions for individuals and populations: a Dynamic Energy Budget analysis for Corbicula fluminea in the Rhine
• Picoche et al 2014: Towards the Determination of Mytilus edulis Food Preferences Using the Dynamic Energy Budget (DEB) Theory
• Filgueira et al 2014: A fully-spatial ecosystem-DEB model of oyster (Crassostrea virginica) carrying capacity in the Richibucto Estuary, Eastern Canada
• Bèjaoui-Omri et al 2014: Dynamic energy budget model: a monitoring tool for growth and reproduction performance of Mytilus galloprovincialis in Bizerte Lagoon (Southwestern Mediterranean Sea)
• Matzelle et al 2014: Dynamic Energy Budget model parameter estimation for the bivalve Mytilus californianus: Application of the covariation method.
• Lavaud et al 2014: Feeding and energetics of the great scallop, Pecten maximus, through a DEB model
• Sarà et al 2013: Predicting biological invasions in marine habitats through eco-physiological mechanistic models: a case study with the bivalve Brachidontes pharaonis
• Saraiva et al 2012: Validation of a Dynamic Energy Budget (DEB) model for the blue mussel Mytilus edulis
• Wijsman and Smaal 2011: Growth of cockles (Cerastoderma edule) in the Oosterschelde described by a Dynamic Energy Budget model
• Thomas et al 2011: Application of a bioenergetic growth model to larvae of the pearl oyster Pinctada margaritifera L.
• Pouvreau et al 2006: Application of a dynamic energy budget model to the Pacific oyster Crassostrea gigas, reared under various environmental conditions
• Flye Sainte Marie et al 2007: Impact of Brown Ring Disease on the energy budget of the Manila clam Ruditapes philippinarum
• Ren and Ross 2005: Environmental influence on mussel growth: A dynamic energy budget model and its application to the greenshell mussel Perna canaliculus
• Ren and Ross 2001: A dynamic energy budget model of the Pacific oyster Crassostrea gigas
• Visser et al 1994: Energy budgets and reproductive allocation in the simultaneous hermaphrodite pond snail, Lymnaea stagnalis (L.): A trade-off between male and female function
• Haren and Kooijman 1993: Application of the dynamic energy budget model to Mytilus edulis (L.)
• Ross and Nisbet 1990: Dynamic models of growth and reproduction of the mussel Mytilus edulis L.
• Zonneveld and Kooijman 1989: Application of a Dynamic Energy Budget Model to Lymnaea stagnalis (L.)

annelids

• Galasso et al 2020: Using the Dynamic Energy Budget theory to evaluate the bioremediation potential of the polychaete Hediste diversicolor in an integrated multi-trophic aquaculture system
• Rakel et al 2020: Individual-based dynamic energy budget modelling of earthworm lifehistories in the context of competition
• de Cubber et al 2019: Annelid polychaetes experience metabolic acceleration as other Lophotrochozoans: Inferences on the life cycle of Arenicola marina with a Dynamic Energy Budget model
• Ducrot et al 2007: Rearing and estimation of life-cycle parameters of the tubicifid worm Branchiura sowerbyi: Application to ecotoxicity testing
• Klok 2007: Effects of earthworm density on growth, development, and reproduction in Lumbricus rubellus (Hoffm.) and possible consequences for the intrinsic rate of population increase.
• Ratsak et al 1993: Modelling of growth of an oligochaete on activated sludge

arthropods

• Klagkou et al 2024: Dynamic Energy Budget Approach for Modeling Growth and Reproduction of Neotropical Stink Bugs
• Liu et al 2022: Determining the Parameters of the Dynamic Energy Budget Model of Litopenaeus vannamei
• Lagos et al 2022: Modelling the effects of food limitation and temperature on the growth and reproduction of the krill Nyctiphanes australis
• Gergs and Baden 2021: A Dynamic Energy Budget Approach for the Prediction of Development Times and Variability in Spodoptera frugiperda Rearing
• Yang et al 2020: A dynamic energy budget model of Fenneropenaeus chinensis with applications for aquaculture and stock enhancement
• Koch and de Schamphelaere 2020: Estimating inter-individual variability of dynamic energy budget model parameters for the copepod Nitocra spinipes from existing life-history data
• Tonk and Rozemeijer 2019: Ecology of the brown crab (Cancer pagurus) and production potential for passive fisheries in Dutch offshore windfarms
• Rozemeijer and Wijsman 2019: Desktop study on autecology and productivity of European lobster (Homarus gammarus, L) in offshore wind farms
• Koch and De Schamphelaere 2018: Two dynamic energy budget models for the harpacticoid copepod Nitocra spinipes
• Llandres et al 2015: A dynamic energy budget for the whole life-cycle of holometabolous insects
• Steenbergen et al 2015: Management options for the brown shrimp (Crangon crangon) fisheries in the North Sea
• Jager and Ravagnan 2015: Parameterising a generic model for the dynamic energy budget of Antarctic krill, Euphausia superba
• Jager et al 2015: Capturing the life history of the marine copepod Calanus sinicus into a generic bioenergetics framework
• McCauley et al 1990: Growth, reproduction, and mortality of Daphnia pulex Leydig: life at low food
• Gurney et al 1990: The physiological ecology of Daphnia: a dynamic model of growth and reproduction
• McCauley et al 1990: The physiological ecology of Daphnia: Development of a model of growth and reproduction
• Evers and Kooijman 1989: Feeding, digestion and oxygen consumption in Daphnia magna; a study in energy budgets

other

• van der Meer et al 2020: Predicting post-natal energy intake of lesser black-backed gull chicks by Dynamic Energy Budget modeling
• Lavaud et al 2020: A Dynamic Energy Budget model for the macroalga Ulva lactuca
• Galli et al 2016: Modelling red coral (Corallium rubrum) growth in response totemperature and nutrition
• van der Molen et al 2015: Modelling survival and connectivity of Mnemiopsis leidyi in the south-western North Sea and Scheldt estuaries
• Augustine et al 2014: Modelling the eco-physiology of the purple mauve stinger, Pelagia noctiluca, using Dynamic Energy Budget theory
• Teixeira et al 2014: A new perspective on the growth pattern of the Wandering Albatross (Diomedea exulans) through DEB theory
• Augustine et al 2014: Mechanisms behind the metabolic flexibility of an invasive comb jelly
• Augustine et al 2012: The trade-off between maturation and growth during accelerated development in frogs
• Hendrata and Birner 2010: Dynamic-energy-budget-driven fruiting-body formation in myxobacteria
• Alver et al 2006: An individual-based population model for rotifer (Brachionus plicatilis) cultures
• Dougherty et al 2002: Energy-based dynamic model for variable temperature batch fermentation by Lactococcus lactis

Patterns in parameter values

• Kooijman 2024: The comparative energetics of branchiopods: adaptations to volatile environments SI
• Kooijman et al 2022: The comparative energetics of the carnivorans and pangolins SI
• Augustine et al 2022: The comparative energetics of the chondrichthyans reveals universal links between respiration, reproduction and lifespan SI
• Lika et al 2022: The comparative energetics of the ray-finned fish in an evolutionary context SI
• Marn et al 2022: The comparative energetics of the turtles and crocodiles SI
• Kooijman and Augustine 2022: The comparative energetics of the cephalopods: they neither grow nor reproduce fast SI
• Kooijman et al 2021: Multidimensional scaling for animal traits in the context of dynamic energy budget theory SI
• van der Meer 2020: Production efficiency differences between poikilotherms and homeotherms have little to do with metabolic rate
• Kooijman et al 2020: The energetic basis of population growth in animal kingdom SI
• Kooijman 2020: The comparative energetics of petrels and penguins SI
• Augustine et al 2019: Altricial-precocial spectra in animal kingdom SI
• Augustine et al 2019: Why big-bodied animal species cannot evolve a waste-to-hurry strategy SI
• Lika et al 2019: Body size as emergent property SI
• Baas et al 2015: Sensitivity of animals to chemical compounds links to metabolic rate SI
• Kooijman et al 2014: Comparative energetics of the 5 fish classes on the basis of Dynamic Energy Budgets SI
• Kooijman 2014: Metabolic acceleration in animal ontogeny: an evolutionary perspective SI
• Kooijman et all 2014: Resource allocation to reproduction in animals SI
• Lika et al 2014: Bijection between data and parameter space quantifies the supply-demand spectrum SI
• Kooijman 2013: "Waste-to-hurry" Dynamic Energy Budgets explain the need of wasting to fully exploit blooming resources SI
• Kooijman et al 2011: Scenarios for acceleration in fish development and the role of metamorphosis
• Kooijman et al 2007: Scaling relationships based on partition coefficients and body sizes have similarities and interactions
• Cardoso et al 2006: Body size scaling relationships in bivalves: a comparison of field data with predictions by Dynamic Energy Budgets (DEB theory)
• van der Veer et al 2006: The estimation of DEB parameters for various Northeast Atlantic bivalve species
• van der Veer et al 2003: Body size scaling relationships in flatfish as predicted by Dynamic Energy Bugets (DEB theory): implications for recruitment
• Kooijman 1986: Energy budgets can explain body size relations

Population Dynamics

• Kooijman 2024: Ways to reduce or avoid juvenile-driven cycles in individual-based population models
• DeCubber et al 2024: Unravelling mechanisms behind population dynamics, biological traits and latitudinal distribution in two benthic ecosystem engineers: A modelling approach
• Kooijman et al 2020: The energetic basis of population growth in animal kingdom
• de Roos 2020: The impact of population structure on population and community dynamics
• Desforges et al 2020: Environment and physiology shape Arctic ungulate population dynamics
• Arnould-Pétré et al 2020: Individual-based model of population dynamics in a sea urchin of the Kerguelen Plateau (Southern Ocean), Abatus cordatus, under changing environmental conditions
• Kooi and Kooijman 2020: A cohort projection method to follow DEB-structured populations with periodic, synchronized and iteroparous reproduction
• Goedegebuure et al 2018: Modelling southern elephant seals Mirounga leonina using an individual-based model coupled with a dynamic energy budget
• Grossowicz et al 2017: A dynamic energy budget (DEB) model to describe population dynamics of the marine cyanobacterium Prochlorococcus marinus
• McFarland 2015: Population dynamics of the invasive green mussel, Perna viridis, in southwest Florida and individual energetics through the application of the Dynamic Energy Budget Theory
• Beaudouin et al 2015: An Individual-Based Model of Zebrafish Population Dynamics Accounting for Energy Dynamics
• Kooi and van der Meer 2010: Bifurcation theory, adaptive dynamics and DEB-structured populations of iteroparous species
• de Roos et al 2008: Simplifying a physiologically structured population model to a stage-structured biomass model
• Kooijman et al 2007: A new class of non-linear stochastic population models with mass conservation
• Klanjscek et al 2006: Integrating dynamic energy budgets into matrix population models
• Kooijman et al 2004: Dynamic Energy Budget representations of stoichiometric constraints to population models
• Brandt et al 2003: A general model for multiple substrate biodegradation. Application to co-metabolism of non structurally analogous compounds
• Kooi and Boer 2001: Bifurcations in ecosystem models and their biological interpretation
• Nisbet et al 2000: From molecules to ecosystems through Dynamic Energy Budget models
• Kooijman and Nisbet 2000: How light and nutrients affect life in a closed bottle
• Kooijman et al 1999: The Application of Mass and Energy Conservation Laws in Physiologically Structured Population Models of Heterotrophic Organisms
• Kooi et al 1998: Consequences of population models on the dynamics of food chains
• de Roos 1997: A gentle introduction to physiologically structured population models
• de Roos et al 1997: What individual life histories can (and cannot) tell about population dynamics
• Kooi and Kooijman 1996: Catastrophic behavior of myxamoebae
• McCauley et al 1996: Structured population models of herbiverous zooplankton
• Gurney et al 1996: Individual energetics and the equilibrium demography of structured populations
• Kooi and Kooijman 1995: Many limiting behaviours in microbial food chains
• Kooi and Kooijman 1994: The transient behaviour of food chains in chemostats
• Kooijman 1992: Biomass conversion at population level
• Nisbet et al 1991: Population Dynamics and Element Recycling in an Aquatic Plant-Herbivore System
• Kooijman et al 1989: Population consequences of a physiological model for individuals
• Hallam et al 1989: Effects of toxicants on aquatic populations
• Nisbet et al 1989: Structured population models: a tool for linking effects at individual and population level
• Kooijman et al 1987: Research on the physiological basis of population dynamics in relation to ecotoxicology
• Kooijman 1986: Population dynamics on the basis of budgets
• Kooijman 1985: Toxicity at population level
• Diekmann et al 1984: Continuum population dynamics with an application to Daphnia magna
• Kooijman and Metz 1984: On the dynamics of chemically stressed populations; The deduction of population consequences from effects on individuals

Tumor growth

• Tosca et al 2021: A Dynamic Energy Budget (DEB) based modeling framework to describe tumor-in-host growth inhibition and cachexia onset during anticancer treatment in in vivo xenograft studies
• Tosca et al 2019: A Population Dynamic Energy Budget-Based Tumor Growth Inhibition Model for Etoposide Effects on Wistar Rats
• Terranova et al 2018: Modeling tumor growth inhibition and toxicity outcome after administration of anticancer agents in xenograft mice: A Dynamic Energy Budget (DEB) approach
• van Leeuwen et al 2003: The embedded tumor: host physiology is important for the interpretation of tumor growth