Publications

2020

Girardot, B., Gauduchon, M., Ménard, F.  and Poggiale, J.-C., Does evolution design robust food webs? Proc. R. Soc. B 287: 20200747. doi.org/10.1098/rspb.2020.0747

Poggiale, J.-C., Kooi, B.W., Aldebert, C. and Girardot, B., Analysis of a predator–prey model with specific time scales: a geometrical approach proving the occurrence of canard solutions, J. Math. Biol.  doi: 10.1007/s00285-019-01337-4 (pdf)

Poggiale, J.-C., Regime shifts at the origin of a long transient methodological development for predictive ecology, Physics of Life Reviews, doi: 10.1016/j.plrev.2019.12.001, (pdf)

Legras, G., Loiseau, N., Gaertner, J.-C., Poggiale, J.-C., Gaertner-Mazouni, N., Assessing functional diversity: the influence of the number of the functional traits, Theoretical Ecology, 13, 117-126, doi: 10.1007/s12080-019-00433-x

2019

Clement, A., Kooi, B. W.; Nerini, D., Gauduchon, M. and  Poggiale J.-C., Three-dimensional bifurcation analysis of a predator-prey model with uncertain formulation, SIAM J. Appl. Math., 79 (1), 377-395.

Maury, O., Poggiale, J.-C., Aumont, O., Damage-related protein turnover explains inter-specific patterns of maintenance rate and suggests modifications of the DEB theory, Journal of Sea Research, 143, 35-47 (pdf).

Dunn, R.J.K., Welsh, D.T., Teasdale, P.R., Gilbert, F., Poggiale, J.-C., Waltham, N.J., Effects of the Bioturbating Marine Yabby Trypaea australiensis on Sediment Properties in Sandy Sediments Receiving Mangrove Leaf Litter, J. Mar. Sci. Eng. 7(12), 426; doi: 10.3390/jmse7120426

Legras, G., Loiseau, N., Gaertner J.-C., Poggiale, J.-C., Ienco, D., Mazouni, N., Mérigot, B., Assessment of congruence between co-occurrence and functional networks: A new framework for revealing community assembly rules, Scientific reports, 9, doi: 10.1038/s41598-019-56515-7

2018

Kooi, B.W., Poggiale, J.-C., Modelling, singular perturbation and bifurcation analyses of bitrophic food chains, Mathematical Biosciences, 301, 93-110 (pdf).

Aldebert, C., Kooi, B.W., Nérini, D., Poggiale, J.-C., Is structural sensitivity a problem of oversimplified biological models? Insights from nested Dynamic Energy Budget models, Journal of Theoretical Biology, 448, 1-8 (pdf).

2017

F. Pennekamp, M.W. Adamson, O.L. Petchey, J.-C. Poggiale, M. Aguiar, B.W. Kooi, D. Botkin, D.L. DeAngelis,  The practice of prediction: What can ecologists learn from applied, ecology-related fields? Ecological  Complexity, 32, 156-167 (pdf)

Thibaut, T., Blanfune, A. Boudouresque, C.F., Personnic, S., Ruitton, S., Ballesteros, E., Bellan-Santini, D., Bianchi, C.N., Bussotti, S, Cebrian, E., More..., An ecosystem-based approach to assess the status of Mediterranean algae-dominated shallow rocky reefs, Marine Pollution Bulletin, 117; 311-329. doi: 10.1016/j.marpolbul.2017.01.029

2016

J. Guiet, J.-C. Poggiale, O. Maury, Modelling the community size-spectrum: recent developments and new directions, Ecological Modelling 337, 4-14 (pdf)

J. Guiet, O. Aumont, J.-C. Poggiale, O. Maury, Effects of lower trophic level biomass and water temperature on fish communities : A modeling study, Progress in Oceanography, 46, 22-37 (pdf)

C. Aldebert, D. Nérini, M. Gauduchon, J.-C. Poggiale, Structural sensitivity and resilience in a predator–prey model with density-dependent mortality, Ecological  Complexity, in press (pdf).

C. Aldebert, D. Nérini, M. Gauduchon, J.-C. Poggiale, Does structural sensitivity alter stability - complexity relationship? Ecological Complexity, in press (pdf)

2015

C. Accolla, D. Nérini, O. Maury and J.-C. Poggiale, Analysis of functional response in presence of schooling phenomena: An IBM approach, Progress in Oceanography, 134, 232-243 (pdf)

M. Marvá, J.-G. Alcázar, J.-C. Poggiale, R. Bravo de la Parra, A simple geometrical condition for the existence of periodic solutions of planar periodic systems. Applications to some biological models. Journal of Mathematical Analysis and Applications 423 (2), 1469-1479 (pdf).

2014

S. Augustine, S. Rosa, S.A.L.M. Kooijman, F. Carlotti, J.-C. Poggiale, Modeling the eco-physiology of the purple mauve stinger, Pelagia nocticula, using Dynamic Energy Budget theory, Journal of Sea Research, 94, 52-64 (pdf).

S. Augustine, C. Jaspers, S.A.L.M. Kooijman, F. Carlotti, J.-C. Poggiale, V. Freitas, H. van der Veer, L. van Walraven, Mechanisms behind the metabolic flexibility of an invasive comb jelly, Journal of Sea Research, 94, 156-165 (pdf). 

Dugenne, M. Thyssen, D. Nérini, C. Manté, J.-C. Poggiale, N. Garcia, F. Garcia, G. Grégori, Consequence of a sudden wind event on the dynamics of a coastal phytoplankton community: an insight into specific population growth rates using a single cell high frequency approach,  Frontiers in Microbiology, Vol. 5, Article 485, doi:10.3389/fmicb.2014.00485.

S. Personnic, C.-F. Boudouresque, P. Astruch, et al., An Ecosystem-Based Approach to Assess the Status of a Mediterranean Ecosystem, the Posidonia oceanica Seagrass Meadow, Plos One, Volume: 9   Issue: 6     Article Number: e98994   Published: JUN 16 2014.

2013

F. Cordoleani, D. Nérini, A. Morozov, M. Gauduchon, J.-C. Poggiale, Scaling up the predator functional response in heterogeneous environment: when Holling type III can emerge? Journal of Theoretical Biology, 336, 200-208, (pdf).

J.-C. Poggiale, Y. Eynaud, M. Baklouti, Impact of periodic nutrient input rate on trophic chain properties, Ecological Complexity, Ecological Complexity, 56-63, (pdf).

M. Marva, R. Bravo de la Parra, J.-C. Poggiale, Reduction of slow-fast asymptotically autonomous systems with applications to gradostat models, Ecological Complexity, 14, 75-84, (pdf).

O. Maury, J.-C. Poggiale, From individuals to populations to communities: A dynamic energy budget model of marine ecosystem size-spectrum including life history diversity, Journal of Theoretical Biology, 324, 52-71 (pdf).

Y. Eynaud, D. Nérini, M. Baklouti, J.-C. Poggiale,  Towards a simplification of models using regression trees, Journal of the Royal Society Interface, 10, 20120613, (pdf)

2012

M. Marva, J.-C. Poggiale, R. Bravo de la Parra, Reduction of slow-fast periodic systems with applications to population dynamics models, Mathematical Models and Methods in Applied Sciences, 22 (10) (pdf).

A. Morozov, J.-C. Poggiale, F. Cordoleani, Implementation of the zooplankton functional response in plankton models: state of the art, recent challenges and future directions, Progress in Oceanography 103, 80-91 (pdf).

A. Morozov, J.-C. Poggiale, From spatially explicit ecological models to mean-field dynamics: The state of the art and perspectives, Ecological Complexity 10, 1-11 (pdf)

P. Auger, J.-C. Poggiale, E. Sanchez, A review on spatial aggregation methods involving several time scales, Ecological Complexity 10, 12-25 (pdf)

M. Marva, R. Bravo de la Parra, J.-C. Poggiale, Approximate aggregation of a two time scales periodic multi-strain SIS epidemic model: a patchy environment  with fast migrationsEcological Complexity 10, 34-41 (pdf) 

Pischedda,  P. Cuny, J.-L. Esteves, J.-C. Poggiale, F. Gilbert Spatial oxygen heterogeneity in a Hediste diversicolor irrigated burrow, Hydrobiologia,  680 (1), 109-124 (pdf)

2011

The Mermex group, X. Durrieu de Madron, C. Guieu, R. Sempéré et al., (2011), Marine ecosystems’ responses to climatic and anthropogenic forcings in the Mediterranean, Progress in Oceanography, 91, 97-166 (pdf)

F. Cordoleani, D. Nérini, M. Gauduchon, A. Morozov, J.-C. Poggiale, (2011), Structural sensitivity of biological models revisited, Journal of Theoretical Biology, 283, 82-91 (pdf)

E. Sánchez, P. Auger, J.-C. Poggiale, Two-time scales in spatially structured models of population dynamics: A semigroup approach, Journal of Mathematical Analysis and Applications, 375, 149-165 (pdf).

2010

T. Souza, T. Domingos, J.-C. Poggiale and S.A.L.M., Kooijman, (2010), Dynamic energy budget theory restores coherence in biology, Philosophical Transactions of the Royal Society - B, Vol. 365, 3413-3428.

S. Massarin, F. Alonzo, L. Garcia-Sanchez, R. Gilbin, J. Garnier-Laplacec, J.-C. Poggiale, (2010), Effects of chronic uranium exposure on life history and physiology of Daphnia magna over three successive generations, Aquatic Toxicology, Vol. 99 (3), 309-319 (pdf)

J.-C. Poggiale, M. Baklouti, B. Queguiner and S.A.L.M. Kooijman, (2010), How far details are important in ecosystem modelling: the case of multi-limiting nutrients in phytoplankton - zooplankton interactions, Philosophical Transactions of the Royal Society - B, Vol. 365, 3495-3507.

M. Eichinger, R. Sempéré, G. Grégori, B. Charrière, J. C. Poggiale and D. Lefèvre, (2010), Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments, Biogeosciences, Vol. 7 (6), 1861-1876 (pdf)

F. Carlotti, J.-C. Poggiale, (2010), Towards methodological approaches to implement the zooplankton component in ‘‘end to end” food-web models, Progress in Oceanography, Vol. 84, 20-38 (pdf)

2009

J.-C. Poggiale, P. Auger, F. Cordoléani, T. Nguyen-Huu, (2009),  Study of a virus-bacteria interaction model in a chemostat: application of geometrical singular perturbation theory, Philosophical Transactions of the Royal Society - A, Vol. 367, 4685-4697 

M. Eichinger, S.A.L.M. Kooijman, R. Sempéré, D. Lefèvre, G. Grégori, B. Charrière, J.-C. Poggiale, (2009), DOC consumption and release by marine bacteria in a pulsed-substrate environment: from experiments to modelling, Aquatic Microbial Ecology, Vol. 56, 41-54 (pdf)

2008

J.-C. Poggiale, M. Gauduchon and P. Auger, (2008), Enrichment Paradox Induced by Spatial Heterogeneity in a Phhytoplankton - Zooplankton System, Mathematical Models of Natural Phenomena, Vol. 3 (3), 87-102 (pdf)

F. Mermillod-Blondin, J.-C. Poggiale, C. Tolla, W. Thuillier, P. Auger and M. Creuzé des Châtelliers, (2008), Modelling the impact of tubicid worms (Oligochaeta) on oxygen concentrations in hyporheic sediments: importance of vertical distributions, Fundamentals and Applied Limnology, 172 (2): 135–145

P. Auger, R. Bravo de la Parra, J.-C. Poggiale, E. Sanchez, L. Sanz, (2008), Aggregation methods in dynamical systems and applications in population and community dynamics, Physics of Life Reviews, 5, 79-105 (pdf)

L. Pischedda,  J.-C. Poggiale, P. Cuny, F. Gilbert, (2008),  Imaging Oxygen Distribution in Marine Sediments. The Importance of Bioturbation and Sediment Heterogeneity, Actabiotheoretica, Vol. 56, 123-135 (pdf).

P. Auger, R. Bravo de la Parra, J.-C. Poggiale, E. Sanchez, and T. Nguyen-Huu, (2008), « Aggregation of Variables and Applications to Population Dynamics »  in Structured Population Models in Biology and Epidemiology Series: Lecture Notes in Mathematics, Subseries: Mathematical Biosciences Subseries, Vol. 1936 Magal, Pierre; Ruan, Shigui (Eds.) , 345 p.

2007

O. Maury, B. Faugeras, Y.-J. Shin, J.-C. Poggiale, T. Ben Ari, F. Marsac, (2007), Modeling environmental effects on the size-structured energy flow through marine ecosystems. Part 1: The model,          Progress in Oceanography, 74, 479-499, (pdf)

F. Gilbert, S. Hulth, V. Grossi, J.-C. Poggiale, G. Desrosiers, R. Rosenberg, M. Gérino, F. François, E. Michaud, G. Stora, (2007), Sediment reworking by marine benthic species from Gullmar Fjord
    (Western Sweden): Importance of faunal biovolume,
J. Experimental Marine Biology and Ecology, 348, 133-144, (pdf)

R. Mchich, P.Auger, J.-C. Poggiale, (2007), Effect of predator density dependent dispersal of prey on stability of a predator-prey system, Mathematical Biosciences, 206, 343-356 (pdf). 

E. Duport, F. Gilbert, J.-C. Poggiale, K. Dedieu and G. Stora, (2007), Benthic macrofauna and sediment reworking quantification in contrasted environment in the Thau Lagoon, Estuarine, Coastal and Shelf Science, 72, 522-533 (pdf)

C. Tolla, S. A. L. M. Kooijman and J.-C. Poggiale, (2007), A kinetic inhibition mechanism for maintenance , Journal of Theoretical Biology, 244, (4), 576-587 (pdf).

2006

 T. Nguyen-Huu, C. Lett, J.C. Poggiale and P. Auger, (2006), Effect of movement frequency on global host-parasitoid spatial dynamics with unstable local dynamics , Ecological                     Modelling,197, 290-295 (pdf).

T. Nguyen-Huu, C. Lett, P. Auger, J.-C. Poggiale, (2006), Spatial synchrony of host-parasitoid models using aggregation of variables, Mathematical Biosciences, 203, 204-221 (pdf).

M. Eichinger, J.-C., Poggiale, F. Van Wambeke, D. Lefèvre, R. Sempéré, (2006), Modelling DOC assimilation and bacterial growth efficiency in biodegradation experiments: a case study in the Northeast Atlantic Ocean, Aquatic Microbial Ecology, 43, 139-151, (pdf).

P. Auger, B.W.Kooi, R. Bravo de la Parra, J.-C. Poggiale, (2006), Bifurcation analysis of a predator-prey model with predators using hawk and dove tactics, Journal of Theoretical Biology, 238, 597-607, (pdf).

2005

 J.-C. Poggiale, P. Auger, D. Nérini, C. Manté, F. Gilbert, (2005), Global production increased by spatial heterogeneity in a population dynamics model, Actabiotheoretica, 53, 359-370, (pdf).

 R. Bravo de la Parra,  J.-C. Poggiale, (2005), Theoretical ecology and mathematical modelling: Problems and methods, Ecological Modelling, 188,  (1), 1-2 (Editorial), (pdf).

 2004

J.-C. Poggiale , P. Auger, (2004), Impact of spatial heterogeneity on a predator–prey system dynamics, C. R. Biologies, 327, 1058–1063 (pdf).

D. Ouellette, G. Desrosiers, J.-P. Gagné, F. Gilbert, J.-C. Poggiale, G. Stora, P. Blier, (2004), Effect of temperature on the in vitro bioturbation activities of the polychaete Nereis virens (Sars), Marine Ecology - Progress Series, vol. 266, pp.185-193 (pdf).

2003

M. Gérino, G. Stora, F. François-Carcaillet, F. Gilbert, J.C. Poggiale, F. Mermillod-Blondin, G. Desrosiers, P. Vervier, (2003), Macro-Invertebrate functional groups in freshwater and marine sediments : a common mechanistic classification, Vie et Milieu, 53 (4), pp. 221-231.

F. Talin, C. Tolla, C. Rabouille, J.C. Poggiale, (2003), Relations between bacterial biomass and carbon cycle in marine sediments : An early diagenetic model, ActaBiotheoretica, Vol. 51, 4, pp. 295 - 315 (pdf).

S.A.L.M.  Kooijman, P. Auger, J.C.  Poggiale, B.W. Kooi,, (2003), Eight quantitative steps in the evolution of endosymbiosis and homeostasis, Biol. Review, vol. 78, pp. 435-463 (pdf).

F. Gilbert, S. Hulth, N. Strömberg, Katja Ringdahl, JC Poggiale, (2003),  2-D optical quantification of particle reworking activities in marine surface sediments, J. Experimental Marine Biology and Ecology, 4059, pp. 1-12  (pdf).

2002

B.W. Kooi, J.C.  Poggiale, P. Auger, S.A.L.M Kooijman, (2002), Aggregation methods in food chains with nutrient recycling, Ecological modelling, Vol. 157, 1, pp 69 – 86, (pdf).

F. François, M. Gérino, G. Stora, J.P. Durbec, J.C. Poggiale (2002), A functional approach of the sediment reworking due to gallery digging macrobenthic organisms : modelling and application with the polychaete Nereis diversicolor, Marine Ecology Progress Series, Vol. 229, pp. 127-136, (pdf).

2001

F. Gilbert, G. Stora, G. Desrosiers, B. Deflandre, J.C. Bertrand, J.C. Poggiale, J.P. Gagné, (2001), Alteration and release of aliphatic compounds by the polychaete Nereis virens (Sars) experimentally fed with hydrocarbons, J. Experimental Marine Biology and Ecology, Vol. 256, 2, pp. 199-231, (pdf).

J.C. Poggiale, J.C. Dauvin, (2001), Long term dynamics of three benthic Ampelisca (Crustacea-Amphipoda) populations from the Bay of Morlaix (western English Channel) related to their disappearance after the Amoco Cadiz oil spill, Marine Ecology Progress Series, Vol. 214,  P 201-209, (pdf).

2000

P. Auger, S. Charles, M. Viala, J.C. Poggiale, (2000), Aggregation and emergence in ecological modelling : integration of the ecological levels, Ecological Modelling, 127, pp. 11-20, (pdf).

P. Auger, J.C. Poggiale, S. Charles, (2000), Emergence of Individual Behaviour at the population level : effects of density dependent migration on population dynamics, Compte Rendus de l'Académie des Sciences, Sciences de la Vie, 323, pp. 119-127, (pdf).

1999

T. Moutin, P. Raimbaut, J.C Poggiale, (1999), Production primaire dans les eaux de surface de la Méditerranée occidentale : calcul de la production journalière, Compte Rendus de l'Académie des Sciences, Sciences de la Vie, 322, 651-659, (pdf).

P. Auger, G. Chiorino, J.C. Poggiale, (1999), Aggregation, emergence and immergence in hierarchically organized systems, Int. J. General Systems, 27 (4-5), pp. 349-371

C. Bernstein, P. Auger, J.C. Poggiale, (1999), Predator Migration decisions, the Ideal Free Distribution and predator-prey dynamics, American Naturalist, 153 (3), pp. 267-281.

1998

F. François, J.C. Poggiale, J.P. Durbec, G. Stora, (1998), A new model of bioturbation for a functional approach to sediment reworking resulting from macrobenthic communities, Belle W. Baruch Library in Marine Science, Univ. South Carolina Press.

P. Auger, J.C. Poggiale (1998), Aggregation and Emergence in Systems of Ordinary Differential Equations, Mathematical Computer Modelling, 27, 4, pp. 1-22, (pdf).

J.C. Poggiale, J.Michalski, R. Arditi (1998), Emergence of Donor Control in Patchy Predator-Prey Systems, Bulletin of Mathematical Biology, 60(6), pp. 1149-1166, (pdf).

J.C. Poggiale, (1998),  Predator-Prey Models in Heterogeneous Environment : Emergence of Functional Response, Mathematical Computer Modelling, 27, 4, pp. 63-71, (pdf).

J.C. Poggiale, (1998), Lotka-Volterra’s Model and Migrations : breaking of the well-known center, Mathematical Computer Modelling, 27, 4, pp. 51-62, (pdf).

J.C. Poggiale, (1998), From Behavioural to Population level : growth and competition, Mathematical Computer Modelling, 27, 4, pp. 41-50, (pdf).

B.W. Kooi, J.C. Poggiale, P.M. Auger, (1998), Aggregation Methods in Food Chains, Mathematical Computer Modelling, 27, 4, pp. 109-120, (pdf).

1997

J. Michalski, J.C. Poggiale, R. Arditi, P. Auger, (1997), Effects of migrations modes on patchy predator-prey systems, Journal of Theoretical Biology, 185, 459-474, (pdf).

F. François, J.C. Poggiale, G. Stora, J.P. Durbec, (1997), A new approach for the modelling of sediment reworking induced by a macrobenthic community, ActaBiotheoretica 45, 295-319.

1996

P. Auger, J.C. Poggiale, (1996), Reduction of complexity and emergence in hierarchically organized systems : population dynamics, Systems Analysis Modelling Simulation, 26, 217-237.

P. Auger, J.C. Poggiale, (1996), Emergence of  Population  Growth Models : Fast Migration and Slow Growth, Journal of Theoretical Biology 182, 99-108, (pdf).

J.C. Poggiale, P. Auger, (1996), Fast Oscillating Migrations in a predator-prey model, Mathematical Models and Methods in Applied Sciences, Vol.6, 2, 217-226 , (pdf).

P. Auger, J.C. Poggiale, (1996), Aggregation and Emergence in Hierarchically Organized Systems : Population Dynamics, ActaBiotheoretica, 44, 301-316 (pdf)

1995

P. Auger, J.C. Poggiale, (1995), Emerging properties in population dynamics with different time scales, Journal of Biological Systems, Vol.3, 2, 591-602

J.C. Poggiale, P. Auger, R. Roussarie, (1995), Perturbations of the Classical Lotka-Volterra System by Behavioural Sequences, ActaBiotheoretica 43, 27-39