Bibliography

Major publications by the team in recent years

[1]

J. Arino, J.-L. Gouzé, A. Sciandra.
A discrete, size-structured model of phytoplankton growth in the chemostat. Introduction of non constant cell division., in: J. Math. Biol., 2002, vol. 45, p. 313-336.

[2]

O. Bernard, G. Bastin.
On the estimation of the pseudo-stoichiometric matrix for mass balance modeling of biotechnological processes, in: Math. Biosciences, 2005, vol. 193, p. 51-77.

[3]

O. Bernard, J.-L. Gouzé.
Closed loop observers bundle for uncertain biotechnological models, in: J. Process. Contr., 2004, vol. 14:7, p. 765-774.

[4]

O. Bernard, Z. Hadj-Sadok, D. Dochain, A. Genovesi, J.-P. Steyer.
Dynamical model development and parameter identification for an anaerobic wastewater treatment process, in: Biotech.Bioeng., 2001, vol. 75, n^o 75, p. 424-438.

[5]

M. Chaves.
Input-to-state stability of rate-controlled biochemical networks, in: SIAM Journal of Control and Optimization, 2005, vol. 44, p. 704-727.

[6]

B. Faugeras, O. Bernard, A. Sciandra, M. Levy.
A modelling and data assimilation approach to estimate the carbon/chlorophyl and carbon/nitrogen ratios in a coupled hydrodynamical-biological model, in: Nonlinear Processes in Geophysics, 2004, vol. 11, p. 515-533.

[7]

J.-L. Gouzé.
Positive and negative circuits in dynamical systems, in: Journal Biol. Syst., 1998, vol. 6, n^o 1, p. 11-15.

[8]

J.-L. Gouzé, A. Rapaport, Z. Hadj-Sadok.
Interval observers for uncertain biological systems, in: Ecological modelling, 2000, vol. 133, p. 45-56.

[9]

F. Grognard, F. Mazenc, A. Rapaport.
Polytopic Lyapunov functions for persistence analysis of competing species, in: Discrete and Continuous Dynamical Systems-Series B, 2007, vol. 8, n^o 1, p. 73-93.

[10]

L. Mailleret, O. Bernard, J.-P. Steyer.
Nonlinear adaptive control for bioreactors with unknown kinetics, in: Automatica, 2004, vol. 40-8, p. 1379-1385.

Publications of the year

Doctoral Dissertations and Habilitation Theses

[11]

C. Mocquet.
Interférence entre les processus mitotiques et la prise d'azote chez Thalassiosira weissflogii. Implications en modélisation et sur les flux globaux, Université Paris VI, 2009, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

[12]

E. Altman, P. Bernhard, M. Debbah, A. Silva.
Continuum Equilibria for Routing in Dense static Ad-hoc Networks, in: Computer Networks, 2009, to appear.

[13]

E. Benoît.
Bifurcation delay - the case of the sequence: stable focus - unstable focus - unstable node, in: Discrete and Continuous Dynamical Systems, 2009, vol. 2, n^o 4, p. 911–929.

[14]

O. Bernard, A. Sciandra, S. Rabouille.
Carbon fixation prediction during a bloom of Emiliania huxleyi is highly sensitive to the assumed regulation mechanism, in: Biogeosciences Discussions, 2009, vol. 6, n^o 3, p. 5339–5372
http://www.biogeosciences-discuss.net/6/5339/2009/.

[15]

J. Blanchard, S. Jennings, R. Law, M. Castle, P. McCloghrie, M.-J. Rochet, E. Benoît.
How does abundance scale with body size in coupled size-structured food webs, in: Journal of Animal Ecology, 2009, vol. 78, p. 270-280.

[16]

M. Chaves, A. Sengupta, E. D. Sontag.
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks, in: J. of Math. Biol., 2009, vol. 59(3), p. 315-358.

[17]

A. Dayarian, M. Chaves, A. Sengupta, E. D. Sontag.
Shape, size and robustness: feasible regions in the parameter space of biochemical networks, in: PLoS Comp. Biol., 2009, vol. 5(1), e1000256 p.

[18]

T. Eissing, M. Chaves, F. Allgöwer.
Live and let die - a systems biology view on cell death, in: Computers & Chemical Engineering, 2009, vol. 33(3), p. 583-589.

[19]

N. el Farouq, G. Barles, P. Bernhard.
Deterministic minimax impulse control, in: Applied Mathematics and Optimization, 2010, to appear.

[20]

E. Farcot, J.-L. Gouzé.
Limit cycles in piecewise-affine gene network models with multiple interaction loops, in: International Journal of Systems Science, 2009, to appear.

[21]

E. Farcot, J.-L. Gouzé.
Periodic solutions of piecewise affine gene network models: the case of a negative feedback loop, in: Acta Biotheoretica, 2009, vol. 57(4), p. 429-455.

[22]

G. Goffaux, A. V. Wouwer, O. Bernard.
Continuous - Discrete Interval Observers Applied to the Monitoring of Cultures of Microalga, in: J. Proc. Contr., 2009, vol. 19, p. "1182-1190".

[23]

G. Goffaux, A. V. Wouwer, O. Bernard.
Continuous - Discrete Interval Observers for Monitoring Microalgae Cultures, in: Biotech. Progress, 2009, vol. 25, p. 667-675.

[24]

J. Hess, O. Bernard.
Advanced dynamical risk analysis for monitoring anaerobic digestion process, in: Biotechnology Progress , 2009, vol. 25, p. 643 - 653.

[25]

A. Karama, O. Bernard, J.-L. Gouzé.
Constrained Hybrid Neural Modelling of Biotechnological Processes, in: International Journal of Chemical Reactor Engineering , 2009, to appear.

[26]

L. Lardon, A. Hélias, B. Sialve, J.-P. Steyer, O. Bernard.
Life-Cycle Assessment of Biodiesel Production from Microalgae, in: Environ. Sci. Technol., 2009, vol. 43, p. 6475-6481.

[27]

F. Lombard, F. Renaud, C. Sainsbury, A. Sciandra, G. Gorsky.
Appendicularian ecophysiology. I. Food concentration dependent clearance rate, assimilation efficiency, growth and reproduction of Oikopleura dioica, in: Journal of Marine Systems, 2010, to appear.

[28]

F. Lombard, A. Sciandra, G. Gorsky.
Appendicularian ecophysiology. II. Modeling nutrition, metabolism, growth and reproduction of the appendicularian Oikopleura dioica, in: Journal of Marine Systems, 2010, to appear.

[29]

L. Mailleret, F. Grognard.
Global stability and optimisation of a general impulsive biological control model, in: Mathematical Biosciences, 2009, vol. 221, n^o 2, p. 91-100.

[30]

F. Mazenc, O. Bernard.
Interval observers for planar systems with complex poles, in: IEEE Transactions on Automatic Control, 2010, to appear.

[31]

F. Mazenc, M. Malisoff, O. Bernard.
A Simplified Design for Strict Lyapunov Functions under Matrosov Conditions, in: IEEE Transactions on Automatic Control, 2009, vol. 54, p. 177-183.

[32]

M. Moisan, O. Bernard, J.-L. Gouzé.
Near optimal interval observers bundle for uncertain bioreactors, in: Automatica, 2009, vol. 45, p. 291-295.

[33]

S. Nundloll, L. Mailleret, F. Grognard.
Two models of interfering predators in impulsive biological control, in: Journal of Biological Dynamics, 2010, vol. 4, n^o 1, p. 102-114.

[34]

B. Sialve, N. Bernet, O. Bernard.
Anaerobic digestion of microalgae as a necessary step to make microalgal biodiesel sustainable, in: Biotechnol. Advances, 2009, vol. 27, p. 409-416.

[35]

L. Tournier, M. Chaves.
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics, in: J. Theor. Biol., 2009, vol. 260(2), p. 196-209.

Invited Conferences

[36]

P. Bernhard.
Nonzero-sum dynamic games in the management of biological systems, in: Third International Conference on Game Theory and Management, Sankt Petersburg, Russia, 2009.

International Peer-Reviewed Conference/Proceedings

[37]

A. Akhmetzhanov, P. Bernhard, F. Grognard, L. Mailleret.
Competition between foraging predators and hiding preys as a nonzero-sum differential game, in: Proceedings of the International Conference on Game Theory for Networks (GameNets 2009), Istanbul, Turkey, 2009, 10 pp p.

[38]

O. Bernard, P. Masci, A. Sciandra.
A photobioreactor model in nitrogen limited conditions, in: Proceedings of the Mathmod 09 conference, Vienna, Austria, 2009.

[39]

O. Bernard, A. Sciandra, S. Rabouille.
Predictions of carbon fixation during a bloom of Emiliania huxleyi as a function of the regulating inorganic carbon species, in: Proceedings of the Mathmod 09 conference, Vienna, Austria, 2009.

[40]

G. Bougaran, O. Bernard, A. Sciandra.
Modelling continuous cultures of microalgae colimited with nitrogen and phosphorus, in: Proceedings of the Mathmod 09 conference, Vienna, Austria, 2009.

[41]

M. Chaves.
Methods for qualitative analysis of genetic networks, in: Proc. of the 10th ECC Conference, Budapest, Hungary, 2009, p. 671-676.

[42]

M. Chaves, T. Eissing, F. Allgöwer.
Regulation of apoptosis via the NFkB pathway: modeling and analysis, in: Dynamics on and of complex networks: applications to biology, computer science and the social sciences, N. Ganguly, A. Deutsch, A. Mukherjee (editors), Modeling and Simulation in Science, Engineering and Technology, Birkhäuser, Boston, 2009.

[43]

C. G. Diéguez, E. Roca, O. Bernard.
Reduction of the Anaerobic Digestion Model N 1 for an industrial wastewater treatment plant by Principal Component Analysis, in: Proc. of the 10th ECC conference, Budapest, Hungary, 2009.

[44]

F. Mairet, O. Bernard.
Coupling framers to get enhanced interval observers. Application to growth rate estimation in a photobioreactor, in: Proceedings of the 48th CDC conference, Shangai, China, 2009.

[45]

P. Masci, O. Bernard, F. Grognard, E. Latrille, J.-B. Sorba, J.-P. Steyer.
Driving competition in a complex ecosystem: application to anaerobic digestion, in: Proc. of the 10th ECC conference, Budapest, Hungary, 2009.

[46]

F. Mazenc, O. Bernard.
Interval observers for planar systems with complex poles, in: Proc. of the 10th ECC conference, Budapest, Hungary, 2009.

[47]

F. Mazenc, S. Niculescu, O. Bernard.
Interval Observers for Linear Systems with Delay, in: Proceedings of the 48th CDC conference, Shangai, China, 2009.

[48]

L. Tournier, M. Chaves.
Operational interactions in genetic networks: application to an apoptosis signalling pathway, in: Proc. of the 10th European Control Conf., Budapest, Hungary, 2009, p. 1889-1894.

National Peer-Reviewed Conference/Proceedings

[49]

P. Collet, A. Hélias, L. Lardon, O. Bernard, B. Sialve, J.-P. Steyer.
Analyse du Cycle de Vie de la production de biodiesel à partir d algues couplée avec une digestion anaérobie, in: Proceedings of the 2009 Stic & Environnement conference, Calais, France, 2009.

[50]

F. Mairet, M. Moisan, O. Bernard.
Interval observer based estimator of specific growth rate in bioreactors, in: Proceedings of the 2009 Stic & Environnement conference, Calais, France, 2009.

Scientific Books (or Scientific Book chapters)

[51]

E. Benoît, J.-L. Gouzé.
An algorithmic approach to orders of magnitude in a biochemical system, in: International Symposium on Positive Systems: Theory and Applications (POSTA 2009), R. Bru, S. Romero (editors), Lecture Notes in Control and Information Sciences, Springer Verlag, 2009, vol. 389.

[52]

P. Bernhard.
ESS, Population games, replicator dynamics: dynamics and games if not dynamic games, in: Advances in the Theory and Applications of Dynamic Games, K. Szajowski, G. Zaccour (editors), Annals of the International Society of Dynamic Games, Birkhaüser, 2010, n^o 11.

[53]

A. Shaiju, P. Bernhard.
Evolutionarily Stable Strategies: Two Nontrivial Examples and a Theorem, in: Advances in Dynamic Games and their Applications (also in 12th International Symposium on Dynamic Games and Applications, Sophia Antipolis, France, 2006), P. Bernhard, V. Gaitsgory, O. Pourtallier (editors), Annals of the International Society of Dynamic Games, Birkhaüser, 2009, n^o 10, p. 377–398.

Internal Reports

[54]

M. Chaves, L. Tournier, J.-L. Gouzé.
Comparison between Boolean and piecewise affine differential models for genetic networks, INRIA, HAL, 2009, n^o RR-7070
http://hal.archives-ouvertes.fr/inria-00426414/fr, Technical report.

[55]

E. Farcot, J.-L. Gouzé.
Limit cycles in piecewise-affine gene network models with multiple interaction loops, INRIA, 2009, n^o RR-6875
http://hal.inria.fr/inria-00367186/fr/, INRIA Research Report.

[56]

E. Farcot, J.-L. Gouzé.
Qualitative control of periodic solutions in piecewise affine systems; application to genetic networks, INRIA, dec 2009, n^o RR-7130
http://hal.archives-ouvertes.fr/inria-00437928/fr/, Research Report.

[57]

A. Morvan.
Stratégie optimale de consommation/reproduction des ravageurs des cultures, Ecole Polytechnique Universitaire de Nice - Sophia Antipolis, 2009, Internship report.

[58]

A.-L. Mouly.
Première approche pour la modélisation du couplage d'une culture d'algues et d'un digesteur anaérobie, Université Lyon I, 2009, Internship report.

[59]

E. Pruvost.
Automatisation d'un photobioréacteur de production de micro-algues, CREUFOP, Université Montpellier II, 2009, Internship report.

[60]

M. d. M. Quiroga.
Mathematical and Computational Analysis of Genetic Regulatory Networks, University of Cordoba, Argentina, 2009, Internship report.

Scientific Popularization

[61]

O. Bernard.
Les carburants extraits de micro-algues, in: Pour la science, january 2009, vol. 375, p. 18-19.

Patents and standards

[62]

B. Sialve, J.-P. Steyer, E. Latrille, O. Bernard, G. Bougaran, R. Kaas, J.-P. Cadoret.
Procédé de fixation de CO2 et de traitement des déchets organiques par couplage d'un système de digestion anaérobie et d'un système de production de microorganismes phytoplanctoniques, 2009, n^o 09/50334.

References in notes

[63]

A. Akhmetzhanov, L. Mailleret, F. Grognard.
Inter- and intraseason dynamics of prey-predator optimal control models, in: preprint, 2010, in preparation.

[64]

O. Barrou, A. Karama, E. Lakhal, O. Bernard, M.-N. Pons, J.-P. Corriou.
Estimation of a Reduced Model of the BSM1 Activated Sludge Wastewater Treatment Plant, in: International Journal of Chemical Reactor Engineering, 2008, vol. 6, A63 p.

[65]

G. Bastin, D. Dochain.
On-line estimation and adaptative control of bioreactors, Elsevier, 1990.

[66]

E. Benoît, M.-J. Rochet.
A continuous model of biomass size spectra governed by predation and the effects of fishing on them, in: Journal of Theoretical Biology, 1 2004, vol. 226, n^o 1, p. 9-21.

[67]

O. Bernard, G. Bastin.
Identification of reaction schemes for bioprocesses: determination of an incompletely known yield matrix, in: Bioprocess and Biosystem Engineering, 2005, vol. 27, p. 293-302.

[68]

O. Bernard, G. Bastin.
On the estimation of the pseudo-stoichiometric matrix for mass balance modeling of biotechnological processes, in: Math. Biosciences, 2005, vol. 193, p. 51-77.

[69]

O. Bernard.
TELEMAC Deliverable 3.4: Final version of the Telemac advanced control module, 2004.

[70]

O. Bernard.
Use of modulating functions for reaction network identification, in: Proceedings of the 10th CAB conference, Cancun, Mexico, 2007.

[71]

O. Bernard, B. Chachuat, A. Hélias, J. Rodríguez.
Can we assess the model complexity for a bioprocess ? Theory and example of the anaerobic digestion process, in: Wat. Sci. Tech., 2005, vol. 53, p. 85-92.

[72]

O. Bernard, J.-L. Gouzé.
Closed loop observers bundle for uncertain biotechnological models, in: J. Process. Contr., 2004, vol. 14:7, p. 765-774.

[73]

O. Bernard, J.-L. Gouzé.
State estimation for bioprocesses, in: Bioprocess Control, D. Dochain (editor), Wiley, Hoboken, 2008.

[74]

O. Bernard, J. Hess, J.-P. Steyer, E. Latrille.
Bioréacteur et procédé pour la production de biogaz, 2007, n^o 07/08731.

[75]

O. Bernard, P. Masci, F. Mairet, A. Sciandra.
A photobioreactor model in nitrogen limited conditions, in: Biotech Bioeng, 2010, submitted.

[76]

O. Bernard, I. Queinnec.
Dynamic models of biochemical processes: properties of the models, in: Automatic Control of Bioprocesses, D. Dochain (editor), ISTE, 2006, chap. 2, p. 23-52.

[77]

O. Bernard, I. Queinnec.
Dynamic models of biochemical processes: properties of models, in: Bioprocess Control, D. Dochain (editor), Wiley, Hoboken, 2008.

[78]

O. Bernard, A. Sciandra.
Generic analysis of the response of calcifying microalgae to an elevation of pCO₂ : qualitative vs quantitative analysis, in: ARIMA, 2008, vol. 9, p. 57-84.

[79]

O. Bernard, A. Sciandra, S. Madani.
Multimodel analysis of the response of the coccolithophore Emiliania huxleyi to an elevation of pCO₂ under nitrate limitation, in: Ecol. Model., 2008, vol. 211, p. 324-338.

[80]

M. Chaves, T. Eissing, F. Allgöwer.
Bistable biological systems: a characterization through local compact input-to-state stability, in: IEEE Trans. Autom. Control, 2008, vol. 53(1), p. 87-100.

[81]

M. Chaves, J.-L. Gouzé.
Control of piecewise affine systems: the bistable switch, in: preprint, 2009.

[82]

H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann.
Qualitative simulation of genetic regulatory networks using piecewise-linear models, in: Bulletin of Mathematical Biology, 2004, vol. 66, n^o 2, p. 301-340.

[83]

E. Farcot, J.-L. Gouzé.
Qualitative control of periodic solutions in piecewise affine systems; application to genetic networks, in: Hybrid Systems, Computation and Control HSCC 2010, Lecture Notes in Computer Sciences (LNCS), Springer-Verlag, 2010, submitted.

[84]

J.-L. Gouzé, M. Moisan, O. Bernard.
A simple improvement of interval asymptotic observers for biotechnological processes, in: Proceedings of the ROCOND 2006 conference, Toulouse, France, 2006.

[85]

J.-L. Gouzé, T. Sari.
A class of piecewise linear differential equations arising in biological models, in: Dynamical systems, 2002, vol. 17, p. 299–316.

[86]

S. Hansen, S. Hubbel.
Single-nutrient microbial competition, in: Science, 1980, vol. 207, n^o 28, p. 1491-1493.

[87]

J. Hess, O. Bernard.
Advanced dynamical risk analysis for monitoring anaerobic digestion process, in: Proceedings of the 10th CAB conference, Cancun, Mexico, 2007.

[88]

J. Hess.
Modélisation de la qualité du biogaz produit par un fermenteur méthanogène et stratégie de régulation en vue de sa valorisation, Université de Nice-Sophia Antipolis, 2007, Ph. D. Thesis.

[89]

J. Hess, E. Latrille, O. Bernard, J.-P. Steyer.
Control of the biogas quality produced during anaerobic digestion of wine distillery wastewater, in: Proceedings of the 10th latin american workshop and symposium on anaerobic digestion, Easter Island, Chile, 2008.

[90]

T. Lacour, A. Sciandra, A. Gelay, P. Mayzaud, O. Bernard.
Tryglycerids content vs productivity as a response to the nitrogen status in Isochysis galbana , in: Journal of Phycology, 2010, submitted.

[91]

F. Mairet, P. Masci, O. Bernard, T. Lacour, A. Sciandra.
Modelling lipid production in microalgae, in: Proceedings of the 11th CAB conference, Leuven, Belgium, 2010, submitted.

[92]

F. Mairet, M. Titica, O. Bernard, J. Pruvost.
Coupling biological and radiative models to describe microalgal growth in a photobioreactor, in: Proceedings of the 11th CAB conference, Leuven, Belgium, 2010, submitted.

[93]

P. Masci, O. Bernard, F. Grognard.
Continuous Selection of the Fastest Growing Species in the Chemostat, in: Proceedings of the IFAC conference, Seoul, Korea, 2008.

[94]

P. Masci, O. Bernard, F. Grognard.
Microalgal biomass surface productivity optimization based on a photobioreactor model, in: Proceedings of the 11th CAB conference, Leuven, Belgium, 2010, submitted.

[95]

P. Masci, F. Grognard, O. Bernard, E. Benoît.
Theoretical study of the competition for substrate between N microorganism species, 2010, in preparation.

[96]

F. Mazenc, O. Bernard.
Interval observers for linear time-invariant systems with disturbances, in: Automatica, 2010, submitted.

[97]

C. Mocquet, O. Bernard, A. Sciandra.
Cell cycle modelling for microalgae grown under light/dark cycles, in: Proceedings of the 11th CAB conference, Leuven, Belgium, 2010, submitted.

[98]

M. Moisan, O. Bernard, J.-L. Gouzé.
Near optimal interval observers bundle for uncertain bioreactors, in: Proceedings of the 9th European Control Conference, Kos, Greece, 2007.

[99]

M. Moisan, O. Bernard, J.-L. Gouzé.
Robust estimation using direct–reverse time interval observers: Application to an industrial bioreactor, in: Proceedings of the STIC et Environnement 2007 Conference, Lyon, France, 2007.

[100]

M. Moisan, O. Bernard.
An interval observer for non-monotone systems: Application to an industrial anaerobic digestion process, in: Proceedings of the 10th CAB Conference, Cancún, Mexico, 2007.

[101]

M. Moisan.
Synthèse d'observateurs par intervalles pour des systèmes biologiques mal connus, Université de Nice Sophia–Antipolis, 2007, Ph. D. Thesis.

[102]

I. Ndiaye, M. Chaves, J.-L. Gouzé.
Study and parameter identification of a model coupling cell signaling and gene expression, in: Proc. 16th Mediterranean Conf. Control and Automation (MED'08), Ajaccio, France, 2008.

[103]

I. Ndiaye, J.-L. Gouzé.
Unicité et stabilité globale de l'équilibre de modèles métaboliques réversibles, in: Actes de CIFA 2010, Springer-Verlag, 2010, submitted.

[104]

S. Nundloll, L. Mailleret, F. Grognard.
Impulsive biological control with intra-specific predator competition: global stability and convergence, in: Bulletin of Mathematical Biology, 2010, submitted.

[105]

J. Rault.
Réalisation d'un modèle mathématique de dynamique des populations, structuré en taille, pour le zooplancton, Ecole Polytechnique Universitaire de Nice - Sophia Antipolis, 2008, Rapport de stage de fin d'études.

[106]

J. Rodriguez, E. Roca, J. Lema, O. Bernard.
Determination of the adequate minimum model complexity required in anaerobic bioprocesses using experimental data, in: J. Chem. Tech. Biotech., 2008, vol. 83, p. 1694-1702.

[107]

J.-P. Steyer, O. Bernard, D. Batstone, I. Angelidaki.
Lessons learnt from 15 years of ICA in anaerobic digestion processes, in: Wat. Sci. Tech. , 2006, vol. 53, p. 25-33.