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

Articles in International Peer-Reviewed Journal

[11]

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.

[12]

O. Bernard, A. Sciandra.
Generic analysis of the response of calcifying microalgae to an elevation of pCO₂ : qualitative vs quantitative analysis, in: ARIMA, to appear, 2008.

[13]

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.

[14]

M. Chaves, R. Albert.
Studying the effect of cell division on expression patterns of the segment polarity genes, in: J. Royal Society Interface, 2008, vol. 5, p. S71-S84.

[15]

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.

[16]

M. Chaves, A. Sengupta, E. D. Sontag.
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks, in: J. Mathematical Biology, to appear, 2008.

[17]

A. Dayarian, M. Chaves, E. D. Sontag, A. Sengupta.
Shape, size and robustness: feasible regions in the parameter spaceof biochemical networks, in: PLoS Computational Biology, to appear, 2008.

[18]

T. Eissing, M. Chaves, F. Allgöwer.
Live and let die - a systems biology view on cell death, in: Computers & Chemical Eng., to appear, 2008.

[19]

E. Farcot, J.-L. Gouzé.
A mathematical framework for the control of piecewise affine models of gene networks, in: Automatica, 2008, vol. 44, p. 2326-2332.

[20]

E. Farcot, J.-L. Gouzé.
Periodic solutions of piecewise affine gene network models: the case of a negative feedback loop, in: Acta Biotheoretica, to appear, 2008.

[21]

G. Goffaux, A. Vande Wouwer, O. Bernard.
Continuous - Discrete Interval Observers for Monitoring Microalgae Cultures, in: Biotech. Progress, to appear, 2008.

[22]

J.-L. Gouzé, V. Lemesle.
Two simple growth models in the chemostat, in: ARIMA, to appear, 2008.

[23]

J. Hess, O. Bernard.
Advanced dynamical risk analysis for monitoring anaerobic digestion process, in: Biotechnology Progress, to appear, 2008.

[24]

J. Hess, O. Bernard.
Design and study of a risk management criterion for an unstable anaerobic wastewater treatment process, in: J. Process. Contr., 2008, vol. 18, p. 71-79.

[25]

V. Lemesle, J.-L. Gouzé.
A simple unforced oscillatory growth model in the chemostat, in: Bulletin of Mathematical Biology, 2008, vol. 70, p. 344-357.

[26]

L. Mailleret, J.-L. Gouzé, O. Bernard.
Global stabilization of a class of partially known positive systems, in: Automatica, 2008, vol. 44, p. 2128-2134.

[27]

F. Mazenc, M. Malisoff, O. Bernard.
A Simplified Design for Strict Lyapunov Functions under Matrosov Conditions, in: IEEE Trans. Autom. Control, to appear, 2009.

[28]

M. Moisan, O. Bernard, J.-L. Gouzé.
Near optimal interval observers bundle for uncertain bioreactors, in: Automatica, to appear, 2008.

[29]

S. Nundloll, L. Mailleret, F. Grognard.
The effect of partial crop harvest on biological pest control, in: Rocky Mountain Journal of Mathematics, 2008, vol. 38, n^o 5, p. 1633-1661.

[30]

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.

[31]

L. Tournier, J.-L. Gouzé.
Hierarchical analysis of piecewise affine models of gene regulatory networks, in: Theory in Biosciences, 2008, vol. 127, p. 125-134.

Articles in Non Peer-Reviewed Journal

[32]

J.-P. Cadoret, O. Bernard.
La production de biocarburants lipidiques avec des microalgues: promesses et défis, in: Journal de la société de biologie, 2008, vol. 202, p. 201-211.

International Peer-Reviewed Conference/Proceedings

[33]

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.

[34]

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.

[35]

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.

[36]

F. Mazenc, M. Malisoff, O. Bernard.
Lyapunov Functions and Robustness Analysis under Matrosov Conditions with an Application to Biological Systems, in: Proceedings of the ACC conference, Seattle, USA, 2008.

[37]

M. Moisan, O. Bernard, J.-L. Gouzé.
High/low gain bundle of observers: application to the input estimation of a bioreactor model, in: Proceedings of the IFAC conference, Seoul, Korea, 2008.

[38]

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.

[39]

S. Nundloll, L. Mailleret, F. Grognard.
Global Stability in a General Impulsive Biological Control Model with Harvest, in: Proceedings of the IFAC World Congress, Seoul, Korea, 2008.

[40]

L. Tournier, J.-L. Gouzé.
Qualitative stability patterns for Lotka-Volterra systems on rectangles, in: Hybrid Systems, Computation and Control HSCC 08, M. Egerstedt, B. Mishra (editors), Lecture Notes in Computer Sciences (LNCS) 4981, Springer-Verlag, Saint-Louis, USA, 2008, p. 662-665.

Scientific Books (or Scientific Book chapters)

[41]

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

[42]

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

Internal Reports

[43]

E. Benoît.
Notes sur les techniques d'étude des champs lents-rapides, Technical report, INRIA, 2008.

[44]

L. Mailleret, F. Grognard.
Global stability and optimisation of a general impulsive biological control model, Research report, INRIA, 2008, n^o 6637
http://hal.inria.fr/inria-00320578/en/.

[45]

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

[46]

V. Rosano.
Réalisation d'une maquette informatique pour la réduction de modèles biochimiques, Rapport de stage de master MASS, Université de Nice Sophia-Antipolis, 2008.

[47]

L. Tournier, M. Chaves.
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics, Research report, INRIA, 2008, n^o 6703
http://hal.inria.fr/inria-00325914/en.

Scientific Popularization

[48]

O. Bernard, A. Sciandra.
Des micro-algues numériques, in: La Recherche, 2008, vol. Juillet/Aout 2008 - 421.

Other Publications

[49]

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

References in notes

[50]

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

[51]

A. Akhmetzhanov, L. Mailleret, F. Grognard, P. Bernhard.
Reproduction dynamics in a differential game between foraging predators and hiding preys, in preparation.

[52]

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

[53]

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.

[54]

E. Benoît.
Bifurcation delay - the case of the sequence: stable focus - unstable focus - unstable node, in: Discrete and Continuous Dynamical Systems, submitted, 2008.

[55]

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.

[56]

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.

[57]

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

[58]

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

[59]

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.

[60]

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

[61]

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.

[62]

M. Chaves, E. D. Sontag, R. Albert.
Methods of robustness analysis for Boolean models of gene control networks, in: IEE Proc. Systems Biology, 2006, vol. 153(4), p. 154-167.

[63]

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.

[64]

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: Proceedings of the ECC conference, submitted, Budapest, Hungary.

[65]

G. Goffaux, A. Vande Wouwer, O. Bernard.
Discrete-time interval observers applied to continuous cultures of phytoplankton, in: Proceedings of the 7th NOLCOS conference, Pretoria, South Africa, 2007.

[66]

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.

[67]

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.

[68]

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

[69]

A. Hélias, O. Bernard.
Assessing the main reactions in a bioprocess: application to cheese ripening, in: Proceedings of the 10th CAB conference, Cancun, Mexico, 2007.

[70]

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

[71]

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

[72]

L. Mailleret, J.-L. Gouzé, O. Bernard.
Nonlinear control for algae growth models in the chemostat, in: Bioprocess and Biosystem Engineering, 2005, vol. 27, p. 319-328.

[73]

L. Mailleret, F. Grognard.
Global stability and optimisation of a general impulsive biological control model, in: Mathematical Biosciences, submitted.

[74]

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: Proceedings of the ECC conference, submitted, Budapest, Hungary.

[75]

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

[76]

F. Mazenc, O. Bernard.
Interval observers for planar systems with complex poles, in: Proceedings of the ECC conference, submitted, Budapest, Hungary.

[77]

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.

[78]

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.

[79]

M. Moisan, O. Bernard.
A direct-reverse time interval observer. A pplication to biotechnological models, in: Proceedings of the 7th IFAC Symposium on Nonlinear Control Systems, Pretoria, South Africa, 2007.

[80]

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.

[81]

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

[82]

S. Nundloll, L. Mailleret, F. Grognard.
Impulsive biological control with intra-specific predator competition: global stability and convergence, in: Mathematical Biosciences and Engineering, in preparation.

[83]

S. Nundloll, L. Mailleret, F. Grognard.
Two models of interfering predators in impulsive biological control, in: Journal of Biological Dynamics, submitted.

[84]

D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann.
Qualitative simulation of the carbon starvation response in Escherichia Coli, in: Biosystems, 2006, vol. 84 (2).

[85]

A. Sciandra, L. Pawlowski, O. Bernard.
A growth model for autotrophic phytoplankton and its validation using chemostat experiments co-limited by light and nitrogen, in: Ecol. Model., submitted.

[86]

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.

[87]

A. Vande Wouwer, G. Goffaux, O. Bernard.
Continuous - Discrete Interval Observers Applied to the Monitoring of Cultures of Microalgae, in: J. Proc. Contr., In revision, 2008.