Bibliography

• 1J. 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.
• 2O. 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.
• 3O. Bernard, J.-L. Gouzé.
  
  Closed loop observers bundle for uncertain biotechnological models, in: J. Process. Contr., 2004, vol. 14:7, p. 765-774.
• 4O. 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.
• 5M. Chaves.
  
  Input-to-state stability of rate-controlled biochemical networks, in: SIAM Journal of Control and Optimization, 2005, vol. 44, p. 704-727.
• 6B. 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.
• 7J.-L. Gouzé.
  
  Positive and negative circuits in dynamical systems, in: Journal Biol. Syst., 1998, vol. 6, n^o 1, p. 11-15.
• 8J.-L. Gouzé, A. Rapaport, Z. Hadj-Sadok.
  
  Interval observers for uncertain biological systems, in: Ecological modelling, 2000, vol. 133, p. 45-56.
• 9L. Mailleret, O. Bernard, J.-P. Steyer.
  
  Nonlinear adaptive control for bioreactors with unknown kinetics, in: Automatica, 2004, vol. 40-8, p. 1379-1385.
• 10L. 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.

Articles in International Peer-Reviewed Journal

• 11W. Abou-Jaoudé, M. Chaves, J.-L. Gouzé.
  
  A theoretical exploration of birhythmicity in the p53-Mdm2 network, in: PLoS One, 2011, vol. 6(2), e17075 p.
  
  http://dx.doi.org/10.1371/journal.pone.0017075
• 12A. R. Akhmetzhanov, F. Grognard, L. Mailleret.
  
  Optimal life-history strategies in seasonal consumer-resource dynamics., in: Evolution, 2011, vol. 65, n^o 11, p. 3113–3125.
  
  http://dx.doi.org/10.1111/j.1558-5646.2011.01381.x
• 13O. Bernard.
  
  Hurdles and challenges for modelling and control of microalgae for CO2 mitigation and biofuel production, in: Journal of Process Control, 2011, vol. 21, n^o 10, p. 1378–1389.
  
  http://dx.doi.org/10.1016/j.jprocont.2011.07.012
• 14M. Chaves, J.-L. Gouzé.
  
  Exact control of genetic networks in a qualitative framework: the bistable switch example, in: Automatica, 2011, vol. 47, p. 1105-1112.
  
  http://dx.doi.org/10.1016/j.automatica.2011.01.071
• 15P. Collet, A. Hélias, L. Lardon, M. Ras, R.-A. Goy, J.-P. Steyer.
  
  Life-cycle assessment of microalgae culture coupled to biogas production, in: Bioresource Technology, 2011, vol. 102, p. 207-214.
  
  http://dx.doi.org/10.1016/j.biortech.2010.06.154
• 16F. Fabre, E. Rousseau, L. Mailleret, B. Moury.
  
  Durable strategies to deploy plant resistance in agricultural landscapes, in: New Phytologist, 2011, to appear.
  
  http://dx.doi.org/10.1111/j.1469-8137.2011.04019.x
• 17F. Hamelin, M. Castel, S. Poggi, D. Andrivon, L. Mailleret.
  
  Seasonality and the evolutionary divergence of plant parasites, in: Ecology, 2011, vol. 92, p. 2159-2166.
  
  http://dx.doi.org/10.1890/10-2442.1
• 18T. Lacour, A. Sciandra, A. Talec, P. Mayzaud, O. Bernard.
  
  Diel variations of carbohydrates and neutral lipids in N-sufficient and N-starved cyclostat cultures of Isochrysis sp., in: Journal of Phycology, 2011, to appear.
• 19X.-D. Li, C.-Z. Xu.
  
  Infinite-dimensional Luenberger-like observers for a rotating body-beam system, in: Systems and Control Letters, Jan 2011, vol. 60, n^o 2, p. 138-145.
  
  http://hal.archives-ouvertes.fr/hal-00647239/en/
• 20X.-D. Li, C.-Z. Xu.
  
  Synthèse des observateurs pour une classe de systèmes de dimension infinie, in: Journal Européen des Systèmes Automatisés, Nov 2011, vol. 45, n^o Nouvelles tendances en automatique, p. 363-383.
  
  http://hal.archives-ouvertes.fr/hal-00647281/en/
• 21L. Mailleret, M. Castel, J. Montarry, F. Hamelin.
  
  From elaborate to compact seasonal plant epidemic models and back: is competitive exclusion in the details?, in: Theoretical Ecology, 2011, to appear.
  
  http://dx.doi.org/10.1007/s12080-011-0126-0
• 22F. Mairet, O. Bernard, E. Cameron, M. Ras, L. Lardon, J.-P. Steyer, B. Chachuat.
  
  Three-reaction model for the anaerobic digestion of microalgae, in: Biotechnology and Bioengineering, 2011, to appear.
  
  http://dx.doi.org/10.1002/bit.23350
• 23F. Mairet, O. Bernard, P. Masci, T. Lacour, A. Sciandra.
  
  Modelling neutral lipid production by the microalga Isochrysis affinis galbana under nitrogen limitation, in: Biores. Technol., 2011, vol. 102, p. 142-149.
  
  http://dx.doi.org/10.1016/j.biortech.2010.06.138
• 24F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer.
  
  Modeling anaerobic digestion of microalgae using ADM1., in: Biores. Technol., 2011, vol. 102, n^o 13, p. 6823–6829.
  
  http://dx.doi.org/10.1016/j.biortech.2011.04.015
• 25F. Mazenc, O. Bernard.
  
  Interval observers for linear time-invariant systems with disturbances, in: Automatica, 2011, vol. 47, n^o 1, p. 140 - 147. [ DOI : 10.1016/j.automatica.2010.10.019 ]
  
  http://www.sciencedirect.com/science/article/pii/S0005109810004334
• 26F. Mazenc, S. Niculescu, O. Bernard.
  
  Exponentially stable interval observers for linear systems with delay, in: Siam Journal Contr. Optim., 2011, to appear.
• 27D. A. Oyarzún, M. Chaves, M. Hoff-Hoffmeyer-Zlotnik.
  
  Multistability and oscillations in genetic control of metabolism, in: Journal of Theoretical Biology, 2012, vol. 295, p. 139-153, to appear.
  
  http://dx.doi.org/10.1016/j.jtbi.2011.11.017
• 28G. Robledo, F. Grognard, J.-L. Gouzé.
  
  Global stability for a model of competition in the chemostat with microbial inputs, in: Nonlinear Analysis: Real World Applications, 2012, vol. 13, n^o 2, p. 582 - 598. [ DOI : 10.1016/j.nonrwa.2011.07.049 ]
  
  http://www.sciencedirect.com/science/article/pii/S1468121811002185

Invited Conferences

• 29P. Bernhard.
  
  On the Dynamics of the Handicap Principle, in: Mathematical Apsects of Game theory, Toulouse, France, R. Laraki, M. Quincampoix, J. Renault, S. Sorin, T. Tomala, X. Venel (editors), Toulouse School of Economics, 2011.
• 30P. Bernhard.
  
  Robust Optimization in Finance, in: Optimization Days 2011, Montréal, Quebec, Canada, E. Delage, D. Orban, J.-F. Plante, G. Zaccour (editors), GERAD, HEC, 2011.

International Conferences with Proceedings

• 31W. Abou-Jaoudé, M. Chaves, J.-L. Gouzé.
  
  Mechanisms for coexistence of two limit cycles in a biochemical model, in: Proc. 18th IFAC World Congress, Milan, Italy, August 2011.
• 32E. Cameron, F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer, B. Chachuat.
  
  Anaerobic Digestion of Microalgae: Identification for Optimization and Control, in: IFAC World Congress, Milano, Italy, 2011, n^o 1.
• 33M. Chaves, L. Tournier.
  
  Predicting the asymptotic dynamics of large biological networks by interconnections of Boolean modules, in: 50th IEEE Conference on Decision and Control and European Control Conference, Orlando, Florida, USA, December 2011.
• 34P. Hartmann, O. Bernard.
  
  Investigating photo inhibition processes in a novel Droop-Han modelling approach, in: Proceedings of the Watermatex conference, San Sebastian, Spain, 2011.
• 35X.-D. Li, J.-L. Gouzé, M. Chaves.
  
  An observer for a piecewise affine genetic network model with Boolean observations, in: 50th IEEE Conference on Decision and Control and European Control Conference, 2011.
• 36F. Mairet, O. Bernard, T. Lacour, A. Sciandra.
  
  Modelling microalgae growth in nitrogen limited photobiorector for estimating biomass, carbohydrate and neutral lipid productivities, in: IFAC World Congress, 2011.
• 37F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer.
  
  A Dynamic Model for Anaerobic Digestion of Microalgae, in: IFAC World Congress, Milano, Italy, 2011.
• 38F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer.
  
  Testing the ability of ADM1 to represent the anaerobic digestion of microalgae, in: Proceedings of the Watermatex conference, San Sebastian, Spain, 2011.
• 39F. Mairet, M. Moisan, O. Bernard.
  
  Interval estimation of lipid quota in microalgae culture using dynamic tuning parameter, in: 9th IEEE International Conference on Control & Automation (IEEE ICCA 2011), Santiago, Chile, 2011.
• 40D. A. Oyarzún, M. Chaves.
  
  Global Gene Regulation in Metabolic Networks, in: Proc. 18th IFAC World Congress, Milan, Italy, August 2011.

National Conferences with Proceeding

• 41F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer.
  
  Anaerobic digestion of microalgae: evaluation of process performances using ADM1, in: Stic & Environnement 2011, Saint-Etienne, France, 2011.

Conferences without Proceedings

• 42A. R. Akhmetzhanov, P. Bernhard, F. Grognard, L. Mailleret.
  
  Dynamic game for optimal resource allocation of annual plants and grazing consumers, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
• 43S.-D. Ayata, O. Aumont, O. Bernard, M. Lévy.
  
  Comparison of biogeochemical models with increasing complexity in photosynthesis formulation: the importance of taking into account photoadaptation in marine ecosystem models, in: Advances in Marine Ecosystem Modelling Symposium 2011, Plymouth, United-Kingdom, 2011.
• 44M. Castel, F. Hamelin, S. Poggi, D. Andrivon, L. Mailleret.
  
  Evolutionary insights from semi-discrete plant epidemic models, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
• 45M. Chaves, J.-L. Gouzé.
  
  Qualitative Control of a Bistable Genetic Network, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
• 46P. Collet, J. Langlois, M. Cornelus, L. Lardon, J.-P. Steyer, O. Bernard, A. Hélias.
  
  Environmental assessment and ecodesign perspectives, in: Ecotech-tools conference, Montpellier, France, 2011.
• 47P. Collet, L. Lardon, A. Hélias, S. Bricout, I. Lombaert-Valot, B. Perrier, O. Lépine, J.-P. Steyer, O. Bernard.
  
  Can we produce biofuel from microalgae without a renewable source of electricity and heat?, in: Algn'n'Chem conference, Montpellier, France, 2011.
• 48P. Hartmann, A.-C. Boulanger, J. Sainte-Marie, M.-O. Bristeau, K. Ebert, A. Sciandra, O. Bernard.
  
  Numerical prediction of microalgae productivity and energy requirement during the cultivation process in raceway, in: Alg'n'Chem conference, Montpellier, France, 2011.
• 49L. Mailleret, M. Castel, F. Hamelin.
  
  From elaborate to compact seasonal plant epidemic models, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
• 50J. Rault, E. Benoît.
  
  Stability results on some zooplankton size-structured models, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
• 51M. Teixeira-Alves, L. Mailleret, F. Grognard.
  
  Optimal foraging predators in Leslie Gower models with alternative prey, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.

Scientific Books (or Scientific Book chapters)

• 52A. R. Akhmetzhanov, L. Mailleret, F. Grognard, P. Bernhard.
  
  Join forces or cheat: evolutionary analysis of a consumer-resource system, in: Annals of the International Society of Dynamic Games, 2011, to appear.
• 53G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, F. Dayan.
  
  Modeling and analysis of gene regulatory networks, in: Modeling in Computational Biology and Biomedicine: Current Trends, F. Cazals, P. Kornprobst (editors), Springer, 2011, to appear.

Internal Reports

• 54I. Belgacem.
  
  Les réseaux de régulation génétique : controle d'un oscillateur, Université Tlemcen, 2011.
• 55H. Bonnefond.
  
  Effets de chocs osmotiques sur la production de lipides chez Dunaliella salina, INSA Toulouse, 2011.
• 56A. Lebon.
  
  Elaboration d'un modèle plante-ravageur dans le cadre de la lutte biologique, Montpellier Supagro, 2011.
• 57X.-D. Li, J.-L. Gouzé, M. Chaves.
  
  An observer for a piecewise affine genetic network model with Boolean observations, INRIA, December 2011.
  
  http://hal.archives-ouvertes.fr/hal-00647317
• 58E. Rousseau.
  
  Conception et étude d'un modèle de gestion durable des variétés de plantes résistantes aux virus dans un paysage, INSA Lyon, 2011.
• 59B. Rémond.
  
  Modélisation de l?effet de la température sur le taux de croissance spécifique du phytoplancton, Université Paris VI, 2011.

• 60O. 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.
• 61G. Bastin, D. Dochain.
  
  On-line estimation and adaptative control of bioreactors, Elsevier, 1990.
• 62O. 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.
• 63O. Bernard.
  
  TELEMAC Deliverable 3.4: Final version of the Telemac advanced control module, 2004.
• 64O. Bernard, J.-L. Gouzé.
  
  Closed loop observers bundle for uncertain biotechnological models, in: J. Process. Contr., 2004, vol. 14:7, p. 765-774.
• 65O. 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.
• 66O. Bernard, I. Queinnec.
  
  Dynamic models of biochemical processes: properties of models, in: Bioprocess Control, D. Dochain (editor), Wiley, Hoboken, 2008.
• 67O. 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/
• 68O. 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.
• 69G. Bougaran, O. Bernard, A. Sciandra.
  
  Modelling continuous cultures of microalgae colimited with nitrogen and phosphorus, in: Journal of Theoretical Biology, 2010, vol. 265, n^o 3, p. 443–454.
• 70C. Breindl, M. Chaves, J.-L. Gouzé, F. Allgöwer.
  
  Structure estimation for unate Boolean models of gene regulation networks, in: Proc.SYSID, Brussels, Belgium, 2011, submitted.
• 71C. G. Diéguez, E. Roca, O. Bernard.
  
  Reduction of the Anaerobic Digestion Model N${}^{\circ }$1 for an industrial wastewater treatment plant by Principal Component Analysis, in: Proc. of the 10th ECC conference, Budapest, Hungary, 2009.
• 72F. Grognard, A. R. Akhmetzhanov, P. Masci, O. Bernard.
  
  Optimization of a photobioreactor biomass production using natural light, in: Proceedings of the 49th IEEE CDC conference, Atlanta, USA, 2010.
• 73F. Grognard, A. R. Akhmetzhanov, P. Masci, O. Bernard.
  
  Optimization of a photobioreactor biomass production using natural light, INRIA, Sep 2010, n^o RR-7378.
  
  http://hal.archives-ouvertes.fr/hal-00516705/en/
• 74T. Lacour.
  
  Influence du statut azoté et du cycle lumineux diurne sur le métabolisme lipidique d'Isochrysis sp, Université P.M. Curie, 2010.
• 75L. 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.
• 76X.-D. Li, M. Chaves, J.-L. Gouzé.
  
  Robust estimation for a hybrid model of genetic network, in: 20th Mediterranean Conference on Control and Automation, 2012, submitted.
• 77L. Mailleret, V. Lemesle.
  
  A note on semi-discrete modelling in the life sciences, in: Philosophical Transactions of the Royal Society A: Mathematical,Physical and Engineering Sciences, 2009, vol. 367, n^o 1908, p. 4779-4799. [ DOI : 10.1098/rsta.2009.0153 ]
  
  http://rsta.royalsocietypublishing.org/content/367/1908/4779.abstract
• 78P. Masci, O. Bernard, F. Grognard.
  
  Continuous Selection of the Fastest Growing Species in the Chemostat, in: Proceedings of the IFAC conference, Seoul, Korea, 2008.
• 79P. Masci, F. Grognard, O. Bernard.
  
  Microalgal biomass surface productivity optimization based on a photobioreactor model, in: Proceedings of the 11th CAB conference, Leuven, Belgium, 2010.
• 80F. Mazenc, O. Bernard.
  
  Interval observers for planar systems with complex poles, in: IEEE Transactions on Automatic Control, 2010, vol. 55, n^o 2, p. 523–527.
• 81C. 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.
• 82C. 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.
• 83M. Moisan, O. Bernard.
  
  Robust interval observers for global Lipschitz uncertain chaotic systems, in: Systems & Control Letters, 2010, vol. 59, n^o 11, p. 687 - 694. [ DOI : 10.1016/j.sysconle.2010.08.005 ]
  
  http://www.sciencedirect.com/science/article/pii/S016769111000109X
• 84I. Ndiaye, J.-L. Gouzé.
  
  Global stability of reversible enzymatic metabolic chains, in: Acta Biotheoretica, 2011, submitted.
• 85S. Nundloll.
  
  Dos and don'ts in augmentative biological control: insights from mathematical modelling, Université de Nice-Sophia Antipolis, 2010.
• 86J. Rault, E. Benoît, J.-L. Gouzé.
  
  Stabilizing effect of cannibalism in a discrete size-structured model, in: Acta Biotheoretica, 2011, submitted.
• 87J. 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.
• 88L. Rosso, J. Lobry, J. Flandrois.
  
  An Unexpected Correlation between Cardinal Temperatures of Microbial Growth Highlighted by a New Model, in: Journal of Theoretical Biology, 1993, vol. 162, n^o 4, p. 447 - 463. [ DOI : 10.1006/jtbi.1993.1099 ]
  
  http://www.sciencedirect.com/science/article/pii/S0022519383710994
• 89B. 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.
• 90B. 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.
• 91 Task Group for Mathematical Modelling of Anaerobic Digestion Processes, I. W. A..
  
  Anaerobic Digestion Model No. 1 (ADM1), IWA Publishing, London, 2002.