Project Team Biocore

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
PDF e-pub XML


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, no 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, no 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]
L. Mailleret, O. Bernard, J.-P. Steyer.
Nonlinear adaptive control for bioreactors with unknown kinetics, in: Automatica, 2004, vol. 40-8, p. 1379-1385.
[10]
L. Mailleret, F. Grognard.
Global stability and optimisation of a general impulsive biological control model, in: Mathematical Biosciences, 2009, vol. 221, no 2, p. 91-100.
Publications of the year

Articles in International Peer-Reviewed Journal

[11]
W. 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
[12]
A. R. Akhmetzhanov, F. Grognard, L. Mailleret.
Optimal life-history strategies in seasonal consumer-resource dynamics., in: Evolution, 2011, vol. 65, no 11, p. 3113–3125.
http://dx.doi.org/10.1111/j.1558-5646.2011.01381.x
[13]
O. Bernard.
Hurdles and challenges for modelling and control of microalgae for CO2 mitigation and biofuel production, in: Journal of Process Control, 2011, vol. 21, no 10, p. 1378–1389.
http://dx.doi.org/10.1016/j.jprocont.2011.07.012
[14]
M. 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
[15]
P. 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
[16]
F. 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
[17]
F. 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
[18]
T. 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.
[19]
X.-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, no 2, p. 138-145.
http://hal.archives-ouvertes.fr/hal-00647239/en/
[20]
X.-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, no Nouvelles tendances en automatique, p. 363-383.
http://hal.archives-ouvertes.fr/hal-00647281/en/
[21]
L. 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
[22]
F. 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
[23]
F. 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
[24]
F. Mairet, O. Bernard, M. Ras, L. Lardon, J.-P. Steyer.
Modeling anaerobic digestion of microalgae using ADM1., in: Biores. Technol., 2011, vol. 102, no 13, p. 6823–6829.
http://dx.doi.org/10.1016/j.biortech.2011.04.015
[25]
F. Mazenc, O. Bernard.
Interval observers for linear time-invariant systems with disturbances, in: Automatica, 2011, vol. 47, no 1, p. 140 - 147. [ DOI : 10.1016/j.automatica.2010.10.019 ]
http://www.sciencedirect.com/science/article/pii/S0005109810004334
[26]
F. Mazenc, S. Niculescu, O. Bernard.
Exponentially stable interval observers for linear systems with delay, in: Siam Journal Contr. Optim., 2011, to appear.
[27]
D. 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
[28]
G. 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, no 2, p. 582 - 598. [ DOI : 10.1016/j.nonrwa.2011.07.049 ]
http://www.sciencedirect.com/science/article/pii/S1468121811002185

Invited Conferences

[29]
P. 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.
[30]
P. 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

[31]
W. 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.
[32]
E. 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, no 1.
[33]
M. 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.
[34]
P. Hartmann, O. Bernard.
Investigating photo inhibition processes in a novel Droop-Han modelling approach, in: Proceedings of the Watermatex conference, San Sebastian, Spain, 2011.
[35]
X.-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.
[36]
F. 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.
[37]
F. 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.
[38]
F. 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.
[39]
F. 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.
[40]
D. A. Oyarzún, M. Chaves.
Global Gene Regulation in Metabolic Networks, in: Proc. 18th IFAC World Congress, Milan, Italy, August 2011.

National Conferences with Proceeding

[41]
F. 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

[42]
A. 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.
[43]
S.-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.
[44]
M. 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.
[45]
M. Chaves, J.-L. Gouzé.
Qualitative Control of a Bistable Genetic Network, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
[46]
P. 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.
[47]
P. 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.
[48]
P. 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.
[49]
L. Mailleret, M. Castel, F. Hamelin.
From elaborate to compact seasonal plant epidemic models, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
[50]
J. Rault, E. Benoît.
Stability results on some zooplankton size-structured models, in: European Conference on Mathematical and Theoretical Biology, Krakow, Poland, 2011.
[51]
M. 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)

[52]
A. 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.
[53]
G. 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

[54]
I. Belgacem.
Les réseaux de régulation génétique : controle d'un oscillateur, Université Tlemcen, 2011.
[55]
H. Bonnefond.
Effets de chocs osmotiques sur la production de lipides chez Dunaliella salina, INSA Toulouse, 2011.
[56]
A. Lebon.
Elaboration d'un modèle plante-ravageur dans le cadre de la lutte biologique, Montpellier Supagro, 2011.
[57]
X.-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
[58]
E. Rousseau.
Conception et étude d'un modèle de gestion durable des variétés de plantes résistantes aux virus dans un paysage, INSA Lyon, 2011.
[59]
B. Rémond.
Modélisation de l?effet de la température sur le taux de croissance spécifique du phytoplancton, Université Paris VI, 2011.
References in notes
[60]
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.
[61]
G. Bastin, D. Dochain.
On-line estimation and adaptative control of bioreactors, Elsevier, 1990.
[62]
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.
[63]
O. Bernard.
TELEMAC Deliverable 3.4: Final version of the Telemac advanced control module, 2004.
[64]
O. Bernard, J.-L. Gouzé.
Closed loop observers bundle for uncertain biotechnological models, in: J. Process. Contr., 2004, vol. 14:7, p. 765-774.
[65]
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.
[66]
O. Bernard, I. Queinnec.
Dynamic models of biochemical processes: properties of models, in: Bioprocess Control, D. Dochain (editor), Wiley, Hoboken, 2008.
[67]
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, no 3, p. 5339–5372.
http://www.biogeosciences-discuss.net/6/5339/2009/
[68]
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.
[69]
G. Bougaran, O. Bernard, A. Sciandra.
Modelling continuous cultures of microalgae colimited with nitrogen and phosphorus, in: Journal of Theoretical Biology, 2010, vol. 265, no 3, p. 443–454.
[70]
C. 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.
[71]
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.
[72]
F. 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.
[73]
F. Grognard, A. R. Akhmetzhanov, P. Masci, O. Bernard.
Optimization of a photobioreactor biomass production using natural light, INRIA, Sep 2010, no RR-7378.
http://hal.archives-ouvertes.fr/hal-00516705/en/
[74]
T. Lacour.
Influence du statut azoté et du cycle lumineux diurne sur le métabolisme lipidique d'Isochrysis sp, Université P.M. Curie, 2010.
[75]
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.
[76]
X.-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.
[77]
L. 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, no 1908, p. 4779-4799. [ DOI : 10.1098/rsta.2009.0153 ]
http://rsta.royalsocietypublishing.org/content/367/1908/4779.abstract
[78]
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.
[79]
P. 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.
[80]
F. Mazenc, O. Bernard.
Interval observers for planar systems with complex poles, in: IEEE Transactions on Automatic Control, 2010, vol. 55, no 2, p. 523–527.
[81]
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.
[82]
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.
[83]
M. Moisan, O. Bernard.
Robust interval observers for global Lipschitz uncertain chaotic systems, in: Systems & Control Letters, 2010, vol. 59, no 11, p. 687 - 694. [ DOI : 10.1016/j.sysconle.2010.08.005 ]
http://www.sciencedirect.com/science/article/pii/S016769111000109X
[84]
I. Ndiaye, J.-L. Gouzé.
Global stability of reversible enzymatic metabolic chains, in: Acta Biotheoretica, 2011, submitted.
[85]
S. Nundloll.
Dos and don'ts in augmentative biological control: insights from mathematical modelling, Université de Nice-Sophia Antipolis, 2010.
[86]
J. Rault, E. Benoît, J.-L. Gouzé.
Stabilizing effect of cannibalism in a discrete size-structured model, in: Acta Biotheoretica, 2011, submitted.
[87]
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.
[88]
L. 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, no 4, p. 447 - 463. [ DOI : 10.1006/jtbi.1993.1099 ]
http://www.sciencedirect.com/science/article/pii/S0022519383710994
[89]
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.
[90]
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, no 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.