Bibliography
Major publications by the team in recent years
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1N. Bajeux, F. Grognard, L. Mailleret.
Augmentative biocontrol when natural enemies are subject to Allee effects, in: Journal of Mathematical Biology, 2017, vol. 74, no 7, pp. 1561 - 1587. [ DOI : 10.1007/s00285-016-1063-8 ]
https://hal.archives-ouvertes.fr/hal-01402250 -
2C. Baroukh, R. Muñoz-Tamayo, J.-P. Steyer, O. Bernard.
DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae, in: PLoS ONE, August 2014, vol. 9, no 8, e104499. [ DOI : 10.1371/journal.pone.0104499 ]
https://hal.inria.fr/hal-01097327 -
3O. 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, pp. 1378–1389. [ DOI : 10.1016/j.jprocont.2011.07.012 ]
http://hal.inria.fr/hal-00848385 -
4V. Calcagno, F. Grognard, F. M. Hamelin, E. Wajnberg, L. Mailleret.
The functional response predicts the effect of resource distribution on the optimal movement rate of consumers, in: Ecology Letters, December 2014, vol. 17, no 12, pp. 1570-1579. [ DOI : 10.1111/ele.12379 ]
https://hal.inria.fr/hal-01084299 -
5N. Giordano, F. Mairet, J.-L. Gouzé, J. Geiselmann, H. De Jong.
Dynamical allocation of cellular resources as an optimal control problem: Novel insights into microbial growth strategies, in: PLoS Computational Biology, March 2016, vol. 12, no 3, e1004802 p. [ DOI : 10.1371/journal.pcbi.1004802 ]
https://hal.inria.fr/hal-01332394 -
6N. Go, C. Bidot, C. Belloc, S. Touzeau.
Integrative Model of the Immune Response to a Pulmonary Macrophage Infection: What Determines the Infection Duration?, in: PLoS ONE, September 2014, vol. 9, no 9, e107818. [ DOI : 10.1371/journal.pone.0107818 ]
https://hal.inria.fr/hal-01099937 -
7F. 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, pp. 142-149.
http://dx.doi.org/10.1016/j.biortech.2010.06.138 -
8M. Moisan, O. Bernard, J.-L. Gouzé.
Near optimal interval observers bundle for uncertain bioreactors, in: Automatica, January 2009, vol. 45, no 1, pp. 291–295. [ DOI : 10.1016/j.automatica.2008.07.006 ]
https://hal.archives-ouvertes.fr/hal-01109396 -
9C. Poignard, M. Chaves, J.-L. Gouzé.
Periodic Oscillations for Non Monotonic Smooth Negative Feedback Circuits, in: SIAM Journal on Applied Dynamical Systems, 2016, vol. 15, no 1, pp. 257–286. [ DOI : 10.1137/15M1033368 ]
https://hal.archives-ouvertes.fr/hal-01242157 -
10L. Tournier, M. Chaves.
Interconnection of asynchronous Boolean networks, asymptotic and transient dynamics, in: Automatica, 2013, vol. 49, no 4, pp. 884-893. [ DOI : 10.1016/j.automatica.2013.01.015, ]
http://hal.inria.fr/hal-00848450
Doctoral Dissertations and Habilitation Theses
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11N. Bajeux.
Modélisation de stratégies d’introduction de populations, effets Allee et stochasticité, Université Côte d'Azur, July 2017. -
12S. Casagranda.
Modeling, analysis and reduction of biological systems, Université Côte d’Azur, Nice Sophia Antipolis, France, June 2017, Spéciality: Control, Signal and Image Processing.
Articles in International Peer-Reviewed Journals
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13N. Bajeux, F. Grognard, L. Mailleret.
Augmentative biocontrol when natural enemies are subject to Allee effects, in: Journal of Mathematical Biology, 2017, vol. 74, no 7, pp. 1561 - 1587. [ DOI : 10.1007/s00285-016-1063-8 ]
https://hal.archives-ouvertes.fr/hal-01402250 -
14V. Baldazzi, M. Génard, N. Bertin.
Cell division, endoreduplication and expansion processes: setting the cell and organ control into an integrated model of tomato fruit development, in: Acta Horticulturae, November 2017, no 1182, pp. 257 - 264. [ DOI : 10.17660/ActaHortic.2017.1182.31 ]
https://hal.inria.fr/hal-01661920 -
15C. Baroukh, V. Turon, O. Bernard.
Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes, in: PLoS Computational Biology, June 2017, vol. 13, no 6. [ DOI : 10.1371/journal.pcbi.1005590 ]
https://hal.inria.fr/hal-01576858 -
16T. Bayen, F. Mairet.
Optimisation of strain selection in evolutionary continuous culture, in: International Journal of Control, July 2017, pp. 1 - 12. [ DOI : 10.1080/00207179.2016.1264631 ]
https://hal.inria.fr/hal-01577972 -
17I. Belgacem, S. Casagranda, E. Grac, D. Ropers, J.-L. Gouzé.
Reduction and stability analysis of a transcription-translation model of RNA polymerase, in: Bulletin of Mathematical Biology, 2017, pp. 1-25, forthcoming. [ DOI : 10.1007/s11538-017-0372-4 ]
https://hal.inria.fr/hal-01655367 -
18H. Bonnefond, G. M. Grimaud, J. Rumin, G. Bougaran, A. Talec, M. O. Gachelin, M. O. Boutoute, E. Pruvost, O. Bernard, A. Sciandra.
Continuous selection pressure to improve temperature acclimation of Tisochrysis lutea, in: PLoS ONE, August 2017.
https://hal.inria.fr/hal-01576865 -
19H. Bonnefond, N. Moelants, A. Talec, P. Mayzaud, O. Bernard, A. Sciandra.
Coupling and uncoupling of triglyceride and beta-carotene production by Dunaliella salina under nitrogen limitation and starvation, in: Biotechnology for Biofuels, January 2017, vol. 10, no 1, 25 p. [ DOI : 10.1186/s13068-017-0713-4 ]
https://hal.inria.fr/hal-01450081 -
20Q. Béchet, M. Laviale, N. Arsapin, H. Bonnefond, O. Bernard.
Modeling the impact of high temperatures on microalgal viability and photosynthetic activity, in: Biotechnology for Biofuels, December 2017, vol. 10, no 1, 136 p. [ DOI : 10.1186/s13068-017-0823-z ]
https://hal.inria.fr/hal-01530933 -
21A. Camuel, B. Guieysse, C. Alcántara, Q. Béchet.
Fast algal eco-toxicity assessment: Influence of light intensity and exposure time on Chlorella vulgaris inhibition by atrazine and DCMU, in: Ecotoxicology and Environmental Safety, March 2017, vol. 140, pp. 141 - 147. [ DOI : 10.1016/j.ecoenv.2017.02.013 ]
https://hal.inria.fr/hal-01578039 -
22H. De Jong, S. Casagranda, N. Giordano, E. Cinquemani, D. Ropers, J. Geiselmann, J.-L. Gouzé.
Mathematical modelling of microbes: metabolism, gene expression and growth, in: Journal of the Royal Society Interface, November 2017, vol. 14, no 136, 20170502 p. [ DOI : 10.1098/rsif.2017.0502 ]
https://hal.inria.fr/hal-01666954 -
23R. De-Luca, F. Bezzo, Q. Béchet, O. Bernard.
Exploiting meteorological forecasts for the optimal operation of algal ponds, in: Journal of Process Control, July 2017, vol. 55, pp. 55 - 65. [ DOI : 10.1016/j.jprocont.2017.03.010 ]
https://hal.inria.fr/hal-01666404 -
24D. Demory, L. Arsenieff, N. Simon, C. Six, F. Rigaut-Jalabert, D. Marie, P. Ge, E. Bigeard, S. Jacquet, A. Sciandra, O. Bernard, S. Rabouille, A.-C. Baudoux.
Temperature is a key factor in Micromonas-virus interactions, in: ISME Journal, 2017, vol. 11, pp. 601-612. [ DOI : 10.1038/ismej.2016.160 ]
http://hal.upmc.fr/hal-01464528 -
25E. Desnoues, M. Génard, B. Quilot-Turion, V. Baldazzi.
A kinetic model of sugar metabolism in peach fruit allows the exploration of genetic variability, in: Acta Horticulturae, November 2017, no 1182, pp. 169 - 176. [ DOI : 10.17660/ActaHortic.2017.1182.20 ]
https://hal.archives-ouvertes.fr/hal-01662057 -
26D. Figueiredo, M. A. Martins, M. Chaves.
Applying differential dynamic logic to reconfigurable biological networks, in: Mathematical Biosciences, 2017, vol. 291, pp. 10 - 20. [ DOI : 10.1016/j.mbs.2017.05.012 ]
https://hal.inria.fr/hal-01568597 -
27G. M. Grimaud, F. Mairet, A. Sciandra, O. Bernard.
Modeling the temperature effect on the specific growth rate of phytoplankton: a review, in: Reviews in Environmental Science and Biotechnology, August 2017.
https://hal.inria.fr/hal-01576871 -
28S. Nilusmas, M. Mercat, T. Perrot, S. Touzeau, V. Calcagno, C. Djian Caporalino, P. Castagnone-Sereno, L. Mailleret.
A multi-seasonal model of plant-nematode interactions and its use to identify durable plant resistance deployment strategies, in: Acta Horticulturae, November 2017, no 1182, pp. 211 - 218. [ DOI : 10.17660/ActaHortic.2017.1182.25 ]
https://hal.inria.fr/hal-01661995 -
29B. Polizzi, O. Bernard, M. Ribot.
A time-space model for the growth of microalgae biofilms for biofuel production, in: Journal of Theoretical Biology, August 2017. [ DOI : 10.1016/j.jtbi.2017.08.017 ]
https://hal.archives-ouvertes.fr/hal-01408045 -
30V. Ravigné, V. Lemesle, A. A. Walter, L. Mailleret, F. M. Hamelin.
Mate Limitation in Fungal Plant Parasites Can Lead to Cyclic Epidemics in Perennial Host Populations, in: Bulletin of Mathematical Biology, 2017, vol. 73, pp. 1 - 447. [ DOI : 10.1007/s11538-016-0240-7 ]
https://hal.inria.fr/hal-01569465 -
31E. E. Rousseau, B. Moury, L. Mailleret, R. Senoussi, A. Palloix, V. Simon, S. Valière, F. Grognard, F. Fabre.
Estimating virus effective population size and selection without neutral markers, in: PLoS Pathogens, November 2017, vol. 13, no 11, pp. 1-25. [ DOI : 10.1371/journal.ppat.1006702 ]
https://hal.inria.fr/hal-01658535 -
32J.-A. Sepulchre, F. Mairet, J.-L. Gouzé.
Optimization and control of bio-conversion of polymeric substrate in the chemostat, in: AIChE Journal, 2017, vol. 107, 16 p. [ DOI : 10.1016/B978-0-408-10617-7.50007-9 ]
https://hal.inria.fr/hal-01569696 -
33M. Sourisseau, M. Plus, A. Chapelle, V. Le Guennec, G. Le Gland.
How competition for resources drive specific niches and community structure of phytoplankton by using a trait-based model, in: Frontiers in Marine Science, 2017, vol. 4, 00000. [ DOI : 10.3389/fmars.2017.00052 ]
http://hal.univ-brest.fr/hal-01510343 -
34L. Tamisier, E. Rousseau, S. Barraillé, G. Nemouchi, M. Szadkowski, L. Mailleret, F. Grognard, F. Fabre, B. Moury, A. Palloix.
Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation, in: Journal of General Virology, July 2017, vol. 98, no 7, pp. 1923 - 1931. [ DOI : 10.1099/jgv.0.000835 ]
https://hal.inria.fr/hal-01571391 -
35L. Van Oudenhove, L. Mailleret, X. Fauvergue.
Infochemical use and dietary specialization in parasitoids: a meta-analysis, in: Ecology and Evolution, 2017, vol. 7, no 13, pp. 4804 - 4811. [ DOI : 10.1002/ece3.2888 ]
https://hal.inria.fr/hal-01569455 -
36I. Yegorov, F. Mairet, J.-L. Gouzé.
Optimal feedback strategies for bacterial growth with degradation, recycling and effect of temperature, in: Optim. Control Appl. Meth., 2017, pp. 1 - 36.
https://hal.inria.fr/hal-01655960
Invited Conferences
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37S. Touzeau.
Épidémiologie mathématique : applications en élevage et en agriculture, in: MADEV17 - Mathématiques Appliquées à des questions de DEVeloppement, Rabat, Morocco, Académie des Sciences, France and Académie Hassan II des Sciences et Techniques, Maroc, October 2017.
https://hal.inria.fr/hal-01651426
International Conferences with Proceedings
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38s. Almeida, M. Chaves, F. Delaunay, C. Feillet.
A comprehensive reduced model of the mammalian cell cycle, in: IFAC World Congress 2017, Toulouse, France, July 2017. [ DOI : 10.1016/j.ifacol.2017.08.2204 ]
https://hal.inria.fr/hal-01568507 -
39S. Casagranda, J.-L. Gouzé.
Principal Process Analysis and reduction of biological models with order of magnitude, in: IFAC World Congress, Toulouse, France, July 2017. [ DOI : 10.1016/j.ifacol.2017.08.2241 ]
https://hal.inria.fr/hal-01529448 -
40C. Martínez, O. Bernard, F. Mairet.
Maximizing microalgae productivity by shading outdoor cultures , in: IFAC 2017 - 20th World Congress of the International Federation of Automatic Control, Toulouse, France, IFAC papers online, Elsevier, July 2017, vol. 50, no 1, pp. 8734 - 8739. [ DOI : 10.1016/j.ifacol.2017.08.1725 ]
https://hal.inria.fr/hal-01666463 -
41S. Nilusmas, M. Mercat, T. Perrot, S. Touzeau, V. Calcagno, C. Djian-Caporalino, P. Castagnone, L. Mailleret.
A multi-seasonal model of plant-nematode interactions and its use for durable plant resistance deployment strategies, in: EASYs 2017 - Ecology & Agriculture Summit for Young scientists, Chizé, France, March 2017.
https://hal.archives-ouvertes.fr/hal-01606132 -
42I. Yegorov, F. Grognard, L. Mailleret, F. Halkett.
Optimal resource allocation for biotrophic plant pathogens, in: IFAC 2017 - 20th World Congress of the International Federation of Automatic Control, Toulouse, France, July 2017, pp. 1-6.
https://hal.inria.fr/hal-01572090 -
43I. Yegorov, F. Mairet, J.-L. Gouzé.
Optimal resource allocation for bacterial growth with degradation, in: IFAC World Congress, Toulouse, France, July 2017. [ DOI : 10.1016/j.ifacol.2017.08.1593 ]
https://hal.inria.fr/hal-01524917
Conferences without Proceedings
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44N. Go, S. Touzeau, C. Belloc, A. Doeschl-Wilson.
Neutralising antibodies prevent PRRS viremia rebound: evidence from a data-supported model of immune response, in: ModAH 2017 - Modelling in Animal Health conference, Nantes, France, INRA, June 2017.
https://hal.inria.fr/hal-01577647 -
45L. Pereira, M. Meyer, P. Hofman, J.-L. Gouzé, M. Chaves, J. Roux.
Modeling cell death dynamics at the receptor level, in: CompSysBio, Advanced Lecture Course on Computational Systems Biology, Aussois, France, March 2017.
https://hal.inria.fr/hal-01568506
Internal Reports
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46J. Guillaumont, C. Bidot, S. Touzeau.
Modélisation du portage des salmonelles dans un élevage porcin, INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, 2017, no 2017-2, 47 p.
https://hal.inria.fr/hal-01605512
Patents
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47O. Bernard, A. Sciandra, F. Mairet, H. Bonnefond, E. Pruvost.
Selective bioreactor for microalgae , April 2017, no WO2017174907A1.
https://hal.inria.fr/hal-01671566
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48C. Baroukh, R. Munoz Tamayo, O. Bernard, J.-P. Steyer.
Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production, in: Current Opinion in Biotechnology, 2015, vol. 33, pp. 198-205. [ DOI : 10.1016/j.copbio.2015.03.002 ]
https://hal.archives-ouvertes.fr/hal-01163456 -
49C. Baroukh, R. Muñoz-Tamayo, O. A. Bernard, J.-P. Steyer.
Reply to the Comment on “Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production” by Baroukh et al. [Curr. Opin. Biotechnol. 2015, 33:198–205], in: Current Opinion in Biotechnology, March 2016, vol. 38, pp. 200 - 202. [ DOI : 10.1016/j.copbio.2016.02.018 ]
https://hal.inria.fr/hal-01410975 -
50O. Bernard.
La production de micro-algues sous serre photovoltaique : évolution ou révolution ?, in: Revue de l'Energie, November 2014, vol. 621, pp. 385-392.
https://hal.inria.fr/hal-01101142 -
51O. Bernard, A.-C. Boulanger, M.-O. Bristeau, J. Sainte-Marie.
A 2D model for hydrodynamics and biology coupling applied to algae growth simulations, in: ESAIM: Mathematical Modelling and Numerical Analysis, September 2013, vol. 47, no 5, pp. 1387-1412. [ DOI : 10.1051/m2an/2013072 ]
https://hal.archives-ouvertes.fr/hal-00936859 -
52O. Bernard, F. Mairet, B. Chachuat.
Modelling of Microalgae Culture Systems with Applications to Control and Optimization, in: Advances in Biochemical Engineering/Biotechnology, 2015. [ DOI : 10.1007/10_2014_287 ]
https://hal.inria.fr/hal-01245875 -
53O. Bernard, F. Mairet, C. Combe, A. Sciandra, E. Pruvost.
BIOREACTOR FOR MICROALGAE, March 2016, no WO/2016/151219.
https://hal.inria.fr/hal-01671573 -
54P. Bernhard.
Robust Control and Dynamic Games, in: Handbook of Dynamic Game Theory, June 2018, pp. 1-30.
https://hal.inria.fr/hal-01658681 -
55H. Bonnefond, N. Moelants, A. Talec, O. Bernard, A. Sciandra.
Concomitant effects of light and temperature diel variations on the growth rate and lipid production of Dunaliella salina, in: Algal Research, March 2016, vol. 14, pp. 72–78. [ DOI : 10.1016/j.algal.2015.12.018 ]
http://hal.upmc.fr/hal-01266717 -
56Q. Béchet, P. Moussion, O. A. Bernard.
Calibration of a productivity model for the microalgae Dunaliella salina accounting for light and temperature, in: Algal Research, November 2016, vol. 21, pp. 156 - 160. [ DOI : 10.1016/j.algal.2016.11.001 ]
https://hal.inria.fr/hal-01410980 -
57S. Casagranda, D. Ropers, J.-L. Gouzé.
Model reduction and process analysis of biological models, in: 2015 23th Mediterranean Conference on Control and Automation (MED), Torremolinos, Spain, Proceedings of 23th Mediterranean Conference on Control and Automation (MED), June 2015. [ DOI : 10.1109/MED.2015.7158908 ]
https://hal.inria.fr/hal-01239356 -
58M. Chaves, A. Carta.
Attractor computation using interconnected Boolean networks: testing growth rate models in E. Coli, in: Theoretical Computer Science, 2014, 17 p. [ DOI : 10.1016/j.tcs.2014.06.021 ]
https://hal.inria.fr/hal-01095196 -
59C. Combe, P. Hartmann, S. Rabouille, A. Talec, O. Bernard, A. Sciandra.
Long-term adaptive response to high-frequency light signals in the unicellular photosynthetic eukaryote Dunaliella salina, in: Biotechnology and Bioengineering, January 2015, 20 p. [ DOI : 10.1002/bit.25526 ]
https://hal.inria.fr/hal-01102019 -
60D. Demory.
Étude théorique et expérimentale de l'effet de l'hydrodynamique sur la photosynthèse du phytoplancton par un dispositif novateur à base de LED, Université Pierre and Marie Curie, Paris VI, 2013.
http://hal.inria.fr/hal-00852252 -
61J.-L. Gouzé, A. Rapaport, Z. Hadj-Sadok.
Interval observers for uncertain biological systems, in: Ecological modelling, 2000, vol. 133, pp. 45-56.
http://dx.doi.org/10.1016/S0304-3800(00)00279-9 -
62G. M. Grimaud.
Modelling the temperature effect on phytoplankton : from acclimation to adaptation, Université Nice Sophia Antipolis, June 2016.
https://tel.archives-ouvertes.fr/tel-01383294 -
63M. Haond, T. Morel Journel, E. Lombaert, E. Vercken, L. Mailleret, L. Roques.
Higher carrying capacities lead to faster propagation, in: in preparation. -
64P. Hartmann, D. Demory, C. Combe, R. Hamouda, J. Sainte-Marie, M.-O. Bristeau, A.-C. Boulanger, B. Sialve, J.-P. Steyer, S. Rabouille, A. Sciandra, O. Bernard.
Growth Rate Estimation of Algae in Raceway Ponds: A Novel Approach, in: 19th IFAC World Congress, Cape Town, South Africa, August 2014. [ DOI : 10.3182/20140824-6-ZA-1003.02408 ]
https://hal.inria.fr/hal-01097313 -
65L. 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, pp. 6475-6481. -
66L. Mailleret, F. Grognard.
Global stability and optimisation of a general impulsive biological control model, in: Mathematical Biosciences, 2009, vol. 221, no 2, pp. 91-100.
http://dx.doi.org/10.1016/j.mbs.2009.07.002 -
67L. 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, pp. 4779-4799. [ DOI : 10.1098/rsta.2009.0153 ]
http://rsta.royalsocietypublishing.org/content/367/1908/4779.abstract -
68F. Mairet, O. A. Bernard.
Robustness of Bioprocess Feedback Control to Biodiversity, in: AIChE Journal, 2016, 24 p. [ DOI : 10.1002/aic.15604 ]
https://hal.inria.fr/hal-01410765 -
69F. Mairet, O. Bernard.
The Photoinhibistat: Operating Microalgae Culture under Photoinhibition for Strain Selection, in: 11th IFAC Symposium on Dynamics and Control of Process Systems Including Biosystems DYCOPS-CAB , Trondheim, Norway, IFAC-PapersOnLine, June 2016, vol. 49, no 7. [ DOI : 10.1016/j.ifacol.2016.07.344 ]
https://hal.inria.fr/hal-01410835 -
70F. Mairet, R. Muñoz-Tamayo, O. Bernard.
Driving Species Competition in a Light-limited Chemostat, in: 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), Toulouse, France, 2013.
http://hal.inria.fr/hal-00852258 -
71P. Masci, O. Bernard, F. Grognard.
Continuous Selection of the Fastest Growing Species in the Chemostat, in: Proceedings of the IFAC conference, Seoul, Korea, 2008. -
72R. Muñoz-Tamayo, F. Mairet, O. Bernard.
Optimizing microalgal production in raceway systems, in: Biotechnology Progress, 2013, vol. 29, no 2, pp. 543–552. [ DOI : 10.1002/btpr.1699 ]
http://hal.inria.fr/hal-00850376 -
73S. Nundloll.
Dos and don'ts in augmentative biological control: insights from mathematical modelling, Université de Nice-Sophia Antipolis, 2010. -
74B. Sialve, N. Bernet, O. Bernard.
Anaerobic digestion of microalgae as a necessary step to make microalgal biodiesel sustainable, in: Biotechnol. Advances, 2009, vol. 27, pp. 409-416.