Team Digiplante

Members
Overall Objectives
Scientific Foundations
Software
New Results
Partnerships and Cooperations
Bibliography
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Bibliography

Major publications by the team in recent years
[1]
J. Bertheloot, P.-H. Cournède, B. Andrieu.
NEMA, a functional-structural model of N economy within wheat culms after flowering: I. Model description, in: Annals of Botany, 2011, vol. 108, no 6, p. 1085-1096.
[2]
P.-H. Cournède, M. Kang, A. Mathieu, J.-F. Barczi, H. Yan, P. de Reffye.
Structural factorization of plants to compute their functional and architectural growth, in: Simulation - Transaction of the Society for modeling and simulation international, July 2006, vol. 82, no 7, p. 427-438.
[3]
P.-H. Cournède, A. Mathieu, F. Houllier, D. Barthélémy, P. de Reffye.
Computing competition for light in the GreenLab model of plant growth: a contribution to the study of the effects of density on resource acquisition and architectural development, in: Annals of Botany, 2008, vol. 101, no 8.
[4]
P.-H. Cournède, V. Letort, A. Mathieu, M.-Z. Kang, S. Lemaire, S. Trevezas, F. Houllier, P. de Reffye.
Some Parameter Estimation Issues in Functional-Structural Plant Modelling, in: Mathematical Modelling of Natural Phenomena, 2011, vol. 6, no 2, p. 133-159.
[5]
M. Kang, P.-H. Cournède, P. de Reffye, D. Auclair, B. Hu.
Analytical study of a stochastic plant growth model: application to the GreenLab model, in: Mathematics and Computers in Simulation, 2008, vol. 78, no 1, p. 57-75.
[6]
V. Le Chevalier, M. Jaeger, X. Mei, P.-H. Cournède.
Simulation and visualisation of functional landscapes: effects of the water resource competition between plants, in: Journal of computer science and technology, Nov. 2007, vol. 22, no 6, p. 835-845.
[7]
V. Letort, P.-H. Cournède, A. Mathieu, P. de Reffye, T. Constant.
Parametric identification of a functional-structural tree growth model and application to beech trees (Fagus sylvatica), in: Functional Plant Biology, 2008, vol. 35(10), p. 951-963.
[8]
V. Letort, P. Heuret, P.-C. Zalamea, P. de Reffye, E. Nicolini.
Analysing the effects of local environment on the source-sink balance of Cecropia sciadophylla: a methodological approach based on model inversion., in: Annals of Forest Science, 2011.
[9]
V. Letort, P. Mahe, P.-H. Cournède, P. de Reffye, B. Courtois.
Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization, in: Annals of Botany, 2008, vol. 101, no 8.
[10]
C. Loi, P.-H. Cournède, J. Françon.
A symbolic method to compute the probability distribution of the number of pattern occurences in random texts generated by stochastic 0L-systems, in: 21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms (AofA'10). DMTCS Proceedings, 2010, vol. AM, p. 473-488.
[11]
C. Loi, P.-H. Cournède.
Generating Functions of Stochastic L-Systems and Application to Models of Plant Development, in: Discrete Mathematics and Theoretical Computer Science Proceedings, 2008, vol. AI, p. 325-338.
[12]
A. Mathieu, P.-H. Cournède, D. Barthélémy, P. de Reffye.
Rhythms and alternating patterns in plants as emergent properties of a model of interaction between development and functioning, in: Annals of Botany, 2008, vol. 101, no 8.
[13]
A. Mathieu, P.-H. Cournède, V. Letort, D. Barthélémy, P. de Reffye.
A dynamic model of plant growth with interactions between development and functional mechanisms to study plant structural plasticity related to trophic competition, in: Annals of Botany, 2009, vol. 103, no 8, p. 1173-1186.
[14]
Q. Wu, P.-H. Cournède, A. Mathieu.
An efficient computational method for global sensitivity analysis and its application to tree growth modelling, in: Reliability Engineering & System Safety, 2011, vol. In Press:DOI: 10.1016/j.ress.2011.07.001.
Publications of the year

Doctoral Dissertations and Habilitation Theses

[15]
C. Loi.
Analyse probabiliste, étude combinatoire et estimation paramétrique pour une classe de modèles de croissance de plantes avec développement stochastique, Ecole Centrale Paris, May 2011.
http://hal.inria.fr/tel-00635011/en

Articles in International Peer-Reviewed Journal

[16]
J. Bertheloot, P.-H. Cournède, B. Andrieu.
NEMA, a functional-structural model of N economy within wheat culms after flowering: I. Model description, in: Annals of Botany, 2011, vol. 108, no 6, p. 1085-1096.
[17]
J. Bertheloot, Q. Wu, P.-H. Cournède, B. Andrieu.
NEMA, a functional-structural model of N economy within wheat culms after flowering: II. Evaluation and sensitivity analysis, in: Annals of Botany, 2011, vol. 107, no 5, p. 1097-1109.
[18]
P.-H. Cournède, V. Letort, M. Z. Kang, A. Mathieu, S. Lemaire, S. Trevezas, F. Houllier, P. de Reffye.
Some parameter estimation issues in functional-structural plant modelling, in: Mathematical Modelling of Natural Phenomena, 2011, vol. 6, no 2, p. 133-159. [ DOI : 10.1051/mmnp/20116205 ]
http://hal.inria.fr/halsde-00612622/en
[19]
P.-H. Cournède, V. Letort, A. Mathieu, M. Z. Kang, S. Lemaire, S. Trevezas, F. Houllier, P. de Reffye.
Some Parameter Estimation Issues in Functional-Structural Plant Modelling, in: Mathematical Modelling of Natural Phenomena, 2011, vol. 6, no 2, p. 133-159. [ DOI : 10.1051/mmnp/20116205 ]
http://hal.inria.fr/hal-00631509/en
[20]
J. Diao, P. de Reffye, X. Lei, H. Guo, V. Letort.
Simulation of the topological development of young eucalyptus using a stochastic model and sampling measurement strategy, in: Computers and Electronics in Agriculture, 2012, vol. 80, p. 105-114. [ DOI : 10.1016/j.compag.2011.10.019 ]
http://hal.inria.fr/hal-00651975/en
[21]
A. Jullien, A. Mathieu, J.-M. Allirand, A. Pinet, P.-H. Cournède, P. de Reffye, B. Ney.
Characterization of the interactions between architecture and source-sink relationships in winter oilseed rape (Brassica napus) using the GreenLab model, in: Annals of Botany -London- Oup then Academic Press then Oxford University Press-, 2011, vol. 107, no 5, p. 765-779. [ DOI : 10.1093/aob/mcq205 ]
http://hal.inria.fr/halsde-00613649/en
[22]
V. Letort, P. Heuret, P.-C. Zalamea, P. de Reffye, E. Nicolini.
Analysing the effects of local environment on the source-sink balance of Cecropia sciadophylla: a methodological approach based on model inversion., in: Annals of Forest Science, 2011.
[23]
Y. Ma, A. M. Wubs, E. Heuvelink, A. Mathieu, J. Y. Zhu, B.-G. Hu, P.-H. Cournède, P. de Reffye.
Simulation of fruit-set and trophic competition and optimization of yield advantages in six Capsicum cultivars using functional-structural plant modelling, in: Annals of Botany, 2011, vol. 107, no 5, p. 793-803. [ DOI : 10.1093/aob/mcq223 ]
http://hal.inria.fr/halsde-00613645/en
[24]
B. Pallas, C. Loi, A. Christophe, P.-H. Cournède, J. Lecoeur.
Comparison of three approaches to model grapevine organogenesis in conditions of fluctuating temperature, solar radiation and soil water content, in: Annals of Botany, 2011, vol. 107, no 5, p. 729-745. [ DOI : 10.1093/aob/mcq173 ]
[25]
S. Trevezas, N. Limnios.
Exact MLE and asymptotic properties for nonparametric semi-Markov models, in: Journal of Nonparametric Statistics, September 2011, vol. 23, no 3, p. 719-739. [ DOI : 10.1080/10485252.2011.555543 ]
http://hal.inria.fr/inria-00625293/en
[26]
F. Wang, M. Kang, Q. Lu, V. Letort, H. Han, Y. Guo, P. de Reffye, B. Li.
A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines, in: Annals of Botany, 2011, vol. 107, no 5, p. 781-792.
[27]
X. Wang, A. Mathieu, P.-H. Cournède, A. Jullien, J.-M. Allirand, P. de Reffye, B. Zhang.
Variability and regulation of the number of ovules, seeds and pods according to assimilate availability in winter oilseed rape (Brassica napus L.), in: Field Crops Research, 2011, vol. 122, no 1, p. 60-69.
[28]
Q.-L. Wu, P.-H. Cournède, A. Mathieu.
An efficient computational method for global sensitivity analysis and its application to tree growth modelling, in: Reliability Engineering and System Safety, July 2011. [ DOI : 10.1016/j.ress.2011.07.001 ]
http://hal.inria.fr/hal-00639539/en
[29]
G. Yang, W. Cao, D. Liu, M. Kang, V. Letort, M. Xing, H. Xinyuan.
Growth and development simulation based on functional-structural model GreenLab for poplar (Salicaceae), in: African Journal of Agricultural Research, 2011, vol. 6, no 13, p. 3071-3077.

International Conferences with Proceedings

[30]
C. Baey, P.-H. Cournède.
Using a hierarchical segmented model to assess the dynamics of leaf appearance in plant populations., in: 14th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2011), Rome, Italy, 2011.
http://hal.inria.fr/inria-00602419/en
[31]
F. Kang, P.-H. Cournède, J. Lecoeur.
Irrigation Demand Simulation of Large-scale Scenarios and Crop Genotype Selection in Water Shortage Context, in: Proceedings of the 3rd International Conference on Environmental Science and Information Application Technology (ESIAT 2011), 2011.
[32]
Z. Li, P.-H. Cournède, J.-C. Mailhol.
Irrigation Optimization by Modeling of Plant-Soil Interaction, in: Applied Simulation and Modelling, Crete, Greece, C. Angeli (editor), ACTA Press, June 22-24 2011.
[33]
C. Loi, P.-H. Cournède, S. Trevezas.
Bayesian Estimation in Functional-Structural Plant Models with Stochastic Organogenesis, in: 14th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2011), Rome, Italy, June 2011.
http://hal.inria.fr/hal-00653672/en
[34]
S. Sabatier, D. Andrianasolo, J.-J. Rakotomalala, P. Hamon, P. de Reffye, V. Letort.
Plant architectural and genetic diversities in Coffea native from Madagascar: towards an architecturalfunctional plant growth model applied to Coffea biodiversity perservation, in: XVIII International botanical congress, 2011, vol. Melbourne Australia, 23-30 july 2011, p. 77-78.
[35]
Q.-L. Wu, P.-H. Cournède.
A methodology to study Complex Biophysical Systems with Global Sensitivity Analysis, in: ESREL2011, Troyes, France, C. Berenguer, A. Grall, C. G. Soares (editors), CRC press, September 2011.
http://hal.inria.fr/hal-00639549/en
References in notes
[36]
F. Campillo, V. Rossi.
Convolution Particle Filter for Parameter Estimation in General State-Space Models, in: IEEE Transactions in Aerospace and Electronics., 2009, vol. 45, no 3, p. 1063-1072.
[37]
J. Cariboni, D. Gatelli, R. Liska, A. Saltelli.
The role of sensitivity analysis in ecological modelling, in: Ecological modelling, 2007, vol. 203, p. 167-182.
[38]
J. Helton, J. Johnson, C. Salaberry, C. Storlie.
Survey of sampling based methods for uncertainty and sensitivity analysis, in: Reliability Engineering and System Safety, 2006, vol. 91, p. 1175-1209.
[39]
P. Heuret, D. Barthélémy, Y. Guédon, X. Coulmier, J. Tancre.
Synchronization of growth, branching and flowering processes in the south american tropical tree Cecropia obtusa (Cecropiaceae), in: American Journal of Botany, 2000, vol. 89, no 7, p. 1180-1187.
[40]
T. Homma, A. Saltelli.
Importance measures in global sensitivity analysis of nonlinear models, in: Reliability Engineering and System Safety, 1996, vol. 52, p. 1-17.
[41]
A. Mathieu, P. Cournède, D. Barthélémy, P. de Reffye.
Rhythms and alternating patterns in plants as emergent properties of a model of interaction between development and functioning, in: Annals of Botany, 2008, vol. 101, no 8, p. 1233-1242.
[42]
V. Rossi.
Filtrage non linéaire par noyaux de convolution - Application à un procédé de dépollution biologique, Ecole Nationale Supérieure Agronomique de Montpellier, 2004.
[43]
A. Saltelli, Annoni.P, Azzini.I, Campolongo.F, Ratto.M, Tarantola.S.
Variance based sensitivity analysis of model output. Design and estimator for the total sensitivity index, in: Computer Physics Communications, 2010, vol. 181, no 2, p. 259-270.
[44]
A. Saltelli, M. Ratto, T. Andres, F. Campolongo, J. Cariboni, D. Gatelli, M. Saisana, S. Tarantola.
Global Sensitivity Analysis, The Primer, John Wiley&Sons, 2008.
[45]
A. Saltelli.
Making best use of model evaluations to compute sensitivity indices, in: Computer Physics Communications, 2002, vol. 145, p. 280-297.
[46]
A. Saltelli, S. Tarantola.
On the relative importance of input factors in mathematical models: safety assessment for nuclear waste disposal, in: Journal of American Statistical Association, 2002, vol. 97, p. 702-709.
[47]
I. Sobol.
Sensitivity analysis for non-linear mathematical models, in: Mathematical Modeling and Computational Experiment, 1993, vol. 1, p. 407-414.
[48]
Q.-L. Wu, P.-H. Cournède.
The use of Sensitivity Analysis for the design of Functional Structural Plant Models, in: Procedia - Social and Behavioral Sciences, 2010, vol. 2, no 6, p. 7768 - 7769, Sixth International Conference on Sensitivity Analysis of Model Output. [ DOI : DOI: 10.1016/j.sbspro.2010.05.219 ]
[49]
P. Zalamea, P. Stevenson, S. Madrin, P.-M. Aubert, P. Heuret.
Growth pattern and age determination for Cecropia sciadophylla (Urticaceae), in: American Journal of Botany, 2008, vol. 95, p. 263-271.