Bibliography

Major publications by the team in recent years

[1]

B. Hu, M. Jaeger (editors)
Plant growth Modelling and Applications - PMA03, Tsinghua University Press, Springer, Beijing, China, October 2003.

[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, n^o 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, n^o 8.

[4]

P. de Reffye, M. Goursat, J.-P. Quadrat, B. Hu.
The Dynamic equations of the tree morphogenesis GreenLab model, in: Proceedings of PMA03, Beijing, China, B. Hu, M. Jaeger (editors), Tsinghua University Press, Springer, October 2003, p. 108-117.

[5]

P. de Reffye, E. Heuvelink, D. Barthélémy, P.-H. Cournède.
Biological and mathematical concepts for modelling plant growth and architecture, in: Encyclopedia of Ecology, D. Jorgensen, B. Fath (editors), Elsevier, 2008, p. 101-107.

[6]

P. de Reffye, B. Hu.
Relevant qualitative and quantitative choices for building efficient dynamic plant growth models: GreenLab case., in: Proceedings of PMA03, Beijing, China, B. Hu, M. Jaeger (editors), Tsinghua University Press, Springer, October 2003, p. 87-107.

[7]

Y. Guo, Y. Ma, Z. Zhan, B. Li, M. Dingkuhn, D. Luquet, P. de Reffye.
Parameter optimization and field validation of the functional-structural model GREENLAB for maize., in: Annals of Botany, February 2006, vol. 97, n^o 2, p. 217-230.

[8]

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, n^o 1, p. 57-75.

[9]

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, n^o 6, p. 835-845.

[10]

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.

[11]

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, n^o 8.

[12]

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.

[13]

Y. Ma, M. Wen, Y. Guo, B. Li, P.-H. Cournède, P. de Reffye.
Parameter optimization and field validation of the functional-structural model GreenLab for maize at different population densities, in: Annals of Botany, 2008, vol. 101(8).

[14]

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, n^o 8.

[15]

A. Mathieu, P.-H. Cournède, P. de Reffye.
A dynamical model of plant growth with full retroaction between organogenesis and photosynthesis., in: ARIMA, 2006, vol. 4, p. 101-107.

[16]

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.

[17]

C. Soler, F. Sillion, F. Blaise, P. de Reffye.
An Efficient Instantiation Algorithm for Simulating Radiant Energy Transfer in Plant Models, in: ACM Transactions On Graphics, April 2003, vol. 22, n^o 2.

[18]

H. Yan, M. Kang, P. de Reffye, M. Dingkuhn.
A dynamic, architectural plant model simulating resource-dependent growth, in: Annals of Botany, 2004, vol. 93, p. 591-602.

Publications of the year

Articles in International Peer-Reviewed Journal

[19]

Q. Deng, X. Zhang, Y. Gang, M. Jaeger.
Multiresolution Foliage for Forest Rendering, in: Computer Anination and Virtual Words, 2009, vol. 20, n^o 1.

[20]

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.

[21]

B. Pallas, A. Christophe, P.-H. Cournède, J. Lecoeur.
Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine (Vitis vinifera L.), in: Functional Plant Biology, 2009, vol. 36, p. 156-170.

[22]

R. Qi, V. Letort, M. Kang, P.-H. Cournède, P. de Reffye, T. Fourcaud.
Application of the GreenLab model to simulate and optimize wood production and tree stability: a theoretical study, in: Silva Fennica, 2009, vol. 43(3), p. 465-487.

[23]

R. Qi, Y. Ma, B. Hu, P. de Reffye, P.-H. Cournède.
Optimization of source-sink dynamics in plant growth for ideotype breeding: a case study on maize, in: Computers and Electronics in Agriculture, 2009, vol. Accepted.

[24]

X. Zhang, J. Liu, Z. Li, M. Jaeger.
Volume Decomposition and Hierarchical Skeletonization, in: International Journal of Virtual Reality, 2009, vol. 8, n^o 1, p. 79-80.

International Peer-Reviewed Conference/Proceedings

[25]

J. Bertheloot, P.-H. Cournède, B. Andrieu.
Nitrogen acquisition and utilization by crops: review of different approaches and proposition of a mechanistic modeling, in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[26]

P.-H. Cournède, T. Guyard, B. Bayol, S. Griffon, F. de Coligny, P. Borianne, M. Jaeger, P. de Reffye.
A Forest Growth Simulator Based on Functional-Structural Modelling of Individual Trees., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[27]

P. de Reffye, S. Lemaire, N. Srivastava, F. Maupas, P.-H. Cournède.
Modeling Inter-Individual Variability in Sugar Beet Populations., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[28]

H. Guo, V. Letort, X.-D. Lei, Y.-C. Lu, P. Jaeger.
Application GreenLab model to adult Chinese Pine trees with topology simplification., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[29]

M.-Z. Kang, P. de Reffye, E. Heuvelink.
Modelling growth of inflorescence., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[30]

V. Le Chevalier, M. Jaeger, P.-H. Cournède.
Synchronisation Formalism, Resource and Plant Models for Plant Ecosystem Simulation., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[31]

S. Lemaire, F. Maupas, P.-H. Cournède, J.-M. Allirand, P. de Reffye, B. Ney.
Analysis of the density effects on the source-sink dynamics in Sugar-Beet growth., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[32]

V. Letort, P.-H. Cournède, P. de Reffye.
Impact of topology on plant functioning: a theoretical analysis based on the GreenLab model equations., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[33]

V. Letort, P. Heuret, P.-C. Zalamea, E. Nicolini, P. de Reffye.
Analysis of Cecropia sciadophylla Morphogenesis Based on a Sink-Source Dynamic Model., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[34]

Z. Li, V. Le Chevalier, P.-H. Cournède.
Towards a continuous approach of functional-structural plant growth, in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[35]

D. Li, V. Letort, Y. Guo, P. de Reffye, Z.-G. Zhan.
Modeling branching effects on source-sink relationships of the cotton plant., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[36]

H.-J. Li, X.-P. Zhang, W.-J. Che, M. Jaeger.
Smooth Transition between Different Plant Leaves Models., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[37]

C. Loi, P.-H. Cournède, J. Françon.
Plants as Combinatorial Structures and Applications, in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[38]

Y.-T. Ma, A. Mathieu, A.-M. Wubs, E. Heuvelink, J.-Y. Zhu, B. Hu, P.-H. Cournède, P. de Reffye.
Parameter estimation and growth variation analysis in six Capsicum cultivars with functional-structural model GreenLab., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[39]

A. Mathieu, V. Letort, R. Gosset, J. Gignoux, P.-H. Cournède.
Simulation of morphological plasticity of Acacia tortilis in response to herbivore attacks, in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[40]

X.-J. Nin, X.-P. Zhang, Y.-G. Wang, M. Jaeger.
Segmentation of Architecture Shape Information from 3D Point Cloud., in: VRCAI 2009, Yokohoma, Japan, B.-G. Li, M. Jaeger, Y. Guo (editors), December 9-12 2009, to appear.

[41]

R. Qi, P.-H. Cournède, P. de Reffye.
Tri-trophic Ecosystem Oil palm-Pests-Parasites: II. Sensitivity Analysis, Parameter Identification and Control., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[42]

R. Qi, P.-H. Cournède, R. Lecoustre, P. de Reffye.
Tri-trophic Ecosystem Oil palm-Pests-Parasites: I. Modeling and Simulation Modeling and Simulation., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[43]

R.-X. Sun, J.-Y. Jia, H.-G. Li, M. Jaeger.
Image-based Lightweight Tree Modeling., in: VRCAI 2009, Yokohoma, Japan, B.-G. Li, M. Jaeger, Y. Guo (editors), December 9-12 2009, to appear.

[44]

F. Wang, M.-Z. Kang, H. Han, Q. Lu, V. Letort, P. de Reffye, B.-G. Li.
Calibration of topological development in the procedure of parametric identification: application to the stochastic GreenLab model for Pinus Sylvestris var. Mongolica., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[45]

X.-J. Wang, A. Mathieu, P.-H. Cournède, J.-M. Allirand, A. Jullien, P. de Reffye, B.-G. Zhang.
Stochastic Models in Floral Biology and Application to the Study of Oilseed rape Fertility., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[46]

Q. Wu, P.-H. Cournède.
Sensitivity analysis of GreenLab model for maize, in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[47]

H.-W. Wu, M. Jaeger, M. Wang, B.-G. Li, B.-G. Zhang.
3D-Reconstruction and Visualization of Xylem Vessels of Wheat Nodal Root., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[48]

F. Yang, Y.-M. Wang, M.-Z. Kang, G. Louarn, Q.-X. Dong, P. de Reffye.
Link between tomato flower abortion and trophic competition - a modelling approach., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[49]

B.-G. Zhang, M.-Z. Kang, V. Letort, X.-J. Wang, P. de Reffye.
Comparison between empirical and functional sinks of organs - Application on Tomato plants., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

[50]

C. Zhu, X.-P. Zhang, M. Jaeger.
Cluster-Based Construction of Tree Crown from Scanned Data., in: 3rd international symposium on Plant Growth and Applications(PMA09), Beijing, China, B.-G. Li, M. Jaeger, Y. Guo (editors), IEEE, November 9-12 2009, to appear.

Other Publications

[51]

P.-H. Cournède.
Dynamic System of Plant Growth, 2009, HDR, University of Montpellier II.

References in notes

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Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny, in: Annals of Botany, 2007, vol. 99, n^o 3, p. 375-407.

[53]

A. Christophe, V. Letort, I. Hummel, P.-H. Cournède, P. de Reffye, J. Lecoeur.
Model-based analysis of the dynamics of trophic competition during ArabidopsisThaliana development, in: Functional Plant Biology, 2008, vol. In press..

[54]

P. de Reffye, M. Jaeger, C. Edelin, J. Francon, C. Puech.
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H. Guo, V. Letort, L. Hong, T. Fourcaud, P.-H. Cournède, Y. Lu, P. de Reffye.
Adaptation of the GreenLab model for analyzing sink-source relationships in Chinese Pine saplings., in: Plant growth Modeling, simulation, visualization and their Applications (PMA06)., T. Fourcaud, X. Zhang (editors), IEEE Computer Society (Los Alamitos, California), 2007.

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H. Jones.
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M. Kang, P.-H. Cournède, J.-P. Quadrat, P. de Reffye.
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[61]

M. Kang, E. Heuvelink, V. Letort, P.-H. Cournède, S. Carvalho, P. de Reffye.
Visualizing reaction of chrysanthemum to temperature and light: model calibration and validation, in: Proceedings of the 5th international workshop on Functional-Structural Plant Models (FSPM07), P. Prusinkiewicz, J. Hanan, B. Lane (editors), HortResearch (Napier, New Zealand), 2007.

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V. Le Chevalier, M. Jaeger, X. Mei, A. Lesluye, P.-H. Cournède.
A functional landscape prototype to simulate water resource competition between plants, in: Plant growth Modeling, simulation, visualization and their Applications., T. Fourcaud, X. Zhang (editors), IEEE Computer Society (Los Alamitos, California), 2007.

[63]

S. Lemaire, F. Maupas, P.-H. Cournède, P. de Reffye.
A morphogenetic crop model for sugar-beet (Beta vulgaris L. )., in: International Symposium on Crop Modeling and Decision Support: ISCMDS 2008, April 19-22, 2008, Nanjing, China, Tsinghua University press and Springer, 2008.

[64]

V. Letort.
Multi-scale analysis of source-sink relationships in plant growth models for parameter identification. Case of the GreenLab model., Ecole Centrale Paris, 2008, Ph. D. Thesis.

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Calibration of fruit cyclic patterns in cucumber plants as a function of source-sink ratio with the GreenLab model, in: Proceedings of the 5th international workshop on FSPM, P. Prusinkiewicz, J. Hanan, B. Lane (editors), November 2007.

[69]

B. Pallas, A. Christophe, P.-H. Cournède, J. Lecoeur.
Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine (Vitis vinifera L.), in: Functional Plant Biology, 2008, vol. In press.

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[75]

Z. Zhan, H. Rey, D. Li, Y. Guo, P.-H. Cournède, P. de Reffye.
Study on the Effects of Defoliation on the Growth of Cotton Plant Using the Functional Structural Model GREENLAB, in: Plant growth Modeling, simulation, visualization and their Applications., T. Fourcaud, X. Zhang (editors), IEEE Computer Society (Los Alamitos, California), 2007.

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Multiresolution Plant Models with complex organs., in: Proceedings of ACM VRCIA, Hong Kong, China, 2006, p. 331-334.

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X. Zhang, J. Liu, Z. Li, M. Jaeger.
Volume Decomposition and Hierarchical Skeletonization, in: International Journal of Virtual Reality, 2008, vol. In press..

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Interactive simulations of plant architecture based on a dual-scale automaton model., in: Proceedings of PMA03, Beijing, China, B. Hu, M. Jaeger (editors), Tsinghua University Press, Springer, October 2003, p. 144-153.

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C. Zhu, X. Zhang, B. Hu, M. Jaeger.
Reconstruction of Tree Crown Shape from Scanned Data, in: Proceedings of the Third International Conference of E-Learning and Games - Edutainment 08. Nanjing, China, Z. Pan, etal. (editors), Springer, 2008.