# 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.

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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. - [57]
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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]
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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]
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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. - [70]
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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. - [79]
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