Bibliography

Major publications by the team in recent years

[1]

P. Barbier de Reuille, I. Bohn-Courseau, K. Ljung, H. Morin, N. Carraro, C. Godin, J. Traas.
Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in Arabidopsis, in: PNAS, 2006, vol. 103, p. 1627-1632
http://www-sop.inria.fr/virtualplants/Publications/2006/BBLMCGT06.

[2]

J.-B. Durand, P. Gonçalvès, Y. Guédon.
Computational methods for hidden Markov tree models - An application to wavelet trees, in: IEEE Transactions on Signal Processing, 2004, vol. 52, n^o 9, p. 2551-2560.

[3]

J.-B. Durand, Y. Guédon, Y. Caraglio, E. Costes.
Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models., in: New Phytol, Jun 2005, vol. 166, n^o 3, p. 813–825
http://dx.doi.org/10.1111/j.1469-8137.2005.01405.x.

[4]

P. Ferraro, C. Godin.
An edit distance between quotiented trees, in: Algorithmica, 2003, vol. 48, p. 385-406.

[5]

P. Ferraro, C. Godin, P. Prusinkiewicz.
Toward a quantification of self-similarity in plants, in: Fractals, 2005, vol. 13, n^o 2, p. 91-109
http://www-sop.inria.fr/virtualplants/Publications/2005/FGP05.

[6]

C. Godin, Y. Caraglio.
A multiscale model of plant topological structures, in: Journal of Theoretical Biology, 1998, vol. 191, p. 1-46
http://www-sop.inria.fr/virtualplants/Publications/1998/GC98.

[7]

C. Godin, E. Costes, H. Sinoquet.
Plant architecture modelling - virtual plants and complex systems, in: Plant Architecture and its Manipulation, C. Turnbull (editor), Annual plant reviews, Blackwell, 2005, vol. 17, p. 238-287
http://www-sop.inria.fr/virtualplants/Publications/2005/GCS05.

[8]

Y. Guédon, Y. Caraglio, P. Heuret, E. Lebarbier, C. Meredieu.
Analyzing growth components in trees, in: Journal of Theoretical Biology, 2007, vol. 248, n^o 3, p. 418–447
http://www-sop.inria.fr/virtualplants/Publications/2007/GCHLM07.

[9]

Y. Guédon, D. Barthelemy, Y. Caraglio, E. Costes.
Pattern analysis in branching and axillary flowering sequences, in: Journal of Theoretical Biology, 2001, vol. 212, p. 481-520.

[10]

Y. Guédon.
Estimating hidden semi Markov chains from discrete sequences, in: Journal of Computational and Graphical Statistics, 2003, vol. 12, n^o 3, p. 604-639.

Publications of the year

Articles in International Peer-Reviewed Journal

[11]

F. Chaubert - Pereira, Y. Caraglio, C. Lavergne, Y. Guédon.
Identifying ontogenetic, environmental and individual components of forest tree growth., in: Annals of Botany, 2009, vol. 104, n^o 5, p. 883–896
http://www-sop.inria.fr/virtualplants/Publications/2009/CCLG09.

[12]

F. Chaubert - Pereira, Y. Guédon, C. Lavergne, C. Trottier.
Markov and semi-Markov switching linear mixed models used to identify forest tree growth components., in: Biometrics, 2009
http://www-sop.inria.fr/virtualplants/Publications/2009/CGLT09.

[13]

E. Farcot, J.-L. Gouzé.
Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop, in: Acta Biotheoretica, 2009, vol. 57, n^o 4, p. 429–455
http://www-sop.inria.fr/virtualplants/Publications/2009/FG09a.

[14]

S. Mondet, W. Cheng, G. Morin, R. Grigoras, F. Boudon, W. Tsang Ooi.
Compact and Progressive Plant Models for Streaming in Networked Virtual Environments, in: ACM Transactions on Multimedia Computing, Communications, and Applications (TOMCCAP), aug 2009, vol. 5, n^o 3, p. 1–22
http://www-sop.inria.fr/virtualplants/Publications/2009/MCMGBT09.

[15]

C. Pradal, F. Boudon, C. Nouguier, J. Chopard, C. Godin.
PlantGL : a Python-based geometric library for 3D plant modelling at different scales, in: Graphical Models, jan 2009, vol. 71, n^o 1, p. 1–21
http://www-sop.inria.fr/virtualplants/Publications/2009/PBNCG09.

International Peer-Reviewed Conference/Proceedings

[16]

A. Doran, S. Mondet, R. Grigoras, G. Morin, W. Tsang Ooi, F. Boudon.
A Demonstration of MobiTree: Progressive 3D Tree Models Streaming on Mobile Clients, in: ACM Multimedia 2009, Beijing, ACM, oct 2009
http://www-sop.inria.fr/virtualplants/Publications/2009/DMGMTB09.

[17]

J. Wither, F. Boudon, M.-P. Cani, C. Godin.
Structure from silhouettes: a new paradigm for fast sketch-based design of trees, in: Computer Graphic Forum. Special issue: Eurographics 2009, 2009, vol. 28 (2), p. 541–550
http://www-sop.inria.fr/virtualplants/Publications/2009/WBCG09.

[18]

D.-M. Yan, J. Wintz, B. Mourrain, W. Wang, F. Boudon, C. Godin.
Efficient and robust reconstruction of botanical branching structure from laser scanned points, in: 11th IEEE International conference on Computer-Aided Design and Computer Graphics (CAD/Graphics 2009), 2009
http://www-sop.inria.fr/virtualplants/Publications/2009/YWMWBG09.

Workshops without Proceedings

[19]

T. Cokelaer, C. Pradal, C. Fournier.
Plant modelling with Python components in OpenAlea, in: EuroSciPy 2009, 2009
http://www-sop.inria.fr/virtualplants/Publications/2009/CPF09.

Internal Reports

[20]

E. Farcot, J.-L. Gouzé.
Limit cycles in piecewise-affine gene network models with multiple interaction loops, INRIA, Mar 2009, n^o RR-6875
http://www-sop.inria.fr/virtualplants/Publications/2009/FG09, INRIA Research Report.

[21]

E. Farcot, J.-L. Gouzé.
Qualitative control of periodic solutions in piecewise affine systems; application to genetic networks, INRIA, Dec 2009, n^o RR-7130
http://www-sop.inria.fr/virtualplants/Publications/2009/FG09b, INRIA Research Report.

References in notes

[22]

A. Arber.
Natural philosophy of plant form, University Press, Cambridge, 1950.

[23]

D. Barthelemy, Y. Caraglio, E. Costes.
Architecture, gradients morphogénétiques et âge physiologique chez les végétaux, in: Modélisation et Simulation de l'Architecture des Végétaux, J. Bouchon, P. de Reffye, D. Barthelemy (editors), 1997, p. 89-136.

[24]

E. Costes, C. Smith, M. Renton, Y. Guédon, P. Prusinkiewicz, C. Godin.
MAppleT: simulation of apple tree development using mixed stochastic and biomechanical models, in: Functional Plant Biology, 2008, vol. 35, n^o 9 & 10, p. 936–950
http://www-sop.inria.fr/virtualplants/Publications/2008/CSRGPG08.

[25]

P. Ferraro, C. Godin.
A distance measure between plant architectures, in: Annals of Forest Science, 2000, vol. 57, n^o 5/6, p. 445-461
http://www-sop.inria.fr/virtualplants/Publications/2000/FG00.

[26]

D. Fumey, P. Lauri, Y. Guédon, C. Godin, E. Costes.
Effects of pruning on the apple tree: from tree architecture to modeling, in: International Symposium on Integrating Canopy, Rootstock and Environmental Physiology in Orchard Systems, 2008
http://www-sop.inria.fr/virtualplants/Publications/2008/FLGGC08.

[27]

L. E. Gatsuk, O. V. Smirnova, L. I. Vorontzova, L. B. Zaugolnova, L.A. Zhukova.
Age states of plants of various growth forms: a review, in: Journal of Ecology, 1980, vol. 68, p. 675-696.

[28]

C. Godin, E. Costes, H. Sinoquet.
A method for describing plant architecture which integrates topology and geometry, in: Annals of Botany, 1999, vol. 84, p. 343-357.

[29]

Y. Guédon, Y. Caraglio, P. Heuret, E. Lebarbier, C. Meredieu.
Analyzing growth components in trees, in: Journal of Theoretical Biology, 2007, vol. 248, n^o 3, p. 418–447
http://www-sop.inria.fr/virtualplants/Publications/2007/GCHLM07.

[30]

F. Hallé, R. A. A. Oldeman, P. B. Tomlinson.
Tropical trees and forests. An architectural analysis, Springer-Verlag, New-York, 1978.

[31]

J. L. Harper, B. R. Rosen, J. White.
The growth and form of modular organisms, The Royal Society, London, UK, 1986.

[32]

H. Jönsson, M. Heisler, G. V. Reddy, V. Agrawal, V. Gor, B. E. Shapiro, E. Mjolsness, E. M. Meyerowitz.
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem, in: Bioinformatics, 2005, vol. 21, n^o 1, p. 232–240
http://dx.doi.org/10.1093/bioinformatics/bti1036.

[33]

M. Lucas, Y. Guédon, C. Jay-Allemand, C. Godin, L. Laplaze.
An auxin transport-based model of root branching in Arabidopsis thaliana, in: PLoS ONE, 2008, vol. 3, n^o 11
http://www-sop.inria.fr/virtualplants/Publications/2008/LGJGL08.

[34]

M. Lucas.
Etude et modélisation des déterminismes de mise en place et de développement des racines latérales chez Arabidopsis Thaliana , Université Montpellier II, 2008, Ph. D. Thesis.

[35]

S. Mondet, W. Cheng, G. Morin, R. Grigoras, F. Boudon, W. Tsang Ooi.
Streaming of Plants in Distributed Virtual Environments, in: ACM Multimedia 2008 - Systems and Networking Track, 2008
http://www-sop.inria.fr/virtualplants/Publications/2008/MCMGBT08.

[36]

R. Nozeran.
Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, p. 375-401.

[37]

D. Reinhardt, E.-R. Pesce, P. Stieger, T. Mandel, K. Baltensperger, M. Bennett, J. Traas, J. Friml, C. Kuhlemeier.
Regulation of phyllotaxis by polar auxin transport, in: Nature, November 2003, vol. 426, n^o 6964, p. 255–260
http://dx.doi.org/10.1038/nature02081.

[38]

M. Renton, Y. Guédon, C. Godin, E. Costes.
Similarities and gradients in growth-unit branching patterns during ontogeny in Fuji apple trees: A stochastic approach., in: Journal of Experimental Botany, 2006, vol. 57, n^o 12, p. 3131–3143
http://www-sop.inria.fr/virtualplants/Publications/2006/RGGC06.

[39]

A. Runions, B. Lane, P. Prusinkiewicz.
Modeling Trees with a Space Colonization Algorithm, in: Eurographics Workshop on Natural Phenomena, 2007, p. 63-70
http://www.eg.org/EG/DL/WS/NPH/NPH07/063-070.pdf.

[40]

H. Sinoquet, P. Rivet, C. Godin.
Assessment of the three-dimensional architecture of walnut trees using digitizing, in: Silva Fennica, 1997, vol. 3, p. 265–273.