Bibliography

Major publications by the team in recent years

• 1P. 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, pp. 1627-1632.
  
  http://www-sop.inria.fr/virtualplants/Publications/2006/BBLMCGT06
• 2F. Boudon, C. Pradal, T. Cokelaer, P. Prusinkiewicz, C. Godin.
  
  L-Py: an L-system simulation framework for modeling plant architecture development based on a dynamic language, in: Frontiers in plant science, May 2012, vol. 3, n^o 76. [ DOI : 10.3389/fpls.2012.00076 ]
  
  http://hal.inria.fr/cirad-00703085
• 3F. 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, sept 2010, vol. 66, n^o 3, pp. 753–762.
  
  http://www-sop.inria.fr/virtualplants/Publications/2010/CGLT10
• 4R. Fernandez, P. Das, V. Mirabet, E. Moscardi, J. Traas, J.-L. Verdeil, G. Malandain, C. Godin.
  
  Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution, in: Nature Methods, jul 2010, vol. 7, pp. 547–553.
  
  http://www-sop.inria.fr/virtualplants/Publications/2010/FDMMTVMG10
• 5C. Godin, P. Ferraro.
  
  Quantifying the degree of self-nestedness of trees: application to the structural analysis of plants, in: IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2010, vol. 7, pp. 688–703.
  
  http://www-sop.inria.fr/virtualplants/Publications/2010/GF10
• 6C. La Rota, J. Chopard, P. Das, S. Paindavoine, F. Rozier, E. Farcot, C. Godin, J. Traas, F. Monéger.
  
  A data-driven integrative model of sepal primordium polarity in Arabidopsis, in: The Plant cell, December 2011, vol. 23, n^o 12, pp. 4318–4333.
• 7C. 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, pp. 1–21.
  
  http://www-sop.inria.fr/virtualplants/Publications/2009/PBNCG09
• 8C. Pradal, S. Dufour-Kowalski, F. Boudon, C. Fournier, C. Godin.
  
  OpenAlea: A visual programming and component-based software platform for plant modeling, in: Functional Plant Biology, 2008, vol. 35, n^o 9 & 10, pp. 751–760.
  
  http://www-sop.inria.fr/virtualplants/Publications/2008/PDBFG08a
• 9S. Stoma, M. Lucas, J. Chopard, M. Scheadel, J. Traas, C. Godin.
  
  Flux-based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development, in: PLOS Computational Biology, 2008, vol. 4, n^o 10.
  
  http://www-sop.inria.fr/virtualplants/Publications/2008/SLCSTG08
• 10T. Vernoux, G. Brunoud, E. Farcot, V. Morin, H. Van den Daele, J. Legrand, M. Oliva, P. Das, A. Larrieu, D. Wells, Y. Guédon, L. Armitage, F. Picard, S. Guyomarc'h, C. Cellier, G. Parry, R. Koumproglou, J. Doonan, M. Estelle, C. Godin, S. Kepinski, M. J. Bennett, L. de Veylder, J. Traas.
  
  The auxin signalling network translates dynamic input into robust patterning at the shoot apex, in: Molecular Systems Biology, 2011, vol. 7, n^o 508.
  
  http://www-sop.inria.fr/virtualplants/Publications/2011/VBFMVLODLWGAPGCPKDEG

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 11J. Peyhardi.
  
  Une nouvelle famille de modèles linéaires généralisés (GLMs) pour l'analyse de données catégorielles ; application à la structure et au développement des plantes, Université Montpellier II - Sciences et Techniques du Languedoc, December 2013.
  
  http://hal.inria.fr/tel-00936845

Articles in International Peer-Reviewed Journals

• 12J.-P. Bernard, E. Frenod, A. Rousseau.
  
  Paralic confinement computations in coastal environment with interlocked areas, in: Discrete and Continuous Dynamical Systems - Series S, May 2014.
  
  http://hal.inria.fr/hal-00833340
• 13F. Besnard, Y. Refahi, V. Morin, B. Marteaux, G. Brunoud, P. Chambrier, F. Rozier, V. Mirabet, J. Legrand, S. Lainé, E. Thévenon, E. Farcot, C. Cellier, P. Das, A. Bishopp, R. Dumas, F. Parcy, Y. Helariutta, A. Boudaoud, C. Godin, J. Traas, Y. Guédon, T. Vernoux.
  
  Cytokinin signalling inhibitory fields provide robustness to phyllotaxis, in: Nature, 2013, vol. 505, n^o 7483, pp. 417-421. [ DOI : 10.1038/nature12791 ]
  
  http://hal.inria.fr/hal-00926908
• 14M. Chaves, E. Farcot, J.-L. Gouzé.
  
  Probabilistic approach for predicting periodic orbits in piecewise affine differential models, in: Bulletin of Mathematical Biology, 2013, vol. 75, n^o 6, pp. 967-987. [ DOI : 10.1007/s11538-012-9773-6 ]
  
  http://hal.inria.fr/hal-00828847
• 15R. Choquet, Y. Guédon, A. Besnard, M. Guillemain, R. Pradel.
  
  Estimating stop over duration in the presence of trap-effects, in: Ecological Modelling, 2013, vol. 250, pp. 111-118. [ DOI : 10.1016/j.ecolmodel.2012.11.002 ]
  
  http://hal.inria.fr/hal-00828839
• 16A. Dambreville, P.-E. Lauri, C. Trottier, Y. Guédon, F. Normand.
  
  Deciphering structural and temporal interplays during the architectural development of mango trees, in: Journal of Experimental Botany, 2013, vol. 64, n^o 8, pp. 2467-2480. [ DOI : 10.1093/jxb/ert105 ]
  
  http://hal.inria.fr/hal-00806978
• 17J.-B. Durand, B. Guitton, J. Peyhardi, Y. Holtz, Y. Guédon, C. Trottier, E. Costes.
  
  New insights for estimating the genetic value of F1 apple progenies for irregular bearing during the first years of tree production, in: Journal of Experimental Botany, November 2013, vol. 64, n^o 16, pp. 5099-5113. [ DOI : 10.1093/jxb/ert297 ]
  
  http://hal.inria.fr/hal-00845353
• 18E. Farcot, Y. Yuan.
  
  Homogeneous Auxin Steady States and Spontaneous Oscillations in Flux-Based Auxin Transport Models, in: SIAM Journal on Applied Dynamical Systems, 2013, vol. 12, n^o 3, pp. 1330-1353. [ DOI : 10.1137/120891538 ]
  
  http://hal.inria.fr/hal-00850927
• 19Y. Guédon.
  
  Exploring the latent segmentation space for the assessment of multiple change-point models, in: Computational Statistics, 2013, pp. 1-38. [ DOI : 10.1007/s00180-013-0422-9 ]
  
  http://hal.inria.fr/hal-00850847
• 20Y. Guédon, Y. Refahi, F. Besnard, E. Farcot, C. Godin, T. Vernoux.
  
  Pattern identification and characterization reveal permutations of organs as a key genetically controlled property of post-meristematic phyllotaxis, in: Journal of Theoretical Biology, 2013, vol. 338, pp. 94-110. [ DOI : 10.1016/j.jtbi.2013.07.026 ]
  
  http://hal.inria.fr/hal-00859831
• 21S. Kenouche, J. Larionova, N. Bezzi, Y. Guari, N. Bertin, M. Zanca, L. Lartigue, M. Cieslak, C. Godin, G. Morrot, C. Goze-Bac.
  
  NMR investigation of functionnalized magnetic nanoparticles Fe3O4 as T1-T2 contrast agents, in: Powder Technology, November 2013. [ DOI : 10.1016/j.powtec.2013.07.038 ]
  
  http://hal.inria.fr/hal-00881594
• 22M. Lucas, K. Kenobi, D. Von Wangenheim, U. Voß, K. Swarup, I. De Smet, D. Van Damme, T. Lawrence, B. Péret, E. Moscardi, D. Barbeau, C. Godin, D. Salt, S. Guyomarc'H, E. H. K. Stelzer, A. Maizel, L. Laplaze, M. J. Bennett.
  
  Lateral root morphogenesis is dependent on the mechanical properties of the overlaying tissues, in: Proceedings of the National Academy of Sciences, March 2013, vol. 110, n^o 13, pp. 5229-34. [ DOI : 10.1073/pnas.1210807110 ]
  
  http://hal.inria.fr/cea-00848569
• 23D. Muraro, N. Mellor, M. P. Pound, H. Help, M. Lucas, J. Chopard, H. M. Byrne, C. Godin, T. C. Hodgman, J. R. King, T. P. Pridmore, Y. Helariutta, M. J. Bennett, A. Bishopp.
  
  Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots, in: Proceedings of the National Academy of Sciences, 2014, vol. 111, n^o 2, pp. 857-862. [ DOI : 10.1073/pnas.1221766111 ]
  
  http://hal.inria.fr/hal-00941028
• 24C. M. Negron, L. Contador, B. D. Lampinen, S. G. Metcalf, T. M. DeJong, Y. Guédon, E. Costes.
  
  Systematic Analysis of Branching Patterns of Three Almond Cultivars with Different Tree Architectures, in: Journal of the American Society for Horticultural Science, 2013, vol. 138, n^o 6, pp. 407–415.
  
  http://hal.inria.fr/hal-00931170
• 25M. Oliva, E. Farcot, T. Vernoux.
  
  Plant hormone signaling during development: insights from computational models, in: Current Opinion in Plant Biology, 2013, vol. 16, n^o 1, pp. 19-24. [ DOI : 10.1016/j.pbi.2012.11.006 ]
  
  http://hal.inria.fr/hal-00850918
• 26C. Pradal, G. Varoquaux, H. P. Langtangen.
  
  Publishing scientific software matters, in: Journal of Computational Science, 2013, vol. 4, n^o 5, pp. 311 - 312. [ DOI : 10.1016/j.jocs.2013.08.001 ]
  
  http://hal.inria.fr/hal-00858663
• 27M. L. Walker, E. Farcot, J. Traas, C. Godin.
  
  The Flux-Based PIN Allocation Mechanism Can Generate Either Canalyzed or Diffuse Distribution Patterns Depending on Geometry and Boundary Conditions, in: PLoS ONE, 2013, vol. 8, n^o 1, pp. 1-16. [ DOI : 10.1371/journal.pone.0054802 ]
  
  http://hal.inria.fr/hal-00850845

International Conferences with Proceedings

• 28M. Abichou, C. Fournier, T. Dornbusch, C. Chambon, R. Baccar, J. Bertheloot, T. Vidal, C. Robert, G. David, B. Andrieu.
  
  Re-parametrisation of Adel-wheat allows reducing the experimental effort to simulate the 3D development of winter wheat, in: 7th International Conference on Functional-Structural Plant Models, Saariselka, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 304-306.
  
  http://hal.inria.fr/hal-00851389
• 29M. Balduzzi, F. Boudon, C. Godin.
  
  Optimal 3D reconstruction of plants canopy from terrestrial laser scanner data by fusion of the 3D point information and the intensity value, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 58-60, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850793
• 30F. Boudon, C. Preuksakarn, P. Ferraro, J. Diener, E. Nikinmaa, C. Godin.
  
  Quantitative assessment of automatic reconstructions of branching systems, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 64-66, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850796
• 31M. Cieslak, M. Génard, F. Boudon, V. Baldazzi, C. Godin, N. Bertin.
  
  Integrating architecture and physiological perspectives in fruit development, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 127-130, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850801
• 32A. Dambreville, P. Fernique, C. Pradal, P.-E. Lauri, F. Normand, Y. Guédon, J.-B. Durand.
  
  Deciphering mango tree asynchronisms using Markov tree and probabilistic graphical models, in: FSPM2013 - 7th International Workshop on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), 2013, pp. 210-212, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00847614
• 33J. Diener, P. Nacry, C. Périn, A. Diévart, X. Draye, F. Boudon, A. Gojon, B. Muller, C. Pradal, C. Godin.
  
  An automated image-processing pipeline for high-throughput analysis of root architecture in OpenAlea, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 85-87, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850814
• 34J.-B. Durand, B. Guitton, J. Peyhardi, Y. Holtz, Y. Guédon, C. Trottier, E. Costes.
  
  Estimating the genetic value of F1 apple progenies for irregular bearing during first years of production, in: FSPM2013 - 7th International Workshop on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 13-15.
  
  http://hal.inria.fr/hal-00847593
• 35C. Fournier, C. Pradal, M. Abichou, B. Andrieu, M.-O. Bancal, C. Bedos, P. Benoit, C. Chambon, R. Chapuis, E. Cotteux, L. Mamy, N. Paveley, V. Pot, S. Saint-Jean, C. Sinfort, C. Richard, A. Ter Halle, E. Van Den Berg, A.-S. Walker, C. Robert.
  
  An integrated and modular model for simulating and evaluating how canopy architecture can help reduce fungicide applications, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 345-348, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850818
• 36G. Garin, C. Pradal, B. Andrieu, V. Houlès, C. Robert, C. Fournier.
  
  A generic model of interactions between FSPM, foliar pathogens and microclimate, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 339-341.
  
  http://hal.inria.fr/hal-00850823
• 37L. Guignard, C. Godin, U.-M. Fiuza, L. Hufnagel, P. Lemaire, G. Malandain.
  
  Spatio-temporal registration of embryo images, in: ISBI - International Symposium on Biomedical Imaging, Pekin, China, IEEE, April 2014.
  
  http://hal.inria.fr/hal-00919142
• 38Y. Guédon, O. Taugourdeau, Y. Caraglio, S. Sabatier.
  
  Characterizing the balance between ontogeny and environmental constraints in forest tree development using growth phase duration distributions, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 237-239, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850838
• 39G. Michelin, L. Guignard, U.-M. Fiuza, G. Malandain.
  
  Embryo Cell Membranes Reconstruction by Tensor Voting, in: ISBI - International Symposium on Biomedical Imaging, Beijing, China, IEEE, April 2014.
  
  http://hal.inria.fr/hal-00915000
• 40J. Peyhardi, E. Costes, Y. Caraglio, P.-E. Lauri, C. Trottier, Y. Guédon.
  
  Integrative models for analyzing jointly shoot growth and branching patterns, in: 7th International Workshop on Functional Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), 2013, pp. 207-209, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00808264
• 41J. Peyhardi, C. Trottier, Y. Guédon.
  
  A unifying framework for specifying generalized linear models for categorical data, in: 28th International Workshop on Statistical Modeling, Italy, 2013, pp. 331-335.
  
  http://hal.inria.fr/hal-00808270
• 42C. Pradal, J. Coste, F. Boudon, C. Fournier, C. Godin.
  
  OpenAlea 2.0: Architecture of an integrated modeling environment on the web, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, 213 p.
  
  http://hal.inria.fr/hal-00850931
• 43M. Rakocevic, F. Takeshi Matsunaga, E. Costes, J. Barbosa Tosti, Y. Guédon, L. De Cassia Santin, A. Luiz Johann.
  
  Protocol for foliage modeling and light partitioning in Coffea arabica, in: 7th International Conference on Functional-Structural Plant Models, Saariselkä, Finland, R. Sievänen, E. Nikinmaa, C. Godin, A. Lintunen, P. Nygren (editors), June 2013, pp. 284-286, ISBN 978-951-651-408-9.
  
  http://hal.inria.fr/hal-00850843

Conferences without Proceedings

• 44J.-B. Durand, P. Fernique.
  
  Approche graphique pour la modélisation statistique de la dépendance entre activités journalières, in: Workshop "Statistique, Transport et Activités", Grenoble, France, November 2013.
  
  http://mistis.inrialpes.fr/workshop-statistique-transport.html, http://hal.inria.fr/hal-00919372
• 45P. Fernique, J.-B. Durand, Y. Guédon.
  
  Parametric Modelling of Multivariate Count Data Using Probabilistic Graphical Models, in: AIGM13 - 3rd Workshop on Algorithmic issues for Inference in Graphical Models, Paris, France, September 2013.
  
  http://hal.inria.fr/hal-00918597

Scientific Books (or Scientific Book chapters)

• 46J. Guénard, G. Morin, F. Boudon, V. Charvillat.
  
  Reconstructing Plants in 3D from a Single Image Using Analysis-by-Synthesis, in: Advances in Visual Computing, G. Bebis, R. Boyle, B. Parvin, D. Koracin, B. Li, F. Porikli, V. Zordan, J. Klosowski, S. Coquillart, X. Luo, M. Chen, D. Gotz (editors), Lecture Notes in Computer Science, Springer Berlin Heidelberg, 2013, vol. 8033, pp. 322–332. [ DOI : 10.1007/978-3-642-41914-0_32 ]
  
  http://hal.inria.fr/hal-00931231

Internal Reports

• 47A. Rousseau, A. Darnaud, B. Goglin, C. Acharian, C. Leininger, C. Godin, C. Holik, C. Kirchner, D. Rives, E. Darquie, E. Kerrien, F. Neyret, F. Masseglia, F. Dufour, G. Berry, G. Dowek, H. Robak, H. Xypas, I. Illina, I. Gnaedig, J. Jongwane, J. Ehrel, L. Viennot, L. Guion, L. Calderan, L. Kovacic, M. Collin, M.-A. Enard, M.-H. Comte, M. Quinson, M. Olivi, M. Giraud, M. Dorémus, M. Ogouchi, M. Droin, N. Lacaux, N. Rougier, N. Roussel, P. Guitton, P. Peterlongo, R.-M. Cornus, S. Vandermeersch, S. Maheo, S. Lefebvre, S. Boldo, T. Viéville, V. Poirel, A. Chabreuil, A. Fischer, C. Farge, C. Vadel, I. Astic, J.-P. Dumont, L. Féjoz, P. Rambert, P. Paradinas, S. De Quatrebarbes, S. Laurent.
  
  Médiation Scientifique : une facette de nos métiers de la recherche, March 2013, 34 p.
  
  http://hal.inria.fr/hal-00804915

References in notes

• 48A. Arber.
  
  Natural philosophy of plant form, University Press, Cambridge, 1950.
• 49L. Band, J. Fozard, C. Godin, O. Jensen, T. Pridmore, M. Bennett, J. King.
  
  Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales, in: The Plant Cell, 2012.
  
  http://www-sop.inria.fr/virtualplants/Publications/2012/BFGJPBK12
• 50D. Barthelemy, Y. Caraglio, E. Costes.
  
  Architecture, gradients morphogntiques et âge physiologique chez les vgtaux, in: Modélisation et Simulation de l'Architecture des Végétaux, J. Bouchon, P. de Reffye, D. Barthelemy (editors), INRA, 1997, pp. 89-136.
• 51L. 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, pp. 675-696.
• 52C. Godin, Y. Caraglio.
  
  A multiscale model of plant topological structures, in: Journal of Theoretical Biology, 1998, vol. 191, pp. 1-46.
  
  http://www-sop.inria.fr/virtualplants/Publications/1998/GC98
• 53C. Godin, E. Costes, H. Sinoquet.
  
  A method for describing plant architecture which integrates topology and geometry, in: Annals of Botany, 1999, vol. 84, pp. 343-357.
• 54F. Hallé, R. A. A. Oldeman, P. B. Tomlinson.
  
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• 55J. L. Harper, B. R. Rosen, J. White.
  
  The growth and form of modular organisms, The Royal Society, London, UK, 1986.
• 56J. Murray, A. Jones, C. Godin, J. Traas.
  
  Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling, in: The Plant Cell, 2012.
  
  http://www-sop.inria.fr/virtualplants/Publications/2012/MJGT12
• 57R. Nozeran.
  
  Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, pp. 375-401.
• 58D. Reinhardt, E.R. Pesce, P. Stieger, T. Mandel, K. Baltensperger, M. J. Bennett, J. Traas, J. Friml, C. Kuhlemeier.
  
  Regulation of phyllotaxis by polar auxin transport, in: Nature, November 2003, vol. 426, n^o 6964, pp. 255–260.
  
  http://www.nature.com/nature/journal/v426/n6964/abs/nature02081.html
• 59H. Sinoquet, P. Rivet, C. Godin.
  
  Assessment of the three-dimensional architecture of walnut trees using digitizing, in: Silva Fennica, 1997, vol. 3, pp. 265–273.