Bibliography

Major publications by the team in recent years

• 1F. 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, 2014, vol. 505, n^o 7483, pp. 417-421. [ DOI : 10.1038/nature12791 ]
  https://hal.inria.fr/hal-00926908
• 2F. Boudon, J. Chopard, O. Ali, B. Gilles, O. Hamant, A. Boudaoud, J. Traas, C. Godin.
  A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution, in: PLoS Computational Biology, January 2015, vol. 11, n^o 1, pp. 1-16. [ DOI : 10.1371/journal.pcbi.1003950 ]
  https://hal.archives-ouvertes.fr/hal-01142486
• 3F. 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
• 4F. 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
• 5R. 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
• 6C. 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
• 7M. Lievre, C. C. Granier, Y. Guédon.
  Identifying developmental phases in the Arabidopsis thaliana rosette using integrative segmentation models, in: New Phytologist, 2016, vol. 210, pp. 1466–1478. [ DOI : 10.1111/nph.13861 ]
  https://hal.inria.fr/hal-01360976
• 8G. Lobet, M. P. Pound, J. Diener, C. Pradal, X. Draye, C. Godin, M. Javaux, D. Leitner, F. Meunier, P. Nacry, T. P. Pridmore, A. Schnepf.
  Root System Markup Language: toward a unified root architecture description language, in: Plant Physiology, January 2015, vol. 167, n^o 3, pp. 617-627. [ DOI : 10.1104/pp.114.253625 ]
  https://hal.archives-ouvertes.fr/hal-01113767
• 9J. Peyhardi, C. Trottier, Y. Guédon.
  A new specification of generalized linear models for categorical responses, in: Biometrika, 2015, vol. 102, n^o 4, pp. 889–906. [ DOI : 10.1093/biomet/asv042 ]
  https://hal.inria.fr/hal-01240023
• 10C. Pradal, S. Artzet, J. Chopard, D. Dupuis, C. Fournier, M. Mielewczik, V. Negre, P. Neveu, D. Parigot, P. Valduriez, S. Cohen-Boulakia.
  InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid, in: Future Generation Computer Systems, June 2016. [ DOI : 10.1016/j.future.2016.06.002 ]
  https://hal.inria.fr/hal-01336655
• 11C. 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
• 12Y. Refahi, G. Brunoud, E. Farcot, A. Jean-Marie, M. Pulkkinen, T. Vernoux, C. Godin.
  A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis, in: eLife, July 2016, vol. 71, 50 p. [ DOI : 10.7554/eLife.14093.048 ]
  https://hal.inria.fr/hal-01390155
• 13T. 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

Articles in International Peer-Reviewed Journals

• 14O. Ali, J. Traas.
  Force-Driven Polymerization and Turgor-Induced Wall Expansion, in: Trends in Plant Science, 2016, vol. 21, pp. 398 - 409. [ DOI : 10.1016/j.tplants.2016.01.019 ]
  https://hal.archives-ouvertes.fr/hal-01398409
• 15M.-R. Amini, J.-B. Durand, O. Gaudoin, E. Gaussier, A. Iouditski.
  Data Science: an international training program at master level, in: Statistique et Enseignement (ISSN 2108-6745), June 2016, vol. 7, n^o 1, pp. 95-102.
  https://hal.inria.fr/hal-01342469
• 16F. Ben-Naoum, C. Godin.
  Algorithmic Height Compression of Unordered Trees, in: Journal of Theoretical Biology, 2016, vol. 389, pp. 237 - 252. [ DOI : 10.1016/j.jtbi.2015.10.030 ]
  https://hal.archives-ouvertes.fr/hal-01412215
• 17M. Cieslak, I. CHEDDADI, F. Boudon, V. Baldazzi, M. Génard, C. Godin, N. Bertin.
  Integrating Physiology and Architecture in Models of Fruit Expansion, in: Frontiers in Plant Science, November 2016, vol. 7, 19 p. [ DOI : 10.3389/fpls.2016.01739 ]
  https://hal.inria.fr/hal-01400062
• 18J.-B. Durand, Y. Guédon.
  Localizing the latent structure canonical uncertainty: entropy profiles for hidden Markov models, in: Statistics and Computing, 2016, vol. 26, n^o 1, pp. 549-567, The final publication is available at Springer via http://dx.doi.org/10.1007/s11222-014-9494-9. [ DOI : 10.1007/s11222-014-9494-9 ]
  https://hal.inria.fr/hal-01090836
• 19C. S. Galvan-­‐ampudia, A. M. Chaumeret, C. Godin, T. S. Vernoux.
  Phyllotaxis: from patterns of organogenesis at the meristem to shoot architecture, in: Wiley Interdisciplinary Reviews: Developmental Biology, 2016, vol. 5, pp. 460 - 473. [ DOI : 10.1002/wdev.231 ]
  https://hal.archives-ouvertes.fr/hal-01413095
• 20J. Legrand, J.-B. Leger, S. S. Robin, T. Vernoux, Y. Guédon.
  Modelling the influence of dimerisation sequence dissimilarities on the auxin signalling network, in: BMC Systems Biology, 2016, vol. 10, n^o 22, 17 p. [ DOI : 10.1186/s12918-016-0254-7 ]
  https://hal.inria.fr/hal-01361020
• 21M. Lievre, C. C. Granier, Y. Guédon.
  Identifying developmental phases in the Arabidopsis thaliana rosette using integrative segmentation models, in: New Phytologist, 2016, vol. 210, pp. 1466–1478. [ DOI : 10.1111/nph.13861 ]
  https://hal.inria.fr/hal-01360976
• 22D. Muraro, A. Larrieu, M. Lucas, J. Chopard, H. Byrne, C. Godin, J. King.
  A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana, in: Journal of Theoretical Biology, 2016, vol. 404, pp. 182 - 205. [ DOI : 10.1016/j.jtbi.2016.04.036 ]
  https://hal.archives-ouvertes.fr/hal-01412252
• 23S. Passot, F. Gnacko, D. Moukouanga, M. Lucas, S. Guyomarc'h, B. Moreno-Ortega, J. A. Atkinson, M. N. Belko, M. J. Bennett, P. Gantet, D. M. Wells, Y. Guédon, Y. Y. Vigouroux, J.-L. Verdeil, B. Muller, L. Laplaze.
  Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots, in: Frontiers in Plant Science, 2016, vol. 7, n^o 829, 11 p. [ DOI : 10.3389/fpls.2016.00829 ]
  https://hal.inria.fr/hal-01398441
• 24J. Perrotte, Y. Guédon, A. Gaston, B. Denoyes.
  Identification of successive flowering phases highlights a new genetic control of the flowering pattern in strawberry, in: Journal of Experimental Botany, 2016, vol. 67, n^o 19, pp. 5643 - 5655. [ DOI : 10.1093/jxb/erw326 ]
  https://hal.inria.fr/hal-01398331
• 25J. Peyhardi, C. Trottier, Y. Guédon.
  Partitioned conditional generalized linear models for categorical responses, in: Statistical Modelling, 2016, vol. 16, n^o 4, pp. 297–321. [ DOI : 10.1177/1471082X16644874 ]
  https://hal.inria.fr/hal-01361041
• 26C. Pradal, S. Artzet, J. Chopard, D. Dupuis, C. Fournier, M. Mielewczik, V. Negre, P. Neveu, D. Parigot, P. Valduriez, S. Cohen-Boulakia.
  InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid, in: Future Generation Computer Systems, June 2016. [ DOI : 10.1016/j.future.2016.06.002 ]
  https://hal.inria.fr/hal-01336655
• 27Y. Refahi, G. Brunoud, E. Farcot, A. Jean-Marie, M. Pulkkinen, T. Vernoux, C. Godin.
  A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis, in: eLife, July 2016, vol. 71, 50 p. [ DOI : 10.7554/eLife.14093.048 ]
  https://hal.inria.fr/hal-01390155
• 28J. Starlinger, S. Cohen-Boulakia, S. Khanna, S. Davidson, U. Leser.
  Effective and Efficient Similarity Search in Scientific Workflow Repositories, in: Future Generation Computer Systems, 2016, vol. 56, pp. 584-594. [ DOI : 10.1016/j.future.2015.06.012 ]
  https://hal.archives-ouvertes.fr/hal-01170597
• 29W. Yang, B. Pallas, J.-B. Durand, S. S. Martinez, m. han, E. Costes.
  The impact of long-term water stress on tree architecture and production is related to changes in transitions between vegetative and reproductive growth in the ‘Granny Smith’ apple cultivar, in: Tree Physiology, September 2016. [ DOI : 10.1093/treephys/tpw068 ]
  https://hal.inria.fr/hal-01377095

International Conferences with Proceedings

• 30R. Albasha, C. C. Fournier, C. Pradal, J. Alejando Prieto, G. Louarn, E. Lebon.
  HydroShoot: a new FSPM model for simulating hydraulic structure and gas-exchange dynamics of complex plants canopies under water deficit, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, November 2016.
  https://hal.inria.fr/hal-01396972
• 31T.-W. Chen, C. Fournier, S. Artzet, N. Brichet, J. Chopard, C. Pradal, S. Alvarez Prado, L. C. Cabrera-Bosquet, C. Welcker, F. F. Tardieu.
  Genetic variability in light-related parameters of maize models revealed by linking 3D-reconstruction of plant architecture with light model and phenotyping platform, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, November 2016.
  https://hal.inria.fr/hal-01396935
• 32P. Fernique, A. DAMBREVILLE, J.-B. Durand, C. Pradal, P.-E. P.-E. Lauri, F. Normand, Y. Guédon.
  Characterization of mango tree patchiness using a tree-segmentation/clusteringapproach, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, November 2016.
  https://hal.inria.fr/hal-01398291
• 33C. Fournier, A. Danthony, S. Pointet, B. Perriot, M. Abichou, S. Poidevin, J. Da Costa, E. Cotteux, B. Andrieu, S. Saint-Jean, C. Robert.
  Modeling and simulating the distribution of fungicide among leaves in wheat, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Quingdao, China, November 2016.
  https://hal.inria.fr/hal-01400029
• 34C. Godin, F. Boudon, C. Pradal.
  Reducing algorithm complexity in trees, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, November 2016.
  https://hal.inria.fr/hal-01398289
• 35Y. Guédon, B. Moreno-Ortega, B. Muller.
  Identification of developmental zones in maize lateral roots on the basis of longitudinal epidermis cell length profiles, in: IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), November 2016, vol. Book of abstracts, 42 p.
  https://hal.inria.fr/hal-01398404
• 36G. Michelin, Y. Refahi, R. Wightman, H. Jönsson, J. J. Traas, C. Godin, G. Malandain.
  Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis floral meristems, in: ISBI - International Symposium on Biomedical Imaging, Prague, Czech Republic, April 2016. [ DOI : 10.1109/ISBI.2015.7163872 ]
  https://hal.inria.fr/hal-01251151
• 37B. Pallas, W. Yang, J.-B. Durand, S. S. Martinez, E. E. Costes.
  Impact of Long Term Water Deficit on Production and Flowering Occurrence in the 'Granny Smith' Apple Tree Cultivar, in: XI International Symposium on Integrating Canopy, Rootstock and Environmental Physiology in Orchard Systems, Bologna, Italy, XI International Symposium on Integrating Canopy, Rootstock and Environmental Physiology in Orchard Systems, Prof. Dr. Luca Corelli-Grappadelli, Department of Agricultural Sciences, Università di Bologna, August 2016.
  https://hal.inria.fr/hal-01377104
• 38A. Schneiders, R. Barillot, C. Fournier, C. Pradal, B. Andrieu.
  A functional structural model of wheat leaf metabolism during extension, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, November 2016.
  https://hal.inria.fr/hal-01398296

National Conferences with Proceedings

• 39J.-B. Durand, A. Guérin-Dugué, S. Achard.
  Analyse de séquences oculométriques et d'électroencéphalogrammes par modèles markoviens cachés, in: 48èmes Journées de Statistique, Montpellier, France, May 2016.
  https://hal.inria.fr/hal-01339458

Conferences without Proceedings

• 40P. Fernique.
  AutoWIG : automatisation de l'encapsulation de librairies C++ en Python et en R, in: 48èmes Journées de Statistique de la SFdS Montpellier, Montpellier, France, May 2016, 6 p.
  https://hal.inria.fr/hal-01316276

Internal Reports

• 41S. Cohen-Boulakia, P. Valduriez.
  Bioinformatics big data processing, Inria Sophia Antipolis ; LRI - CNRS, University Paris-Sud, May 2016, n^o RR-8915, 8 p.
  https://hal.inria.fr/hal-01321033

Other Publications

• 42R. Azaïs, J.-B. Durand, C. Godin.
  Approximation of trees by self-nested trees, September 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01294013
• 43A. Barbieri, J. Peyhardi, T. Conroy, S. Gourgou, C. Lavergne, C. Mollevi.
  Item response models for the longitudinal analysis of health-related quality of life in cancer clinical trials, November 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01246368
• 44F. Boudon, S. Persello, A. Jestin, A.-S. Briand, P. Fernique, Y. Guédon, M. Léchaudel, I. Grechi, F. Normand.
  An FSPM approach for modeling fruit yield and quality in mango trees, November 2016, IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Poster.
  https://hal.inria.fr/hal-01400016
• 45A. Bucksch, A. Atta-Boateng, A. F. Azihou, M. Balduzzi, D. Battogtokh, A. Baumgartner, B. Binder, S. Braybrook, C. Chang, V. Coneva, T. DeWitt, A. Fletcher, M. Gehan, D. H. D. Martinez, L. Hong, A. Iyer-Pascuzzi, L. Klein, S. Leiboff, M. Li, J. Lynch, A. Maizel, J. Maloof, R. C. Markelz, C. Martinez, L. Miller, W. Mio, W. Palubicki, H. Poorter, C. Pradal, C. Price, E. Puttonen, J. Reese, R. Rellan-Alvarez, E. Spalding, E. Sparks, C. Topp, J. Williams, D. Chitwood.
  Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences, October 2016, working paper or preprint. [ DOI : 10.1101/078832 ]
  https://hal.inria.fr/hal-01412691
• 46P. Fernique, J. Legrand, J.-B. Durand, Y. Guédon.
  Semi-parametric Markov Tree for cell lineage analysis, June 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01286298
• 47P. Fernique, J. Peyhardi, J.-B. Durand.
  Multinomial distributions for the parametric modeling of multivariate count data, April 2016, working paper or preprint.
  https://hal.inria.fr/hal-01286171
• 48P. Fernique, C. Pradal.
  AutoWIG: Automatic generation of Python bindings for C++ libraries, March 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01286163
• 49C. Fournier, F. Boudon, M. Chelle, M. Saudreau, J. Ngao, G. Louarn, D. Combes, C. Pradal.
  Toward the inter-comparison of radiation transfert model for plant modelling application, November 2016, IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Poster.
  https://hal.inria.fr/hal-01400026
• 50M. Labadie, B. Denoyes, Y. Guédon.
  Identification of flowering patterns specific to strawberry varieties in production condition using longitudinal data analysis, November 2016, vol. poster abstracts, n^o 26, IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Poster.
  https://hal.inria.fr/hal-01400048
• 51S. Liu, F. Baret, F. Boudon, C. Fournier, B. Andrieu, M. Abichou, M. Hemmerlé, B. De Solan.
  Estimating canopy characteristics from ground-based LiDAR measurement assisted with 3D AdelWheat model, November 2016, IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Poster.
  https://hal.inria.fr/hal-01400001
• 52V. Migault, B. Pallas, J.-M. Legave, Y. Guédon, E. Costes.
  Using genome-wide predictions in a functional-structural plant model to simulate the genetic variation of 1-year-old apple tree development under contrasted soil water conditions, 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), November 2016, vol. poster abstracts, n^o 96, IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Poster.
  https://hal.inria.fr/hal-01400054
• 53J. Peyhardi, P. Fernique.
  New characterizations of discrete distributions and graphical models, March 2016, working paper or preprint.
  https://hal.inria.fr/hal-01286173

References in notes

• 54A. Arber.
  Natural philosophy of plant form, University Press, Cambridge, 1950.
• 55R. Azaïs, J.-B. Durand, C. Godin.
  Lossy compression of unordered rooted trees, December 2015, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01236088
• 56D. 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.
• 57F. Boudon, J. Chopard, O. Ali, B. Gilles, O. Hamant, A. Boudaoud, J. Traas, C. Godin.
  A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution, in: PLoS Computational Biology, January 2015, vol. 11, n^o 1, pp. 1-16. [ DOI : 10.1371/journal.pcbi.1003950 ]
  https://hal.archives-ouvertes.fr/hal-01142486
• 58F. Boudon, A. Jestin, A.-S. Briand, P. Fernique, P.-E. Lauri, A. Dambreville, Y. Guédon, I. Grechi, F. Normand.
  The Role of Structural and Temporal Factors in the Architectural Development of the Mango Tree: Evidences from Simulation, in: International Symposium on Modelling in Fruit Research and Orchard Management, Montpellier, France, June 2015.
  https://hal.inria.fr/hal-01237402
• 59F. Boudon, C. Preuksakarn, P. Ferraro, J. Diener, P. Nacry, E. Nikinmaa, C. Godin.
  Quantitative assessment of automatic reconstructions of branching systems obtained from laser scanning, in: Annals of Botany, April 2014, epub ahead of print. [ DOI : 10.1093/aob/mcu062 ]
  https://hal.archives-ouvertes.fr/hal-01064917
• 60I. CHEDDADI, C. Godin, F. Boudon, V. Baldazzi, M. M. Génard, N. Bertin.
  Toward a mechanical model of 3D fruit development, in: International Symposium on Modelling in Fruit Research and Orchard Management, Montpellier, France, June 2015.
  https://hal.inria.fr/hal-01237387
• 61G. Cerutti, C. Godin.
  Meshing Meristems - An Iterative Mesh Optimization Method for Modeling Plant Tissue at Cell Resolution, in: BIOIMAGING, Lisbonne, Portugal, January 2015.
  https://hal.archives-ouvertes.fr/hal-01100808
• 62G. Cerutti, S. Ribes, C. Godin, C. Galvan Ampudia, T. Vernoux.
  3D Tessellation of Plant Tissue A dual optimization approach to cell-level meristem reconstruction from microscopy images, in: International Conference on 3D Vision, Lyon, France, October 2015. [ DOI : 10.1109/3DV.2015.57 ]
  https://hal.archives-ouvertes.fr/hal-01246580
• 63M. 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
• 64J.-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
• 65C. Fournier, S. Artzet, J. Chopard, M. Mielewczik, N. Brichet, L. Cabrera, X. Sirault, S. Cohen-Boulakia, C. Pradal.
  Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data, September 2015, IAMPS 2015 (International Workshop on Image Analysis Methods for the Plant Sciences), Poster.
  https://hal.inria.fr/hal-01253627
• 66L. 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.
• 67C. 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
• 68C. 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.
• 69Y. 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. [ DOI : 10.1016/j.jtbi.2013.07.026 ]
  http://hal.inria.fr/hal-00859831
• 70F. Hallé, R. A. A. Oldeman, P. B. Tomlinson.
  Tropical trees and forests. An architectural analysis, Springer-Verlag, New-York, 1978.
• 71J. L. Harper, B. R. Rosen, J. White.
  The growth and form of modular organisms, The Royal Society, London, UK, 1986.
• 72C. 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.
• 73M. Léchaudel, M. Génard, F. Lescourret, L. Urban, M. Jannoyer.
  Modeling effects of weather and source–sink relationships on mango fruit growth, in: Tree Physiology, 2005, vol. 25, n^o 5, pp. 583-597. [ DOI : 10.1093/treephys/25.5.583 ]
  http://treephys.oxfordjournals.org/content/25/5/583.abstract
• 74M. Léchaudel, G. Vercambre, F. Lescourret, F. Normand, M. Génard.
  An analysis of elastic and plastic fruit growth of mango in response to various assimilate supplies, in: Tree Physiology, 2007, vol. 27, n^o 2, pp. 219-230. [ DOI : 10.1093/treephys/27.2.219 ]
  http://treephys.oxfordjournals.org/content/27/2/219.abstract
• 75R. Nozeran.
  Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, pp. 375-401.
• 76C. 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 10, pp. 751-760. [ DOI : 10.1071/FP08084 ]
  https://hal.inria.fr/hal-00831811
• 77C. Pradal, C. Fournier, P. Valduriez, S. Cohen-Boulakia.
  OpenAlea: Scientific Workflows Combining Data Analysis and Simulation, in: SSDBM 2015: 27th International Conference on Scientific and Statistical Database Management, San Diego, United States, June 2015. [ DOI : 10.1145/2791347.2791365 ]
  https://hal.archives-ouvertes.fr/hal-01166298
• 78C. Preuksakarn, F. Boudon, P. Ferraro, J.-B. Durand, E. Nikinmaa, C. Godin.
  Reconstructing Plant Architecture from 3D Laser scanner data, in: 6th International Workshop on Functional-Structural Plant Models, Davis, United States, September 2010, pp. 12–17.
  https://hal.archives-ouvertes.fr/hal-00490064
• 79Y. Refahi, E. Farcot, Y. Guédon, F. Besnard, T. Vernoux, C. Godin.
  A Combinatorial Model of Phyllotaxis Perturbations in Arabidopsis thaliana, in: 22nd Annual Symposium on Combinatorial Pattern Matching, Palermo, Italy, Palermo, Italy, Lecture Notes in Computer Science - LNCS, 2011, vol. 6661, pp. 323–335.
  https://hal.inria.fr/hal-00828852
• 80A. Runions, M. Fuhrer, B. Lane, P. Federl, A.-G. Rolland-Lagan, P. Prusinkiewicz.
  Modeling and Visualization of Leaf Venation Patterns, in: ACM Transaction on Graphics, July 2005, vol. 24, n^o 3, pp. 702–711.
  http://doi.acm.org/10.1145/1073204.1073251
• 81H. 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.