Project-Team Virtual plants
Members
Overall Objectives
Research Program
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
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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. 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, no 7483, pp. 417-421. [ DOI : 10.1038/nature12791 ]
    https://hal.inria.fr/hal-00926908
  • 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, no 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, no 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
  • 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, no 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, no 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, no 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, no 508.
    http://www-sop.inria.fr/virtualplants/Publications/2011/VBFMVLODLWGAPGCPKDEG
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 12O. Ali, V. Mirabet, C. Godin, J. Traas.
    Physical Models of Plant Development, in: Annual Review of Cell and Developmental Biology, October 2014, vol. 30, no 1, 8 p. [ DOI : 10.1146/annurev-cellbio-101512-122410 ]
    https://hal.inria.fr/hal-01090778
  • 13R. Barillot, J. Escobar-Gutierrez, C. Fournier, P. Huynh, D. Combes.
    Assessing the effects of architectural variations on light partitioning within virtual wheat – pea mixtures, in: Annals of Botany, June 2014, vol. 114, no 4, 13 p. [ DOI : 10.1093/aob/mcu099 ]
    https://hal.inria.fr/hal-01095288
  • 14J.-P. Bernard, E. Frenod, A. Rousseau.
    Paralic confinement computations in coastal environment with interlocked areas, in: Discrete and Continuous Dynamical Systems - Series S, February 2015, vol. 8, no 1, pp. 45-54. [ DOI : 10.3934/dcdss.2015.8.45 ]
    https://hal.archives-ouvertes.fr/hal-00833340
  • 15F. 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, no 7483, pp. 417-421. [ DOI : 10.1038/nature12791 ]
    https://hal.inria.fr/hal-00926908
  • 16F. 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
  • 17R. Choquet, A. Béchet, Y. Guédon.
    Applications of hidden hybrid Markov/semi-Markov models: from stopover duration to breeding success dynamics, in: Ecology and Evolution, 2014, vol. 4, no 6, pp. 817 - 826. [ DOI : 10.1002/ece3.962 ]
    https://hal.inria.fr/hal-01084498
  • 18A. Dambreville, P.-É. Lauri, F. Normand, Y. Guédon.
    Analysing growth and development of plants jointly using developmental growth stages, in: Annals of Botany, 2015, vol. 115, no 1, 13 p. [ DOI : 10.1093/aob/mcu227 ]
    https://hal.inria.fr/hal-01100553
  • 19J.-B. Durand, Y. Guédon.
    Localizing the latent structure canonical uncertainty: entropy profiles for hidden Markov models, in: Statistics and Computing, 2014, 19 p, 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
  • 20J. Dutra Schmitz, Y. Guédon, F. G. Herter, G. B. Leite, P.-E. Lauri.
    Exploring bud dormancy completion with a combined architectural and phenological analysis: the case of the apple tree in contrasting winter temperature conditions, in: American Journal of Botany, 2014, vol. 101, pp. 398 - 407. [ DOI : 10.3732/ajb.1300335 ]
    https://hal.inria.fr/hal-01089580
  • 21G. Garin, C. Fournier, B. Andrieu, V. Houlès, C. Robert, C. Pradal.
    A modelling framework to simulate foliar fungal epidemics using functional–structural plant models, in: Annals of Botany, 2014, mcu101. [ DOI : 10.1093/aob/mcu101 ]
    https://hal.inria.fr/hal-01025689
  • 22S. Kenouche, M. Perrier, N. Bertin, J. Larionova, A. Ayadi, M. Zanca, J. Long, N. Bezzi, P. C. Stein, Y. Guari, M. Cieslak, C. Godin, C. Goze-Bac.
    In vivo quantitative NMR imaging of fruit tissues during growth using Spoiled Gradient Echo sequence, in: Magnetic Resonance Imaging, September 2014, no 32, pp. 1418-1427. [ DOI : 10.1016/j.mri.2014.08.005 ]
    https://hal.archives-ouvertes.fr/hal-01065440
  • 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 U S A, 2014, vol. 111, no 2, pp. 857-862. [ DOI : 10.1073/pnas.1221766111 ]
    https://hal.inria.fr/hal-00941028
  • 24C. Negrón, L. Contador, B. D. Lampinen, S. G. Metcalf, Y. Guédon, E. Costes, T. M. DeJong.
    Differences in proleptic and epicormic shoot structures in relation to water deficit and growth rate in almond trees (Prunus dulcis), in: Annals of Botany, 2014, vol. 113, no 3, pp. 545–554. [ DOI : 10.1093/aob/mct282 ]
    https://hal.inria.fr/hal-01084462
  • 25M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas.
    An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis, in: Current Biology, October 2014, vol. 24, no 19, pp. 1 - 8. [ DOI : 10.1016/j.cub.2014.08.036 ]
    https://hal.inria.fr/hal-01074821
  • 26R. Sievänen, C. Godin, T. De Jong, E. Nikinmaa.
    Functional – structural plant models: a growing paradigm for plant studies, in: Annals of Botany, 2014, pp. 599-603. [ DOI : 10.1093/aob/mcu175 ]
    https://hal.inria.fr/hal-01075790
  • 27J. Starlinger, B. Brancotte, S. Cohen-Boulakia, U. Leser.
    Similarity Search for Scientific Workflows, in: Proceedings of the VLDB Endowment (PVLDB), September 2014, 12 p.
    https://hal.inria.fr/hal-01066046
  • 28O. Taugourdeau, Y. Caraglio, S. Sabatier, Y. Guédon.
    Characterizing the respective importance of ontogeny and environmental constraints in forest tree development using growth phase duration distributions, in: Ecological Modelling, 2015, vol. 300, pp. 61 - 72. [ DOI : 10.1016/j.ecolmodel.2014.12.022 ]
    https://hal.inria.fr/hal-01110350
  • 29J. Zhu, B. Andrieu, J. Vos, W. van der Werf, C. Fournier, J. B. Evers.
    Towards modelling the flexible timing of shoot development: simulation of maize organogenesis based on coordination within and between phytomers, in: Annals of Botany, April 2014, vol. 114, no 4, 10 p. [ DOI : 10.1093/aob/mcu051 ]
    https://hal.inria.fr/hal-01096700

International Conferences with Proceedings

  • 30J.-P. Bernard, B. Gilles, C. Godin.
    Combining Finite Element Method and L-Systems Using Natural Information Flow Propagation to Simulate Growing Dynamical Systems, in: Theory and Practice of Natural Computing, Granada, Spain, C. M.-V. Adrian-Horia Dediu (editor), Springer, December 2014, vol. 8890, pp. 218 - 230. [ DOI : 10.1007/978-3-319-13749-0_19 ]
    https://hal.inria.fr/hal-01096602
  • 31G. 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
  • 32J.-B. Durand, Y. Guédon.
    Quantifying and localizing state uncertainty in hidden Markov models using conditional entropy profiles, in: COMPSTAT 2014 - 21st International Conference on Computational Statistics, Genève, Switzerland, M. Gilli, G. González-Rodríguez, A. Nieto-Reyes (editors), Université de Genève, August 2014, pp. 213-221, ISBN 978-2-8399-1347-8. Please check publisher.
    https://hal.inria.fr/hal-01058278
  • 33P. Fernique, J.-B. Durand, Y. Guédon.
    Estimation of Discrete Partially Directed Acyclic Graphical Models in Multitype Branching Processes, in: COMPSTAT 2014, 21st International Conference on Computational Statistics, Geneva, Switzerland, The International Association for Statistical Computing (IASC), August 2014.
    https://hal.inria.fr/hal-01084524
  • 34P. Fernique, J.-B. Durand, Y. Guédon.
    Learning Discrete Partially Directed Acyclic Graphical Models in Multitype Branching Processes, in: COMPSTAT 2014 - 21st International Conference on Computational Statistics, Genève, Switzerland, M. Gilli, G. González-Rodríguez, A. Nieto-Reyes (editors), Université de Genève, August 2014, pp. 579-586, ISBN 978-2-8399-1347-8.
    https://hal.inria.fr/hal-01058284
  • 35L. 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.
    https://hal.inria.fr/hal-00919142
  • 36G. 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.
    https://hal.inria.fr/hal-00915000
  • 37J. Peyhardi, C. Trottier, Y. Guédon.
    Modèles de références de régression multinomiale. Propriétés et applications en classification supervisée, in: 46 ème journée de Statistique, Rennes, France, June 2014.
    https://hal.inria.fr/hal-01101058
  • 38J. Peyhardi, C. Trottier, Y. Guédon.
    Partitioned conditional generalized linear models for categorical data, in: 29th International Workshop on Statistical Modelling (IWSM 2014), Göttingen, Germany, Statistical Modelling Society, July 2014, vol. 1.
    https://hal.inria.fr/hal-01084505
  • 39J. Starlinger, S. Cohen-Boulakia, S. Khanna, S. Davidson, U. Leser.
    Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity, in: IEEE e-Science conference, Guarujá, Brazil, October 2014.
    https://hal.inria.fr/hal-01066076

National Conferences with Proceedings

  • 40J.-B. Durand, Y. Guédon.
    Quantification de l'incertitude sur la structure latente dans des modèles de Markov cachés, in: 46èmes Journées de Statistique, Rennes, France, June 2014.
    https://hal.inria.fr/hal-01058317
  • 41P. Fernique, J.-B. Durand, Y. Guédon.
    Modèles graphiques paramétriques pour la modélisation des lois de génération dans des processus de branchement multitypes, in: 46èmes Journées de Statistique, Rennes, France, June 2014.
    https://hal.inria.fr/hal-01058313

Scientific Books (or Scientific Book chapters)

  • 42J. Guénard, G. Morin, F. Boudon, V. Charvillat.
    Realistic Plant Modeling from Images Based on Analysis-by-Synthesis, in: Mathematical Methods for Curves and Surfaces, M. Floater, T. Lyche, M.-L. Mazure, K. Mørken, L. Schumaker (editors), Lecture Notes in Computer Science, Springer-Verlag, 2014, vol. 8177, pp. 213-229. [ DOI : 10.1007/978-3-642-54382-1_12 ]
    https://hal.inria.fr/hal-01089744

Other Publications

  • 43B. Moreno-Ortega, E. Chandezon, G. Fort, Y. Guédon, B. Muller.
    Why is lateral root growth so variable? A framework to analyze growth variability among lateral roots and the possible roles of auxin and carbon, September 2014, 7th International Symposium on Root Development.
    https://hal.inria.fr/hal-01090030
  • 44J. Peyhardi, C. Trottier, Y. Guédon.
    A new specification of generalized linear models for categorical data, April 2014, 31 pages, 13 figures.
    https://hal.inria.fr/hal-00985595
  • 45J. Peyhardi, C. Trottier, Y. Guédon.
    Partitioned conditional generalized linear models for categorical data, January 2015, 25 pages, 13 figures.
    https://hal.inria.fr/hal-01101036
References in notes
  • 46A. Arber.
    Natural philosophy of plant form, University Press, Cambridge, 1950.
  • 47L. 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
  • 48D. 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.
  • 49M. 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
  • 50L. 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.
  • 51C. 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
  • 52C. 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.
  • 53Y. 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
  • 54F. Hallé, R. A. A. Oldeman, P. B. Tomlinson.
    Tropical trees and forests. An architectural analysis, Springer-Verlag, New-York, 1978.
  • 55J. L. Harper, B. R. Rosen, J. White.
    The growth and form of modular organisms, The Royal Society, London, UK, 1986.
  • 56C. 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, no 12, pp. 4318–4333.
  • 57M. 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, no 13, pp. 5229-34. [ DOI : 10.1073/pnas.1210807110 ]
    http://hal.inria.fr/cea-00848569
  • 58J. 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
  • 59R. Nozeran.
    Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, pp. 375-401.
  • 60Y. 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
  • 61H. 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.

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