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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1M. Alber, C. Godin, P. K. Maini, R. M. Merks, E. Mjolsness.

    Introduction, in: Bulletin of Mathematical Biology, July 2019. [ DOI : 10.1007/s11538-019-00649-2 ]

    https://hal.archives-ouvertes.fr/hal-02424621
  • 2O. Ali, H. Oliveri, J. Traas, C. Godin.

    Simulating Turgor-Induced Stress Patterns in Multilayered Plant Tissues, in: Bulletin of Mathematical Biology, May 2019, pp. 1-23. [ DOI : 10.1007/s11538-019-00622-z ]

    https://hal.inria.fr/hal-02154814
  • 3R. Azaïs.

    Nearest embedded and embedding self-nested trees, in: Algorithms, August 2019, vol. 12, no 9, pp. 1-16, https://arxiv.org/abs/1709.02334. [ DOI : 10.3390/a12090180 ]

    https://hal.archives-ouvertes.fr/hal-01584078
  • 4R. Azaïs, G. Cerutti, D. Gemmerlé, F. Ingels.

    treex: a Python package for manipulating rooted trees, in: Journal of Open Source Software, June 2019, vol. 4, no 38, pp. 1-2. [ DOI : 10.21105/joss.01351 ]

    https://hal.archives-ouvertes.fr/hal-02164364
  • 5R. Azaïs, A. Genadot, B. Henry.

    Inference for conditioned Galton-Watson trees from their Harris path, in: ALEA : Latin American Journal of Probability and Mathematical Statistics, 2019, vol. 16, no 1, pp. 1-45, https://arxiv.org/abs/1609.01057. [ DOI : 10.30757/ALEA.v16-21 ]

    https://hal.archives-ouvertes.fr/hal-01360650
  • 6J. Bertheloot, F. Barbier, F. Boudon, M. Dolores Perez-Garcia, T. Peron, S. Citerne, E. Dun, C. Beveridge, C. Godin, S. Sakr.

    Sugar availability suppresses the auxin-induced strigolactone pathway to promote bud outgrowth, in: New Phytologist, September 2019, pp. 1-14. [ DOI : 10.1111/nph.16201 ]

    https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-02402977
  • 7I. Cheddadi, M. Génard, N. Bertin, C. Godin.

    Coupling water fluxes with cell wall mechanics in a multicellular model of plant development, in: PLoS Computational Biology, June 2019, vol. 15, no 6, e1007121. [ DOI : 10.1371/journal.pcbi.1007121 ]

    https://hal.archives-ouvertes.fr/hal-02196768
  • 8B. Leggio, J. Laussu, A. Carlier, C. Godin, P. Lemaire, E. Faure.

    MorphoNet: an interactive online morphological browser to explore complex multi-scale data, in: Nature Communications, June 2019, vol. 10, no 2812, pp. 1-8. [ DOI : 10.1038/s41467-019-10668-1 ]

    https://hal.archives-ouvertes.fr/hal-01938153
  • 9B. Leggio, A. Napoli, H. Nakazato, A. Messina.

    Bounds on mixed state entanglement, in: Entropy, 2020, vol. 22, no 1, 62 p. [ DOI : 10.3390/e22010062 ]

    https://hal.archives-ouvertes.fr/hal-02395355
  • 10A. Schneider, C. Godin, F. Boudon, S. Demotes-Mainard, S. Sakr, J. Bertheloot.

    Light Regulation of Axillary Bud Outgrowth Along Plant Axes: An Overview of the Roles of Sugars and Hormones, in: Frontiers in Plant Science, 2019, vol. 10, pp. 1-17, This review was conducted in the framework of a PhD thesis funded by the Environment and Agronomy department of the French National Institute for Agricultural Research (INRA). [ DOI : 10.3389/fpls.2019.01296 ]

    https://hal.archives-ouvertes.fr/hal-02327576

International Conferences with Proceedings

Conferences without Proceedings

  • 13G. Cerutti, C. Galvan-Ampudia, J. Legrand, C. Godin, T. Vernoux.

    Quantifying cell polarities in confocal images using 3D wall meshes, in: IAMPS 2019 - 7th International Workshop on Image Analysis Methods in the Plant Sciences, Bron, France, July 2019, pp. 1-2.

    https://hal.archives-ouvertes.fr/hal-02176398
  • 14F. Greciet, R. Azaïs, A. Gégout-Petit.

    Régression polynomiale par morceaux sous contrainte de régularité pour la propagation de fissures, in: JdS 2019 - 51èmes Journées de Statistique, Nancy, France, June 2019, pp. 1-5.

    https://hal.archives-ouvertes.fr/hal-02172747
  • 15F. Ingels, R. Azaïs.

    De l'importance de la fonction de poids dans le noyau des sous-arbres, in: JdS 2019 - 51èmes Journées de Statistique, Nancy, France, June 2019, pp. 1-6.

    https://hal.archives-ouvertes.fr/hal-02129866

Software

  • 16C. Pradal, C. Fournier, F. Boudon, P. Valduriez, E. Pacitti, Y. Y. Guédon, C. Godin.

    OpenAlea, April 2019, OpenAlea 2.0 adds to OpenAlea 1.0 a high-level formalism dedicated to the modeling of morphogenesis that makes it possible to use several modeling paradigms (Blackboard, L-systems, Agents, Branching processes, Cellular Automata) expressed with different languages (Python, L-Py, R, Visual Programming, ...) to analyse and simulate shapes and their development.

    https://hal.inria.fr/hal-02100181

Other Publications

References in notes
  • 24F. 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, no 1, pp. 1-16. [ DOI : 10.1371/journal.pcbi.1003950 ]

    https://hal.archives-ouvertes.fr/hal-01142486
  • 25R. 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, 2010, vol. 7, pp. 547–553.
  • 26L. Guignard, U.-M. Fiuza, B. Leggio, E. Faure, J. Laussu, L. Hufnagel, G. Malandain, C. Godin, P. Lemaire.

    Contact-dependent cell-cell communications drive morphological invariance during ascidian embryogenesis, November 2018, working paper or preprint. [ DOI : 10.1101/238741 ]

    https://hal.archives-ouvertes.fr/hal-01938126
  • 27Y. Long, I. Cheddadi, V. Mirabet, M. Dumond, C. Godin, A. Boudaoud.

    Cellular heterogeneity in pressure and growth emerges from tissue topology and geometry, 2018. [ DOI : 10.1101/334664 ]

    https://www.biorxiv.org/content/early/2018/05/30/334664
  • 28G. Michelin, Y. Refahi, R. Wightman, H. Jonsson, J. Traas, C. Godin, G. Malandain.

    Spatio-temporal registration of 3D microscopy image sequences of arabidopsis floral meristems, in: Proceedings - International Symposium on Biomedical Imaging, 2016, vol. 2016-June, pp. 1127–1130. [ DOI : 10.1109/ISBI.2016.7493464 ]
  • 29H. Oliveri, J. J. Traas, C. Godin, O. Ali.

    Regulation of plant cell wall stiffness by mechanical stress: a mesoscale physical model, in: Journal of Mathematical Biology, September 2018, pp. 1-29. [ DOI : 10.1007/s00285-018-1286-y ]

    https://hal.inria.fr/hal-01691110
  • 30R. S. Smith, S. Guyomarc’h, T. Mandel, D. Reinhardt, C. Kuhlemeier, P. Prusinkiewicz.

    A plausible model of phyllotaxis, in: Proceedings of the National Academy of Sciences, 2006, vol. 103, no 5, pp. 1301–1306. [ DOI : 10.1073/pnas.0510457103 ]

    http://www.pnas.org/content/103/5/1301
  • 31S. Stoma, M. Lucas, J. Chopard, M. Schaedel, J. Traas, C. Godin.

    Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development, in: PLOS Computational Biology, 10 2008, vol. 4, no 10, pp. 1-15.

    https://doi.org/10.1371/journal.pcbi.1000207


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