Team, Visitors, External Collaborators
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

[1]
M. 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
[2]
O. 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
[3]
R. 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
[4]
R. 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
[5]
R. 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
[6]
J. 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
[7]
I. 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
[8]
B. 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
[9]
B. 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
[10]
A. 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

[11]
R. Azaïs, J.-B. Durand, C. Godin.
Approximation of trees by self-nested trees, in: ALENEX 2019 - Algorithm Engineering and Experiments, San Diego, United States, SIAM, 2019, pp. 39-53, https://arxiv.org/abs/1810.10860. [ DOI : 10.1137/1.9781611975499.4 ]
https://hal.archives-ouvertes.fr/hal-01294013
[12]
B. Henry, S. R. Chowdhury, A. Lahmadi, R. Azaïs, J. François, R. Boutaba.
SPONGE: Software-Defined Traffic Engineering to Absorb Influx of Network Traffic, in: 44th IEEE Conference on Local Computer Networks (LCN), Osnabrück, Germany, October 2019.
https://hal.archives-ouvertes.fr/hal-02403616

Conferences without Proceedings

[13]
G. 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
[14]
F. 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
[15]
F. 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

[16]
C. 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

[17]
R. Azaïs, F. Ingels.
The Weight Function in the Subtree Kernel is Decisive, November 2019, https://arxiv.org/abs/1904.05421v2 - 35 pages.
https://hal.archives-ouvertes.fr/hal-02097593
[18]
A. Chaudhury, C. Godin.
Geometry Reconstruction of Plants, December 2019, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02414486
[19]
C. Galvan-Ampudia, G. Cerutti, J. Legrand, G. Brunoud, R. Martin Arevalillo, R. Azaïs, V. Bayle, S. Moussu, C. Wenzl, Y. Jaillais, J. U. Lohmann, C. Godin, T. Vernoux.
Temporal integration of auxin information for the regulation of patterning, November 2019, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02368529
[20]
C. Godin, C. Golé, S. Douady.
Phyllotaxis: a remarkable example of developmental canalization in plants, November 2019, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02370969
[21]
B. Leggio, R. Azaïs.
Estimation of Piecewise-Deterministic Trajectories in a Quantum Optics Scenario, December 2019, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02389225
[22]
B. Leggio, J. Laussu, E. Faure, P. Lemaire, C. Godin.
Multiscale mechanical model for cell division orientation in developing biological systems, November 2019, working paper or preprint. [ DOI : 10.1101/785337 ]
https://hal.archives-ouvertes.fr/hal-02367600
[23]
F. Zhao, F. Du, H. Oliveri, L. Zhou, O. Ali, W. Chen, S. Feng, Q. Wang, S. , M. Long, R. Schneider, A. Sampathkumar, C. Godin, J. Traas, Y. Jiao.
A microtubule-mediated mechanical feedback controls leaf blade development in three dimensions, November 2019, working paper or preprint. [ DOI : 10.1101/604710 ]
https://hal.archives-ouvertes.fr/hal-02370615
References in notes
[24]
F. 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
[25]
R. 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.
[26]
L. 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
[27]
Y. 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
[28]
G. 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 ]
[29]
H. 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
[30]
R. 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
[31]
S. 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