Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

• 1A. Armezzani, U. Abad, O. Ali, A. Andres Robin, L. Vachez, A. Larrieu, E. Mellerowicz, L. Taconnat, V. Battu, T. Stanislas, M. Liu, T. Vernoux, J. Traas, M. Sassi.
  
  Transcriptional induction of cell wall remodelling genes is coupled to microtubule-driven growth isotropy at the shoot apex in Arabidopsis, in: Development (Cambridge, England), June 2018, vol. 145, n^o 11. [ DOI : 10.1242/dev.162255 ]
  
  https://hal.archives-ouvertes.fr/hal-01894645
• 2R. Azaïs, A. Genadot.
  
  Estimation of the average number of continuous crossings for non-stationary non-diffusion processes, in: Journal of Statistical Planning and Inference, 2018, https://arxiv.org/abs/1703.10192.
  
  https://hal.archives-ouvertes.fr/hal-01499914
• 3S. Bertrand, R. Ben Ameur, G. Cerutti, D. Coquin, L. Valet, L. Tougne.
  
  Bark and Leaf Fusion Systems to Improve Automatic Tree Species Recognition, in: Ecological Informatics, June 2018. [ DOI : 10.1016/j.ecoinf.2018.05.007 ]
  
  https://hal.archives-ouvertes.fr/hal-01811039
• 4K. Biasuz, B. Leggio, E. Faure, P. Lemaire.
  
  The “computable egg”: Myth or useful concept?, in: Current Opinion in Systems Biology, October 2018, vol. 11, pp. 91-97. [ DOI : 10.1016/j.coisb.2018.09.003 ]
  
  https://hal.archives-ouvertes.fr/hal-01919148
• 5H. 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
• 6S. Verger, G. Cerutti, O. Hamant.
  
  An Image Analysis Pipeline to Quantify Emerging Cracks in Materials or Adhesion Defects in Living Tissues, in: Bio-protocol , 2018, vol. 8, n^o 19.
  
  https://hal.inria.fr/hal-01940178

International Conferences with Proceedings

• 7R. Azaïs, J.-B. Durand, C. Godin.
  
  Approximation of trees by self-nested trees, in: ALENEX 2019 - Algorithm Engineering and Experiments, San Diego, United States, January 2019, pp. 1-24, https://arxiv.org/abs/1810.10860. [ DOI : 10.10860 ]
  
  https://hal.archives-ouvertes.fr/hal-01294013

Scientific Books (or Scientific Book chapters)

• 8R. Azaïs, A. Genadot.
  
  Level Crossings and Absorption of an Insurance Model, in: Statistical Inference for Piecewise-deterministic Markov Processes, R. Azaïs, F. Bouguet (editors), Wiley, August 2018, pp. 65-105. [ DOI : 10.1002/9781119507338.ch3 ]
  
  https://hal.archives-ouvertes.fr/hal-01862266
• 9R. Azaïs, A. Gégout-Petit, F. Greciet.
  
  Rupture Detection in Fatigue Crack Propagation, in: Statistical Inference for Piecewise-deterministic Markov Processes, Wiley, August 2018, pp. 173-207. [ DOI : 10.1002/9781119507338.ch6 ]
  
  https://hal.archives-ouvertes.fr/hal-01862267

Books or Proceedings Editing

• 10R. Azaïs, F. Bouguet (editors)
  
  Statistical Inference for Piecewise-deterministic Markov Processes, Wiley, August 2018, pp. i-xxxiv 1-260. [ DOI : 10.1002/9781119507338 ]
  
  https://hal.archives-ouvertes.fr/hal-01862248

Scientific Popularization

• 11F. Greciet, R. Azaïs, A. Gégout-Petit.
  
  Detection and modeling of the propagation regimes in fatigue crack propagation, in: ENBIS 2018 - 18th Annual Conference of the European Network for Business and Industrial Statistics, Nancy, France, September 2018.
  
  https://hal.inria.fr/hal-01942243

Other Publications

• 12R. Azaïs, A. Genadot, B. Henry.
  
  Inference for conditioned Galton-Watson trees from their Harris path, November 2018, https://arxiv.org/abs/1609.01057 - working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01360650
• 13S. Bertrand, G. Cerutti, L. Tougne.
  
  Visualization of Leaf Botanical Features Extracted from AlexNet Convolutional Layers, January 2018, IAMPS - International Workshop on Image Analysis Methods for the Plant Sciences 2018, Poster.
  
  https://hal.archives-ouvertes.fr/hal-01691924
• 14G. Cerutti, C. Galvan-Ampudia, J. Legrand, T. Vernoux, C. Godin.
  
  A parametric active 4D model for the automatic construction of developmental atlases from confocal images of shoot apical meristems, January 2018, IAMPS - International Workshop on Image Analysis Methods for the Plant Sciences 2018, Poster.
  
  https://hal.inria.fr/hal-01692584
• 15C. Galvan-Ampudia, G. Cerutti, J. Legrand, R. Azaïs, G. Brunoud, S. Moussu, C. Wenzl, J. U. Lohmann, C. Godin, T. Vernoux.
  
  From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex, November 2018, working paper or preprint. [ DOI : 10.1101/469718 ]
  
  https://hal.inria.fr/hal-01937928
• 16L. 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
• 17B. Leggio, J. Laussu, A. Carlier, C. Godin, P. Lemaire, E. Faure.
  
  MorphoNet: An interactive online morphological browser to explore complex multi-scale data, November 2018, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01938153
• 18H. Oliveri, F. Zhao, O. Ali, J. Traas, C. Godin.
  
  Stress-based regulation of multicellular plant growth: a finite element modeling approach applied to planar leaf morphogenesis, October 2018, ICSB 2018 - 19th International Conference on Systems Biology, Poster.
  
  https://hal.inria.fr/hal-01897027

References in notes

• 19K. Bharath, P. Kambadur, D. Dey, R. Arvin, V. Baladandayuthapani.
  
  Statistical tests for large tree-structured data, in: Journal of the American Statistical Association, 2016.
• 20F. 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
• 21Y. 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
• 22Y. 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, jul 2016, vol. 5, e14093 p.
  
  https://doi.org/10.7554/eLife.14093
• 23R. 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, n^o 5, pp. 1301–1306. [ DOI : 10.1073/pnas.0510457103 ]
  
  http://www.pnas.org/content/103/5/1301
• 24A. J. Smola, S. Vishwanathan.
  
  Fast kernels for string and tree matching, in: Advances in neural information processing systems, 2003, pp. 585–592.
• 25S. 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, n^o 10, pp. 1-15.
  
  https://doi.org/10.1371/journal.pcbi.1000207
• 26S. Verger, Y. Long, A. Boudaoud, O. Hamant.
  
  A tension-adhesion feedback loop in plant epidermis, in: eLife, apr 2018, vol. 7, e34460 p.
  
  https://doi.org/10.7554/eLife.34460