Bibliography

Major publications by the team in recent years

• 1R. 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, 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), November 2016.
  https://hal.inria.fr/hal-01396972
• 2O. Ali, V. Mirabet, C. Godin, J. Traas.
  Physical Models of Plant Development, in: Annual Review of Cell and Developmental Biology, October 2014, vol. 30, n^o 1, 8 p. [ DOI : 10.1146/annurev-cellbio-101512-122410 ]
  https://hal.inria.fr/hal-01090778
• 3O. 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
• 4R. 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
• 5F. 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
• 6F. 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
• 7F. 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
• 8A. 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
• 9F. 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
• 10R. 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
• 11P. Fernique, A. Dambreville, J.-B. Durand, C. Pradal, P.-E. Lauri, F. Normand, Y. Guédon.
  Characterization of mango tree patchiness using a tree-segmentation/clustering approach, in: 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Qingdao, China, IEEE, November 2016, pp. 68-74. [ DOI : 10.1109/FSPMA.2016.7818290 ]
  https://hal.inria.fr/hal-01398291
• 12C. Godin, E. Azpeitia, E. Farcot.
  An introduction to modelling flower primordium initiation, in: From Molecules to Living Organisms: An Interplay Between Biology and Physics, Lecture Notes of the Les Houches School of Physics, December 2015, vol. 102.
  https://hal.inria.fr/hal-01254880
• 13C. 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
• 14M. Labadie, B. Denoyes, Y. Guédon.
  Identification of flowering patterns specific to strawberry varieties in production condition using longitudinal data analysis, 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), 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
• 15M. 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
• 16G. 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
• 17B. Muller, Y. Guédon, B. Moreno-Ortega, G. Fort.
  Identifying Developmental Zones in Maize Lateral Root Cell Length Profiles using Multiple Change-Point Models, in: Frontiers in Plant Science, October 2017, vol. 8, pp. 1-19. [ DOI : 10.3389/fpls.2017.01750 ]
  https://hal.inria.fr/hal-01651169
• 18S. 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
• 19J. 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
• 20J. Peyhardi, Y. Caraglio, E. Costes, P.-E. Lauri, C. Trottier, Y. Guédon.
  Integrative models for joint analysis of shoot growth and branching patterns, in: New Phytologist, 2017, np p, UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières. [ DOI : 10.1111/nph.14742 ]
  https://hal.archives-ouvertes.fr/hal-01606754
• 21J. 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
• 22J. 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
• 23C. 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
• 24C. 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
• 25Y. 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
• 26M. 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 - CB, October 2014, vol. 24, n^o 19, pp. 1 - 8. [ DOI : 10.1016/j.cub.2014.08.036 ]
  https://hal.inria.fr/hal-01074821
• 27T. 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

• 28E. Azpeitia, S. Munoz, D. Gonzalez-Tokman, M. E. Martinez-Sanchez, N. Weinstein, A. Naldi, E. R. Alvarez-Buylla, D. A. Rosenblueth, L. Mendoza.
  Erratum: The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks (vol 7, 42023, 2017), in: Scientific Reports, 2017, vol. 7, 1 p. [ DOI : 10.1038/srep44964 ]
  https://hal.archives-ouvertes.fr/hal-01604935
• 29E. Azpeitia, S. Munoz, D. Gonzalez-Tokman, M. E. Martinez-Sanchez, N. Weinstein, A. Naldi, E. R. Alvarez-Buylla, D. A. Rosenblueth, L. Mendoza.
  The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks, in: Scientific Reports, 2017, vol. 7, pp. 1-14. [ DOI : 10.1038/srep42023 ]
  https://hal.archives-ouvertes.fr/hal-01606130
• 30M. Balduzzi, B. M. Binder, A. Bucksch, C. Chang, L. Hong, A. S. Iyer-Pascuzzi, C. Pradal, E. E. Sparks.
  Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology, in: Frontiers in Plant Science, February 2017, vol. 8, 117 p. [ DOI : 10.3389/fpls.2017.00117 ]
  https://hal.inria.fr/hal-01455754
• 31N. Brichet, C. Fournier, O. Turc, O. Strauss, S. Artzet, C. Pradal, C. Welcker, F. Tardieu, L. Cabrera-Bosquet.
  A robot-assisted imaging pipeline for tracking the growths of maize ear and silks in a high-throughput phenotyping platform, in: Plant Methods, November 2017, vol. 13, n^o 1, 12 p. [ DOI : 10.1186/s13007-017-0246-7 ]
  https://hal.inria.fr/hal-01631186
• 32A. B. Bucksch, A. Atta-Boateng, A. F. Azihou, D. P. Battogtokh, A. B. Baumgartner, B. N. Binder, S. A. Braybrook, C. Chang, V. C. Coneva, T. P. Dewitt, A. A. Fletcher, M. A. Gehan, D. H. H. Diaz-Martinez, L. Hong, A. S. Iyer-Pascuzzi, L. B. Klein, S. Leiboff, M. L. Li, J. P. Lynch, A. A. Maizel, J. H. Maloof, R. Cody Markelz, C. C. Martinez, L. A. Miller, W. L. Mio, W. P. Palubicki, H. H. Poorter, C. N. Pradal, C. N. Price, E. N. Puttonen, J. N. Reese, R. N. Rellán-Álvarez, E. E. Spalding, E. E. Sparks, C. N. Topp, J. H. Williams, D. H. Chitwood.
  Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences, in: Frontiers in Plant Science, June 2017, vol. 8, n^o 900, 16 p. [ DOI : 10.3389/fpls.2017.00900 ]
  https://hal.inria.fr/hal-01537909
• 33G. Cerutti, O. Ali, C. Godin.
  DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution, in: Frontiers in Plant Science, 2017, vol. 8, 353 p. [ DOI : 10.3389/fpls.2017.00353 ]
  https://hal.archives-ouvertes.fr/hal-01573521
• 34S. Cohen-Boulakia, K. Belhajjame, O. Collin, J. Chopard, C. Froidevaux, A. Gaignard, K. Hinsen, P. Larmande, Y. Le Bras, F. Lemoine, F. Mareuil, H. Ménager, C. Pradal, C. Blanchet.
  Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, in: Future Generation Computer Systems, 2017. [ DOI : 10.1016/j.future.2017.01.012 ]
  https://hal.archives-ouvertes.fr/hal-01516082
• 35J.-B. Durand, A. Allard, B. Guitton, E. Van de Weg, M. Bink, E. Costes.
  Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping, in: Frontiers in Plant Science, June 2017, vol. 8, pp. 858–872. [ DOI : 10.3389/fpls.2017.00858 ]
  https://hal.inria.fr/hal-01564977
• 36M. L. Garcia-Gomez, E. Azpeitia, E. R. Alvarez-Buylla.
  A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana, in: PLoS Computational Biology, 2017, vol. 13, n^o 4, 36 p. [ DOI : 10.1371/journal.pcbi.1005488 ]
  https://hal.archives-ouvertes.fr/hal-01607284
• 37S. Lacube, C. Fournier, C. Palaffre, E. J. Millet, F. Tardieu, B. Parent.
  Distinct controls of leaf widening and elongation by light and evaporative demand in maize, in: Plant, Cell and Environment, 2017, vol. 40, n^o 9, pp. 2017-2028. [ DOI : 10.1111/pce.13005 ]
  https://hal.archives-ouvertes.fr/hal-01548684
• 38S. Liu, F. Baret, M. Abichou, F. Boudon, S. Thomas, K. Zhao, C. Fournier, B. Andrieu, K. Irfan, M. Hemmerlé, B. De Solan.
  Estimating wheat green area index from ground-based LiDAR measurement using a 3D canopy structure model, in: Agricultural and Forest Meteorology, December 2017, vol. 247, pp. 12 - 20. [ DOI : 10.1016/j.agrformet.2017.07.007 ]
  https://hal.inria.fr/hal-01573077
• 39B. Moreno-Ortega, G. Fort, B. Muller, Y. Guédon.
  Identifying Developmental Zones in Maize Lateral Root Cell Length Profiles using Multiple Change-Point Models, in: Frontiers in Plant Science, October 2017, vol. 8, pp. 1-19. [ DOI : 10.3389/fpls.2017.01750 ]
  https://hal.inria.fr/hal-01651169
• 40A. Ndour, V. Vadez, C. Pradal, M. Lucas.
  Virtual Plants Need Water Too: Functional-Structural Root System Models in the Context of Drought Tolerance Breeding, in: Frontiers in Plant Science, September 2017, vol. 8, pp. 1-18. [ DOI : 10.3389/fpls.2017.01577 ]
  https://hal.inria.fr/hal-01596093
• 41J. Peyhardi, P. Fernique.
  Characterization of convolution splitting graphical models, in: Statistics and Probability Letters, February 2017, vol. 126. [ DOI : 10.1016/j.spl.2017.02.018 ]
  https://hal.inria.fr/hal-01286173
• 42C. 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, February 2017, vol. 67, pp. 341–353. [ DOI : 10.1016/j.future.2016.06.002 ]
  https://hal.inria.fr/hal-01336655

International Conferences with Proceedings

• 43J.-B. Durand, A. Allard, B. GUITTON, E. Van de Weg, M. C. A. M. Bink, E. Costes.
  Genetic determinism of flowering regularity over years in an apple multi-family population, in: International Symposium on Flowering, Fruit Set and Alternate Bearing, Palermo, Italy, June 2017.
  https://hal.inria.fr/hal-01565681

Conferences without Proceedings

• 44S. BERTRAND, G. Cerutti, L. Tougne.
  Bark Recognition to Improve Leaf-based Classification in Didactic Tree Species Identification, in: VISAPP 2017 - 12th International Conference on Computer Vision Theory and Applications, Porto, Portugal, February 2017.
  https://hal.archives-ouvertes.fr/hal-01486591
• 45S. BERTRAND, G. Cerutti, L. Tougne.
  Segmentation Algorithm on Smartphone Dual Camera: Application to Plant Organs in the Wild, in: 10th International Conference on Machine Vision, Vienna, Austria, November 2017.
  https://hal.archives-ouvertes.fr/hal-01675655

Other Publications

• 46P. Fernique, C. Pradal.
  AutoWIG: Automatic Generation of Python Bindings for C++ Libraries, June 2017, working paper or preprint.
  https://hal.inria.fr/hal-01531771

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