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, 2014, vol. 505, n^o 7483, pp. 417-421. [ DOI : 10.1038/nature12791 ]
  
  https://hal.inria.fr/hal-00926908
• 3F. 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
• 4F. 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
• 5F. 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
• 6R. 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
• 7C. 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
• 8J. 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
• 9C. 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
• 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, n^o 508.
  
  http://www-sop.inria.fr/virtualplants/Publications/2011/VBFMVLODLWGAPGCPKDEG

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 11S. Cohen-Boulakia.
  
  Data Integration in the Life Sciences: Scientific Workflows, Provenance, and Ranking, Université Paris-Sud, June 2015, Habilitation à diriger des recherches.
  
  https://hal.archives-ouvertes.fr/tel-01245229

Articles in International Peer-Reviewed Journals

• 12J.-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, n^o 1, pp. 45-54. [ DOI : 10.3934/dcdss.2015.8.45 ]
  
  https://hal.archives-ouvertes.fr/hal-00833340
• 13F. 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
• 14A. 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, n^o 1, 13 p. [ DOI : 10.1093/aob/mcu227 ]
  
  https://hal.inria.fr/hal-01100553
• 15J.-B. Durand, Y. Guédon.
  
  Localizing the latent structure canonical uncertainty: entropy profiles for hidden Markov models, in: Statistics and Computing, 2016, vol. 26, n^o 1, pp. 549-567. [ DOI : 10.1007/s11222-014-9494-9 ]
  
  https://hal.inria.fr/hal-01090836
• 16M. Grand-Brochier, A. Vacavant, G. Cerutti, C. Kurtz, J. Weber, L. Tougne.
  
  Tree leaves extraction in natural images: Comparative study of pre-processing tools and segmentation methods, in: IEEE Transactions on Image Processing, 2015, vol. 24, n^o 5, pp. 1549-1560. [ DOI : 10.1109/TIP.2015.2400214 ]
  
  https://hal.archives-ouvertes.fr/hal-01176699
• 17Y. Guédon.
  
  Segmentation uncertainty in multiple change-point models, in: Statistics and Computing, 2015, vol. 25, n^o 2, pp. 303 - 320. [ DOI : 10.1007/s11222-013-9433-1 ]
  
  https://hal.inria.fr/hal-01117013
• 18J.-M. Legave, Y. Guédon, G. Malagi, A. El Yaacoubi, M. Bonhomme.
  
  Differentiated Responses of Apple Tree Floral Phenology to Global Warming in Contrasting Climatic Regions, in: Frontiers in Plant Science, December 2015, vol. 6, n^o 1054, 13 p. [ DOI : 10.3389/fpls.2015.01054 ]
  
  https://hal.inria.fr/hal-01244070
• 19G. 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
• 20E. Marza, S. Taouji, K. Barroso, A.-A. Raymond, L. Guignard, M. Bonneu, N. Pallares-Lupon, J.-W. Dupuy, M. E. Fernandez-Zapico, J. Rosenbaum, F. Palladino, D. Dupuy, E. Chevet.
  
  Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription, in: EMBO Reports, 2015, vol. 16, n^o 3, pp. 332–340. [ DOI : 10.15252/embr.201439123 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163728
• 21C. Negrón, L. Contador, B. D. Lampinen, S. G. Metcalf, Y. Guédon, E. Costes, T. M. DeJong.
  
  How different pruning severities alter shoot structure: a modelling approach in young 'Nonpareil' almond trees, in: Functional Plant Biology, 2015, vol. 42, n^o 3, pp. 325–335. [ DOI : 10.1071/FP14025 ]
  
  https://hal.inria.fr/hal-01120092
• 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
• 23A. Ravasio, I. CHEDDADI, T. Chen, T. Pereira, H. T. Ong, C. Bertocchi, A. Brugues, A. Jacinto, A. J. Kabla, Y. Toyama, X. Trepat, N. Gov, L. Neves de Almeida, B. Ladoux.
  
  Gap geometry dictates epithelial closure efficiency, in: Nature Communications, July 2015, vol. 6. [ DOI : 10.1038/ncomms8683 ]
  
  https://hal.archives-ouvertes.fr/hal-01245750
• 24A. Rodriguez, L. Torres, U. Juarez, D. Sosa, E. Azpeitia, B. Garcia-de Teresa, E. Cortes, R. Ortiz, A. M. Salazar, P. Ostrosky-Wegman, L. Mendoza, S. Frias.
  
  Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process, in: Theoretical Biology and Medical Modelling, 2015, vol. 12, n^o 1, 19 p. [ DOI : 10.1186/s12976-015-0011-4 ]
  
  https://hal.inria.fr/hal-01217314
• 25J. Starlinger, S. Cohen-Boulakia, S. Khanna, S. Davidson, U. Leser.
  
  Effective and Efficient Similarity Search in Scientific Workflow Repositories, in: Future Generation Computer Systems, September 2015, 79 p. [ DOI : 10.1016/j.future.2015.06.012 ]
  
  https://hal.archives-ouvertes.fr/hal-01170597
• 26O. 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

Invited Conferences

• 27C. Pradal.
  
  Multiscale topological and geometrical representation of plant architecture, in: NimBIOS: Morphological Plant Models, Knoxville, United States, Alexander Bucksch and Dan Chitwood, September 2015.
  
  https://hal.inria.fr/hal-01245386

International Conferences with Proceedings

• 28G. 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
• 29Y. Guédon.
  
  Slope heuristics for multiple change-point models, in: 30th International Workshop on Statistical Modelling (IWSM 2015), Linz, Austria, H. Friedl, H. Wagner (editors), Statistical Modelling Society, July 2015.
  
  https://hal.inria.fr/hal-01240037
• 30G. Michelin, L. Guignard, U.-M. Fiuza, P. Lemaire, C. Godin, G. Malandain.
  
  Cell Pairings for Ascidian Embryo Registration, in: ISBI - International Symposium on Biomedical Imaging, New York, United States, April 2015. [ DOI : 10.1109/ISBI.2015.7163872 ]
  
  https://hal.inria.fr/hal-01113166
• 31G. Michelin, Y. Refahi, R. Wightman, H. Jönsson, J. J. Traas, C. Godin, G. Malandain.
  
  Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis floral meristems, in: ISBI - International Symposium on Biomedical Imaging, Prague, Czech Republic, April 2016. [ DOI : 10.1109/ISBI.2015.7163872 ]
  
  https://hal.inria.fr/hal-01251151
• 32J. Peyhardi.
  
  New qualitative choice models incorporating individual and choice characteristics, in: 30th International Workshop on Statistical Modelling (IWSM 2015), Linz, Austria, H. Friedl, H. Wagner (editors), Statistical Modelling Society, July 2015, vol. 1, pp. 319-323.
  
  https://hal.inria.fr/hal-01242841
• 33J. Peyhardi.
  
  Nouveaux modèles de choix qualitatifs prenant en compte des caractéristiques individuelles et des caractéristiques de choix, in: 47èmes Journées de Statistique, Lille, France, Société Française de Statistique, June 2015.
  
  https://hal.inria.fr/hal-01242827
• 34C. Pradal, C. Fournier, P. Valduriez, S. Cohen-Boulakia.
  
  OpenAlea: Scientific Workflows Combining Data Analysis and Simulation, in: SSDBM 2015: 27th International Conference on Scientific and Statistical Database Management, San Diego, United States, June 2015. [ DOI : 10.1145/2791347.2791365 ]
  
  https://hal.archives-ouvertes.fr/hal-01166298

National Conferences with Proceedings

• 35P. Fernique, J.-B. Durand, Y. Guédon.
  
  Détection de motifs disruptifs au sein de plantes : une approche de quotientement/classification d'arborescences, in: 47èmes Journées de Statistique, Lille, France, Société Française de Statistique, June 2015.
  
  https://hal.inria.fr/hal-01240305
• 36Y. Guédon.
  
  Heuristique de pente pour les modèles de détection de ruptures multiples, in: 47èmes Journées de Statistique, Lille, France, Société Française de Statistique, June 2015.
  
  https://hal.inria.fr/hal-01240298

Conferences without Proceedings

• 37F. Boudon, A. Jestin, A.-S. Briand, P. Fernique, P.-E. Lauri, A. Dambreville, Y. Guédon, I. Grechi, F. Normand.
  
  The Role of Structural and Temporal Factors in the Architectural Development of the Mango Tree: Evidences from Simulation, in: International Symposium on Modelling in Fruit Research and Orchard Management, Montpellier, France, June 2015.
  
  https://hal.inria.fr/hal-01237402
• 38I. CHEDDADI, C. Godin, F. Boudon, V. Baldazzi, M. M. Génard, N. Bertin.
  
  Toward a mechanical model of 3D fruit development, in: International Symposium on Modelling in Fruit Research and Orchard Management, Montpellier, France, June 2015.
  
  https://hal.inria.fr/hal-01237387
• 39G. Cerutti, S. Ribes, C. Godin, C. Galvan Ampudia, T. Vernoux.
  
  3D Tessellation of Plant Tissue A dual optimization approach to cell-level meristem reconstruction from microscopy images, in: International Conference on 3D Vision, Lyon, France, October 2015. [ DOI : 10.1109/3DV.2015.57 ]
  
  https://hal.archives-ouvertes.fr/hal-01246580
• 40I. Grechi, F. Boudon, M. Léchaudel, F. Normand.
  
  A crop simulation model to predict fruit yield and quality on mango tree: overview, progresses and perspectives, in: International Mango Symposium, Darwin, Australia, September 2015.
  
  https://hal.inria.fr/hal-01237410
• 41S. Passot, F. Gnacko, J. Atkinson, B. Atkinson, M. Lucas, S. Guyomarc'H, F. Boudon, M. Couderc, L. Zekraoui, C. Sturrock, N. Kane, C. T. Hash, P. Gantet, M. J. Bennett, D. Wells, Y. Y. Vigouroux, Y. Guédon, L. Laplaze.
  
  Exploring root development and architecture in one of the most heat and drought tolerant cereals, pearl millet, in: Plant Phenotyping Symposium, Barcelone, Spain, November 2015.
  
  https://hal.inria.fr/hal-01237385
• 42F. Reyes, B. Pallas, C. Pradal, E. Costes.
  
  A Multi-Scale Model to explore Carbon Allocation in Plants, in: International Symposium on Modelling in Fruit Research and Orchard Management, Montpellier, France, June 2015.
  
  https://hal.inria.fr/hal-01245366

Scientific Books (or Scientific Book chapters)

• 43C. 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

Internal Reports

• 44C. Robert, C. C. Fournier, C. Bedos, D. Gouache, B. B. Perriot.
  
  ECHAP « L’architecture des couverts végétaux : un levier pour réduire l’utilisation des fongicides ? », INRA, January 2015, n^o 1879/10, 43 p.
  
  https://hal.inria.fr/hal-01253658

Scientific Popularization

• 45C. Godin.
  
  L'importance capitale du travail de fourmis des chercheurs, in: 1024 – Bulletin de la société informatique de France, January 2016, n^o 5, 10 p.
  
  https://hal.inria.fr/hal-01256863

Other Publications

• 46R. Azaïs, J.-B. Durand, C. Godin.
  
  Lossy compression of unordered rooted trees, December 2015, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01236088
• 47A. Barbieri, J. Peyhardi, C. Lavergne, T. Conroy, S. Gourgou, C. Mollevi.
  
  Selection of item response theory models for the longitudinal analysis of health-related quality of life in cancer clinical trials, December 2015, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01246368
• 48B. Brancotte, B. Rance, A. Denise, S. Cohen-Boulakia.
  
  Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-Bio, July 2015, JOBIM (Journées Ouvertes Biologie Informatique Mathématiques), Poster.
  
  https://hal.archives-ouvertes.fr/hal-01167840
• 49C. Fournier, S. Artzet, J. Chopard, M. Mielewczik, N. Brichet, L. Cabrera, X. Sirault, S. Cohen-Boulakia, C. Pradal.
  
  Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data, September 2015, IAMPS 2015 (International Workshop on Image Analysis Methods for the Plant Sciences), Poster.
  
  https://hal.inria.fr/hal-01253627
• 50I. Grechi, F. Boudon, M. Léchaudel, T. Nordey, M. Génard, F. Normand.
  
  Modelling fruit yield and quality on the Mango tree: Recent progresses and future steps, June 2015, International Symposium on Modelling in Fruit Research and Orchard Management, Poster.
  
  http://hal.univ-reunion.fr/hal-01193184
• 51J. 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

• 52A. Arber.
  
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• 53L. Band, J. Fozard, C. Godin, O. Jensen, T. Pridmore, M. Bennett, J. King.
  
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• 55F. Boudon, C. Preuksakarn, P. Ferraro, J. Diener, P. Nacry, E. Nikinmaa, C. Godin.
  
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• 68M. Léchaudel, M. Génard, F. Lescourret, L. Urban, M. Jannoyer.
  
  Modeling effects of weather and source–sink relationships on mango fruit growth, in: Tree Physiology, 2005, vol. 25, n^o 5, pp. 583-597. [ DOI : 10.1093/treephys/25.5.583 ]
  
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• 70J. 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
• 71R. Nozeran.
  
  Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, pp. 375-401.
• 72J. 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
• 73C. Preuksakarn, F. Boudon, P. Ferraro, J.-B. Durand, E. Nikinmaa, C. Godin.
  
  Reconstructing Plant Architecture from 3D Laser scanner data, in: 6th International Workshop on Functional-Structural Plant Models, Davis, United States, September 2010, pp. 12–17.
  
  https://hal.archives-ouvertes.fr/hal-00490064
• 74Y. Refahi, E. Farcot, Y. Guédon, F. Besnard, T. Vernoux, C. Godin.
  
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