Paul-Henry Cournède

209
Documents

Présentation

2009 HDR Montpellier University

2001 PhD in Applied Mathematics, Ecole Centrale Paris

1997 Ingénieur Ecole Centrale Paris

1997 Certificate of Advanced Studies in Mathematics, Part III, Cambridge University

1992-1994 BJ

Publications

Publications

Beyond handcrafted radiomics in oncologic imaging: Innovations in deep, explainable, multi-site and multi-omics radiomics approaches

Jules Dupont , Fiona Frau , Victor Robic , Marina Manso Jimeno , Letuan Phan et al.

Diagnostic and Interventional Imaging, 2026, ⟨10.1016/j.diii.2026.02.001⟩

Article dans une revue hal-05549203v1
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Prognostic significance of early on-treatment evolution of circulating tumor DNA in advanced ER+/HER2- breast cancer

A Mamann , Y Pradat , F C Bidard , S Delaloge , L Cabel et al.

Annals of Oncology, 2025, 36 (11), pp.1342-1355. ⟨10.1016/j.annonc.2025.06.015⟩

Article dans une revue hal-05299939v1
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Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology

Hakim Benkirane , Maria Vakalopoulou , David Planchard , Julien Adam , Ken Olaussen et al.

PLoS Computational Biology, 2025, 21 (6), pp.e1013012. ⟨10.1371/journal.pcbi.1013012⟩

Article dans une revue inserm-05144693v1

Novae: a graph-based foundation model for spatial transcriptomics data

Quentin Blampey , Hakim Benkirane , Nadège Bercovici , Fabrice André , Paul-Henry Cournède Article dans une revue hal-05396711v1

Mathematical modelling, selection and hierarchical inference to determine the minimal dose in IFNα therapy against myeloproliferative neoplasms

Gurvan Hermange , William Vainchenker , Isabelle Plo , Paul-Henry Cournède

Mathematical Medicine and Biology, 2024, 41 (2), pp.110-134. ⟨10.1093/imammb/dqae006⟩

Article dans une revue hal-05269717v1
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Confidence intervals of survival predictions with neural networks trained on molecular data

Elvire Roblin , Paul-Henry Cournède , Stefan Michiels

Informatics in Medicine Unlocked, 2024, 44 (2024), pp.101426. ⟨10.1016/j.imu.2023.101426⟩

Article dans une revue inserm-04642336v1
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A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization

Lily Monnier , Paul-Henry Cournède

PLoS Computational Biology, 2024, 20 (2), pp.e1011880. ⟨10.1371/journal.pcbi.1011880⟩

Article dans une revue hal-05236067v1
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Moving toward precision medicine to predict drug sensitivity in patients with metastatic breast cancer

M. Bottosso , F. Mosele , S. Michiels , Paul-Henry P.-H. Cournède , S. Dogan et al.

ESMO Open, 2024, 9 (3), pp.102247. ⟨10.1016/j.esmoop.2024.102247⟩

Article dans une revue inserm-04638434v1
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Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Field Crops Research, 2024, 310, pp.109368. ⟨10.1016/j.fcr.2024.109368⟩

Article dans une revue hal-04644963v1
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Machine learning identifies a profile of inadequate responder to methotrexate in rheumatoid arthritis

Julien Duquesne , Vincent Bouget , Paul-Henry Cournede , Bruno Fautrel , Francis Guillemin et al.

Rheumatology, 2023, 62 (7), pp.2402-2409. ⟨10.1093/rheumatology/keac645⟩

Article dans une revue hal-03986625v1

Better than RECIST and Faster than iRECIST: Defining the Immunotherapy Progression Decision Score to Better Manage Progressive Tumors on Immunotherapy

Younes Belkouchi , Hugues Talbot , Nathalie Lassau , Littisha Lawrance , Siham Farhane et al.

Clinical Cancer Research, 2023, 29 (8), pp.1528-1534. ⟨10.1158/1078-0432.CCR-22-0890⟩

Article dans une revue hal-04396436v1
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Optimizing IFN Alpha Therapy against Myeloproliferative Neoplasms

Gurvan Hermange , Paul-Henry Cournède , Isabelle Plo

Journal of Pharmacology and Experimental Therapeutics, 2023, 387 (1), pp.31-43. ⟨10.1124/jpet.122.001561⟩

Article dans une revue hal-04308358v1
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A biology-driven deep generative model for cell-type annotation in cytometry

Quentin Blampey , Nadège Bercovici , Charles-Antoine Dutertre , Isabelle Pic , Joana Mourato Ribeiro et al.

Briefings in Bioinformatics, 2023, 24 (5), ⟨10.1093/bib/bbad260⟩

Article dans une revue hal-04287005v1

Moving toward precision oncology centers V2.0

S. Dogan , Paul-Henry P.-H. Cournède , E. Solary , J.-M. Heard , M. Aldea et al.

Annals of Oncology, 2023, 34 (12), pp.1088-1089. ⟨10.1016/j.annonc.2023.09.3115⟩

Article dans une revue hal-04372621v1
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Integrative Pan-Cancer Genomic and Transcriptomic Analyses of Refractory Metastatic Cancer

Yoann Pradat , J. Viot , Andrey A. Yurchenko , Konstantin Vladimirovich Gunbin , L. Cerbone et al.

Cancer Discovery, 2023, 13 (5), pp.1116-1143. ⟨10.1158/2159-8290.CD-22-0966⟩

Article dans une revue hal-04122846v1
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CustOmics: A versatile deep-learning based strategy for multi-omics integration

Hakim Benkirane , Yoann Pradat , Stefan Michiels , P. H. Cournède

PLoS Computational Biology, 2023, 19 (3), ⟨10.1371/journal.pcbi.1010921⟩

Article dans une revue hal-04069315v1
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New calibration setup for quantitative DCE‐US imaging protocol: Toward standardization

Isaline Hoferer , Laurene Jourdain , Charly Girot , Baya Benatsou , Ingrid Leguerney et al.

Medical Physics : The international journal of medical physics research and practice, 2023, 50 (9), pp.5541-5552. ⟨10.1002/mp.16362⟩

Article dans une revue hal-04261753v1
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Synergic prognostic value of 3D CT scan subcutaneous fat and muscle masses for immunotherapy-treated cancer

Pierre Decazes , Samy Ammari , Younes Belkouchi , Léo Mottay , Littisha Lawrance et al.

Journal for Immunotherapy of Cancer, 2023, 11 (9), pp.e007315. ⟨10.1136/jitc-2023-007315⟩

Article dans une revue hal-04287256v1

BR55 Ultrasound Molecular Imaging of Clear Cell Renal Cell Carcinoma Reflects Tumor Vascular Expression of VEGFR-2 in a Patient-Derived Xenograft Model

Jean Courcier , Ingrid Leguerney , Baya Benatsou , Sibylle Pochon , Isabelle Tardy et al.

International Journal of Molecular Sciences, 2023, 24 (22), pp.16211. ⟨10.3390/ijms242216211⟩

Article dans une revue hal-04372573v1
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Improving HLA typing imputation accuracy and eplet identification with local next‐generation sequencing training data

Romain Lhotte , Véronique Letort , Cédric Usureau , Debora Jorge-Cordeiro , Jérémy Siemowski et al.

HLA: Immune Response Genetics, 2023, 103 (1), pp.e15222. ⟨10.1111/tan.15222⟩

Article dans une revue hal-04573496v1
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Full Bayesian inference in hidden Markov models of plant growth

Gautier Viaud , Yuting Chen , Paul-Henry P.-H. Cournède

Annals of Applied Statistics, 2022, 16 (4), ⟨10.1214/21-AOAS1594⟩

Article dans une revue hal-04292956v1

Better than RECIST and faster than iRECIST: Defining the immunotherapy progression decision score to better manage progressive tumors on immunotherapy

Younes Belkouchi , Hugues Talbot , Nathalie Lassau , L. Lawrance , S. Farhane et al.

Annals of Oncology, 2022, 33, pp.S595-S596. ⟨10.1016/j.annonc.2022.07.159⟩

Article dans une revue hal-03940635v1
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Modélisation mathématique de l'hématopoïèse et des hémopathies : développement, dynamique et traitement

Gurvan Hermange , Paul-Henry P.-H. Cournède , Isabelle Plo

Hématologie, 2022, 28 (4), pp.183-200. ⟨10.1684/hma.2022.1762⟩

Article dans une revue hal-04134893v1
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Inferring the initiation and development of myeloproliferative neoplasms

Gurvan Hermange , Alicia Rakotonirainy , Mahmoud Bentriou , Amandine Tisserand , Mira El-Khoury et al.

Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (37), ⟨10.1073/pnas.2120374119⟩

Article dans une revue hal-03844872v1

Leveraging conditional generative models in a general explanation framework of classifier decisions

Martin Charachon , Paul-Henry Cournède , Céline Hudelot , Roberto Ardon

Future Generation Computer Systems, 2022, 132, pp.223-238. ⟨10.1016/j.future.2022.02.020⟩

Article dans une revue hal-04574152v1
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Predicting immunotherapy outcomes in patients with MSI tumors using NLR and CT global tumor volume

Younes Belkouchi , Laetitia Nebot-Bral , Littisha Lawrance , Michele Kind , Clémence David et al.

Frontiers in Oncology, 2022, 12, pp.982790. ⟨10.3389/fonc.2022.982790⟩

Article dans une revue hal-04266174v1
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Machine Learning Predicts Response to TNF Inhibitors in Rheumatoid Arthritis: Results on the ESPOIR and ABIRISK Cohorts

Vincent Bouget , Julien Duquesne , Signe Hassler , Paul-Henry P.-H. Cournède , Bruno Fautrel et al.

RMD Open : Rheumatic & Musculoskeletal Diseases, 2022, 8 (2), pp.e002442. ⟨10.1136/rmdopen-2022-002442⟩

Article dans une revue hal-03979132v1
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Prediction of Early Response to Immunotherapy: DCE-US as a New Biomarker

Raphael Naccache , Younes Belkouchi , Littisha Lawrance , Baya Benatsou , Joya Hadchiti et al.

Cancers, 2022, 14 (5), pp.1337. ⟨10.3390/cancers14051337⟩

Article dans une revue hal-03792594v1
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Inferring the dynamic of mutated hematopoietic stem and progenitor cells induced by IFNα in myeloproliferative neoplasms

Matthieu Mosca , Gurvan Hermange , Amandine Tisserand , Robert John Noble , Christophe Marzac et al. Article dans une revue hal-03452002v1

Bayesian Estimation for the GreenLab Plant Growth Model with Deterministic Organogenesis

D. Logothetis , S. Malefaki , S. Trevezas , Paul-Henry P.-H. Cournède

Journal of Agricultural, Biological, and Environmental Statistics, 2021, 27 (1), pp.63-87. ⟨10.1007/s13253-021-00468-w⟩

Article dans une revue hal-04372549v1
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Automaton-ABC: A statistical method to estimate the probability of spatio-temporal properties for parametric Markov population models

Mahmoud Bentriou , Paolo Ballarini , Paul-Henry Cournède

Theoretical Computer Science, 2021, 893, pp.191-219. ⟨10.1016/j.tcs.2021.09.039⟩

Article dans une revue hal-04148855v1

Dynamic monitoring of software use with recurrent neural networks

Chloé Adam , Antoine Aliotti , Fragkiskos Malliaros , Paul-Henry Cournède

Data and Knowledge Engineering, 2020, 125, pp.101781. ⟨10.1016/j.datak.2019.101781⟩

Article dans une revue hal-02520120v1

Association of metastatic pattern and molecular status in stage IV non-small cell lung cancer adenocarcinoma

Alison Dormieux , Laura Mezquita , Paul-Henry P.-H. Cournède , Jordi Remon , Melodie Tazdait et al.

European Radiology, 2020, 30 (9), pp.5021-5028. ⟨10.1007/s00330-020-06784-y⟩

Article dans une revue hal-03127555v1

Optimal control of non-smooth greenhouse models

A. Della Noce , M. Carrier , Paul-Henry P.-H. Cournède

Acta Horticulturae, 2020, 1296, pp.125-132. ⟨10.17660/ActaHortic.2020.1296.17⟩

Article dans une revue hal-03128485v1

Comprehensive landscape of immune-checkpoints uncovered in clear cell renal cell carcinoma reveals new and emerging therapeutic targets.

Diana Tronik-Le Roux , Mathilde Sautreuil , Mahmoud Bentriou , Jérôme Verine , Maria Belén Palma et al.

Cancer Immunology, Immunotherapy, 2020, 69 (7), pp.1237-1252. ⟨10.1007/s00262-020-02530-x⟩

Article dans une revue hal-02879515v1

Prediction of the molecular status in non-small cell lung cancer based on metastatic pattern: A free webtool powered by artificial intelligence.

Benjamin Besse , Alison Dormieux , Laura Mezquita , Renaud Monnet , Melodie Tazdait et al.

Journal of Clinical Oncology, 2020, 38 (15_suppl), pp.9535-9535. ⟨10.1200/JCO.2020.38.15_suppl.9535⟩

Article dans une revue hal-03128125v1

Ultrasound Molecular Imaging of Renal Cell Carcinoma: VEGFR targeted therapy monitored with VEGFR1 and FSHR targeted microbubbles

Alexandre Ingels , Ingrid Leguerney , Paul-Henry P.-H. Cournède , Jacques Irani , Sophie Ferlicot et al.

Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-64433-2⟩

Article dans une revue hal-03128255v1
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Asymptotic distribution of likelihood ratio test statistics for variance components in nonlinear mixed effects models

Charlotte Baey , Paul-Henry P.-H. Cournède , Estelle Kuhn

Computational Statistics and Data Analysis, 2019, 135, pp.107-122. ⟨10.1016/j.csda.2019.01.014⟩

Article dans une revue hal-02367731v1

Insights of Global Sensitivity Analysis in Biological Models with Dependent Parameters

Julien Sainte-Marie , Paul-Henry P.-H. Cournède

Journal of Agricultural, Biological, and Environmental Statistics, 2019, 24 (1), pp.92-111. ⟨10.1007/s13253-018-00343-1⟩

Article dans une revue hal-02367752v1

Association of metastatic pattern and molecular status in metastatic lung non-small cell lung cancer adenocarcinomas

A. Dormieux , L. Mezquita , Paul-Henry P.-H. Cournède , L. Lacroix , Emy Rouleau et al.

Annals of Oncology, 2019, 30, pp.vii14. ⟨10.1093/annonc/mdz413.049⟩

Article dans une revue hal-03128413v1

Échographie moléculaire dans le cancer du rein : modèle pré-clinique de suivi des traitements anti-angiogéniques à partir de microbulles couplées au VEGFR1 et FSHR

I. Alexandre , I. Leguerney , Paul-Henry P.-H. Cournède , J. Irani , S. Ferlicot et al.

Progrès en Urologie, 2019, 29 (13), pp.647. ⟨10.1016/j.purol.2019.08.054⟩

Article dans une revue hal-03128465v1

A new methodology based on sensitivity analysis to simplify the recalibration of functional–structural plant models in new conditions

Amélie Mathieu , Tiphaine Vidal , Alexandra Jullien , Qiongli Wu , Camille Chambon et al.

Annals of Botany, 2018, 127 (3), pp.397-408. ⟨10.1093/aob/mcy080⟩

Article dans une revue hal-01824176v1

Mixed-Effects Estimation in Dynamic Models of Plant Growth for the Assessment of Inter-individual Variability

Charlotte Baey , Amélie Mathieu , Alexandra Jullien , Samis Trevezas , Paul-Henry P.-H. Cournède

Journal of Agricultural, Biological, and Environmental Statistics, 2018, 23 (2), pp.208-232. ⟨10.1007/s13253-017-0307-4⟩

Article dans une revue hal-01766698v1

Leaf density-based modelling of phototropic crown dynamics and long-term predictive application to European beech

Robert Beyer , Veronique Letort , Dominik Bayer , Hans Pretzsch , Paul-Henry Cournède

Ecological Modelling, 2017, 347, pp.63 - 71. ⟨10.1016/j.ecolmodel.2016.12.012⟩

Article dans une revue hal-01630989v1

Model-Driven and Data-Driven Approaches for Crop Yield Prediction: Analysis and Comparison

Xiangtuo Chen , Paul-Henry P.-H. Cournède

International Journal of Mathematical and Computational Sciences, 2017, 11 (7), pp.334-342

Article dans une revue hal-02527764v1
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Indices de Sobol généralisés aux variables dépendantes : tests de performance de l’algorithme HOGS couplé à plusieurs estimateurs paramétriques

Julien Sainte-Marie , Gautier Viaud , Paul-Henry Cournède

Journal de la Société Française de Statistique, 2017, 158 (1), pp.68-89

Article dans une revue hal-01630985v1
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Leaf segmentation and tracking in arabidopsis thaliana combined to an organ-scale plant model for genotypic differentiation

Gautier Viaud , Olivier Loudet , Paul-Henry Cournede

Frontiers in Plant Science, 2017, 7, pp.1-14. ⟨10.3389/fpls.2016.02057⟩

Article dans une revue hal-01602596v1

Reconstructing minimal length tree branch systems from leaf positions

Paul-Henry P.-H. Cournède , Robert Beyer , Dominik Bayer , Hans Pretzsch

Ecological Informatics, 2017, 42, pp.61 - 66. ⟨10.1016/j.ecoinf.2017.09.010⟩

Article dans une revue hal-01630979v1

Validation of a functional-structural tree model using terrestrial Lidar data

Robert Beyer , Dominik Bayer , Veronique Letort , Hans Pretzsch , Paul-Henry Cournède

Ecological Modelling, 2017, 357, pp.55 - 57. ⟨10.1016/j.ecolmodel.2017.02.018⟩

Article dans une revue hal-01630981v1
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Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach

Konstantinos Koutroumpas , Paolo Ballarini , Irene Votsi , Paul-Henry Cournède

Bioinformatics, 2016, 32 (17), pp.i781 - i789. ⟨10.1093/bioinformatics/btw471⟩

Article dans une revue hal-01817488v1

Turgidity-dependent petiole flexibility enables efficient water use by a tree subjected to water stress

David Gonzalez-Rodriguez , Paul-Henry Cournède , Emmanuel de Langre

Journal of Theoretical Biology, 2016, 398, pp.20-31. ⟨10.1016/j.jtbi.2016.03.011⟩

Article dans une revue istex hal-01323343v1
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Learning from User Workflows for the Characterization and Prediction of Software Crashes

Chloé Adam , Antoine Aliotti , Paul-Henry Cournède

2016 IEEE 16th International Conference on Data Mining Workshops (ICDMW), 2016, pp.1023 - 1030. ⟨10.1109/ICDMW.2016.0148⟩

Article dans une revue hal-01616232v1

Modeling spatial competition for light in plant populations with the porous medium equation

Robert Beyer , Octave Etard , Paul-Henry P.-H. Cournède , Pascal Laurent-Gengoux

Journal of Mathematical Biology, 2015, 70 (3), pp.533-547. ⟨10.1007/s00285-014-0763-1⟩

Article dans une revue hal-02404088v1
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A Regularized Particle Filter EM Algorithm Based on Gaussian Randomization with an Application to Plant Growth Modeling

Yuting Chen , Samis Trevezas , Paul-Henry Cournède

Methodology and Computing in Applied Probability, 2015, 17 (4), pp.847-870. ⟨10.1007/s11009-015-9440-0⟩

Article dans une revue hal-00997732v1
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A nonlinear mixed effects model of plant growth and estimation via stochastic variants of the EM algorithm.

Charlotte Baey , Samis Trevezas , Paul-Henry Cournède

Communications in Statistics - Theory and Methods, 2015, pp.00. ⟨10.1080/03610926.2014.930909⟩

Article dans une revue hal-01068327v1
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Application of a probabilistic model for analysing the abortion of seeds and pods in winter oilseed rape (Brassica napus)

Xiu Juan Wang , Amélie Mathieu , Paul-Henry P.-H. Cournède , B G Zhang , Philippe de Reffye

Annals of Applied Biology, 2014, 165 (3), pp.414- 428. ⟨10.1111/aab.12152⟩

Article dans une revue hal-01510245v1

Parameter estimation via stochastic variants of the ECM algorithm with applications to plant growth modeling

Samis Trevezas , Sonia Malefaki , Paul-Henry P.-H. Cournède

Computational Statistics and Data Analysis, 2014, 78, pp.82-99. ⟨10.1016/j.csda.2014.04.004⟩

Article dans une revue hal-02527966v1
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Model-Based Analysis-Synthesis for Realistic Tree Reconstruction and Growth Simulation

Corina Iovan , Paul-Henry Cournède , Thomas Guyard , Benoît Bayol , Dider Boldo et al.

IEEE Transactions on Geoscience and Remote Sensing, 2014, 52 (2), pp.1438-1450. ⟨10.1109/TGRS.2013.2251467⟩

Article dans une revue hal-00826023v1
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Data assimilation to reduce uncertainty of crop model prediction with convolution particle filtering

Yuting Chen , Paul-Henry Cournède

Ecological Modelling, 2014, in press. ⟨10.1016/j.ecolmodel.2014.01.030⟩

Article dans une revue hal-00997728v1

A comprehensive methodology of global sensitivity analysis for complex mechanistic models with an application to plant growth

Qiongli Wu , Paul-Henry Cournède

Ecological Complexity, 2014, 20, pp.219-232. ⟨10.1016/j.ecocom.2013.12.005⟩

Article dans une revue hal-02527976v1
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Sunlab: a Functional-Structural Model for Genotypic and Phenotypic Characterization of the Sunflower Crop

Fenni Kang , Paul-Henry Cournede , Jeremie Lecoeur , Véronique Letort

Ecological Modelling, 2014, 290, pp.21-33. ⟨10.1016/j.ecolmodel.2014.02.006⟩

Article dans une revue hal-01272125v1
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Parametrization of five classical plant growth models applied to sugar beet and comparison of their predictive capacities on root yield and total biomass

Charlotte Baey , Anne Didier , Sébastien Lemaire , Fabienne Maupas , Paul-Henry Cournède

Ecological Modelling, 2014, 290, pp.11-20. ⟨10.1016/j.ecolmodel.2013.11.003⟩

Article dans une revue hal-00919753v1

A Symbolic Method to Analyse Patterns in Plant Structure

Cedric Loi , Paul-Henry P.-H. Cournède , Jean Françon

Combinatorics, Probability and Computing, 2014, 23 (5), pp.842-860. ⟨10.1017/S0963548314000108⟩

Article dans une revue hal-02527843v1
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Modeling tree crown dynamics with 3D partial differential equations

Robert Beyer , Véronique Letort , Paul-Henry Cournède

Frontiers in Plant Science, 2014, 5, pp.329. ⟨10.3389/fpls.2014.00329⟩

Article dans une revue hal-01272213v1
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Modelling the interindividual variability of organogenesis in sugar beet populations using a hierarchical segmented model

Charlotte Baey , Anne Didier , Lemaire Sébastien , Fabienne Maupas , Paul-Henry Cournède

Ecological Modelling, 2013, 263, pp.56-63. ⟨10.1016/j.ecolmodel.2013.04.013⟩

Article dans une revue hal-00819919v1
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Development and Evaluation of Plant Growth Models: Methodology and Implementation in the PYGMALION platform

Paul-Henry Cournède , Yuting Chen , Qiongli Wu , Charlotte Baey , Benoît Bayol

Mathematical Modelling of Natural Phenomena, 2013, 8 (4), pp.112-130. ⟨10.1051/mmnp/20138407⟩

Article dans une revue hal-00860902v1
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A sequential Monte Carlo approach for MLE in a plant growth model

Samis Trevezas , Paul-Henry Cournède

Journal of Agricultural, Biological, and Environmental Statistics, 2013, pp.online first. ⟨10.1007/s13253-013-0134-1⟩

Article dans une revue hal-00796154v1

Parallel Graph Grammars with Instantiation Rules Allow Efficient Structural Factorization of Virtual Vegetation

Katarina Smolenova , Winfried Kurth , Paul-Henry Cournède

Electronic Communications of the EASST, 2012, pp.114-128. ⟨10.14279/tuj.eceasst.61.830.825⟩

Article dans une revue hal-00872370v1

An efficient computational method for global sensitivity analysis and its application to tree growth modelling

Qiongli Wu , Paul-Henry Cournède , Amélie Mathieu

Reliability Engineering and System Safety, 2012, 107, pp.35-43. ⟨10.1016/j.ress.2011.07.001⟩

Article dans une revue istex hal-00639539v1

An optimal control methodology for plant growth--Case study of a water supply problem of sunflower

Lin Wu , François-Xavier Le Dimet , Philippe de Reffye , Bao-Gang Hu , Paul-Henry Cournède et al.

Mathematics and Computers in Simulation, 2012, 82 (5), pp.909-923. ⟨10.1016/j.matcom.2011.12.007⟩

Article dans une revue istex hal-00705066v1
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Oscillations in Functional Structural Plant Growth Models

Amélie Mathieu , Veronique Letort , Paul-Henry Cournède , Baogui Zhang , Patrick Heuret et al.

Mathematical Modelling of Natural Phenomena, 2012, 7 (6), pp.47-66. ⟨10.1051/mmnp/20127603⟩

Article dans une revue hal-00780592v1

Characterization of the effects of inter-tree competition on source-sink balance in Chinese pine trees with the GreenLab model

Hong Guo , Xiangdong Lei , Paul-Henry Cournède , Veronique Letort

Trees - Structure and Function, 2012, 26, pp.1057-1067. ⟨10.1007/s00468-012-0683-x⟩

Article dans une revue istex hal-00780354v1
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Some Parameter Estimation Issues in Functional-Structural Plant Modelling

Paul-Henry Cournède , Veronique Letort , Amélie Mathieu , Meng Zhen Kang , Sébastien Lemaire et al.

Mathematical Modelling of Natural Phenomena, 2011, 6 (2), pp.133-159. ⟨10.1051/mmnp/20116205⟩

Article dans une revue hal-00631509v1

Simulation of fruit-set and trophic competition and optimization of yield advantages in six Capsicum cultivars using functional-structural plant modelling

Yuntao Ma , A. M. Wubs , E. Heuvelink , Amélie Mathieu , J. Y. Zhu et al.

Annals of Botany, 2011, 107 (5), pp.793-803. ⟨10.1093/aob/mcq223⟩

Article dans une revue halsde-00613645v1

Characterization of the interactions between architecture and source-sink relationships in winter oilseed rape (Brassica napus) using the GreenLab model

Alexandra Jullien , Amélie Mathieu , Jean-Michel Allirand , Amélie Pinet , Philippe de Reffye et al.

Annals of Botany, 2011, 107 (5), pp.765-779. ⟨10.1093/aob/mcq205⟩

Article dans une revue halsde-00613649v1

Variability and regulation of the number of ovules, seeds and pods according to assimilate availability in winter oilseed rape (Brassica napus L.).

Xiujuan X. Wang , Amélie A. Mathieu , Paul-Henry P.-H. Cournède , Jean Michel J. M. Allirand , Alexandra A. Jullien et al.

Field Crops Research, 2011, 122 (1), pp.60-69. ⟨10.1016/j.fcr.2011.02.008⟩

Article dans une revue istex hal-01000492v1

NEMA, a functional-structural model of nitrogen economy within wheat culms after flowering. I.Model description

Jessica Bertheloot , Paul-Henry Cournède , Bruno Andrieu

Annals of Botany, 2011, 108 (6), pp.1085-1096. ⟨10.1093/aob/mcr119⟩

Article dans une revue hal-01019789v1

NEMA, a functional-structural model of nitrogen economy within wheat culms after flowering. II. Evaluation and sensitivity analysis

Jessica Bertheloot , Qiongli Wu , Paul-Henry Cournède , Bruno Andrieu

Annals of Botany, 2011, 108 (6), pp.1097-1109. ⟨10.1093/aob/mcr125⟩

Article dans une revue hal-00826101v1

Comparison of three approaches to model grapevine organogenesis in conditions of fluctuating temperature, solar radiation and soil water content

Benoît Pallas , Cedric Loi , Angélique Christophe , Paul-Henry Cournède , Jérémy Lecoeur

Annals of Botany, 2010, 107 (5), pp.Non connues. ⟨10.1093/aob/mcq173⟩

Article dans une revue inria-00546250v1
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Optimization of source-sink dynamics in plant growth for ideotype breeding: a case study on maize

Rui Qi , Yuntao Ma , Baogang Hu , Philippe de Reffye , Paul-Henry Cournède

Computers and Electronics in Agriculture, 2010, 71 (1), pp.96-105. ⟨10.1016/j.compag.2009.12.008⟩

Article dans une revue hal-00493526v3

Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine

Benoit Pallas , Angélique Christophe , Paul-Henry Cournède , Jérémie Lecoeur

Functional Plant Biology, 2009, 36 (2), pp.156-170. ⟨10.1071/fp08178⟩

Article dans une revue hal-02666609v1

A dynamic model of plant growth with interactions between development and functional mechanisms to study plant structural plasticity related to trophic competition.

A. Mathieu , Paul-Henry Cournède , Véronique Letort , Daniel Barthélémy , P. de Reffye

Annals of Botany, 2009, 103 (8), pp.1173-1186. ⟨10.1093/aob/mcp054⟩

Article dans une revue halsde-00418643v1

Une histoire de la modélisation des plantes

Philippe de Reffye , Marc Jaeger , Paul-Henry Cournède

Interstices, 2009

Article dans une revue hal-01350407v1
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Application of the GreenLab model to simulate and optimize wood production and tree stability: a theoretical study

Rui Qi , Véronique Letort , M. Z. Kang , Paul-Henry Cournède , Philippe de Reffye et al.

Silva Fennica, 2009, 43 (3), pp.465-487

Article dans une revue halsde-00436297v1

Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine (Vitis vinifera L.)

Benoit Pallas , Angélique Christophe , Paul-Henry Cournède , Jérémie Lecoeur

Functional Plant Biology, 2009, 36, pp.156-170

Article dans une revue hal-00872383v1

Computing competition for light in the GREENLAB model of plant growth: a contribution to the study of the effects of density on resource acquisition and architectural development.

Paul-Henry Cournède , Amélie Mathieu , François Houllier , Daniel Barthélémy , Philippe de Reffye

Annals of Botany, 2008, 101 (8), pp.1207-1219. ⟨10.1093/aob/mcm272⟩

Article dans une revue halsde-00291875v1

Analytical study of a stochastic plant growth model: application to the GreenLab model

M. Z. Kang , Paul-Henry Cournède , Philippe de Reffye , Daniel Auclair , Bao-Gang Hu

Mathematics and Computers in Simulation, 2008, 78 (1), pp.57-78. ⟨10.1016/j.matcom.2007.06.003⟩

Article dans une revue istex halsde-00306691v1

Rhythms and alternating patterns in plants as emergent properties of a model of interaction between development and functioning

Amélie Mathieu , Daniel Barthélémy , Paul-Henry Cournède , Philippe de Reffye

Annals of Botany, 2008, 101 (8), pp.1233-1242. ⟨10.1093/aob/mcm171⟩

Article dans une revue halsde-00288730v1

A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis thaliana

Angélique Christophe , Veronique Letort , Irène Hummel , Paul-Henry Cournède , P. de Reffye et al.

Functional Plant Biology, 2008, 35, pp.1147-1162. ⟨10.1071/FP08099⟩

Article dans une revue hal-00652522v1

Quantitative genetics and functional-structural plant growth models : Simulation of quantitative trait loci detection for model parameters and application to potential yield optimization

Véronique Letort , Paul Mahe , Paul-Henry Cournède , Philippe de Reffye , Brigitte Courtois

Annals of Botany, 2008, 101 (8), pp.1243-1254. ⟨10.1093/aob/mcm197⟩

Article dans une revue halsde-00288538v1

Structural Identifiability of Generalized Constraint Neural Network Models for Nonlinear Regression

Shuang-Hong Yang , Bao-Gang Hu , Paul-Henry Cournède

Neurocomputing, 2008, 72 (1-3), pp.392-400. ⟨10.1016/j.neucom.2007.12.013⟩

Article dans une revue istex hal-00872379v1

Parameter optimization and field validation of the functional-structural model GREENLAB for Maize at different population densities

Yuntao Ma , Wen Meiping , Yan Guo , Baoguo Li , Paul-Henry Cournède et al.

Annals of Botany, 2008, 101 (8), pp.1185-1194. ⟨10.1093/aob/mcm233⟩

Article dans une revue halsde-00290415v1
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Parametric identification of a functional-structural tree growth model and application to beech trees (Fagus sylvatica)

Veronique Letort , Paul-Henry Cournède , Amélie Mathieu , Philippe de Reffye , Thiéry Constant

Functional Plant Biology, 2008, 35, pp.951-963. ⟨10.1071/fp08065⟩

Article dans une revue inria-00529461v1
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Simulation and Visualisation of Functional Landscapes: Effects of the Water Resource Competition between Plants

Vincent Le Chevalier , Marc Jaeger , Xing Mei , Paul-Henry Cournède

Journal of Computer Science and Technology, 2007, 22 (6), pp.835-845. ⟨10.1007/s11390-007-9105-8⟩

Article dans une revue istex inria-00547631v1
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A dynamical model of plant growth with full retroaction between organogenesis and photosynthesis

Amélie Rostand-Mathieu , Paul-Henry Cournède , Philippe de Reffye

Revue Africaine de Recherche en Informatique et Mathématiques Appliquées, 2006, 7ème Colloque Africain sur la Recherche en Informatique (CARI'04), Volume 4, 2006, pp.101-107. ⟨10.46298/arima.1844⟩

Article dans une revue inria-00122478v2
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Structural Factorization of Plants to Compute their Functional and Architectural Growth

Paul-Henry Cournède , M.Z. Kang , A. Mathieu , Jean-François Barczi , H.P. Yan et al.

SIMULATION: Transactions of The Society for Modeling and Simulation International, 2006, Simulation,Transactions of the society for modelling and simulation international, 82 (7), pp.427-438. ⟨10.1177/0037549706069341⟩

Article dans une revue istex inria-00121231v1

Positivity statements for a Mixed-Element-Volume scheme on fixed and moving grids

Bruno Koobus , Paul-Henry Cournède , Alain Dervieux

Revue Européenne de Mécanique Numérique/European Journal of Computational Mechanics, 2006, 15 (7-8), pp.767-798. ⟨10.3166/remn.15.767-798⟩

Article dans une revue hal-00372831v1
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A Water Supply Optimization Problem for Plant Growth Based on GreenLab Model

Lin Wu , Philippe de Reffye , Bao-Gang Hu , François-Xavier Le Dimet , Paul-Henry Cournède

Revue Africaine de Recherche en Informatique et Mathématiques Appliquées, 2005, Volume 3, Special Issue CARI'04, november 2005, pp.197-207. ⟨10.46298/arima.1836⟩

Article dans une revue hal-01261708v1

GreenLab: A Dynamical Model of Plant Growth for Environmental Applications

Paul-Henry Cournède , Philippe de Reffye

ERCIM News, 2005, Special : Environmental Modelling, 61, pp.39-40

Article dans une revue inria-00121232v1

Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

ESA 2024, Aug 2024, Rennes, France

Communication dans un congrès hal-04936930v1
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Counterfactual Analysis for Digital Histopathology Slides Using Human Interpretable Features

Hakim Benkirane , Maria Vakalopoulou , Stefan Michiels , Paul-Henry Cournède , William Lotter

MIDL 2024 - Medical Imaging with Deep Learning, Jul 2024, Paris, France. Online ahead of print

Communication dans un congrès inserm-05034913v1
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Spatio-Temporal Analysis of Patient-Derived Organoid Videos Using Deep Learning for the Prediction of Drug Efficacy

Leo Fillioux , Emilie Gontran , Jérôme Cartry , Jacques RR Mathieu , Sabrina Bedja et al.

ICCV workshop 2023, Oct 2023, Paris, France

Communication dans un congrès hal-04331446v1

142P Correlating total tumor volume on CT-Scan and liquid biopsy ctDNA in 1017 patients with metastatic cancer: A novel study

Y. Belkouchi , L. Dawi , L. Lawrance , S. Ammari , D. Vasseur et al.

ESMO Congress 2023, European Society for Medical Oncology, Oct 2023, Madrid, Spain. pp.S237, ⟨10.1016/j.annonc.2023.09.2867⟩

Communication dans un congrès hal-04396382v1

1022MO Predicting overall survival of patients with melanoma and NSCLC treated with immunotherapy using AI combining total tumor volume and tumor heterogeneity on CT-Scans

Lama Dawi , Samy Ammari , Younes Belkouchi , Joya Hadchiti , L. Lawrance et al.

ESMO 2023 - Congress of European Society for Medical Oncology, European Society for Medical Oncology, Oct 2023, Madrid, Spain. pp.S622, ⟨10.1016/j.annonc.2023.09.2161⟩

Communication dans un congrès hal-04396366v1
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A Formal Approach for Tuning Stochastic Oscillators

Paolo Ballarini , Mahmoud Bentriou , Paul-Henry P.-H. Cournède

Computational Methods in Systems Biology, Sep 2023, Luxembourg, Luxembourg. pp.1-17, ⟨10.1007/978-3-031-42697-1_1⟩

Communication dans un congrès hal-04570564v1
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Structured State Space Models for Multiple Instance Learning in Digital Pathology

Leo Fillioux , Joseph Boyd , Maria Vakalopoulou , Paul-Henry P.-H. Cournède , Stergios Christodoulidis

MICCAI 2023, Oct 2023, Vancouver, Canada. ⟨10.1007/978-3-031-43907-0_57⟩

Communication dans un congrès hal-04331431v1
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Developing WHEAMM, a new FSPM for the simulation of wheat cultivar mixtures. Feedbacks on model conception, sensitivity analysis and automatic calibration in Julia

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Presentation for the Wageningen FSPM group, Apr 2023, Online, France

Communication dans un congrès hal-04936906v1
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Etude des mélanges de variétés de blé tendre avec une approche interdisciplinaire entre expérimentation au champ et modélisation mécaniste

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

ECOScience, Mar 2023, Palaiseau, France

Communication dans un congrès hal-04936903v1
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WHEAMM: a new functional-structural plant model to study plastic responses to competition for light in wheat cultivar mixtures

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

PlantComp2022, Oct 2022, Gand, Belgium

Communication dans un congrès hal-04936896v1
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Hyper-AdaC: Adaptive clustering-based hypergraph representation of whole slide images for survival analysis

Hakim Benkirane , Maria Vakalopoulou , Stergios Christodoulidis , Ingrid-Judith Garberis , Stefan Michiels et al.

ML4H 2022 - Machine Learning for Health, Nov 2022, New Orelans, France. pp.405-418

Communication dans un congrès hal-04330534v1

Towards the statistical inference of WHEAMM's parameters

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Réunion du groupe de travail Modélisation du projet MoBiDiv, Feb 2022, En ligne, France

Communication dans un congrès hal-04936882v1

Comprendre les normes de réactions dans les mélanges intraspécifiques à l'aide d'un modèle et d'une expérience à l'échelle de la plante

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Colloque interne de l'UMR GQE - Le Moulon, Jun 2021, Gif-sur-Yvette, France

Communication dans un congrès hal-04936828v1

Normes de réaction et plasticité phénotypique des plantes selon l'hétérogénéité de leur voisinage: cas du blé en monoculture versus mélange variétal

Meije Gawinowski , Paul-Henry P.-H. Cournède , Jérôme Enjalbert , Timothée Flutre

Petit Pois Déridé, May 2022, Lille, France

Communication dans un congrès hal-04936889v1

WHEAMM : a functional-structural model to study the quantitative genetics of wheat variety mixtures

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Séminaire INRAE-CIRAD sur la modélisation des cultures, Dec 2021, Montpellier, France

Communication dans un congrès hal-04936879v1

On the Use of Neural Networks with Censored Time-to-Event Data

Elvire Roblin , Paul-Henry P.-H. Cournède , Stefan Michiels

International Symposium on Mathematical and Computational Oncology - ISMCO 2020, Oct 2020, Paris, France. pp.56-67, ⟨10.1007/978-3-030-64511-3_6⟩

Communication dans un congrès hal-03127430v1

Developping WHEAMM, a functional-structural model of wheat variety mixtures to study the genetic basis of phenotypic plasticity in an agricultural context

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

Réunion annuelle du GDR PlasPhen, Nov 2020, Montpellier, France

Communication dans un congrès hal-04936827v1
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Simulation de la densité limite de champ moyen pour des populations hétérogènes avec interactions

Antonin Della Della Noce , Amélie Mathieu , Paul-Henry P.-H. Cournède

22ème Rencontre du Non-Linéaire, Mar 2019, Paris, France

Communication dans un congrès hal-02425831v1

Assimilation de données par filtrage particulaire régularisé dans un modèle d'épidémiologie

Mahmoud Bentriou , Stefanella Boatto , Gautier Viaud , Paul-Henry P.-H. Cournède

50èmes journées de Statistique de a SFdS, May 2018, Palaiseau, France

Communication dans un congrès hal-02860793v1

Crop recognition from sequential sentinel-1 images with lstm recurrent networks

Wendy Hammache , Théophile Lohier , Paul-Henry P.-H. Cournède

6th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA), Nov 2018, Hefei, China

Communication dans un congrès hal-02861019v1

Modèles de population avec interactions : de la limite de champ moyen à l'approximation de champ moyen.

Antonin Della Della Noce , Amelie Mathieu , Paul-Henry P.-H. Cournède

50èmes journées de Statistique de la SFdS, May 2018, Palaiseau, France

Communication dans un congrès hal-02860994v1

Application of Weighted Regression for the Prediction of Soft Wheat Production in France

Xiangtuo Chen , Benoît Bayol , Paul-Henry Cournède

6th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA) 2018, Nov 2018, Hefei, China. pp.141-146, ⟨10.1109/pma.2018.8611566⟩

Communication dans un congrès hal-02860799v1

Sensitivity analysis to help individual plant model parameterization for winter oilseed rape

Amélie Mathieu , Tiphaine Vidal , Alexandra Jullien , Qiongli Wu , Paul-Henry P.-H. Cournède

International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), FSPMA 2016., Nov 2016, Qingdao, China. ⟨10.1109/fspma.2016.7818299⟩

Communication dans un congrès hal-01566311v1

Modeling soil temperature to predict emergence

Etienne Claverie , Jérémie J. Lecoeur , Veronique Letort , Paul-Henry P.-H. Cournède

2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA), Nov 2016, Qingdao, China. ⟨10.1109/FSPMA.2016.7818285⟩

Communication dans un congrès hal-01823953v1

Impact of geometrical traits on light interception in conifers analysis using an FSPM for Scots pine

Katarina Streit , Michael Henke , Benoit Bayol , Paul-Henry P.-H. Cournède , Risto Sievaenen et al.

IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA), Nov 2016, Qingdao, China. ⟨10.1109/FSPMA.2016.7818307⟩

Communication dans un congrès hal-02402783v1
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A data augmentation scheme embedding a sequential Monte Carlo method for Bayesian parameter inference in state space models

Irene Votsi , Paul-Henry Cournède

48èmes Journées de Statistique de la SFdS, May 2016, Montpellier, France

Communication dans un congrès hal-01355334v1
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Modeling the inter-individual variability of single-stemmed plant development

Antonin Della Della Noce , Véronique Letort , Amandine Hansart , Charlotte Baey , Gautier Viaud et al.

International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Nov 2016, Qingdao, China. ⟨10.1109/fspma.2016.7818287⟩

Communication dans un congrès hal-01490367v1

WIP - Promoting good modeling practice with a domain-specific language and statistical algorithms designed for parallel computing

Benoît Bayol , Yuting Chen , Charlotte Baey , Gautier Viaud , Paul-Henry P.-H. Cournède

DEVS '15: Proceedings of the Symposium on Theory of Modeling & Simulation: DEVS Integrative M&S Symposium, Apr 2015, San Diego, United States

Communication dans un congrès hal-02777331v1
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A Comparison of a Generic MCMC-Based Algorithm for Bayesian Estimation in C++, R and Julia. Application to Plant Growth Modeling

Gautier Viaud , Yuting Chen , Benoît Bayol , Paul-Henry Cournède

2015 Spring Simulation Multi-Conference The Society for Modeling & Simulation International, Apr 2015, Alexandria, United States

Communication dans un congrès hal-01250999v1
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Towards an EDSL to enhance good modelling practice for non-linear stochastic discrete dynamical models Application to plant growth models

Benoit Bayol , Yuting Chen , Paul-Henry Cournède

SIMULTECH 2013, Jul 2013, Iceland. pp.132-138, ⟨10.5220/0004481101320138⟩

Communication dans un congrès hal-01001669v1

A comprehensive global sensitivity analysis for biological model diagnosis and parameterization: application to the NEMA model

Qiongli Wu , Jessica Bertheloot , Paul-Henry Cournède

Seventh International Workshop on Functional-Structural Plant Models, Jun 2013, Saariselkä, Finland

Communication dans un congrès hal-00826102v1
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A nonlinear mixed effects model to explain inter-individual variability in plant populations

Charlotte Baey , Samis Trevezas , Paul-Henry Cournède

Applied Stochastic Models and Data Analysis International Conference (ASMDA) 2013, Jun 2013, Barcelona, Spain

Communication dans un congrès hal-00826175v1
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Global sensitivity analysis of the NEMA model for its parameterization and biological diagnosis.

Qiongli Wu , Jessica Bertheloot , Paul-Henry Cournède

7th International Conference on Functional-Structural Plant Models (FSPM 2013), Jun 2013, Saariselkä, Finland

Communication dans un congrès hal-01456018v1

Assessment of Interactions in Complex Mechanistic Models using Global Sensitivity Analysis

Qiongli Wu , Paul-Henry Cournède

International Conference "Interactions in Complex Systems", Jun 2013, Orléans, France

Communication dans un congrès hal-00826105v1

Modelling Competition in Crop Populations via Reaction-­Diffusion Foliage Dynamics. With an Outlook on Tree Modelling

Robert Beyer , Paul-Henry Cournède

7th International Conference on Functional-Structural Plant Models (FSPM 2013), Jun 2013, Saariselkä, Finland. pp.201-203

Communication dans un congrès hal-00829756v1

Optimal Control of Crop Irrigation based on the Hamilton-Jacobi-Bellman Equation

Jacques Ramanathan , Yuting Chen , Paul-Henry Cournède

SIAM Conference on Control and its Applications, Jul 2013, San Diego, United States. pp.21-28, ⟨10.1137/1.9781611973273.4⟩

Communication dans un congrès hal-02777904v1
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Iterative convolution particle filtering for nonlinear parameter estimation and data assimilation with application to crop yield prediction

Yuting Chen , Samis Trevezas , Paul-Henry Cournède

Society for Industrial and Applied Mathematics (SIAM): Control & its Applications 2013, Jul 2013, San Diego, United States. pp.CHEN, ⟨10.1137/1.9781611973273.10⟩

Communication dans un congrès hal-00826052v1
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Some sequential Monte Carlo techniques for Data Assimilation in a plant growth model

Yuting Chen , Samis Trevezas , Aman Gupta , Paul-Henry Cournède

Applied Stochastic Models and Data Analysis International Conference (ASMDA) 2013, Jun 2013, Spain. in press

Communication dans un congrès hal-00997736v1

Sensitivity Analysis for Plant Models with Correlated Parameters: Application to the Characterization of Sun flower Genotypes

Qiongli Wu , Benoît Bayol , Fenni Kang , Jérémie Lecoeur , Paul-Henry Cournède

7th International Conference on Sensitivity Analysis of Model Output, Jul 2013, Nice, France

Communication dans un congrès hal-00826104v1
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SUNLAB: a Functional-Structral Model for Genotypic and Phenotypic Characterization of the Sunflower Crop

Fenni Kang , Veronique Letort , Hugo Magaldi , Paul-Henry Cournède , Jérémie Lecoeur

2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Oct 2012, Shanghai, China. pp.148-151

Communication dans un congrès hal-00781183v1
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Filtrage par noyaux de convolution itératif

Yuting Chen , Benoît Bayol , Cédric Loi , Samis Trevezas , Paul-Henry Cournède

Les 44 Journées de Statistique, May 2012, Bruxelles, Belgique. pp.CHEN

Communication dans un congrès hal-00776397v1
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Assessment of Parameter Uncertainty in Plant Growth Model Identification

Yuting Chen , Paul-Henry Cournède

2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Oct 2012, China. CHEN, page 43

Communication dans un congrès hal-00776551v1
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Evaluation of the Predictive Capacity of Five Plant Growth Models for Sugar Beet

Charlotte Baey , Anne Didier , Li Song , Sébastien Lemaire , Fabienne Maupas et al.

Plant Growth Modeling, Simulation, Visualization and Applications - PMA12, Nov 2012, Shanghai, China. pp.30-37

Communication dans un congrès hal-00776389v2

Effects of pod position and its appearance time on pod and seed abortion in winter oilseed rape (Brassica napus L.)

Xiujuan X. Wang , Amélie A. Mathieu , Paul-Henry P.-H. Cournède , Jean Michel J. M. Allirand , Alexandra A. Jullien et al.

13. International Rapeseed Congress, Jun 2011, Prague, Czech Republic. pp.154-157

Communication dans un congrès hal-01000458v1

A methodology to study Complex Biophysical Systems with Global Sensitivity Analysis

Qiongli Wu , Paul-Henry Cournède

ESREL2011, Antoine Grall, Sep 2011, Troyes, France

Communication dans un congrès hal-00639549v1
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Bayesian Estimation in Functional-Structural Plant Models with Stochastic Organogenesis

Cédric Loi , Paul-Henry Cournède , Samis Trevezas

14th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2011), Jun 2011, Rome, Italy

Communication dans un congrès hal-00653672v1
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Using a hierarchical segmented model to assess the dynamics of leaf appearance in plant populations.

Charlotte Baey , Paul-Henry Cournède

14th Applied Stochastic Models and Data Analysis International Conference (ASMDA 2011), Jun 2011, Rome, Italy

Communication dans un congrès inria-00602419v1
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The use of Sensitivity Analysis for the design of Functional Structural Plant Models

Qiongli Wu , Paul-Henry Cournède

Sixth international conference on sensitivity analysis of model output, Jul 2010, Milan, Italy. pp.7768-7769

Communication dans un congrès hal-00534046v1
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Impact of topology on plant functioning : a theoretical analysis based on the GreenLab model equations

Véronique Letort , Paul-Henry Cournède , Philippe de Reffye

2009 Plant Growth Modeling And Applications, Nov 2009, Beijing, China. pp.341-348

Communication dans un congrès hal-00546801v1

A functional-structural model of nitrogen economy within wheat culms after flowering

Jessica Bertheloot , Paul-Henry P.-H. Cournède , Q. Wu , Bruno Andrieu

12. ESA Congress, Aug 2010, Montpellier, France

Communication dans un congrès hal-01192285v1
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Assessment of Non-Linearity in Functional-Structural Plant Models

Qiongli Wu , Jessica Bertheloot , Amélie Mathieu , Bruno Andrieu , Paul-Henry Cournède

FSPM 2010 - 6th International Workshop on Functional-Structural Plant Models, Sep 2010, Davis, California, United States

Communication dans un congrès hal-01192293v2

Modelling of branch and flower expansion in GreenLab model to account for the whole crop cycle of Winter Oilseed Rape (Brassica Napus L.)

Alexandra Jullien , Amélie Mathieu , Jean Michel Allirand , Amélie Pinet , Philippe Verchère de Reffye et al.

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Ville service., Nov 2009, Beijing, China. 454 p

Communication dans un congrès hal-01192313v1

Calibration of a probabilistic model of oilseed rape fertility to analyze the inter-variety variability in number of seeds

X. Wang , Amélie Mathieu , Paul-Henry P.-H. Cournède , Jean Michel Allirand , Alexandra Jullien et al.

6. International Workshop, Sep 2010, Davis, United States

Communication dans un congrès hal-01192265v1
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A symbolic method to compute the probability distribution of the number of pattern occurences in random texts generated by stochastic 0L-systems

Cedric Loi , Paul-Henry Cournède , Jean Françon

21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms (AofA'10), 2010, Vienna, Austria. pp.473-488, ⟨10.46298/dmtcs.2774⟩

Communication dans un congrès inria-00529137v2
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Stochastic models in floral biology and its application to the study of oilseed rape (Brassica napus L.) fertility

Wang Xiujuan , Amélie Mathieu , Paul-Henry Cournède , Jean-Michel Allirand , Alexandra Jullien et al.

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Beijing, China

Communication dans un congrès inria-00529375v1

Stochastic models in floral biology and application to the study of oilseed rape fertility

Xiujuan Wang , Amélie Mathieu , Paul-Henry P.-H. Cournède , Jean Michel Allirand , Philippe Verchère de Reffye et al.

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Ville service., Nov 2009, Beijing, China. 454 p., ⟨10.1109/PMA.2009.12⟩

Communication dans un congrès hal-01192317v1
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Analysis of the density effects on the source-sink dynamics in Sugar-Beet growth

Sébastien Lemaire , Fabienne Maupas , Paul-Henry Cournède , Jean-Michel Allirand , Bertrand Ney et al.

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Beijing, China. 454 p

Communication dans un congrès inria-00543137v1
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Towards a continuous approach of functional-structural plant growth

Zhongping Li , Vincent Le Chevalier , Paul-Henry Cournède

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Beijing, China. pp.334-340, ⟨10.1109/PMA.2009.69⟩

Communication dans un congrès hal-00529351v1
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Plants as Combinatorial Structures and Applications

Cedric Loi , Paul-Henry Cournède , Jean Françon

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Pékin, China. pp.319-326, ⟨10.1109/pma.2009.27⟩

Communication dans un congrès inria-00546283v1
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Simulation of morphological plasticity of Acacia tortilis in response to herbivore attacks

Amélie Mathieu , Véronique Letort , Renaud Gosset , Jacques Gignoux , Paul-Henry Cournède

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Saisissez le nom du laboratoire, du service ou du département., Ville service., 2009, Beijing, China. 454 p

Communication dans un congrès inria-00543136v1
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Modeling Inter-Individual Variability in Sugar Beet Populations

P. de Reffye , Sébastien Lemaire , Nitish Srivastava , Fabienne Maupas , Paul-Henry Cournède

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Beijing, China

Communication dans un congrès inria-00537646v1
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Sensitivity analysis of GreenLab model for maize

Qiongli Wu , Paul-Henry Cournède

3rd international symposium on Plant Growth and Applications (PMA09), Nov 2010, Beijing, China

Communication dans un congrès inria-00532950v1
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A stochastic growth model of grapevine with full interaction between environment, trophic competition and plant development.

Benoit Pallas , Cedric Loi , Angélique Christophe , Paul-Henry Cournède , Jérémie Lecoeur

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Nov 2009, Pékin, China. pp.95-102

Communication dans un congrès inria-00546291v1
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A Forest Growth Simulator Based on Functional-Structural Modelling of Individual Trees

Paul-Henry Cournède , Thomas Guyard , Benoit Bayol , Sébastien Griffon , François de Coligny et al.

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), IEEE, Nov 2009, Beijing, China. pp.34-41, ⟨10.1109/PMA.2009.55⟩

Communication dans un congrès inria-00529096v1
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A Functional-Structural Plant Model-Theory and Applications in Agronomy

Meng Zhen Kang , Paul-Henry Cournède , Amélie Mathieu , Véronique Letort , Rui Qi et al.

International Symposium on Crop Modeling and Decision Support: ISCMDS 2008, Apr 2008, Nanjing, China

Communication dans un congrès inria-00380520v1

Rhythms and alternating patterns in plants as emergent properties of a model of interaction between development and functioning

Amélie Mathieu , Paul-Henry Cournède , Daniel Barthélémy , Philippe de Reffye

Second International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, PMA06, Nov 2006, Beijin, China. ⟨10.1093/aob/mcm171⟩

Communication dans un congrès hal-02824878v1
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Generating Functions of Stochastic L-Systems and Application to Models of Plant Development

Cedric Loi , Paul Henry Cournède

Fifth Colloquium on Mathematics and Computer Science, 2008, Kiel, Germany. pp.325-338, ⟨10.46298/dmtcs.3574⟩

Communication dans un congrès hal-01194661v1
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A morphogenetic crop model for sugar-beet (Beta vulgaris L.)

Sébastien Lemaire , Fabienne Maupas , Paul-Henry Cournède , Philippe de Reffye

ISCMDS, Apr 2008, Nanjing, China

Communication dans un congrès inria-00336415v3

Analyse et modélisation de l'architecture des Plantes

Daniel Auclair , Jean-François Barczi , Daniel Barthélémy , Frédéric Blaise , Yves Caraglio et al.

Plantes et peuplements virtuels, Institut National de Recherche Agronomique (INRA). UAR Département Adjoint Ecologie des Forêts, Prairies et Milieux Aquatiques (0940)., Mar 2008, Lyon, France

Communication dans un congrès hal-01032386v1

Is it possible to simulate rapeseed organ mass in relation to N nutrition ? Calibration of the functional-structural model GREENLAB for the oilseed rape Brassica napus L. during the vegetative phase for two nitrogen nutrition levels

Alexandra Jullien , Jean Michel Allirand , Paul-Henry P.-H. Cournède , A. Matthieu , P. de Reffye et al.

12. International Rapeseed Congress, Mar 2007, Wuhan, China

Communication dans un congrès hal-01191922v1

Generation of rhythms in plant development controlled by their functioning: theoretical and numerical study

Amélie Mathieu , Paul-Henry Cournède , Daniel Barthélémy , Philippe de Reffye

2. International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, Nov 2006, Beijing, China

Communication dans un congrès hal-02757964v1
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Effect of topological and phenological changes on biomass partitioning in Arabidopsis thaliana inflorescence: a preliminary model-based study

Veronique Letort , Paul-Henry Cournède , Jérémie Lecoeur , Irène Hummel , Philippe de Reffye et al.

PMA06, Plant Growth Modeling, Simulation, Visualization and applications, Nov 2006, Beijing, China. pp.65-69

Communication dans un congrès hal-00576589v1
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Adaptation of the GreenLab model for analyzing sink-source relationships in Chinese Pine saplings

Hong Guo , Veronique Letort , Lingxia Hong , Thierry Fourcaud , Paul-Henry Cournède et al.

PMA06, Plant growth modeling, Simulation, Visualization and Applications, Nov 2006, Beijing, China. pp.236-243

Communication dans un congrès hal-00576583v1
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Optimizing plant growth model parameters for genetic selection based on QTL mapping

Veronique Letort , Paul Mahe , Paul-Henry Cournède , P. de Reffye , Brigitte Courtois

Plant Growth Modeling, Simulation, Visualization and applications, Nov 2006, Beijing, China. pp.16-21

Communication dans un congrès hal-00829810v1

A Water Supply Optimization Problem for Plant Growth Based on GreenLab Model

L. Wu , François-Xavier Le Dimet , B.G. Hu , Paul-Henry Cournède , Philippe de Reffye

7éme Colloque Africain sur la Recherche en Informatique (CARI'04), Nov 2004, Mammamet, Tunisia

Communication dans un congrès inria-00122491v1

Theoretical Study and Numerical Simulation of a Stochastic Model for Plant Growth

M.Z. Kang , Paul-Henry Cournède , J. Le Roux , Philippe de Reffye , B.G. Hu

7th African Conference on Research in Computer Science, Nov 2004, Hammamet, Tunisia

Communication dans un congrès inria-00121499v1
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The Influence of Photosynthesis on the Number of Metamers per Growth Unit in GreenLab Model

Amelie Mathieu , Paul-Henry Cournède , Philippe de Reffye

4TH International Workshop on Functional-Structural Plant Models, Jun 2004, Montpellier, France

Communication dans un congrès hal-00124845v1
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Better than RECIST and faster than iRECIST: defining the Immunotherapy Progression Decision score to better manage progressive tumors on immunotherapy

Younes Belkouchi , Hugues Talbot , Nathalie Lassau , Littisha Lawrance , Siham Farhane et al.

ESMO 2022, Sep 2022, Paris, France.

Poster de conférence hal-03780911v1
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WHEAMM: a functional-structural model to study plant growth and interactions with neighbors in wheat variety mixtures

Meije Gawinowski , Jérôme Enjalbert , Paul-Henry P.-H. Cournède , Timothée Flutre

FSPM 2020 : 9th International Conference on FUNCTIONAL-STRUCTURAL PLANT MODELS, Oct 2020, Hanovre (Virtual Conference), Germany

Poster de conférence hal-02961398v1

Testing variance components in nonlinear mixed effects models. Application to plant growth modelling

Estelle Kuhn , Charlotte Baey , Paul Henry Cournède

31-th European Meeting of Statisticians -EMS, Jul 2017, Helsinki, Finland. 2017

Poster de conférence hal-01607982v1

Testing variance components in nonlinear mixed effects models. Application to plant growth modelling

Estelle Kuhn , Paul Henry Cournède , Charlotte Baey

9. International Conference of the ERCIM WG on Computational and Methodological Statistics (CMStatistics 2016), Dec 2016, Seville, Spain. 2016

Poster de conférence hal-01607339v1
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Multiscale Functional-Structural Plant Modelling at the Example of Apple Trees

Benoit Bayol , Gerhard G. Buck-Sorlin , Faustino Chi , Evelyne Costes , Paul Henry Cournède et al.

International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Nov 2016, Qingdao, China. 2016, ⟨10.1109/FSPMA.2016.7818281⟩

Poster de conférence hal-01602793v1

The Transition from the Single Plant to the Stand

Paul-Henry Cournède , Frédéric Blaise , Philippe de Reffye , Mengzhen Kang

Philippe de Reffye; Mengzhen Kang; Marc Jaeger; Baogui Zhang. Plant Model Greenlab for Botany and Agronomy, Springer Nature Singapore, pp.541-582, 2025, ⟨10.1007/978-981-97-7541-5_11⟩

Chapitre d'ouvrage hal-05107232v1

Approximate Bayesian Inference using the Mean-Field Distribution

Antonin Della Noce , Paul-Henry Cournède

Data Analysis and Related Applications 1: Computational, Algorithmic and Applied Economic Data Analysis, Volume 9, 1, Wiley, 2022, 9781394165513. ⟨10.1002/9781394165513.ch24⟩

Chapitre d'ouvrage hal-04374332v1

Neural Networks to Predict Survival from RNA-seq Data in Oncology

Mathilde Sautreuil , Sarah Lemler , Paul-Henry P.-H. Cournède

Computational Methods in Systems Biology, pp.122-140, 2021, ⟨10.1007/978-3-030-85633-5_8⟩

Chapitre d'ouvrage hal-03347253v1

Reachability Design Through Approximate Bayesian Computation

Mahmoud Bentriou , Paolo Ballarini , Paul-Henry Cournède

Computational Methods in Systems Biology, pp.207-223, 2019, ⟨10.1007/978-3-030-31304-3_11⟩

Chapitre d'ouvrage hal-02317539v1
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Modèles Dynamiques de la Croissance des Plantes : Succès et Défis

Paul-Henry P.-H. Cournède

Potentiels de la science pour une agriculture durable, Académie d'Agriculture de France. Edition: Jean-Claude Pernollet., , 2018

Chapitre d'ouvrage hal-02285935v1

Méthodes inverses et identification paramétrique de modèles d'architecture végétale

Philippe de Reffye , Francois Houllier , Paul-Henry P.-H. Cournède

Philippe de Reffye; Marc Jaeger; Daniel Barthélémy; François Houllier. Architecture et croissance des plantes. Modélisation et applications, , 2016, Synthèses, 978-27592-2622-1

Chapitre d'ouvrage hal-02539715v1

Le passage de la plante au peuplement

Paul-Henry P.-H. Cournède , Philippe de Reffye

Philippe de Reffye; Marc Jaeger; Daniel Barthélémy; François Houllier. Architecture et croissance des plantes. Modélisation et croissances des plantes, 2016, Synthèses, 978-27592-2622-1

Chapitre d'ouvrage hal-02295378v1

Parameterization of plant growth models to characterize genotype by environment interactions: a methodology adapted to breeding programs

Fenni Kang , Thomas Galinier , Paul-Henry Cournède , Jérémie Lecoeur

Halford, N. and Semenov, M. Aspects of Applied Biology 107: Systems Approaches to Crop Improvement, The Association of Applied Biologists, pp.27-35, 2011

Chapitre d'ouvrage hal-00872388v1

Nitrogen acquisition and utilization by crops: review of different approaches and proposition of a mechanistic modeling

Jessica Bertheloot , Paul-Henry Cournède , Bruno Andrieu

Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications: proceedings, 9-13 November 2009, Beijing, China, IEEE Computer Society, 454 p., 2010, Plant Growth Modeling, Simulation, Visualization and Applications, 978-0-7695-3988-1

Chapitre d'ouvrage hal-01192311v1

A Functional-Structural Plant Model: Theories and its Applications in Agronomy

Meng Zhen Kang , Paul-Henry Cournède , Amélie Mathieu , Veronique Letort , Rui Qi

Cao, W. and White, J. and Wang, E. Crop Modeling and Decision Support, Springer, pp.148-160, 2009, 978-3-642-01131-3. ⟨10.1007/978-3-642-01132-0_16⟩

Chapitre d'ouvrage hal-00872390v1

Modélisation et simulation de l'architecture et de la production végétales

Philippe de Reffye , Daniel Barthélémy , Paul-Henry P.-H. Cournède , Marc Jaeger

Aux origines des plantes : des plantes anciennes à la botanique du XXIe siècle, Fayard, 2008, 978-2-213-62836-3

Chapitre d'ouvrage hal-02822356v1

Plant growth models

Philippe de Reffye , E. Heuvalick , Daniel Barthélémy , Paul-Henry P.-H. Cournède

Encyclopedia of Ecology, Elsevier, 2008, 978-0-08-045400-9. ⟨10.1016/B978-008045405-4.00217-2⟩

Chapitre d'ouvrage hal-02821385v1
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STHELAR, a multi-tissue dataset linking spatial transcriptomics and histology for cell type annotation

Félicie Giraud-Sauveur , Quentin Blampey , Hakim Benkirane , Arianna Marinello , Paul-Henry Cournède et al.

2025

Pré-publication, Document de travail hal-05386019v1

Clonal memory of cell division in humans diverges between healthy haematopoiesis and acute myeloid leukaemia

A Donada , G Hermange , T Tocci , A Midoun , G Prevedello et al.

2025

Pré-publication, Document de travail hal-05397031v1
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EVALUATION OF MACHINE-LEARNING MODELS TO MEASURE INDIVIDUALIZED TREATMENT EFFECTS FROM RANDOMIZED CLINICAL TRIAL DATA WITH TIME-TO-EVENT OUTCOMES

Roblin Elvire , Paul-Henry Cournède , Stefan Michiels

2025

Pré-publication, Document de travail inserm-05290368v1

Novae: a graph-based foundation model for spatial transcriptomics data

Quentin Blampey , Hakim Benkirane , Nadège Bercovici , Fabrice André , Paul-Henry Cournède

2025

Pré-publication, Document de travail hal-05392336v1

Likelihood ratio test for variance components in nonlinear mixed effects models

Charlotte Baey , Paul-Henry P.-H. Cournède , Estelle Kuhn

2022

Pré-publication, Document de travail hal-03813686v1
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Neural networks to predict survival from RNA-seq data in oncology

Mathilde Sautreuil , Sarah Lemler , Paul-Henry P.-H. Cournède

2021

Pré-publication, Document de travail hal-03224492v1

Combining Similarity and Adversarial Learning to Generate Visual Explanation: Application to Medical Image Classification

Martin Charachon , Céline Hudelot , Paul-Henry P.-H. Cournède , Camille Ruppli , Roberto Ardon

2021

Pré-publication, Document de travail hal-03127330v1
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Mean field approximation of a heterogeneous population of plants in competition

Antonin Della Noce , Amélie Mathieu , Paul-Henry P.-H. Cournède

2019

Pré-publication, Document de travail hal-02147039v1
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Irrigation Optimization by Modeling of Plant-Soil Interaction

Zhongping Li , Paul-Henry Cournède , Jean-Claude Mailhol

2011

Pré-publication, Document de travail hal-00606408v1
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A symbolic method to analyse patterns in plant structure whose organogenesis is driven by a multitype branching process

Cedric Loi , Paul-Henry Cournède , Jean Françon

2010

Pré-publication, Document de travail inria-00546309v1
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Dynamic System of Plant Growth

Paul-Henry Cournède

Mathematics [math]. Université Montpellier II - Sciences et Techniques du Languedoc, 2009

HDR tel-00377462v2