@article{narci:hal-02475936,
  TITLE = {{Inference for partially observed epidemic dynamics guided by Kalman filtering techniques}},
  AUTHOR = {Narci, Romain and Delattre, Maud and Lar{\'e}do, Catherine and Vergu, Elisabeta},
  URL = {https://hal.archives-ouvertes.fr/hal-02475936},
  JOURNAL = {{Computational Statistics and Data Analysis}},
  PUBLISHER = {{Elsevier}},
  VOLUME = {164},
  YEAR = {2021},
  MONTH = Dec,
  DOI = {10.1016/j.csda.2021.107319},
  KEYWORDS = {Epidemic dynamics ; Approximated maximum likelihood ; SIR model ; Diffusion approach ; Kalman filter ; Measurement errors ; Partially observed Markov process ; Parametric inference},
  PDF = {https://hal.archives-ouvertes.fr/hal-02475936v4/file/csda_2nd_revision.pdf},
  HAL_ID = {hal-02475936},
  HAL_VERSION = {v4},
}

@article{lejal:hal-03287263,
  TITLE = {{Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions}},
  AUTHOR = {Lejal, E. and Chiquet, J. and Aubert, J. and Robin, S. and Estrada-Pe{\~n}a, A. and Rue, O. and Midoux, C. and Mariadassou, M. and Bailly, X. and Cougoul, A. and Gasqui, P. and Cosson, J. and Chalvet-Monfray, K. and Vayssier-Taussat, M. and Pollet, Thomas},
  URL = {https://hal.inrae.fr/hal-03287263},
  JOURNAL = {{Microbiome}},
  PUBLISHER = {{ BioMed Central}},
  VOLUME = {9},
  NUMBER = {1},
  PAGES = {153},
  YEAR = {2021},
  MONTH = Dec,
  DOI = {10.1186/s40168-021-01051-8},
  KEYWORDS = {Microbial Interactions ; Ticks ; Borrelia ; Rickettsia},
  PDF = {https://hal.inrae.fr/hal-03287263/file/s40168-021-01051-8.pdf},
  HAL_ID = {hal-03287263},
  HAL_VERSION = {v1},
}

@article{guerin:hal-03356343,
  TITLE = {{Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen}},
  AUTHOR = {Gu{\'e}rin, Cyprien and Lee, Bo-Hyung and Fradet, Benjamin and Van Dijk, Erwin and Mirauta, Bogdan and Thermes, Claude and Bernardet, Jean-Fran{\c c}ois and Repoila, Francis and Duchaud, Eric and Nicolas, Pierre and Rochat, Tatiana},
  URL = {https://hal.inrae.fr/hal-03356343},
  JOURNAL = {{ISME Communications}},
  VOLUME = {1},
  NUMBER = {1},
  YEAR = {2021},
  MONTH = Dec,
  DOI = {10.1038/s43705-021-00029-9},
  PDF = {https://hal.inrae.fr/hal-03356343/file/2021_Gu%C3%A9rin_ismecomms.pdf},
  HAL_ID = {hal-03356343},
  HAL_VERSION = {v1},
}

@article{jollet:hal-03415988,
  TITLE = {{Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model}},
  AUTHOR = {Jollet, Maxence and Nay, Kevin and Chopard, Ang{\`e}le and Bareille, Marie-Pierre and Beck, Arnaud and Ollendorff, Vincent and Vernus, Barbara and Bonnieu, Anne and Mariadassou, Mahendra and Ru{\'e}, Olivier and Derbr{\'e}, Fr{\'e}d{\'e}ric and Goustard, B{\'e}n{\'e}dicte and Koechlin-Ramonatxo, Christelle},
  URL = {https://hal.inrae.fr/hal-03415988},
  JOURNAL = {{Nutrients}},
  PUBLISHER = {{MDPI}},
  VOLUME = {13},
  NUMBER = {11},
  YEAR = {2021},
  MONTH = Nov,
  DOI = {10.3390/nu13113865},
  KEYWORDS = {hypoactivity ; commensal bacteria ; flora ; phyla ; muscle atrophy ; disuse ; weightlessness ; micro-gravity},
  PDF = {https://hal.inrae.fr/hal-03415988/file/nutrients-13-03865-DMEM.pdf},
  HAL_ID = {hal-03415988},
  HAL_VERSION = {v1},
}

@article{liebermeister:hal-03410872,
  TITLE = {{Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States}},
  AUTHOR = {Liebermeister, Wolfram and Noor, Elad},
  URL = {https://hal.inrae.fr/hal-03410872},
  JOURNAL = {{Metabolites}},
  PUBLISHER = {{MDPI}},
  VOLUME = {11},
  NUMBER = {749},
  PAGES = {1-19},
  YEAR = {2021},
  MONTH = Oct,
  DOI = {10.3390/metabo11110749},
  KEYWORDS = {enzyme kinetic constant ; parameter estimation ; convex optimality problem ; parameter balancing ; enzyme cost minimisation},
  PDF = {https://hal.inrae.fr/hal-03410872/file/Liebermeister_2021_Metabolites_Model_Balancing.pdf},
  HAL_ID = {hal-03410872},
  HAL_VERSION = {v1},
}

@article{bernard:hal-03323846,
  TITLE = {{FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers}},
  AUTHOR = {Bernard, Maria and Ru{\'e}, Olivier and Mariadassou, Mahendra and Pascal, G{\'e}raldine},
  URL = {https://hal.inrae.fr/hal-03323846},
  JOURNAL = {{Briefings in Bioinformatics}},
  PUBLISHER = {{Oxford University Press (OUP)}},
  YEAR = {2021},
  MONTH = Aug,
  DOI = {10.1093/bib/bbab318},
  KEYWORDS = {metagenomics ; metabarcoding ; fungi ; amplicon ; ITS ; workflow},
  PDF = {https://hal.inrae.fr/hal-03323846/file/2021_Bernard_BriefBioInform.pdf},
  HAL_ID = {hal-03323846},
  HAL_VERSION = {v1},
}

@article{helie:hal-03306198,
  TITLE = {{Input/output reduced model of a damped nonlinear beam based on Volterra series and modal decomposition with convergence results}},
  AUTHOR = {H{\'e}lie, Thomas and Laroche, B{\'e}atrice},
  URL = {https://hal.archives-ouvertes.fr/hal-03306198},
  JOURNAL = {{Nonlinear Dynamics}},
  PUBLISHER = {{Springer Verlag}},
  VOLUME = {105},
  NUMBER = {1},
  PAGES = {515-540},
  YEAR = {2021},
  MONTH = Jul,
  DOI = {10.1007/s11071-021-06529-6},
  KEYWORDS = {Beam ; Partial differential equation ; Nonlinear systems ; Volterra series ; Modal truncation ; Convergence ; Error bounds},
  PDF = {https://hal.archives-ouvertes.fr/hal-03306198/file/HAL__NODY_HELIE_LAROCHE.pdf},
  HAL_ID = {hal-03306198},
  HAL_VERSION = {v1},
}

@article{bergou:hal-03285165,
  TITLE = {{Complexity iteration analysis for strongly convex multi-objective optimization using a Newton path-following procedure}},
  AUTHOR = {Bergou, El-Houcine and Diouane, Youssef and Kungurtsev, Vyacheslav},
  URL = {https://hal.inrae.fr/hal-03285165},
  JOURNAL = {{Optimization Letters}},
  PUBLISHER = {{Springer Verlag}},
  VOLUME = {15},
  NUMBER = {4},
  PAGES = {1215-1227},
  YEAR = {2021},
  MONTH = Jun,
  DOI = {10.1007/s11590-020-01623-x},
  KEYWORDS = {Multi-objective optimization ; Strongly convex optimization ; Path-following ; Newton method ; Complexity analysis},
  PDF = {https://hal.inrae.fr/hal-03285165/file/2021_Bergou_Optimization%20Letters.pdf},
  HAL_ID = {hal-03285165},
  HAL_VERSION = {v1},
}

@article{sellem:hal-03233594,
  TITLE = {{Dynamics of cattle sperm sncRNAs during maturation, from testis to ejaculated sperm}},
  AUTHOR = {Sellem, Eli and Marthey, Sylvain and Rau, Andrea and Jouneau, Luc and Allais-Bonnet , Aur{\'e}lie  and Le Danvic, Chrystelle and Guyonnet, Beno{\^i}t and Kiefer, H{\'e}l{\`e}ne and Jammes, H{\'e}l{\`e}ne and Schibler, Laurent},
  URL = {https://hal.archives-ouvertes.fr/hal-03233594},
  JOURNAL = {{Epigenetics \\& Chromatin}},
  HAL_LOCAL_REFERENCE = {MECP2},
  PUBLISHER = {{BioMed Central}},
  VOLUME = {14},
  PAGES = {2-18},
  YEAR = {2021},
  MONTH = May,
  DOI = {10.1186/s13072-021-00397-5},
  KEYWORDS = {RRFs ; TRFs ; MiRNA ; PiRNA ; Epididymis location ; Testicular parenchyma sperm ; Bovine ; SncRNAs ; Sperm epigenetics},
  PDF = {https://hal.archives-ouvertes.fr/hal-03233594/file/Sellem%20et%20al%202021.pdf},
  HAL_ID = {hal-03233594},
  HAL_VERSION = {v1},
}

@article{carpentier:hal-03391093,
  TITLE = {{Siland a R package for estimating the spatial influence of landscape}},
  AUTHOR = {Carpentier, Florence and Martin, Olivier},
  URL = {https://hal-agroparistech.archives-ouvertes.fr/hal-03391093},
  JOURNAL = {{Scientific Reports}},
  PUBLISHER = {{Nature Publishing Group}},
  VOLUME = {11},
  NUMBER = {1},
  PAGES = {7488},
  YEAR = {2021},
  MONTH = Apr,
  DOI = {10.1038/s41598-021-86900-0},
  PDF = {https://hal-agroparistech.archives-ouvertes.fr/hal-03391093/file/s41598-021-86900-0.pdf},
  HAL_ID = {hal-03391093},
  HAL_VERSION = {v1},
}

@article{chiquet:hal-03215628,
  TITLE = {{The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances}},
  AUTHOR = {Chiquet, Julien and Mariadassou, Mahendra and Robin, St{\'e}phane},
  URL = {https://hal.sorbonne-universite.fr/hal-03215628},
  JOURNAL = {{Frontiers in Ecology and Evolution}},
  PUBLISHER = {{Frontiers Media S.A}},
  VOLUME = {9},
  YEAR = {2021},
  MONTH = Mar,
  DOI = {10.3389/fevo.2021.588292},
  PDF = {https://hal.sorbonne-universite.fr/hal-03215628/file/fevo-09-588292.pdf},
  HAL_ID = {hal-03215628},
  HAL_VERSION = {v1},
}

@article{hoscheit:hal-03284092,
  TITLE = {{Dynamic centrality measures for cattle trade networks}},
  AUTHOR = {Hoscheit, Patrick and Anthony, Eric and Vergu, Elisabeta},
  URL = {https://hal.archives-ouvertes.fr/hal-03284092},
  JOURNAL = {{Applied Network Science}},
  PUBLISHER = {{Springer}},
  VOLUME = {6},
  YEAR = {2021},
  MONTH = Mar,
  DOI = {10.1007/s41109-021-00368-5},
  KEYWORDS = {Temporal networks ; Centrality ; Cattle trade ; Epidemic mitigation},
  PDF = {https://hal.archives-ouvertes.fr/hal-03284092/file/s41109-021-00368-5.pdf},
  HAL_ID = {hal-03284092},
  HAL_VERSION = {v1},
}

@article{schwendimann:hal-03365988,
  TITLE = {{Staphylococcal Enterotoxin Gene Cluster: Prediction of Enterotoxin (SEG and SEI) Production and of the Source of Food Poisoning on the Basis of v Sa$\beta$ Typing}},
  AUTHOR = {Schwendimann, Livia and Merda, D. and Berger, T. and Denayer, S. and Feraudet-Tarisse, C. and Kl{\"a}ui, A. J. and Messio, Sabine and Mistou, M. Y. and Nia, Y. and Hennekinne, J. A. and Graber, H. U.},
  URL = {https://hal.inrae.fr/hal-03365988},
  JOURNAL = {{Applied and Environmental Microbiology}},
  PUBLISHER = {{American Society for Microbiology}},
  VOLUME = {87},
  NUMBER = {5},
  YEAR = {2021},
  MONTH = Feb,
  DOI = {10.1128/AEM.02662-20},
  KEYWORDS = {Staphylococcus aureus ; egc ; enterotoxin},
  PDF = {https://hal.inrae.fr/hal-03365988/file/AEM.02662-20.pdf},
  HAL_ID = {hal-03365988},
  HAL_VERSION = {v1},
}

@article{derozier:hal-03131704,
  TITLE = {{Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations}},
  AUTHOR = {D{\'e}rozier, Sandra and Nicolas, Pierre and M{\"a}der, Ulirke and Gu{\'e}rin, Cyprien},
  URL = {https://hal.archives-ouvertes.fr/hal-03131704},
  JOURNAL = {{Bioinformatics}},
  PUBLISHER = {{Oxford University Press (OUP)}},
  YEAR = {2021},
  MONTH = Feb,
  DOI = {10.1093/bioinformatics/btab079},
  PDF = {https://hal.archives-ouvertes.fr/hal-03131704/file/genoscapist_hal.pdf},
  HAL_ID = {hal-03131704},
  HAL_VERSION = {v1},
}

@article{lefeunteun:hal-03117715,
  TITLE = {{Physiologically Based Modeling of Food Digestion and Intestinal Microbiota: State of the Art and Future Challenges. An INFOGEST Review}},
  AUTHOR = {Le Feunteun, Steven and Al-Razaz, Ahmed and Dekker, Matthijs and George, Erwin and Laroche, B{\'e}atrice and Van Aken, George},
  URL = {https://hal.inrae.fr/hal-03117715},
  JOURNAL = {{Annual Review of Food Science and Technology}},
  PUBLISHER = {{Annual Reviews}},
  VOLUME = {12},
  PAGES = {16/1-16/19},
  YEAR = {2021},
  MONTH = Jan,
  DOI = {10.1146/annurev-food-070620-},
  KEYWORDS = {in silico ; gastrointestinal tract ; digestion ; transit ; absorption ; microbiota},
  PDF = {https://hal.inrae.fr/hal-03117715/file/annurev-food-070620-124140.pdf},
  HAL_ID = {hal-03117715},
  HAL_VERSION = {v1},
}

@article{gilquin:hal-01291769,
  TITLE = {{Iterative estimation of Sobol' indices based on replicated designs}},
  AUTHOR = {Gilquin, Laurent and Prieur, Cl{\'e}mentine and Arnaud, Elise and Monod, Herve},
  URL = {https://hal.inrae.fr/hal-01291769},
  JOURNAL = {{Computational and Applied Mathematics}},
  PUBLISHER = {{Springer Verlag}},
  VOLUME = {40},
  NUMBER = {18},
  YEAR = {2021},
  MONTH = Jan,
  DOI = {10.1007/s40314-020-01402-5},
  KEYWORDS = {Sobol' indices ; space-filling designs ; iterative estimator ; space-filling ; recursive estimator ; orthogonal array ; Sobol' index ; sensitivity analysis},
  PDF = {https://hal.inrae.fr/hal-01291769v5/file/manuscript.pdf},
  HAL_ID = {hal-01291769},
  HAL_VERSION = {v5},
}

@article{asenova:hal-02790978,
  TITLE = {{Inference on extremal dependence in the domain of attraction of a structured H{\"u}sler--Reiss distribution motivated by a Markov tree with latent variables}},
  AUTHOR = {Asenova, Stefka and Mazo, Gildas and Segers, Johan},
  URL = {https://hal.inrae.fr/hal-02790978},
  JOURNAL = {{Extremes}},
  PUBLISHER = {{Springer Verlag (Germany)}},
  YEAR = {2021},
  KEYWORDS = {multivariate extremes ; tail dependence ; graphical models ; latent variables ; tail tree ; river network ; H{\"u}sler-Reiss distribution ; Markov tree},
  PDF = {https://hal.inrae.fr/hal-02790978v2/file/hrmt_latent_2021-01-05.pdf},
  HAL_ID = {hal-02790978},
  HAL_VERSION = {v2},
}

@article{david:hal-03213698,
  TITLE = {{Optimization of sampling designs for pedigrees and association studies}},
  AUTHOR = {David, Olivier and Le Rouzic, Arnaud and Dillmann, Christine},
  URL = {https://hal.archives-ouvertes.fr/hal-03213698},
  JOURNAL = {{Biometrics}},
  PUBLISHER = {{Wiley}},
  YEAR = {2021},
  DOI = {10.1111/biom.13476},
  KEYWORDS = {Bayesian statistics ; genetic algorithm ; high-dimensional statistics ; optimal designs ; quantitative genetics},
  PDF = {https://hal.archives-ouvertes.fr/hal-03213698/file/20210501Sampling_hal.pdf},
  HAL_ID = {hal-03213698},
  HAL_VERSION = {v1},
}

@article{tahir:hal-03390655,
  TITLE = {{Accurate determination of epitope for antibodies with unknown 3D structures}},
  AUTHOR = {Tahir, Shifa and Bourquard, Thomas and Musnier, Astrid and Jullian, Yann and Corde, Yannick and Omahdi, Zakaria and Mathias, Laetitia and Reiter, Eric and Crepieux, Pascale and Bruneau, Gilles and Poupon, Anne},
  URL = {https://hal.archives-ouvertes.fr/hal-03390655},
  JOURNAL = {{mAbs}},
  PUBLISHER = {{Taylor \\& Francis}},
  VOLUME = {13},
  NUMBER = {1},
  PAGES = {1-10},
  YEAR = {2021},
  DOI = {10.1080/19420862.2021.1961349},
  KEYWORDS = {MAbTope ; Epitope Mapping ; Molecular docking ; Antibody modeling ; Antibody-antigen docking Antibody ; Epitope mapping ; epitope binning ; bioinformatics ; artificial intelligence ; dupilimumab},
  PDF = {https://hal.archives-ouvertes.fr/hal-03390655/file/Tahir-MAbs2021.pdf},
  HAL_ID = {hal-03390655},
  HAL_VERSION = {v1},
}

@article{morris:hal-03154445,
  TITLE = {{One Health concepts and challenges for surveillance, forecasting and mitigation of plant disease beyond the traditional scope of crop production}},
  AUTHOR = {Morris, Cindy E. and Geniaux, Ghislain and N{\'e}dellec, Claire and Sauvion, Nicolas and Soubeyrand, Samuel},
  URL = {https://hal.inrae.fr/hal-03154445},
  JOURNAL = {{Plant Pathology}},
  PUBLISHER = {{Wiley}},
  VOLUME = {71},
  PAGES = {86-97},
  YEAR = {2021},
  DOI = {10.1111/ppa.13446},
  KEYWORDS = {long distance dissemination ; knowledge inference ; disease forecasting ; agroecology ; spillover ; virulence drivers},
  PDF = {https://hal.inrae.fr/hal-03154445/file/Morris_OneHealth_PlantPathology_manus_27Feb2021.pdf},
  HAL_ID = {hal-03154445},
  HAL_VERSION = {v1},
}

@article{cazelles:hal-03346530,
  TITLE = {{A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic}},
  AUTHOR = {Cazelles, Bernard and Champagne, Clara and Nguyen-Van-Yen, Benjamin and Comiskey, Catherine and Vergu, Elisabeta and Roche, Benjamin},
  URL = {https://hal.sorbonne-universite.fr/hal-03346530},
  JOURNAL = {{PLoS Computational Biology}},
  PUBLISHER = {{Public Library of Science}},
  VOLUME = {17},
  NUMBER = {7},
  PAGES = {e1009211},
  YEAR = {2021},
  DOI = {10.1371/journal.pcbi.1009211},
  KEYWORDS = {COVID 19 ; Ireland ; Vaccination and immunization ; Epidemiology ; France ; Virus testing ; Hospitals ; Pathogens},
  PDF = {https://hal.sorbonne-universite.fr/hal-03346530/file/journal.pcbi.1009211.pdf},
  HAL_ID = {hal-03346530},
  HAL_VERSION = {v1},
}

@article{cazelles:hal-03342941,
  TITLE = {{Dynamics of the COVID-19 epidemic in Ireland under mitigation}},
  AUTHOR = {Cazelles, Bernard and Nguyen-Van-Yen, Benjamin and Champagne, Clara and Comiskey, Catherine},
  URL = {https://hal.sorbonne-universite.fr/hal-03342941},
  JOURNAL = {{BMC Infectious Diseases}},
  PUBLISHER = {{BioMed Central}},
  VOLUME = {21},
  NUMBER = {1},
  PAGES = {735},
  YEAR = {2021},
  DOI = {10.1186/s12879-021-06433-9},
  KEYWORDS = {COVID-19 ; Ireland ; Stochastic model ; Time varying parameters ; Mitigation},
  PDF = {https://hal.sorbonne-universite.fr/hal-03342941/file/s12879-021-06433-9.pdf},
  HAL_ID = {hal-03342941},
  HAL_VERSION = {v1},
}

@article{ezanno:hal-03161705,
  TITLE = {{Research perspectives on animal health in the era of artificial intelligence}},
  AUTHOR = {Ezanno, Pauline and Picault, S{\'e}bastien and Beaun{\'e}e, Ga{\"e}l and Bailly, Xavier and Mu{\~n}oz, Facundo and Duboz, Rapha{\"e}l and Monod, Herv{\'e} and Gu{\'e}gan, Jean-Fran{\c c}ois},
  URL = {https://hal.archives-ouvertes.fr/hal-03161705},
  JOURNAL = {{Veterinary Research}},
  PUBLISHER = {{BioMed Central}},
  VOLUME = {52},
  NUMBER = {1},
  PAGES = {40},
  YEAR = {2021},
  DOI = {10.1186/s13567-021-00902-4},
  KEYWORDS = {Animal disease ; Data ; Livestock ; Modelling ; Artificial intelligence ; Decision support tool},
  PDF = {https://hal.archives-ouvertes.fr/hal-03161705/file/13567_2021_Article_902.pdf},
  HAL_ID = {hal-03161705},
  HAL_VERSION = {v1},
}