Pascal CROISEAU
Présentation
GABI, équipe G2B 2008: Recrutement CRCN à l’INRAE de Jouy en Josas, unité GABI, équipe G2B Mes travaux de recherches portent sur l’exploitation de données génomiques bovine. Je peux en isoler deux composantes complémentaires : (1) D’une part l’identification et la comparaison de méthodes statistiques pour la sélection génomique. La sélection génomique consiste à prédire la valeur génétique d’animaux candidats à la sélection en exploitant les informations apportées par une population de référence. Je contribue à la mise en place et à l’amélioration des modèles de sélection génomique utilisés pour les évaluations génétiques nationales. (2) D’autre part, la sélection génomique s’appuie sur la connaissance des régions QTL. Pour améliorer la qualité de prédiction de nos méthodes, l’identification et la localisation des QTL est une étape clé. Si durant la période 2008-2015, mes travaux ont été guidés par l’accès à de nouvelles technologies (exploitation de la puce 50K pour la mise en place d’une évaluation génomique officielle en France chez les grandes races bovines laitières ; exploitation d’une puce haute densité pour améliorer la précision des évaluations génomiques et étendre ces évaluations aux races régionales), depuis 2015, mes travaux visent à exploiter les propriétés des méthodes d’évaluation génomique ainsi que de la sélection génomique mise en place dans les entreprises de sélection pour répondre aux grands enjeux de demain tel que le maintien de la diversité génétique ou encore le développement d’une évaluation génomique en croisement. 2021: Habilitation à Diriger des Recherches (Université Paris-Saclay) 2004-2008: Doctorat de l’Université de Paris-Sud, Ecole doctorale Gène Génome Cellule, spécialité : génétique statistique (Mention très honorable). Cette thèse a été réalisée sous la direction de E. Génin à l’unité INSERM 535 (Hôpital Paul Brousse, Villejuif, directrice : F. Clerget-Darpoux) et soutenue le 14 janvier 2008 devant le jury : Sujet: Influence et traitement des données manquantes dans les études d’association en génétique: application à la Sclérose en Plaques. 2003-2004: D.E.A. de génétique multifactorielle, Université Paris Sud. 2004: Déterminisme génétique de la Sclérose en Plaques : Rôle de 2 gène candidats (CTLA4 et HLA-DRB1). Directrice de stage : E. Génin ; INSERM U535, stage de DEA : 6 mois. 2007: Post-doctorat à l’Institut de Génétique Humaine de l’Université de Newcastle (Angleterre). Responsable : Heather Cordell.
Domaine de Vilvert,
78352 Jouy en Josas
01-34-65-21-97
pascal.croiseau@inrae.frFORMATIONS et EXPERIENCES PROFESSIONNELLES
Parcours professionnel
Diplômes
2001-2003: Licence-Maîtrise de Biologie Informatique, Université Paris VII.
1999-2001: DEUG de biologie, Université Paris VII.Formations complémentaires en France
2004: Analyse génétique de lignées de poules sélectionnées pour des réponses immunitaires. Directrice de stage : M.H. Pinard ; INRA (Jouy en Josas), stage de DEA, 3 mois.Formations complémentaires à l’étranger
ENSEIGNEMENTS
2008-2020 : Master PRIAM
Encadrements :
EXPERTISES SCIENTIFIQUES
LANGUE et LANGAGES
Langue
Compétences informatiques
COMPETENCES SCIENTIFIQUES ET GESTION DE PROJETS
Compétences en génétique
Montage et Gestion de projets
Production scientifique :
Publications
Publications
Fast and accurate estimation of breed origin of alleles in crossbred populations76th EAAP Annual Meeting, Sep 2025, Innsbruck, Austria |
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Deep Learning for Crossbred Genomic Prediction: Integrating Transfer Learning and Heterosis Effects76th EAAP Annual Meeting, Sep 2025, Innsbruck, Austria |
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Genetic correlations: more than a parameter that defines relationships between traitsInternational Conference of Quantitative Genetics, Feb 2025, Lucca, Italy |
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Genomic prediction integrating indirect breeding values from MIR spectra data in dairy cows76th EAAP Annual Meeting, Sep 2025, Innsbruck, Austria |
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Detecting genetic load: A GWAS model accounting for identity by descent76th EAAP Annual Meeting, Aug 2025, Innsbruck, Austria |
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The impact of using individual-specific genetic correlations on the ranking and genetic covariance parameters of selection candidates76th EAAP Annual Meeting, Sep 2025, Innsbruck, Austria |
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Unraveling the influence of the host genetic on vaginal microbiota composition in Holstein cowsEuropean Federation of Animal Science, Sep 2024, Florence, Italy |
Genetic correlations: a parameter or a latent phenotype in genetic evaluations?Interbull annual meeting, May 2024, Bled (Slovénie), Slovenia |
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Evaluating the Efficiency of Phenomic Selection in Dairy CattleEuropean Federation of Animal Science, Sep 2024, Florence, Italy |
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Genomic prediction using functional annotations and QTL features in dairy and beef cattle.breeds75. Annual Meeting of the European Federation of Animal Science (EAAP 2024), European Federation of Animal Science (EAAP), Sep 2024, Florence, Italy. pp.292 |
Sequence-based GWAS analyses revealed genome regions associated with the fecal microbiota in Holstein27. Rencontres autour des recherches sur les ruminants (3R 2024), Institut de l'Elevage - INRAE, Dec 2024, Paris, France. pp.65-69 |
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Benchmarking predictive models: evaluating parametric, ensemble, and deep learning approaches for animal phenotype prediction from genotypes.AI and biology Symposium, EMBO EMBL, Heidelberg, Mar 2024, Heidelberg, Germany |
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GBLUP AND DEEP LEARNING INTEGRATION: A NOVEL APPROACH TO EVALUATING NONLINEARLY RELATED GENETIC TRAITSInternational Conference of Quantitative Genetics, Jul 2024, Vienne, Austria |
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Host genes shape the lower gut microbiota of Holstein cows: evidence from sequence-based GWASEuropean Federation of Animal Science, Sep 2024, Florence, Italy |
Loss of diversity in the Holstein breedWorld Holstein Conference, Nov 2023, Puy-du-Fou, France |
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Impact of genomic selection on genetic diversity in five European local cattle breedsBook of Abstracts of the 74. Annual Meeting of the European Federation of Animal Science, INRAE, Aug 2023, Lyon, France. pp.180 |
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Host genetics affects the composition of the lower gut microbiota in dairy cows74th Annual Meeting of the European Federation of Animal Science, Aug 2023, Lyon, France. ⟨10.3920/978-90-8686-936-7⟩ |
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Methods to Estimate Erosion Factors of Genomic Breeding Values of Candidates due to Long-Distance Linkage Disequilibrium2023 Interbull Meeting, Interbull, Aug 2023, Lyon, France. pp.33-41 |
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Exploring Non-Linear Genetic Relationships Between Correlated Traits74th Annual Meeting of the European Association for Animal Production, INRAE, Aug 2023, Lyon, France |
Host genetics affect the composition of the lower gut microbiota in dairy cowsBook of Abstracts of the 74. Annual Meeting of the European Federation of Animal Science, EAAP, Aug 2023, Lyon, France. pp.518 |
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Incorporating biological information into genomic prediction modelsVistaMilk Artificial Intelligence in Agriculture Masterclass, Feb 2023, Online, Ireland |
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Characterization of bovine vaginal microbiota and its relationship with host phenotypesEuropean Federation of Animal Science, Sep 2022, Porto, Portugal |
Leveraging multi-omic data for integrative exploratory and predictive analysesJournées Math Bio Santé du GDR MATHSAV, Oct 2022, Besançon, France |
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Long-distance associations generate erosion of genomic breeding values of candidates for selection12th World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands |
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Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde x Holstein x Red Danish)ICAR/Interbull Annual Conference, May 2022, Montréal, Canada |
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Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde x Holstein x Red Danish)26èmes Rencontres Recherches Ruminants, Idele-Inrae, Dec 2022, Paris, France. pp.183-186 |
272. Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde × Holstein × Red Danish)World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands. pp.1148-1151, ⟨10.3920/978-90-8686-940-4_272⟩ |
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Exploiting prior knowledge into genomic prediction models with BayesRCO50th European Mathematical Genetics Meeting (EMGM), Apr 2022, Cambridge, United Kingdom |
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Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde x Holstein x Red Danish)12th World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands |
288. Long-distance associations generate erosion of genomic breeding values of candidates for selectionWorld Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands. pp.1213-1216, ⟨10.3920/978-90-8686-940-4_288⟩ |
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Accuracy of prediction for a genomic evaluation in rotational crossbreeding scheme (Montbéliarde × Holstein × Red Danish)12th World congress of genetics applied to livestock production, Jul 2022, Rotterdam (NL), Netherlands |
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Mise en place d'une évaluation génomique pour les animaux issus d'un croisement trois voies : Montbéliarde X Holstein X Rouge Danoise3R2022 : 26èmes Rencontres autour des Recherches sur les Ruminants., Institut de l'élevage [IDELE] INRAE, Dec 2022, Paris, France |
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Sequence-based GWAS meta-analyses for beef production traits12th World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands |
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Capitalizing on complex annotations in Bayesian genomic prediction for a backcross population of growing pigs12th World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands |
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Evaluating the Interpretability of SNP Effect Size Classes in Bayesian Genomic Prediction Models49th European Mathematical Genetics Meeting (EMGM), Apr 2021, Paris, France. pp.69-100, ⟨10.1159/000516194⟩ |
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The Use of A Priori Biological Information to Evaluate the Ability of BayesRC Model in Genomic Prediction72st Annual Meeting of the European Association for Animal Production, Aug 2021, Davos, Switzerland |
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Sequence -based GWAS for milk production traits, udder health and morphology in French dairy cattle71th Annual Meeting of the European Association for Animal Production, Dec 2020, Virtual, France |
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Impact of multiple ovulation and embryo transfer on genetic gain and diversity in dairy cattle70. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2019, Gant, Belgium |
Evolution of ROH’s distribution along the genome over a decade of genomic selection in dairy cattle70tH Annual meeting of the European Federation of Animal Science, Aug 2019, Ghent, Belgium |
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Impact of multiple ovulation and embryo transfer on genetic gain and diversity in dairy cattle70th Annual Meeting of European Federation of Animal Science, Aug 2019, Ghent, Belgium |
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Use of haploblocks in genomic evaluation of Holsteins.World congress on Genetics Applied to Livestock Production, Feb 2018, Auckland, Australia |
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Inclusion of candidate mutations in genomic evaluation for French dairy cattle breeds69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2018, Dubrovnik, Croatia |
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Use of whole sequence GWAS to improve genomic evaluation in dairy cattleWorld Congress on Genetics Applied to Livestock Production, Feb 2018, Auckland, Australia |
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Evolution of ROH's distribution along the genome over a decade of genomic selection in dairy cattle69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2018, Dubrovnik, Croatia |
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Experience from large scale use of the EuroGenomics custom SNP chip in cattle11. World Congress of Genetics Applied to Livestock Production, Feb 2018, Auckland, New Zealand |
The impact of genomic selection on genetic diversity and genetic gain in French dairy cattle breeds.69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2017, Dubrovnik, Croatia |
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Use of whole sequence GWAS to improve genomic evaluation in dairy cattlePlant and Animal Genome Conference, Jan 2017, San Diego, United States |
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Use of whole sequence GWAS to improve genomic evaluation in dairy cattle24. Plant and Animal Genome Conference, Jan 2017, San Diego, United States |
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French genomic experience: genomics for all ruminant species2016 Interbull Meeting, Oct 2016, Puerto Varas, Chile |
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Identification of candidate causal variants underlying QTL in dairy cattle through GWAS and Bayesian approach at the sequence levelPAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States |
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French genomic experience: genomics for all ruminant species40. Biennal session of ICAR, Oct 2016, Puerto Varas, Chile |
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Mise en place d’une évaluation génomique en races Abondance, Tarentaise et Vosgienne23. Rencontres autour des Recherches sur les Ruminants, Dec 2016, Paris, France |
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How is genomics changing cattle breeding?JAM Joint Annual Meeting, Jul 2016, Salt Lake City, United States |
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Using whole genome sequences to identify QTL for udder health and morphology in French dairy cattle67. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2016, Belfast, United Kingdom |
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Using genomes sequences to identify causal variants for milk fatty acids in dairy cattle66. Annual Meeting of the European Federation of Animal Science (EAAP), European Federation of Animal Science (EAAP). INT., Aug 2015, Warsaw, Poland |
Using sequences data to identify causal variants for milk fatty acids composition in dairy cattle66. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2015, Varsovie, Poland. 577 p |
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Haplotype construction methods to enhance genomic evaluation66. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2015, Varsovie, Poland. 577 p |
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ldentification de mutations candidates affectant la composition du lait en acides gras et protéines par analyse d’association sur la séquence du génome dans les races Holstein, Montbéliarde et Normande22. Rencontres autour des Recherches sur les Ruminants, Dec 2015, Paris, France. 409 p |
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Identification of causal variants for milk protein composition using sequence data in dairy cattle66. Annual Meeting of the European Federation of Animal Science (EAAP), European Federation of Animal Science (EAAP). INT., Aug 2015, Warsaw, Poland |
Multibreed association studies at the sequence level : comparison between meta and joint analyses.66. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2015, Varsovie, Poland |
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Comparison of different Marker-Assisted BLUP models for a new French genomic evaluation66. Annual Meeting of the European Federation of Animal Science (EAAP), European Federation of Animal Science (EAAP). INT., Aug 2015, Warsaw, Poland |
In silico detection of causal mutation in beef cattle.Journée ouvertes en Biologie, Informatique et Mathématique, Sep 2015, Clermont Ferrand, France |
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Genomic evaluation using QTL information10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada |
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Mise en place de l’évaluation génomique française officielle en race Brune21. Rencontres Recherches Ruminants, Dec 2014, Paris, France |
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Mise en place d’évaluations génomiques dans les races bovines laitières à effectifs limités en France21. Rencontres Recherches Ruminants, Dec 2014, Paris, France |
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Genomic evaluation using combined reference populations from Montbéliarde and French Simmental breeds10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada |
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Extension to haplotypes of genomic evaluation algorithms10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada |
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Application of a three-haplotype LDLA model to the French Holstein population10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada |
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Implementation of the French official genomic evaluation in Brown Swiss dairy cattle10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada |
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Comparison of genomic selection approaches for small breedsInterbull Meeting 2013, Aug 2013, Nantes, France. pp.90-94 |
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From the 50K chip to the HD: Imputation efficiency in 9 French dairy cattle breedsEAAP, Aug 2012, Bratislava, Slovakia. pp.308 |
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Could genomic selection methods be efficient to detect QTLs? Application in French dairy cattleQTLMAS, May 2011, Rennes, France. pp.30 |
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Use of phenotypes from multi-trait national evaluations in genomic evaluation62. Annual meeting of the EAAP, Aug 2011, Stavanger, Norway. pp.28 |
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Genomic selection: implementation in dairy cattle5th QTL-MAS workshop, May 2011, Rennes, France |
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State of the art of genomics for selectionWorkshop of ICAR 2011 "New technologies and new challenges for breeding and herd management", Jun 2011, Bourg-en-Bresse, France. 1 p |
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Genomic Selection In French Dairy CattleApplied Genomics for Sustainable Livestock Breeding, May 2011, Melbourne, Australia. 1 p |
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État de l'art de la sélection génomique en France et approche multiracialeColloque International, La génomique bovine Contribution de la génomique à l’avenir de l’élevage bovin - International Workshop, Bovine genomics Contributions to the future of livestock, Oct 2011, Clermont-Ferrand/Cournon, France. 2 p |
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Genomic selection in French dairy cattle.9th World Congress on Genetics Applied to Livestock Production, 2010, Leipzig, pp.Inconnu |
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Lasso bayesiano mejorado para seleccion genomicaXV Reunion Nacional de Mejora Genetica Animal, Jun 2010, Vigo, España. pp.1-6 |
Aptitude of Bayesian lasso for genomic selection9. World Congress on Genetics Applied to Livestock Production, Aug 2010, Leipzig, Germany |
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Application of PLS and Sparse PLS regression in genomic selection9. World Congress on Genetics Applied to Livestock Production, Aug 2010, Leipzig, Germany |
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Intérêt d'une puce basse densité pour l'évalution génomique des vaches laitières.17. Rencontres autour des Recherches sur les Ruminants, Dec 2010, Paris, France |
Improving genomic evaluation strategies in dairy cattle through SNP pre-selection9. World Congress on Genetics Applied to Livestock Production, Aug 2010, Leipzig, Germany |
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Mise en place de la sélection génomique dans les trois principales races françaises de bovins laitiers17. Rencontres autour des Recherches sur les Ruminants, Dec 2010, Paris, France |
Use of the elastic-net algorithm for genomic selection in dairy cattle.60th Annual Meeting of the European Association for Animal Production (EAAP), 2427 August 2009, 2009, Barcelona |
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Use of the Elastic-Net algorithm for genomic selection in dairy cattle13th Quantitative Trait Locus and Marker Assisted Selection Workshop, Apr 2009, Wageningen, Netherlands. pp.Book of Abstracts: 15 |
Modèles d'évaluation génomique : application aux populations bovines laitières françaises16. Rencontres autour des Recherches sur les Ruminants, Dec 2009, Paris, France |
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Marker assisted EBV using a dense SNP markers map: application to the Normande and Montbéliarde breeds.60th Annual Meeting of the European Association for Animal Production (EAAP), 2427 August 2009, 2009, Barcelona |
Sequence-based GWAS identify genomic regions associated with resistance to gastrointestinal strongyles in Holstein heifers76th EAAP Annual Meeting, Aug 2025, Innsbruck, Austria |
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Sequence-based GWAS meta-analyses for beef production traits39th International Society for Animal Genetics Conference, Jul 2023, Cape Town / Le Cap, South Africa |
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Impact of the correlation between SNP effects in different breeds on the accuracy of predictions74th Annual Meeting of the European Federation of Animal Science, Aug 2023, Lyon, France. Wageningen Academic Publishers, Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science, ⟨10.3920/978-90-8686-936-7⟩ |
A hierarchical Bayesian mixture model for predicting phenotypes from genomic data with prior biological informationWorking Group on Model-Based Clustering Summer Session, Jul 2022, Online, France. |
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A SNP-BLUP genomic evaluation with breed-specific SNP effects for three-way dairy crossbreds71st Annual Meeting of the European Association for Animal Production, Dec 2020, Virtual, France |
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Imputation accuracy of crossbred dairy cows71. Annual Meeting of the European Federation of Animal Science (EAAP), Dec 2020, Virtual meeting, Portugal. Wageningen Academic Publishers, Book of abstracts, 26, 2020, Book of abstracts of the 71st annual meeting of the european federation of animal science |
Updating reference population in Genomic Selection for genetic diversity conservation What can we learn from real data and simulations?Gordon Research Conference in Quantitative Genetics and Genomics, Feb 2017, Galveston Texas, United States. 2017 |
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Implementation of genomic selection in three French regional dairy cattle breeds67. Annual meeting of the European Federation of Animal Science EAAP 2016, Aug 2016, Belfast, United Kingdom. 2016, Book of Abstract of the 67th Annual Meeting of the European Federation of Animal Science |
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Using whole genome sequences to identify candidate mutations of bovine milk fatty acids and proteins in fairy cattlePAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States. pp.P0526, 2016 |
Which individual to phenotype? Optimal design of reference population for genomic selection while maintaining genetic diversityICQG 5, Jun 2016, Madison, Wisconsin, United States. 2016 |
Valoriser la diversité génétique en sélection végétale et animaleINRAE. Agroécologie : des recherches pour la transition des filières et des territoires, Editions Quae, pp.59-69, 2020, 978-2-7592-3129-4 |
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Quel futur pour l’amélioration génétique chez les espèces animales domestiques ?Potentiels de la science pour l’avenir de l’agriculture, de l’alimentation et de l’environnement, Académie d'Agriculture, 2014 |
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Deep Learning for genomic prediction accounting for heterosis in crossbreeding systems2025 |
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Characterization of bovine vaginal microbiota and its relationship with host fertility, health, and production2023 |
Analyse génétique de lignées de poules sélectionnées pour des réponses immunitaires.[Stage] Université Paris Sud - Paris 11 (UP11), Inconnu, FRA. 2004 |
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Genomic selection: from technological development to application to the major challenges of tomorrowAnimal genetics. Université paris saclay, 2021 |
BayesRCO2022 |