Recent publications
Lien CY, Tixier-Boichard M, Wu SW, Chen CF. 2024. Identification of quantitative trait locus and positional candidate loci influencing chicken egg quality under tropical conditions. Tropical Animal Health and Production. https://doi.org/10.1007/s11250-024-04197-3
2024
Bédère N, Dupont J, Baumard Y, Staub C, Gourichon D, Frédéric E, Le Roy P, Zerjal T. Genetic background of body reserves in laying hens through backfat thickness phenotyping. Peer Community Journal. https://doi.org/10.24072/pcjournal.412
Bernard M, Lecoeur A, Coville J-L, Bruneau N, Jardet D, Lagarrigue S, Meynadier A, Calenge F, Pascal G, Zerjal T. 2024. Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions. Scientif Rep
Besnard F., Guintard A., Grohs C., Guzylack-Piriou L., Cano M., Escouflaire C., Hoze C., Leclerc H., Buronfosse T., Dutheil L., Jourdain J., Barbat A., Fritz S., Deloche M.C., Remot A., Gausseres B., Clement A., Bouchier M., Contat E., Relun A., Plassard V., Riviere J., Pechoux C., Vilotte M., Eche C., Kuchly C., Charles M., Boulling A., Viard G., Minery S., Barbey S., Birbes C., Danchin-Burge C., Launay F., Mattalia S., Allais-Bonnet A., Ravary B., Millemann Y., Guatteo R., Klopp C., Gaspin C., Iampietro C., Donnadieu C., Milan D., Arcangioli M.A., Boussaha M., Foucras G., Boichard D., Capitan A. Massive detection of cryptic recessive genetic defects in cattle mining millions of life histories ? Genome Biol.
Bortoluzzi C, Restoux G, Rouger R, Desnoues B, Petitjean F, Bosse M, Tixier-Boichard M. 2024. Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds. bioRXiv GiBBS https://doi.org/10.1101/2024.02.22.581528
Bortoluzzi C, Restoux G, Rouger R, Desnoues B, Petitjean F, Bosse M, Tixier-Boichard M. 2024. Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds.Peer Community Journal. https://doi.org/10.24072/pcjournal.474
Collin A, Coustham V, Tona JK, Tesseraud S, Mignon-Grasteau S, Méda B, Vitorino Carvalho A, Guyot Y, Lagarrigue S, Pitel F, Zerjal T. Face au changement climatique, quelles stratégies d’atténuation et d’adaptation pour les productions avicoles ? INRAE Productions Animales. https://doi.org/10.20870/productions-animales.2023.36.4.7384
Coste V, Sellem E, Marthey S, Hoze C, Bonnet A, Schibler L, Kieffer H, Jaffrezic F. 2024. Multi-omics data integration for the identification of predictive biomarkers for bull fertility. PlosOne. https://doi.org/10.1371/journal.pone.0298623
Daniel-Carlier N, Castille J, Passet B, Vilotte M, Le Danvic C, Jaffrezic F, Beauvallet C, Péchoux C, Capitan A, Vilotte J-L. 2024 Targeted mutation and inactivation of the kinesin light chain 3 protein-encoding gene have no impact on mouse fertility. Biology of Reproduction https://doi.org/10.1093/biolre/ioad131
Débare H, Blanc F, Piton G, Leplat JJ, Vincent‑Naulleau S, Rivière J, Vilotte M, Marthey S, Lecardonnel J, Coville JL, Estellé J, Rau A, Bourneuf E, Egidy G. Malignant features of minipig melanomas prior to spontaneous regression. Scientif Rep. https://doi.org/10.1038/s41598-024-59741-w
Degalez F, Charles M, Foissac S, Zhou H, Guan D , Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. 2024. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Scientif Rep https://doi.org/10.1038/s41598-024-56705-y
Degrelle SA, Liu F, Laloe D, Richard C, Le Bourhis D, Rossignol MN, Hue I. 2024. Understanding bovine embryo elongation: a transcriptomic study of trophoblastic vesicles. Front Physiol https://doi.org/10.3389/fphys.2024.1331098
Dufour A, Kurilo C, Stöckl JB, Laloë D, Bailly Y, Manceau P, Martins F, Turhan AG, Ferchaud S, Pain B, Fröhlich T, Foissac S, Artus J, Acloque H. 2024. Cell specification and functional interactions in the pig blastocyst inferred from single cell transcriptomics and uterine fluids proteomics. Genomics https://doi.org/10.1016/j.ygeno.2023.110780
Girardie O, Laloe D, Bonneau M, Billon Y, Bailly J, David I, Canario L. Primiparous sow behaviour on the day of farrowing as one of the primary contributors to the growth of piglets in early lactation. Scientif Rep. https://doi.org/10.1038/s41598-024-69358-8
Ivanova E, Hue-Beauvais C, Castille J, Laubier J, Le Guillou S, Aujean E, Lecardonnel J, Lebrun L, Jaffrezic F, Rousseau-Ralliard D, Péchoux C, Letheule M, Foucras G, Charlier M, Le Provost F. 2024. Mutation of SOCS2 induces structural and functional changes in mammary development. Development. https://doi.org/10.1242/dev.202332
Jacques A, Duclos D, Danchin-Burge C, Mercat M-J, Tixier-Boichard M, Restoux G. 2024. Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank. Peer Community Journal. https://doi.org/10.24072/pcjournal.369
Laubier J, Van De Wiele A, Barboiron A, Laloë D, Saint-Andrieux C, Castille J, Meloni E, Ernst S, Pellerin M, Floriot S, Daniel-Carlier N, Passet B, Merlet J, Verheyden H, Béringue V, Andréoletti O, Houston F, Vilotte J-L, Bourret V, Moazami-Goudarzi K. 2024. Variation in the prion protein gene (PRNP) open reading frame sequence in French cervids. Vet Res. https://doi.org/10.1186/s13567-024-01362-2
Lefevre F, Bojkovskib D, Bou Dagher Kharrat M, Bozzano M, Charvolin-Lemaire E, Hiemstra SJ, Kraigher H, Laloe D, Restoux G, Sharrock S, Sturaro E, van Hintum T, Westergren M, Maxted N, GenRes Bridge Expert Panel. 2024. European genetic resources conservation in arapidly changing world: three existential challengesfor the crop, forest and animal domains in the 21stcentury. Genetic Resources. https://doi.org/10.46265/genresj.REJR689
Paul K, Restoux G, Phocas F. 2024. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Gen Sel Evol. https://doi.org/10.1186/s12711-024-00884-9
Poncet M, Féménia M, Pierre C, Charles M, Capitan A, Boulling A, Rocha D. 2024. Nuclear sequences of mitochondrial origin in domestic yak Scientif Rep. https://doi.org/10.1038/s41598-024-61147-7
The FarmGTEx PigGTEx Consortium,... Giuffra E... Rocha D, Charles M,... Fang L. 2024. A compendium of genetic regulatory effects across pig tissues. Nature comm. https://doi.org/10.1038/s41588-023-01585-7
2024
Bédère N, Dupont J, Baumard Y, Staub C, Gourichon D, Frédéric E, Le Roy P, Zerjal T. Genetic background of body reserves in laying hens through backfat thickness phenotyping. Peer Community Journal. https://doi.org/10.24072/pcjournal.412
Bernard M, Lecoeur A, Coville J-L, Bruneau N, Jardet D, Lagarrigue S, Meynadier A, Calenge F, Pascal G, Zerjal T. 2024. Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions. Scientif Rep
Bortoluzzi C, Restoux G, Rouger R, Desnoues B, Petitjean F, Bosse M, Tixier-Boichard M. 2024. Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds. bioRXiv GiBBS https://doi.org/10.1101/2024.02.22.581528
Collin A, Coustham V, Tona JK, Tesseraud S, Mignon-Grasteau S, Méda B, Vitorino Carvalho A, Guyot Y, Lagarrigue S, Pitel F, Zerjal T. Face au changement climatique, quelles stratégies d’atténuation et d’adaptation pour les productions avicoles ? INRAE Productions Animales. https://doi.org/10.20870/productions-animales.2023.36.4.7384
Coste V, Sellem E, Marthey S, Hoze C, Bonnet A, Schibler L, Kieffer H, Jaffrezic F. 2024. Multi-omics data integration for the identification of predictive biomarkers for bull fertility. PlosOne. https://doi.org/10.1371/journal.pone.0298623
Débare H, Blanc F, Piton G, Leplat JJ, Vincent‑Naulleau S, Rivière J, Vilotte M, Marthey S, Lecardonnel J, Coville JL, Estellé J, Rau A, Bourneuf E, Egidy G. Malignant features of minipig melanomas prior to spontaneous regression. Scientif Rep. https://doi.org/10.1038/s41598-024-59741-w
Degrelle SA, Liu F, Laloe D, Richard C, Le Bourhis D, Rossignol MN, Hue I. 2024. Understanding bovine embryo elongation: a transcriptomic study of trophoblastic vesicles. Front Physiol https://doi.org/10.3389/fphys.2024.1331098
Dufour A, Kurilo C, Stöckl JB, Laloë D, Bailly Y, Manceau P, Martins F, Turhan AG, Ferchaud S, Pain B, Fröhlich T, Foissac S, Artus J, Acloque H. 2024. Cell specification and functional interactions in the pig blastocyst inferred from single cell transcriptomics and uterine fluids proteomics. Genomics https://doi.org/10.1016/j.ygeno.2023.110780
Ivanova E, Hue-Beauvais C, Castille J, Laubier J, Le Guillou S, Aujean E, Lecardonnel J, Lebrun L, Jaffrezic F, Rousseau-Ralliard D, Péchoux C, Letheule M, Foucras G, Charlier M, Le Provost F. 2024. Mutation of SOCS2 induces structural and functional changes in mammary development. Development. https://doi.org/10.1242/dev.202332
Jacques A, Duclos D, Danchin-Burge C, Mercat M-J, Tixier-Boichard M, Restoux G. 2024. Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank. Peer Community Journal. https://doi.org/10.24072/pcjournal.369
Laubier J, Van De Wiele A, Barboiron A, Laloë D, Saint-Andrieux C, Castille J, Meloni E, Ernst S, Pellerin M, Floriot S, Daniel-Carlier N, Passet B, Merlet J, Verheyden H, Béringue V, Andréoletti O, Houston F, Vilotte J-L, Bourret V, Moazami-Goudarzi K. 2024. Variation in the prion protein gene (PRNP) open reading frame sequence in French cervids. Vet Res. https://doi.org/10.1186/s13567-024-01362-2
Lefevre F, Bojkovskib D, Bou Dagher Kharrat M, Bozzano M, Charvolin-Lemaire E, Hiemstra SJ, Kraigher H, Laloe D, Restoux G, Sharrock S, Sturaro E, van Hintum T, Westergren M, Maxted N, GenRes Bridge Expert Panel. 2024. European genetic resources conservation in arapidly changing world: three existential challengesfor the crop, forest and animal domains in the 21stcentury. Genetic Resources. https://doi.org/10.46265/genresj.REJR689
Paul K, Restoux G, Phocas F. 2024. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Gen Sel Evol. https://doi.org/10.1186/s12711-024-00884-9
The FarmGTEx PigGTEx Consortium,... Giuffra E... Rocha D, Charles M,... Fang L. 2024. A compendium of genetic regulatory effects across pig tissues. Nature comm. https://doi.org/10.1038/s41588-023-01585-7
2023
Adel-Patient K, Campeotto F, Grauso M, Guillon B, Moroldo M, Venot E, Dietrich C, Machavoine F, Castelli F, Fenaille F, Molina TJ, Barbet P, Delacourt C, Leite-de-Moraes M, Lezmi G. 2023. Assessment of local and systemic signature of eosinophilic esophagitis (EoE) in children through multi-omics approaches. Frontiers in immunology.
Bi H, Tranell J, Harper DC, Lin W, Li J, Hellstrom AR, Larsson M, Rubin C-J, Wang C, Sayyab S, Kerje S, Bed'hom B, Gourichon D, Ito S, Wakamatsu K, Tixier-Boichard M, Marks MS, Globisch D, Andersson L. 2023. A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken. PLoS genetics.
Couix N, Lauvie A, Verrier E. 2023. Biodiversité domestique animale : à quoi tenons-nous ? Quae Edition (chapitre)
Coustham V, Andrieux C, Cerutti C, Collin A, David I, Demars J, Devailly G, Morisson M, Houssier M, Lagarrigue S, Métayer-Coustard S, Mignon-Grasteau S, Panserat S, Petit A, Vitorino Carvalhos A, Zerjal T, Pitel F Épigénétique, gènes et environnement : quelle importance pour les pratiques d’élevage et les méthodes de sélection des volailles ? INRAE Prod Anim https://doi.org10.20870/productions-animales.2023.36.4.7384
Danchin-Burge C, Tixier-Boichard M, Danvy S, Sabbagh M. 2023. Méthodes et pratiques de gestion et de préservation de la biodiversité domestique animale. Quae Edition (chapitre)
Daniel-Carlier N, Castille J, Passet B, Vilotte M, Le Danvic C, Jaffrezic F, Beauvallet C, Pechoux C, Capitan A, Vilotte J-L. 2023. Targeted mutation and inactivation of the kinesin light chain 3 protein-encoding gene have no impact on mouse fertility. Biology of reproduction.https://doi.org/10.1093/biolre/ioad131
Delosiere M, Bernard L, Hurtaud C, Guilleton M, Viala D, Rau A, Bonnet M, Cebo C. 2023. Protein signatures of spontaneous lipolysis and lipoprotein lipase activity in cow's milk. Journal of proteomics.
Dufour A, Kurilo C, Stöckl JB, Laloë D, Bailly Y, Manceau P, Martins F, Turhan AG, Ferchaud S, Pain B, Fröhlich T, Foissac S, Artus J, Acloque H. 2023. Cell specification and functional interactions in the pig blastocyst inferred from single cell transcriptomics. BioRXIV.
Fiddaman SR, Klopp C, Charles M, Bardou P, Lebrasseur O, Derks M, Schauer J, Reimer C, Geibel J, Gheyas A, Smith A, Schnabel R, Martin Cerezo ML, Nishibori M, Godinez CJP, Layos JKN, Alfieri JM, Blackmon H, Athrey GN, Larson G, Ng’ang’a I, Muir W, Lange M, Wright D, Cheng H, Simianer H, Weigend S, Warren W, Crooijmans R, Hanotte O, Smith J, Tixier-Boichard M, Frantz LAF. 2023. Chicken Genomic Diversity Consortium: Large-Scale Genomics to Unravel the Origins and Adaptations of Chickens. Cytogenetic and Genome Research https://doi.org/10.1159/000529376
Hakimzadeh A, Abdala Asbun A, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Brandstrom Durling M, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Ozkurt E, M Palmer J, Pascal G, Porter TM, Straub D, Vasar M, Vetrovsky T, Zafeiropoulos H, Anslan S.2023. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular ecology resources
Heams T. 2023. The Contrasting Role of Single-cell Studies in the Theoretical Debate on Determinism in Molecular Biology. J Biol Sci. https://doi.org/10.13133/2532-5876/18306.
Jacques A, Leroy G, Rognon X, Verrier E, Tixier‑Boichard M, Restoux G. 2023. Reintroducing genetic diversity in populations from cryopreserved material: the case of Abondance, a French local dairy cattle breed. Genet Sel Evol.
Lauvie A, Audiot A, Verrier E. 2023. La biodiversité domestique : vers de nouveaux liens entre élevage, territoires et société. Quae Editions (ouvrage)
Lauvie A, Alexandre G, Angeon V, Couix N, Fontaine O, Gaillard C, Meuret M, Mougenot C, Moulin CH, Naves M, Nozières-Petit MO, Paoli JC, Perucho L, Sorba JM, Tillard E, Verrier E. 2023. Is the ecosystem services concept relevant to capture the multiple benefits from farming systems using livestock biodiversity? A framework proposal. Genetic Resources. https://doi.org/10.46265/genresj.2023.8
Leduc A, Le Guillou S, Laloë D, Herve L, Laubier J, Poton P, Faulconnier Y, Pires J, Gele M, Martin P, Leroux C, Boutinaud M, Le Provost F. 2023. MiRNome variations in milk fractions during feed restrictions of different intensities in dairy cows. BMC Genomics. https://doi.org/10.1186/s12864-023-09769-5
Le Guillou S, Ciobotaru C, Laubier J, Castille J, Aujean E, Hue-Beauvais C, Cherbuy C, Liuu S, Henry C, David A, Jaffrezic F, Laloe D, Charlier M, Alexandre-Gouabau M-C, Le Provost F. 2023 Specific milk composition of miR-30b transgenic mice associated with early duodenum maturation in offspring with lasting consequences for growth. The Journal of nutrition.
Leroy G, Wang SZ, Lewis T, Licari S. 2023. Ancient and Recent Changes in Breeding Practices for Dogs. Archaeopress.
Mazo G, Karlis D, Rau A. 2023. A randomized pairwise likelihood method for complex statistical inferences. J American Statistical Association. https://doi.org/10.1080/01621459.2023.2257367
Noel A, Dumas C, Rottier E, Beslay D, Costagliola G, Ginies C, Nicole F, Rau A, Le Conte Y, Mondet F. 2023. Detailed chemical analysis of honey bee (Apis mellifera) worker brood volatile profile from egg to emergence. PloS one
Noyer M, Bernard M, Verneau O, Palacios C. 2023. Insights on the particle‑attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. Envir Sci Poll Res
Restoux G. 2023. Caractérisation de la biodiversité animale : approches écologiques et génétiques. Quae Editions (chapitre)
Rice E, Alberdi A, Alfieri J, Athrey G, Balacco J, Bardou P, Blackmon H, Charles M, Cheng H, Fedrigo O, Fiddaman S, Formenti G, Frantz L, Gilbert MT, Hearn C, Jarvis E, Klopp C, Marcos S, Mason A, Velez-Irizarry D, Xu L, Warren W. 2023. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC BIOLOGY https://doi.org/10.1186/s12915-023-01758-0
Smith J, Alfieri J, M, Anthony N, Arensburger P, Athrey G, Balacco J,.......Tixier-Boichard M, ... Yang C, Yin Z, -T, Young M, Zhang G, Zhao B, Zhou H. 2023. Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenet Genome Res.
Verrier E, Badeau F, Basso B, Bertrand C, Boudry P, Bouffartigue B, Charvolin-Lemaire E, Danvy S, Decourtye A, Duclos D, Ducos A, Gourdin JL, Haffray P, Hazard D, Journaux L, Laloë D, Lauvie A, Lenoir H, Naves M, Rouger R, Vandeputte M. 2023. Les races locales menacées d’abandon en France : actualisation des listes et extension de la démarche à de nouvelles espèces. Ethnozootechnie
Verrier E. 2023. Les animaux dans les noms des rues de Paris. Ethnozootechnie
Verrier E. 2023. Rites et monuments funéraires pour les animaux de compagnie. L’exemple du cimetière des chiens d’Asnières-sur-Seine. Ethnozootechnie
Verrier E, Rognon X, Denis B. 2023. Du sauvage au domestique : biodiversité, ressources génétiques et races animales. Quae Editions (chapitre)
2022
Auclair-Ronzaud J, Jaffrézic F, Wimel L, Dubois C, Laloë D, Chavatte-Palmer P. 2022. Estimation of milk production in suckling mares and factors influencing their milk yield. Animal.
Bernard M, Dehaullon A, Gao G, Paul K, Lagarde H, Charles M, Prchal M, Danon J, Jaffrelo L, Poncet C, Patrice P, Haffray P, Quillet E, Dupont-Nivet M, Palti Y, Lallias D, Phocas F. 2022. Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping. Front Genetics
Cazals A, Estelle J, Bruneau N, Coville JL, Menanteau P, Rossignol MN, Jardet D, Bevilacqua C, Rau A, Bed'Hom B, Velge P, Calenge F. 2022. Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens. Gen Sel Evol.
Cerutti C, Leroux S, Gourichon D, Labrune Y, David I, Zerjal T, Coustham V, Devailly G, Pitel F. 2022. Effects of in-ovo injection of endocrine disruptors and methyltransferase inhibitor on quail growth and egg-laying performances. Animal.
Costes V, Chaulot-Talmon A, Sellem E, Perrier JP, Aubert-Frambourg A, Jouneau L, Pontlevoy C, Hozé C, Fritz S, Boussaha M, Le Danvic C, Sanchez MP, Boichard D, Schibler L, Jammes H, Jaffrézic F, Kiefer H. 2022. Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records. Clinical Epigenetics.
Denis B, Verrier E. 2022. Cinquante ans d’activité de la Société d’Ethnozootechnie : bilan et leçons pour demain. Ethnozootechnie
Fiddaman SR, Klopp C, Charles M, Bardou P, Lebrasseur O, Derks M, Schauer J, Reimer C, Geibel J, Gheyas A, Smith A, Schnabel R, Martin Cerezo ML, Nishibori M, Godinez CJP, Layos JKN, Alfieri JM, Blackmon H, Athrey GN, Larson G, Ng’ang’a I, Muir W, Lange M, Wright D, Cheng H, Simianer H, Weigend S, Warren W, Crooijmans R, Hanotte O, Smith J, Tixier-Boichard M, Frantz LAF. 2023 Chicken Genomic Diversity Consortium: Large-Scale Genomics to Unravel the Origins and Adaptations of Chickens. Cytogenetic and Genome Research.
Hue-Beauvais C, Bédin K, Robert R, Gardan-Salmon D, Maupin M, Brun N, Aujean E, Jaffrezic F, Simon S, Charlier M, Le Provost F. 2022. Impact of pre-breeding feeding practices on rabbit mammary gland development at mid-pregnancy Peer Community in Animal Science (bioRxiv).
Gascuel-Odoux C, Lescourret F, Dedieu B, Detang-Dessendre C, Faverdin P, Hazard L, Litrico-Chiarelli I, Petit S, Roques L, Reboud X, Tixier-Boichard M, de Vries H, Caquet T. 2022. A research agenda for scaling up agroecology in European countries. AGRONOMY FOR SUSTAINABLE DEVELOPMENT.
Gastinel PL, Danchin-Burge C, Denis B, Verrier E L’œuvre et l’héritage de Laurent Avon. 2022. Ethnozootechnie
Mazurier M, Drouaud J, Bahrman N, Rau A, Lejeune-Henaut I, Delbreil B, Legrand S. 2022. Integrated sRNA-seq and RNA-seq Analyses Reveal a microRNA Regulation Network Involved in Cold Response in Pisum sativum L. Genes
Mollandin F., Gilbert H., Croiseau P., Rau A. 2022. Accounting for overlapping annotations in genomic prediction models of complex traits. BMC Bioinformatics, 23, 365.
Quéméré P, Denis B, Lauvie A, Verrier E. 2022. Les races en péril : un thème identitaire pour une association lanceuse d’alerte. Ethnozootechnie
Rau A, Manansala R, Flister MJ, Rui H, Jaffrezic F, Laloe D, Auer PL. 2022. Individualized multi-omic pathway deviation scores using multiple factor analysis. BIOSTATISTICS.
Rau A, Passet B, Castille J, Daniel-Carlier N, Asset A, Lecardonnel J, Moroldo M, Jaffrézic F, Laloë D, Moazami-Goudarzi K, Vilotte JL. 2022. Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation. Vet Res.
Restoux G, Rognon X, Vieaud A, Guemene D, Petitjean F, Rouger R, Brard‑Fudulea S, Lubac‑Paye S, Chiron G, Tixier‑Boichard M. 2022. Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds. Gen Sel Evol
Senczuk G, Criscione A, Mastrangelo S, Biscarini F, Marletta D, Pilla F, Laloë D, Ciampolini R. 2022. How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds. Animals.
Verma M, Laloe D, Dige MS, De S, Rout PK. 2022. Landscape and bioclimatic diversity of milk protein variability in tropical goats. Small Ruminant Research
Verrier E, Ducos A. 2022. Aspects génétiques de l’évolution de l’élevage : une histoire de temps, de moyens et d’organisation sociale. Bulletin de l’Académie Vétérinaire de France.
2021
Bernard M, Rué O, Mariadassou M, Pascal G. 2021. FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers. Brief Bioinfo. 1, 6
Boitard S, Paris C, Sevane N, Servin B, Bazi-Kabbaj K, Dunner S. 2021. Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed. Front Genet. 12, 575405
Borey M, Blanc F, Lemonnier G, Leplat JJ, Jardet D, Rossignol MN, Ravon L, Billon Y, Bernard M, Estelle J, Rogel-Gaillard C. 2021. Links between fecal microbiota and the response to vaccination against influenza A virus in pigs. NPJ Vaccines, 6
Charvolin-Lemaire E, Laloë D. 2021. Evolution du concept de race et sa pertinence au début du XXIe siècle. Ethnozootechnie. 109, 47-52
Crisci E, Moroldo M, Manh TPV, Mohammad A, Jourdren L, Urien C, Bouguyon E, Bordet E, Bevilacqua C, Bourge M, Pezant J, Pleau A, Boulesteix O, SchwartzI I, Bertho N, Giuffra E. 2020. Distinctive cellular and metabolic reprogramming in porcine lung mononuclear phagocytes infected with type 1 PRRSV strains. Front Immunol. 11, 588411
David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. 2021. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol. 11
Degalez F, Jehl F, Muret K, Bernard M, Lecerf F, Lagoutte L, Désert C, Pitel F, Klopp C, Lagarrigue S. 2021. Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained. Front Genet.
De Oliveira Silva R, Gardyn OC, Hiemstra SJ, Marques JGO, Tixier-Boichard M, Moran, D. 2021. Ex situ and in situ data for endangered livestock breeds in Spain. Data in Brief, 35
Destoumieux-Garzón D, Bonnet P, Teplitsky C, Criscuolo F, Henry PY, Mazurais D, Prunet P, Salvat G, Usseglio-Polatera P, Verrier E, Friggens N. 2021. OneARK: Strengthening the links between animal production science and animal ecology. Animal, 15:100053
DeVogel N, Auer PL, Manansala R, Rau A, Wang T. 2021. A unified linear mixed model for familial relatedness and population structure in genetic association studies. Genet Epidemiol. in press
Femenia M, Charles M, Boulling A, Rocha D. 2021. Identification and characterisation of mitochondrial sequences integrated into the ovine nuclear genome. Anim Genet
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Jehl F, Degalez F, Bernard M, Lecerf F, Lagoutte L, Désert C, Coulée M, Bouchez O, Leroux S, Abasht B, Tixier-Boichard M, Bed’hom B, Burlot T, Gourichon D, Bardou P, Acloque H, Foissac S, Djebali S, Giuffra E, Zerjal T, Pitel F, Klopp C, Lagarrigue S. 2021. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Front Genet.
Jehl F, Muret K, Bernard M, Boutin M, Lagoutte L, Désert C, Dehais P, Esquerré D, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Pitel F, Zerjal T, Klopp C, Lagarrigue S. 2020. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep. 10, 20457
Lallias D, Bernard M, Ciobotaru C, Dechamp N, Labbé L, Goardon L, Le Calvez JM, Bideau M,Fricot A, Prézelin A, Charles M, Moroldo M, Cousin X, Bouchez O, Roulet A, Quillet E, Dupont-Nivet M. 2021. Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background. Epigenetics. in press.
Leroy G, Verrier E. 2021. Contribution des ressources génétiques animales aux services écosystémiques liés au développement territorial. Essais. 6, 79-87
Mach N, Moroldo M, Rau A, Lecardonnel J, Le Moyec L, Robert C, Barrey E. 2021. Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse. Front. Mol. Biosci. 8, 656204
Mariadassou M, Suez M, Sathyakumar S, Vignal A, Arca M, Nicolas P, Faraut T, Esquerré D, Nishibori M, Vieaud A, Chen CF, Manh Pham H, Roman Y, Hospital F, Zerjal T, Rognon X, Tixier-Boichard M. 2021. Unraveling the history of the genus Gallus through whole genome sequencing. Mol Phylogenet Evol. 158, 107044
Mollandin F, Rau A, Croiseau P. 2021. Evaluating the Interpretability of SNP Effect Size Classes in Bayesian Genomic Prediction Models. Hum Heredity, 85-86
Mollandin F, Rau A, Croiseau P. 2021. An evaluation of the predictive and mapping power of the BayesR model for genomic prediction. G3
Noyer M, Reoyo-Prats B, Aubert D, Bernard M, Verneau O, Palacios C. 2021. Corrrigendum: Particle-attached riverine bacteriome shifts in a pollutant-resistant and pathogenic community during a Mediterranean extreme storm event. Science Total Env. 732, 139047
Ramírez‑Ayala LC, Rocha D, Ramos‑Onsins SE, Leno‑Colorado J, Charles M, Bouchez O, Rodríguez‑Valera5 Y, Pérez‑Enciso, M, Ramayo‑Caldas Y. 2021. Whole‑genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genet Sel Evol. 53, 3
Rau A, Manansala R, Flister MJ, Rui H, Jaffrézzic F, Laloë D, Auer PL. 2021. Individualized multi-omic pathway deviation scores using multiple factor analysis. Biostatistics. in press.
Rognon X, Heams T, Ducos A, Charpentier R, Magnol L, Restoux G, Rigal J, Verrier E. 2021. Evolutions et perspectives des formations pour la génétique et la sélection animale. Ethnozootechnie. 109, 11-18
Sanchez MP, Rocha D, Charles M, Boussaha M, Hozé C, Brochard M, Delacroix-Buchet A, Grosperrin P, Boichard D. 2021. Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1 and ANKH genes and gene regulatory regions on bovine milk minerals. Sci Rep. 11, 7537
Schwochow D, Bornelöv S, Jiang T, Li J, Gourichon D, Bed’Hom B, DorshorstBJ, Chuong, C-M, Tixier-Boichard M, Andersson L. 2021. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus. Pigm cell Melanoma
Sellem E, Marthey S, Rau A, Jouneau L, Bonnet A, Le Danvic C, Guyonnet B, Kiefer H, Jammes H, Schibler L. 2021. Dynamics of cattle sperm sncRNAs during maturation, from testis to ejaculated sperm. Epig Chrom, 14
Silva RD, Gardyn OC, Hiemstra SJ, Marques JGO, Tixier-Boichard M, Moran, D. 2021. Rationalizing ex situ collection of reproductive materials for endangered livestock breed conservation. Ecol Econ. 181, 106916
Tixier-Boichard M, Fabre S, Dhorne-Pollet S, Goubil A, Acloque H, Vincent-Naulleau S, Ross P, Wang Y, Chanthavixay G, Cheng H, Ernst C, Leesburg V, Giuffra E, Zhou H, the Collaborative Working Group. 2021. Tissue Resources for the Functional Annotation of Animal Genomes. Front Genet. 12
Tixier-Boichard M, Lecerf F, Heraulf F, Bardou P, Klopp C. 2020. The "1000 Gallus Genomes" project: sharing sequence data to better exploit them. INRA Prod Anim. 33, 189-202
Verrier E, Markey L, Lauvie A. 2021. Valorisation des races animales locales par des produits liés à leur territoire : cinq leçons tirées de cas variés en France. Essais. 6, 35-45
Verrier E, Rognon X, Patin S, Del Porto P. 2021. L'héritage de Jacques Bougler. Ethnozootechnie. 109, 7-10
Zerjal T, Härtle S, Gourichon D, Guillory V, Bruneau N, Laloë D, Pinard‑van der Laan M-H, Trapp S, Bed’hom B, Quéré P. 2021. Assessment of trade-ofs between feed efciency, growth-related traits, and immune activity in experimental lines of layer chickens. Genet Sel Evol. 53, 44
2020
Auclair-Ronzaud J, Benoist S, Dubois C, Frejaville M, Jousset T, Jaffrézic F, Wimel L, Chavatte-Palmer P. 2020. No-contact microchip monitoring of body temperature in yearling horses. J Equine Vet Sci. 86, 102892
Auclair-Ronzaud J, Jousset T, Dubois C, Wimel L, Jaffrezic F, Chavatte-Palmer P. 2020. No-contact microchip measurements of body temperature and behavioural changes prior to foaling. Theriogenology. 157, 399-406
Bazile J, Jaffrezic F, Dehais P, Reichstadt M, Klopp C, Laloe D, Bonnet M. 2020. Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data. Physiol Genomics. 52, 322-332
Cho Y, Rau A, Reiner A, Auer PL. 2020. Mendelian randomization analysis with survival outcomes. Genet Epidemiol. 2020; 1-8
Destoumieux-Garzón D, Bonnet P, Teplitsky C, Criscuolo F, Henry PY, Mazurais D, Prunet P, Salvat G, Usseglio-Polatera P, Verrier E, Friggens N. 2020. OneARK: Strengthening the links between animal production science and animal ecology. Position Paper. Peer community in Animal Science. 1, 26
Doublet AC, Restoux G, Fritz S, Balberini L, Fayolle G, Hozé C, Laloë D, Croiseau P. 2020. Intensified use of reproductive technologies and reduced dimensions of breeding schemes put genetic diversity at risk in Dairy cattle breeds. Animals (Basel). 10, 1903
Dupont C, Hulot A, Jaffrezic F, Faure C, Czernichow S, di Clemente N, Racine C, Chavatte-Palmer P, Lévy R, Alifert group. 2020. Female ponderal index at birth and idiopathic infertility. J Dev Orig Health Dis. 11, 154-158
Fraslin C, Phocas F, Bestin A, Charles M, Bernard M, Krieg F, Dechamp N, Ciobotaru C, Hozé C, Petitprez F, Milhes M, Lluch J, Bouchez O, Poncet C, Hocdé P, Haffray P, Guiguen Y, Quillet E. 2020. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing. Sci Rep. 10, 17693
Gervais L, Hewison AJM, Morellet N, Bernard M, Merlet J, Cargnelutti B, Chaval Y, Pujol B, Quéméré E. 2020. Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer. J Evol Biol. 33, 595-607
Godichon-Baggioni A, Maugis-Rabusseau C, Rau A. 2020. Multiview cluster aggregation and splitting, with an application to multiomic breast cancer data. Ann Appl Stat. 14, 752-767
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Hammer SE, Ho CH, Ando A, Rogel-Gaillard C, Charles M, Tector M, TectorAJ, Lunney JK. 2020. Importance of the major histocompatibility complex (Swine Leukocyte Antigen) in swine health and biomedical research. Annu Rev Anim Biosci. 8, 171-198
Hulot A, Chiquet J, Jaffrezic F, Rigaill G. 2020. Fast tree aggregation for consensus hierarchical clustering. BMC Bioinformatics. 21, 120
Laoun A, Harkat S, Lafri M, Gaouar SBS, Belabdi I, Ciani E, De Groot M, Blanquet V, Leroy G, Rognon X, Da Silva A. 2020. Inference of breed structure in farm animals: Empirical comparison between SNP and microsatellite performance. Genes (Basel), 11 - pii: E57
Lévy E, Jaffrezic F, Laloë D, Rezaei H, Huang ME, Béringue V, Davy M, Vernis L. 2020. PiQSARS: A pipeline for quantitative and statistical analyses of ratiometric fluorescent biosensors. MethodsX. 7, 101034
Lien CY, Tixier-Boichard M, Wu SW, Chen CF. 2020. Identification of QTL and loci for egg production traits to tropical climate conditions in chickens. Livest Sci. 234, 103980
Mariadassou M, Ramayo-Caldas Y , Charles M, Femenia M, Renand G, Rocha D. 2020. Detection of selection signatures in Limousin cattle using wholegenome resequencing. Anim Genet. 41, 815-819
Moroldo M, Munyaka PM, Lecardonnel J, Lemonnier G, Venturi E, Chevaleyre C, Oswald IP, Estellé J, Rogel-Gaillard C. 2020. Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLAdd minipigs. Sci Rep. 10, 234
Morris KM, Hindle MM, Boitard S, Burt DW, Danner AF, Eory L, Forrest HL, Gourichon D, Gros J, Hillier LW, Jaffredo T, Khoury H, Lansford R, Leterrier C, Loudon A, Mason AS, Meddle SL, Minvielle F, Minx P, Pitel F, Seiler JP, Shimmura T, Tomlinson C, Vignal A, Webster RG, Yoshimura T, Warren WC, Smith J. 2020. The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol, 18-14
Neou M, Villa C, Armignacco R, Jouinot A, Raffin-Sanson ML, Septier A, Letourneur F, Diry S, Diedisheim M, Izac B, Gaspar C, Perlemoine K, Verjus V, Bernier M, Boulin A, Emile JF, Bertagna X, Jaffrezic F, Laloe D, Baussart B, Bertherat J, Gaillard S, Assié G. 2020. Pangenomic classification of pituitary neuroendocrine Tumors. Cancer Cell. 37, 1-12
Noyer M, Reoyo-Prats B, Aubert D, Bernard M, Verneau O, Palacios C. 2020. Particle-attached riverine bacteriome shifts in a pollutant-resistant and pathogenic community during a Mediterranean extreme storm event. Sci Total Environ. 732, 139047
Passet B, Castille J, Makhzami S, Truchet S, Vaiman A, Floriot S, Moazami-Goudarzi K, Vilotte M, Gaillard AL, Helary L, Bertaud M, Andréoletti O, Vaiman D, Calvel P, Daniel-Carlier N, Moudjou M, Beauvallet C, Benharouga M, Laloë D, Mouillet-Richard S, Duchesne A, Béringue V, Vilotte JL. 2020. The Prion-like protein Shadoo is involved in mouse embryonic and mammary development and differentiation. Sci Rep, 10-6765
Pegram CL, Bonnett BN, Skarp H, Arnott G, James H, Hedhammar A, Leroy G, Llewellyn-Zaidi A, Seath IJ, O’Neill DG. 2020. Moving from information and collaboration to action: report from the 4th international dog health workshop, Windsor in May 2019. Canine Med Genet. 7, 4
Sellem E, Marthey S, Rau A, Jouneau L, Bonnet A, Perrier JP, Fritz S, Le Danvic C, Boussaha M, Kiefer H, Jammes H, Schibler L. 2020. A comprehensive overview of bull sperm‑borne small non‑coding RNAs and their diversity across breeds. Epigenetics Chromatin, 13-19
Tixier-Boichard M. 2020. From the jungle fowl to highly performing chickens: are we reaching limits? World Poult Sci J. 76, 2-17
Verrier E. 2020. Les animaux et l’élevage dans les toponymes des Préalpes franco-suisses. Ethnozootechnie. 107, 25-34
Zomerdijk F, Hiemstra SJ, d'Arbaumont M, Tixier-Boichard M, Boettcher P. 2020. Quality management practices of gene banks for livestock: A global review. Biopreserv Biobank. 18, 244-253
2019
Auclair-Ronzaud J, Benoist S, Dubois C, Frejaville M, Jousset T, Jaffrezic F, Wimel L, Chavatte-Palmer P. 2019. No-contact microchip monitoring of body temperature in yearling horses. J Eq Vet Sci. 86, 102892.
Biase FH, Hue I, Dickinson SE, Jaffrezic F, Laloe D, Lewin HA, Sandra O. 2019. Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus. PLoS Biol. 17, e3000046
Boushaba N, Boujenane I, Moazami-Goudarzi K, Flori L, Saïdi-Mehtar N, Tabet-Aoul N, Laloë D. 2019. Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data. Animal. 13, 8-14.
D'Ambrosio J, Phocas F, Haffray P, Bestin A, Brard-Fudulea S, Poncet C, Quillet E, Dechamp N, Fraslin C, Charles M, Dupont-Nivet M. 2019. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding. Genet Sel Evol. 51, 26
Dhara SP, Rau A, Flister MJ, Recka NM, Laiosa MD, Auer PL, Udvadia AJ. 2019. Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors. Sci Rep. 9, 14198
Dhorne-Pollet S, Crisci E, Mach N, Renson P, Jaffrézic F, Marot G, Maroilley T, Moroldo M, Lecardonnel J, Blanc F, Bertho N, Bourry O, Giuffra E. 2019. The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome. Virus. Sci Rep. 9-3160
Doublet AC, Croiseau P, Fritz S, Michenet A, Hozé C, Danchin‑Burge C, Laloë D, Restoux G. 2019. The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds. Genet sel Evol. 51- 52
Dupont C, Hulot A, Jaffrezic F, Faure C, Czernichow S, di Clemente N, Racine C, Chavatte-Palmer P, Lévy R, Alifert group. 2019. Female ponderal index at birth and idiopathic infertility. J Dev Orig Health Dis. in press
Flori L, Moazami-Goudarzi K, Alary V, Araba A, Boujenane I, Boushaba N, Casabianca F, Casu S, Ciampolini R, Coeur D'acier A, Coquelle C, Delgado JV, El-Beltagi A, Hadjipavlou G, Jousselin E, Landi V, Lauvie A, Lecomte P, Ligda C, Marinthe C, Martinez A, Mastrangelo S, Menni D, Moulin CH, Osman MA, Pineau O, Portolano B, Rodellar C, Saidi-Mehtar N, Sechi T, Sempere G, Thevenon S, Tsiokos D, Laloë D, Gautier M. 2019. A genomic map of climate adaptation in Mediterranean cattle breeds. Mol Ecol. in press.
Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, Pinard-Van der Laan MH, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E. 2019. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 17, 108.
Fraslin C, Brard-Fudulea S, D’Ambrosio J, Bestin A, Charles M, Haffray P, Quillet E, Phocas F. 2019. Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm. Anim Genet. 50, 293-297
Gervais L, Perrier C, Bernard M, Merlet J, Pemberton JM, Pujol B, Quéméré E. 2019. RAD-sequencing for estimating genomic relatedness matrix-based heritability in the wild: A case study in roe deer. Mol Ecol Resour, in press
Godichon-Baggioni A, Maugis-Rabusseau C, Rau A. 2019. Clustering transformed compositional data using K-means, with applications in gene expression and bicycle sharing system data. J Appl Stat. 46, 47, 65
Helary L, Castille J, Passet B, Vaiman A, Beauvallet C, Jaffrezic F, Charles M, Tamzini M, Baraige F, Letheule M, Laubier J, Moazami-Goudarzi K, Vilotte JL, Blanquet V, Duchesne A. DNAJC2 is required for mouse early embryonic development. Biochem Biophys Res Commun. 516, 258-263
Hue I, Dufort I, Vitorino Carvalho A, Laloe D, Peynot N, Degrelle SA, Viebahn C, Sirard MA. 2019. Different pre-implantation phenotypes of bovine blastocysts produced in vitro. Reproduction. 157, 163-178
Jehl F, Désert C, Klopp C, Brenet M, Rau A, Leroux S, Boutin M, Lagoutte L, Muret K, Blum Y, Esquerré D, Gourichon D, Burlot T, Collin A, Pitel F, Benani A, Zerjal T, Lagarrigue S. 2019. Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach. BMC Genomics. 20, 1033
Kalo D, Vitorino Carvalho A, Archilla C, Duranthon V, Moroldo M, Levin Y, Kupervaser M, Smith Y, Roth Z. 2019. Mono(2-ethylhexyl) phthalate (MEHP) induces transcriptomic alterations in oocytes and their derived blastocysts. Toxicology. 421, 59-73
Li JY, Bed'hom B, Marthey S, Valade M, Dureux A, Moroldo M, Pechoux C, Coville JL, Gourichon D, Vieaud A, Dorshorst B, Andersson L, Tixier-Boichard M. 2019. A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure. Pigment Cell Melanoma Res. 32, 381-39
Muret K, Désert C, Lagoutte L, Boutin M, Gondret F, Zerjal T, Lagarrigue S. 2019. Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species. BMC Genomics. 20, 882
Plasterer C, Tsaih SW, Lemke A, Schilling R, Dwinell M, Rau A, Aue P, Rui H, Fliste MJ. 2019. Identification of a rat mammary tumor risk locus that Is syntenic with the commonly amplified 8q12.1 and 8q22.1 regions in human breast cancer patients. G3 (Bethesda). 9, 1739-1743
Ramayo-Caldas Y, Zingaretti L, Popova M, Estelle J, Bernard A, Pons N, Bellot P, Mach N, Rau A, Roume H, Perez-Enciso M, Faverdin P, Edouard N, Ehrlich D, Morgavi DP, Renand G. 2019. Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows. J Anim Breed Genet. 137, 49-59
Rau A, Dhara SP, Udvadia AJ, Auer P. 2019. Regeneration Rosetta : an interactive web application to explore regeneration-associated gene expression and chromatin accessibility. G3 (Bethesda). 9, 3953-3959.
Rau A, Flister M Rui H, Auer PL. 2019. Exploring drivers of gene expression in the Cancer Genome Atlas. Bioinformatics. 35, 62-68
Robic A, Morisson M, Leroux S, Gourichon D, Vignal A, Thebault N, Fillon V, Minvielle F, Bed'Hom B, Zerjal T, Pitel F. 2019. Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotypes in Japanese quail. Genet Sel Evol. 51, 12
Sellier P, Boichard D, Verrier E. 2019. La génétique animale à l‘Inra : soixante ans d'une histoire scientifique en prise avec le monde de la sélection et riche en rebondissements technologiques. Histoire Recherche Contemporaine. 8, 86-98
Thelie A, Bailliard A, Seigneurin F, Zerjal T, Tixier-Boichard M, Blesbois E. 2019. Chicken seme cryopreservation and use for the restoration of rare genetic resources. Poult Sci. 98, 447-455
Vignal A, Boitard S, Thebault N, Dayo GK, Yapi-Gnaore V, Karim IYA, Berthouly-Salazar C, Palinkas-Bodzsar N, Guemene D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X. 2019. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour. 19, 997-1014
Wang S, Strandberg E, Viklund A, Windig JJ, Malm S, Lewis T, Laloë D, Leroy G. 2019. Genetic improvement of canine hip dysplasia through sire selection across countries. Vet J. 248, 18-24
2018
Bílková B, Świderská Z, Zita L, Laloë D, Charles M, Benes V, Stopka P, Vinkler M. 2018. Domestic fowl breed variation in egg white protein expression: application of proteomics and transcriptomics. J Agric Food Chem. 66, 11854-11863
Boushaba N, Boujenane I, Moazami-Goudarzi K, Flori L, Saïdi-Mehtar N, Tabet-Aoul N, Laloë D. 2018. Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data. Animal, early print
Chassier M, Barrey E, Robert C, Duluard A, Danvy S, Ricard A. 2018. Genotype imputation accuracy in multiple equine breeds from medium- to high-density genotypes. J Anim Breed Genet. 135, 420-431
Coyral-Castel S, Ramé C, Cognié J, Lecardonnel J, Marthey S, Esquerré D, Hennequet-Antier C, Eli S, Fritz S, Boussaha M, Jaffrézic F, Dupont J. 2018. KIRREL is differentially expressed in adipose tissue from 'fertil plus ' and 'fertil-' cows: in vitro role in ovary? Reproduction. 155, 183-198.
de Verdal H, Komen H, Quillet E, Chatain B, Allal F, Benzie JAH Vandeputte M. 2018. Improving feed efficiency in fish using selective breeding: a review. Rev Aquacult. 10, 833-851
de Verdal H, Vandeputte M, Mekkawy W, Chatain B, Benzie JAH. 2018. Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus. BMC Genet. 19, 105
Demazeau G, Plumecocq A, Lehours P, Martin P, Couedelo L, Billeaud C. 2018. A new high hydrostatic pressure process to assure the microbials safety of human milk while preserving the biological activity of its main components. Front Public Health. 6, 306
Ducrocq V, Laloë D, Swaminathan M, Rognon X, Tixier-Boichard M, Zerjal T. 2018. Genomics for ruminants in developing countries: from principles to practice. Front Genet. 9, 251
Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pasca G. 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solutio. Bioinformatics. 34, 1287-1294
Eynard SE,Croiseau P, Laloë D, Fritz S,Calus MPL, Restoux G. 2018. Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs. G3 (Bethesda). 8, 113-121.
Eynard SE, Windig JJ, Hulsegge I, Hiemstra SJ, Calus MPL. 2018. The impact of using old germplasm on genetic merit and diversityA cattle breed case study. J Anim Breed Sci. 135, 311-322
Fraslin C, Dechamp N, Bernard M, Krieg F, Hervet C, Guyomard R, Esquerré D, Barbieri J, Kuchly C, Duchaud E, Boudinot P, Rochat T, Bernardet JF, Quillet E. 2018. Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions. Genet Sel Evol. 50, 60
Grobler R, Visser C, Capitan A, van Marie-Koster E. 2018. Validation of the POLLED Celtic variant in South African Bonsmara and Drakensberger beef cattle breeds. Livest Sci. 217, 136-139
He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. 2018. Compositional bias in naïve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing. Sci Rep. 8, 1214.
Hubert JN, Zerjal T, Hospital F. 2018. Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrish). PLoS One. 13, e0201838
Lansade L, Foury A, Reigner F, Vidament M, Guettier E, Bouvet G, Soulet D, Parias C, Ruet A, Mach N, Levy F, Moisan MP. 2018. Progressive habituation to separation alleviates the negative effects of weaning in the mother and foal. Psychoneuroendocrinology. 97, 59-68
Legradi JB Di Paolo C, Kraak MHS, van der Geest HG, Schymanski EL, Williams AJ Dingemans, MML Massei, R, Brack W, Cousin X, Begout ML, van der Oost R, Carion A, Suarez-Ulloa V, Silvestre F, Escher BI, Engwall M, Nilen G, Keiter SH, Pollet D, Waldmann, P, Kienle C; Werner I, Haigis AC, Knapen D, Vergauwen L, Spehr M, Schulz W, Busch W, Leuthold D, Scholz S, vom Berg CM, Basu N, Murphy CA, Lampert, A, Kuckelkorn J, Grummt T, Hollert H. 2018. An ecotoxicological view on neurotoxicity assessment. Environ Sci Eur. 30, 46
Marete A, Guldbrandtsen B, Fritz S, Lund MS, Sahana G, Boichard D. 2018. A meta-analysis including pre-selected sequence variants associated with seven traits in three French dairy cattle populations. Front Genet. 9, 522
Maroilley T, Berri M, Lemonnier G, Esquerré D, Chevaleyre C, Mélo S, Meurens F, Coville JL, Leplat JJ, Rau A, Bed’hom B, Vincent-Naulleau S, Mercat MJ, Billon Y, Lepage P, Rogel-Gaillard C, Estellé J. 2018. Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues. Sci Rep, 8-9077
Mondet F, Rau A, Klopp C, Rohmer M, Severac D, Le Conte Y, Alaux C. 2018. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics, 19-328.
Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, García-Casco J, Alves E, Škrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández AI, Óvilo C. 2018. Diversity across major and candidate genes in European local pig breed. PLoS One. 13, e0207475
Narayana SG, Miglior F, Naqvi SA, Malchiodi F, Martin P, Barkema HW. 2018. Genetic analysis of subclinical mastitis in early lactation of heifers using both linear and threshold models. J Dairy Sci. 101, 11120-11131
Rau A, Maugis-Rabusseau C. 2018. Transformation and model choice for RNA-seq co-expression analysis. Brief Bioinform. 19, 425-436.
Rigaill G, Balzergue S, Brunaud V, Blondet E, Rau A, Rogier O, Caius J, Maugis-Rabusseau C, Soubigou-Taconnat, L, Aubourg S, Lurin C, Martin-Magniette ML, Delannoy E. 2018. Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief Bioinform. 19, 65-76.
Rochus CM, Tortereau F, Plisson-Petit F, Restoux G, Moreno-Romieux C, Tosser-Klopp G, Servin B. 2018. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep. BMC Genomics. 19, 71.
Song X, Marandel L, Skiba-Cassy S, Corraze G, Dupont-Nivet M, Quillet E, Geurden I, Panserat S. 2018. Regulation by dietary carbohydrates of intermediary metabolism in liver and muscle of two isogenic lines of Rainbow trout. Front Physiol. 9, 1579
Verrier ER, Genet C, Laloë D, Jaffrezic F, Rau A, Esquerre D, Dechamp N, Ciobotaru C, Hervet H, Krieg F, Jouneau L, Klopp C, Quillet E, Boudinot P. 2018. Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout. BMC Genomics. in press.
Vanbergue E, Peyraud JL, Ferlay A, Miranda G, Martin P, Hurtaud C. 2018. Effects of feeding level, type of forage and milking time on milk lipolytic system in dairy cows. Livest Sci. 217, 116-126
Wang S, Laloë D, Missant FM, Malm S, Lewis T, Verrier E, Strandberg E, Bonnet BN, Leroy G. 2018. Breeding policies and management of pedigree dogs in 15 national kennel clubs. Vet J. 234, 130-135.
2017
Beaumont M, Andriamihaja M, Arman L, Grauso M, Jaffrézic F, Laloë D, Moroldo M, Davila AM, Tomé D, Blachier F and Lan A. 2017. Epithelial response to a high-protein diet in rat colon. BMC Genomics. 18, 116
Danchin-Burge C, Danvy S, Laloë D, Verrier E. 2017. Création d’un observatoire de la VARiabilité génétique des RUMinants et des Equidés (VARUME). Innovations Agronomiques. 55, 235-245
Duchesne A, Vaiman A, Castille J, Beauvallet C, Gaignard P, Floriot S, Rodriguez S, Vilotte M, Boulanger L, Passet B, Albaric O, Guillaume F, Boukadiri A, Richard L, Bertaud M, Timsit E, Guatteo R, Jaffrézic F, Calvel P, Helary L, Mahla R, Esquerré D, Péchoux C, Liuu S, Vallat JM, Boichard D, Slama A, Vilotte JL. 2017. Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health. PLoS Genet. 13, e1006597
Legrand E, Boulange-Lecomte C, Restoux G, Tremolet G, Duflot A, Forget-Leray J. 2017. Individual and mixture acute toxicity of model pesticides chlordecone and pyriproxyfen in the estuarine copepod Eurytemora affinis. Environ Sci Pollut Res. 24, 5976-5984
Leroy G, Baumung R, Notter D, Verrier E, Wurzinger M, Scherf B. 2017. Stakeholder involvement and the management of animal genetic resources across the world. Livest Sci. in press.
Leroux S, Gourichon D, Leterrier C, Labrune Y, Coustham V, Rivière S, Zerjal T, Coville JL, Morisson M, Minvielle F, Pitel F. 2017. Embryonic environment and transgenerational effects in quail. Genet Sel Evol. 49, 14
Lien CY, Tixier-Boichard M, Wu SW, Wang WF, Ng CS, Chen CF. 2017. Detection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens. Genet Sel Evol. 49, 39.
Manirakiza J, Hatungumukama G, Thévenon S, Gautier M, Besbes B, Flori L, Detilleux J. 2017. Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands. Anim Genet. 48, 544-550
Monneret G, Jaffrézic F, Rau A, Zerjal T, Nuel G. 2017. Identification of marginal causal relationships in gene networks from observational and interventional expression data. PLoS One. 12, e0171142
O’Neill DG, Keijser, SFA, Hedhammar A, Kisko C, Leroy G, Llewellyn-Zaidi A, Malm S, Olson PN, Packer RMA, Rousselot JF, Seath IJ, Stull JW, Bonnett BN. 2017. Moving from information and collaboration to action: report from the 3rd international Dog Health Workshop, Paris in April 2017. Canine Genet Epidemiol. 4, 6
Phocas F, Belloc C, Bidanel J, Delaby L, Dourmad JY, Dumont B, Ezanno P, Fortun-Lamothe L, Foucras G, Frappat B, Gonzalez-Garcia E, Hazard D, Larzul C, Lubac S, Mignon-Grasteau S, Moreno-Romieux C, Tixier-Boichard M, Brochard M. 2017. Quels programmes d’amélioration génétique des animaux pour des systèmes d’élevage agro-écologiques ? Inra Prod Anim. 30, 31-46.
Roy J, Tardieu F, Tixier-Boichard M, Schurr U. 2017. European infrastructures for sustainable agriculture. Nat Plants. 3, 756-758
Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S. 2017. Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant J. ahead of print.
Schwochow Thalmann D, Ring H, Sundström E, Cao X, Larsson M, Kerje S, Höglund A, Fogelholm J, Wright D, Jemth P, Hallböök F, Bed'Hom B, Dorshorst B, Tixier-Boichard M, Andersson L. 2017. The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A. PLoS Genet. 13, e1006665.
Tiret M, Hospital F. Blocks of chromosomes identical by descent in a population: Models and predictions. PLoS One. 12, e0187416
Wang S, Leroy G, Malm S, Lewis T, Strandberg E, Fikse WF. 2017. Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK. J Anim Breed Genet. 134, 152-161.
2016
Barret P, Bourguet D, Duée PH, Gerber S, Le Roux X, Tixier-Boichard M. 2016. Éthique et biodiversité : questions posées à et par la recherche agronomique. Nature Sciences Sociétés. 24, 270-276
Boitard S, Boussaha M, Capitan A, Rocha D, Servin B. 2016. Uncovering adaptation from sequence data: Lessons from genome resequencing of four cattle breeds. Genetics. 203, Early Online
Chadi S, Polyte J, Lefevre L, Castille J, Ehanno A, Laubier J, Jaffrézic F, Le Provost F. 2016. Phenotypic and molecular alterations in the mammary tissue of R-spondin1 knock-out mice during pregnancy. PLoS One. 11, e0162566
Couix N, Gaillard C, Lauvie A, Mugnier S, Verrier E. 2016. Breeds both locally adapted and locally adopted, a condition for the sustainability of livestock activities. Cahiers Agriculture. 25, 650009
Davi H, Cailleret M, Restoux G, Amm A, Pichot C, Fady B. 2016. Disentangling the factors driving tree reproduction. EcoSphere. 7, e01389
Eynard SE, Windig JJ, Hiemstra SJ, Calus MPL. 2016. Whole‑genome sequence data uncover loss of genetic diversity due to selection. Genet Sel Evol. 48-33
Hubert JN, Allal F, Hervet C, Ravakarivelo M, Jeney Z, Vergnet A, Guyomard R, Vandeputte M. 2016. How could fully scaled carps appear in natural waters in Madagascar ? Proc Royal Soc Biol Sci. 283, 1-8
Jimenez Mena B, Tataru P, Brondum RF, Sahana G, Guldbrandtsen B, Bataillon T. 2016. One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome. Biol Lett. 12, 1-4
Jimenez Mena B, Hospital F, Bataillon T. 2016. Heterogeneity in effective population size and its implications in conservation genetics and animal breeding. Conservation Genet Res. 8, 35-41
Jimenez Mena B, Schad K, Hanna N, Lacy RC. 2016. Pedigree analysis for the genetic management of group-living species. Ecol Evol. 6, 3067- 3078
Loyau T, Zerjal T, Rodenburg T B, Fablet J, Tixier-Boichard M, Pinard-Van der Laan MH, Mignon-Grasteau S. 2016. Heritability of body surface temperature in hens estimated by infrared thermography at normal or hot temperatures and genetic correlations with egg and feather quality. Animal, in press
Mahammi FZ, Gaouar SB, Laloë D, Faugeras R, Tabet-Aoul N, Rognon X, Tixier-Boichard M, Saidi-Mehtar N. 2016. A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls. J Anim Breed Genet. 133, 59-70
Mazet O, Rodriguez W, Grusea S, Boitard S, Chikhi L. 2016. On the importance of being structured: instantaneous coalescence rates and human evolution-lessons for ancestral population size inference? Heredity. 116, 362-371
Montazer-Torbati F, Boutinaud M, Brun N, Richard C, Neveu A, Jaffrézic F, Laloë D, LeBourhis D, Nguyen M, Chadi S, Jammes H, Renard JP, Chat S, Boukadiri A, Devinoy E. 2016. Differences during the first lactation between cows cloned by somatic cell nuclear transfer and non-cloned cows. J Dairy Sci. Preaccepted
Pham MH, Tran XH, Berthouly-Salazar C, Tixier-Boichard M, Chen CF, Lee YP. 2016. Monitoring of genetic diversity in Taiwan conserved chickens assessed by pedigree and molecular data. Livest Sci. 184, 85- 9
Phocas F, Belloc C, Bidanel J, Delaby L, Dourmad JY, Dumont B, Ezanno P, Fortun-Lamothe L, Foucras G, Frappat B, González-García E, Hazard D, Larzul C, Lubac S, Mignon-Grasteau S, Moreno CR, Tixier-Boichard M, Brochard. 2016. Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes: I-selection goals and criteria. Animal. in press.
Phocas F, Belloc C, Bidanel J, Delaby L, Dourmad JY, Dumont B, Ezanno P, Fortun-Lamothe L, Foucras G, Frappat B, González-García E, Hazard D, Larzul C, Lubac S, Mignon-Grasteau S, Moreno CR, Tixier-Boichard M, Brochard. 2016. Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes: II. Breeding strategies. Animal. in press.
Rigail G, Balzergue S, Brunaud V, Blondet E, Rau A, Rogier O, Caius J, Maugis Rabusseau C, Soubigou Taconnat L, Aubourg S, Lurin C, Martin Magniette ML, Delannoy E. 2016. Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief Bioinform. pii: bbw092.
Roux PF, Frésard L, Boutin M, Leroux S, Klopp C, Djari A, Esquerré D, Martin PG, Zerjal T, Gourichon D, Pitel F, Lagarrigue S. 2016. The extent of mRNA editing is limited in chicken liver and adipose, but impacted by tissular context, genotype, age, and feeding as exemplified with a conserved edited site in COG3. G3 (Bethesda). 6, 321-335
Santana ML, Pereira RJ, Bignardi AB, Ayres DR, Menezes GRO, Silva LOC, Leroy G, Machado CHC, Josahkian LA, Albuquerque LG. 2016. Structure and genetic diversity of Brazilian Zebu cattle breeds assessed by pedigree analysis. Livest Sci. 187, 6-15
Simon M, Lopez-Garcia P, Deschamps P, Restoux G, Bertolino P, Moreira D, Jardillier L. 2016. Resilience of freshwater communities of small microbial eukaryotes undergoing severe drought events. Front Microbiol. 7, 812
Tuggle CK, Giuffra E, White SN, Clarke L, Zhou H, Ross PJ, Acloque H, Reecy JM, Archibald A, Bellone RR, Boichard M, et al. 2016. GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes. Anim Genet. 47, 528-533
Wang S, Leroy G, Malm S, Lewis T, Strandberg E, Fikse WF. 2016. Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK. J Anim Breed Genet. 2016, 1-10
Historique
Barbillon P, Thomas M, Goldringer I, Hospital F, Robin S. 2015. Network impact on persistence in a finite population dynamic diffusion model: application to an emergent seed exchange network. J Theor Biol. 365, 365-376
Berber N, Gaouar S, Leroy G, Kdidi S, Tabet Aouel N, Saïdi Mehtar N. 2014. Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers. J Anim Breed Genet. 131, 387-394
Berthier D, Peylhard M, Dayo GK, Flori, L, Sylla S., Bolly S, Sakande H, Chantal I, Thevenon S. 2015. A comparison of phenotypic traits related to trypanotolerance in five west african cattle breeds highlights the value of shorthorn taurine breeds. PLoS One. 10, e0126498
Boerries M., Grahammer F., Sven Eiselein S., Buck M., Meyer C., Goedel M., Bechtel W., Zschiedrich S., Pfeifer D., Laloe D., Arrondel C., Goncalves S., Kruger M., Harvey SJ., Busch H., Dengjel J., Huber T.B. 2013. Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks. Kidney International 83, 1052-1064
Boije H, Harun-or-Rashid M, Lee YJ, Imsland F, Bruneau N, Vieaud A, Gourichon D, Tixier-Boichard M, Bed’Hom B, Andersson L, Hallböök F. 2013. Sonic Hedgehog-Signalling Patterns the Developing Chicken Comb as Revealed by Exploration of the Peacomb. Plos One. 7, e50890
Bonhomme M, Boitard S, Clemente HS, Dumas B, Young N, Jacquet C. 2015. Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms. Mol Biol Evol. 32, 2097-2110
Brenaut P, Lefèvre L, Rau A, Laloë D, Pisoni G, Moroni P, Bevilacqua C and Martin P. 2014. Contribution of mammary epithelial cells to the immune response during early stages of a bacterial infection to Staphylococcus aureus. Vet Res. 45, 16
Bruford MW, Ginja C., Hoffmann I., Joost S., Orozco-terWengel P., J. Alberto F., J. Amaral A., Barbato M., Biscarini F., Colli L., Costa M., Curik I., Duruz S., Ferenčaković M., Fischer D., Fitak R., F. Groeneveld L., J. G. Hall S., Hanotte O., Hassan FU, HelsenP., Iacolina L., Kantanen K., Leempoel K., A. Lenstra J., Ajmone-Marsan P., Masembe C., Megens HJ, Miele M., Neuditschko M., Nicolazzi E.L., Pompanon F., Roosen J., Sevane N., Smetko A., Štambuk A., Streeter I., Stucki S., Supakorn C., Telo Da Gama L., Tixier-Boichard M., Wegmann D., Zhan X. 2015. Challenges for the conservation of farm animal genomic resources. Front Genet. 6, 314
Chazara O, Chang CS, Bruneau N, Benabdeljelil K, Kayang BK, Loukou NE, Osei-Amponsah R, Yapi-Gnaore V, Youssao IAK, Chen CF, Pinard-van der Laan MH, Tixier-Boichard M, Bed'Hom B. 2013. Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region. Immunogenetics 65, 447-459
Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. 2014. Mapping the epigenetic basis of complex traits. Science. 343, 1145-1148
Desjardin C, Charles C, Benoist-Lasselin C, Riviere J, Gilles M, Chassande O, Morgenthaler C, Laloé D, Lecardonnel J, Flamant F, Legeai-Mallet L, Schibler L. 2014. Chondrocytes play a major role in the stimulation of bone growth by thyroid hormone. Endocrinology. 155, 3123-3135
Desjardin C, Vaiman A, Mata X, Legendre R, Laubier J, Kennedy SP, Laloe D, Barrey E, Jacques C, Cribiu EP, Schibler L. 2014. Next-generation sequencing identifies equine cartilage and subchondral bone miRNAs and suggests their involvement in osteochondrosis physiopathology. BMC Genomics. 15, 798
Dillies MA, Rau A, Aubert J, Hennequet-Antier C., Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Charif D, Le Crom S, Guedj M, Jaffrézic F. 2013. A comprehensive evaluation of normalization methods for high-throughput RNA sequencing data analysis. Briefings in Bioinformatics 14, 671-683
Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L. 2015. A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplexcomb phenotypes. PLoS Genetics. 11, e1004947
Eynard SE, Windig JJ, Leroy G, van Binsbergen R, Calus MPL. 2015. The effect of rare alleles on estimated genomic relationships from whole genome sequence data. BMC Genet. 16, 24
Fariello MI, Servin B, Tosser-Klopp G, Rupp R, Moreno C, International Sheep Genomics Consortium, San Cristobal M, Boitard S. 2014. Selection signatures in worldwide sheep populations. PLoS ONE. 9, e103813
Flori L, Thevenon S, Dayo G-K,Senou M, Sylla S, Berthier D, Moazami-Goudarzi K, Gautier M. 2014. Adaptative admixture in the west African bovine hybrid zone insight from the borgou population. Mol Ecol . 23, 3241-3257
Frésard L, Morisson M, Brun J-M, Collin A, Pain B, Minvielle F, Pitel F. 2013. Epigenetics and phenotypic variability: some interesting insights from birds. Genet Sel Evol. 45, 16
Gallopin M, Celeux G, Jaffrezic F, Rau A. 2015. A model selection criterion for model-based clustering of annotated gene expression data. Stat Appl Genet Mol Biol. 14, 413-428
Gallopin M., Rau A., Jaffrezic F. 2013. A Hierarchical Poisson Log-Normal Model for Network Inference from RNA Sequencing Data. Plos One 8, e77503
Gianola D, Hospital F, Verrier E 2013. Contribution of an additive locus to genetic variance when inheritance is multi-factorial with implications on interpretation of GWAS. Theor Appl Genet. 126, 1457-1472
Heams T. 2013. Understanding the emergence of synthetic biology and its issues: Introduction. MS Medecine Sciences 29, 11-12
Hue-Beauvais C, Koch E, Chavatte Palmer P, Galio L, Chat S, Letheule M, Rousseau Ralliard D, Jaffrezic F, Laloë D, Aujean E, Révillion F, Lhotellier V, Gertler A, Devinoy E, Charlier M. 2015. Milk from dams fed an obesogenic diet combined with a high-fat/high-sugar diet induces long-term abnormal mammary gland development in the rabbit. J Anim Sci. 93, 1641-1655
Ilboudo H, Bras-Gonçalves R, Camara M, Flori L, Camara O, Sakande H, Leno M, Petitdidier E, Jamonneau V, Bucheton B. 2014. Unravelling Human Trypanotolerance: IL8 is Associated with Infection Control whereas IL10 and TNFα Are Associated with Subsequent Disease Development. PLoS Pathog. 10, e1004469
Lambert-Derkimba A, Lauvie A Verrier E. 2013. How the development of products valorizing local breeds changes breeding goals: examples from French cattle breeds. Animal Genetic Resources. 53, 135-140
Lauvie A, Couix N, Verrier E. 2014. No development, no conservation: lessons from the conservation of farm animal genetic resources. Soc Nat Resour. 27, 1331-1338
Le Guillou S, Marthey S, Laloë D, Laubier J, Domagalski J, Mobuchon L, Leroux C, Le Provost F. 2014. Characterization and comparison of lactating mouse and bovine mammary gland miRNomes. Plos One. 9, e91938
Leroy G, Danchin-Burge C, Palhière I, SanCristobal M, Nédélec Y, Verrier E, Rognon X. 2015. How introgression events shape partition of diversity among breeds : a case study in sheep. Genet Sel Evol. 47-48
Leroy G., Mary-Huard T., Verrier E., Danvy S., Charvolin E., Danchin-Burge C. 2013. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genetics Selection Evolution 45, 1
Leroy G, Phocas F, Hedan B, Verrier E, Rognon X. 2015. Inbreeding impact on litter size and survival in selected canine breeds Vet J. 203, 74-78
Leroy G. 2014. Inbreeding depression in livestock species: review and meta-analysis. Anim Genet. 45, 618-628
Leroy G, Vernet E, Pautet MB, Rognon X. 2013. An insight into population structure and gene flow within pure-bred cats. Journal of Animal Breeding and Genetics. 131, 53- 60
Mahammi FZ, Gaouar SBS, Laloë D, Faugeras R, Tabet-Aoul N, Rognon X, Tixier-Boichard M, Saidi-Mehtar N. 2015. A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls. J Anim Breed Genet.
Marris C, Heams T, Kepes F, Campos L, Monsan, P, Toussaint JF, Benoit-Browaeys D, Haiech J, Alix JP, Fellous M. 2013. Measuring an open and responsible science. MS Medecine Sciences. 29, 23-25
Mignon-Grasteau S, Moreri U, Narcy A, Rousseau X, Rodenburg TB, Tixier-Boichard M, Zerjal T. 2015. Robustness to chronic heat stress in laying hens: a meta-analysis. Poultry Science. 94, 586-600
Mir C, Zerjal T, Combes V, Dumas F, Madur D, Bedoya C, Dreisigacker S, Franco J, Grudloyma P, Hao PX, Hearne S, Jampatong C, Laloë D, Muthamia Z, Nguyen T, Prasanna BM, Taba S, Xie CX, Yunus M, Zhang S, Warburton ML, Charcosset A. 2013. Out of America: tracing the genetic footprints of the global diffusion of maize. Theor Appl Genet. 126(S11), 2671-2682
Mobuchon L, Marthey S, Le Guillou S, Laloë D, Le Provost F, Leroux C. 2015. Food deprivation affects the miRNome in the lactating goat mammary gGland. PLoS One. 10, e0140111
Monneret G, Jaffrézic F, Rau A, Nuel G. 2015. Estimation d'effets causaux dans les réseaux de régulation génique: vers la grande dimension. Revue d'intelligence artificielle. 29, 205-227
Moro C, Cornette R, Vieaud A, Bruneau N, Gourichon D, Bed’Hom B, Tixier-Boichard M. 2015. Quantitative effect of a CNV on a morphological trait in chickens. PLoS One. 10, e0118706
Nguyen M, Boutinaud M, Pétridou B, Gabory A, Pannetier M, Chat S, Bouet S, Jouneau L, Jaffrezic F, Laloë D, Klopp C, Brun N, Kress C, Jammes H, Charlier M, Devinoy E. 2014. DNA Methylation and Transcription in a Distal Region Upstream from the Bovine AlphaS1 Casein Gene after Once or Twice Daily Milking. PLoS ONE. 9, e111556
Nuel G, Rau A, Jaffrezic F. 2014. Using pairwise ordering preferences to estimate causal effects in gene expression from a mixture of observational and intervention experiments. Qual Technol Quant Manag. 11, 23-37
Pham MH, Berthouly-Salazar C, Tran XH, Chang WH, Crooijmans, RPMA, Lin DY, Hoang VT, Lee YP, Tixier-Boichard M., Chen CF. 2013. Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies. Animal Genetics 44, 509-521
Pham MH, Chang WH, Berthouly-Salazar C, Lin DY, Yungrahang S, Lee YP, Tixier-Boichard M, Chen CF. 2013. Genetic characterisation of Taiwan commercial native chickens ascertained by microsatellite markers. The Journal of Poultry Science 50, 290-299
Pirault P, Danvy S, Verrier E, Leroy G. 2013. Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale. Plos One 8, e61544
Rau A, Gallopin M, Celeux G, Jaffrézic F. 2013. Data-based filtering for replicated high-throughput transcriptome sequencing experiments. Bioinformatics 29, 2146-2152
Rau A., Jaffrezic F., Nuel G. 2013. Joint estimation of causal effects from observational and intervention gene expression data. BMC Systems Biology 7, 111
Rau A, Maugis-Rabusseau C, Martin-Magniette ML, Celeux G. 2015. Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. Bioinformatics. 31, 1420-1427
Rau A, Marot G, Jaffrézic F. 2014. Differential meta-analysis of RNA-seq data from multiple studies. BMC Bioinformatics. 15, 91
Recoquillay J, Pitel F, Arnould C, Leroux S, Dehais P, Moréno C, Calandreau L, Bertin A, Gourichon D, Bouchez O, Vignal A, Fariello MI, Minvielle F, Beaumont C, Leterrier C, Le Bihan-Duval E. 2015. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genomics. 16, 10
Roux PF, Boitard S, Blum Y, Parks B, Montagner A, Mouisel E, Djari A, Esquerré D, Désert C, Boutin M, Leroux S, Lecerf F, Le Bihan-Duval E, Klopp C, Servin B, Pitel F, Duclos MJ, Guillou H, Lusis AJ, Demeure O, Lagarrigue S. 2015. Combined QTL and Selective Sweep Mappings with Coding SNP Annotation and cis-eQTL Analysis Revealed PARK2 and JAG2 as New Candidate Genes for Adiposity Regulation. G3. 5, 529-2
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