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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech


Recent publications

Beaumont M, Blanc F, Cherbuy C, Egidy G, Giufra E, Lacroix‑Lamandé S, Wiedemann A. 2021. Intestinal organoids in farm animals. Vet Res. 52, 33

Blanc F,  Maroilley T,  Revilla M, Lemonnier G, Leplat JJ,  Billon Y, Ravon L, Bouchez O, Bidanel JP, Bed’Hom B, Pinard‑van der Laan MH, Estellé J, Rogel‑Gaillard C. 2021. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs. Genet Sel Evol. 53, 24

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

Davaine C, Hadadi E, Taylor W, Bennaceur-Griscelli A, Acloque H. 2021. Inducing Sequential Cycles of Epithelial-Mesenchymal and Mesenchymal-Epithelial Transitions in Mammary Epithelial Cells. Methods Mol Biol. 2179, 341-351

Hadadi E, Acloque H. 2021. Role of circadian rhythm disorders on EMT and tumour-immune interactions in endocrine-related cancers. Endocr Relat Cancer. 28, R67-R80

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

Martin P, Vinet A, Denis C, Grohs C, Chanteloup L, Dozias D, Maupetit D, Sapa J, Renand G, Blanc F. 2021. Determination of immunoglobulin concentrations and genetic parameters for colostrum and calf serum in Charolais animals. J Dairy Sci. 104, in press

Minnoye L, Taskiran II, Mauduit D, Fazio M, Van Aerschot L, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, van Rooijen E, Marine JC, Egidy G, Ghanem GE, Zon L, Wouters J, Aerts S. 2020. Cross-species analysis of enhancer logic using deep learning. Genome Res. 30, 1815-1834


Artus J, Hue I, Acloque H. 2020. Preimplantation development in ungulates: a 'ménage à quatre' scenario. Reproduction. 159, R151-R171 GeMS
López-Colom P, Estellé J, Bonet J, Coma J, Martín-Orúe SM. 2020. Applicability of an unmedicated feeding program aimed to reduce the use of antimicrobials in nursery piglets: impact on performance and fecal microbiota. Animals (Basel). 10, pii: E242

Ballester M, Ramayo-Caldas Y, Gonzalez-Rodriguez O, Pascual M, Reixach J, Diaz M, Blanc F, Lopez-Serrano S, Tibau J, Quintanilla R. 2020. Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs. Sci Rep. 10, 18462

Bidanel JP,  Silalahi P, Tribout T, Canario L, Ducos A, Garreau H, Gilbert H, Larzul C, Milan D, Riquet J, Schwob S, Mercat MJ, Hassenfratz C, Bouquet A, Bazin C, Bidanel J. 2020. Cinquante années d’amélioration génétique du porc en France : bilan et perspectives. INRAE Prod Anim. 33, 1-16

Blanc F, Prévost-Blondel A, Piton G, Bouguyon E, Leplat JJ, Andréoletti F, Egidy G, Bourneuf E, Bertho N, Vincent-Naulleau S. 2020. The composition of circulating leukocytes varies with age and melanoma onset in the MeLiM pig biomedical model. Front Immunol. 11, 291

Borey M, Estellé J, Caidi A, Bruneau N, Coville JL,  Hennequet-Antier C, Mignon-Grasteau S, Calenge F. 2020. Broilers divergently selected for digestibility differ for their digestive microbial ecosystems. PLoS One. 15, e0232418.

Carvalho AV, Hennequet-Antier C, Crochet S, Bordeau T, Courousse N, Cailleau-Audouin E, Chartrin P, Darras VM, Zerjal T, Collin A, Coustham V. 2020. Embryonic thermal manipulation has short and long-term effects on the development and the physiology of the Japanese quail. PLoS One. 15, e0227700

Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valiere S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouanno E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y. 2020. Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens. Mol Ecol Resour. 20, 531-543

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

Hadadi E,Taylor W, Li X, Aslan Y, Villote M, Rivière J, Duvallet G, Auriau C, Dulong S, Raymond Letron I, Provot S, Bennaceur-Griscelliand AL, Acloque H. 2020. Chronic circadian disruption modulates breast cancer stemness and immune microenvironment to drive metastasis in mice. Nat Commun. 11, 3193

Li JH, Zhong HZ,  Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G, Estelle-Fabrellas J, Popova M, Yang ZY, Zhang H, Li F, Tang SM, Yang FM, Chen W, Chen B, Li JY,Guo J,  Martin C,Maguin E, Xu X. 2020. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. GigaScience. 9, 1-15

Manjula P, Bed’Hom B,Hoque Md R, Cho S, Seo D, Chazara O, Lee SH, Lee JH. 2020. Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms. Immunogenetics. 72, 367-379.

Marthey S, Estellé J, Blin A, Wahlberg P, Créchet1 F, Lecardonnel J, Tessiot F, Rogel‑Gaillard C,  Bourneuf E. 2020. Transcription from a gene desert in a melanoma porcine model. Mol Genet Genomics, 295. 1239-1252

Massacci FR, Berri EM, Lemonnier G, Guettier E, Blanc F, Jardet D, Rossignol MN, Mercat MJ, Dore J, Lepage P, Rogel Gaillard C, Estelle J. 2020. Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets. Animal Microbiome. 2, 2

Massacci FR, Morelli A, Cucco L, Castinel A, Ortenzi R, Tofani S, Pezzotti G, Estelle J, Paniccia M, Magistrali CF. 2020. Transport to the slaughterhouse affects the Salmonella shedding and modifies the fecal microbiota of finishing pigs. Animals (Basel). 10, 676

Massacci FR, Tofani S, Forte C, Bertocchi M, Lovito C, Orsini S, Tentellini M, Marchi L, Lemonnier G, Luise D, Blanc F, Castinel A Bevilacqua C, Rogel-Gaillard C, Pezzotti G, Estellé J, Trevisi P2, Magistrali CF. 2020. Host genotype and amoxicillin administration affect the incidence of diarrhoea and faecal microbiota of weaned piglets during a natural multiresistant ETEC infection. J Anim Breed Genet. 137, 60-72

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

Munyaka PM, Blanc F, Estellé-Fabrellas J, Lemonnier G, Leplat JJ, Rossignol MN, Jardet D, Plastow G, Billon Y, Willing   BP, Rogel-Gaillard C. 2020. Discovery of predictors of Mycoplasma hyopneumoniae vaccine response efficiency in pigs: 16S rRNA gene fecal microbiota analysis. Microorganisms, 8- 1151

Perez-Pascual D, Estelle J, Dutto G,  Rodde C, Bernardet JF, Marchand Y, Duchaud E, Przybyla C, Ghigo JM. 2020. Growth performance and adaptability of European sea bass (Dicentrarchus labrax) gut microbiota to alternative diets free of fish products. Microorganisms. 9, 1346

Shrestha M, Garreau   H, Balmisse E , Bed'hom B, David I, Guitton E, Helloin E, Lenoir G, Maupin M,  Robert R, Lantier F, Gunia M. 2020. Genetic parameters of resistance to pasteurellosis using novel response traits in rabbits. Genet sel Evol. 52, 34

Terry S, Engelsen AST, Buart S, Elsayed WS, Venkatesh GH, Chouaib S. 2020. Hypoxia-driven intratumor heterogeneity and immune evasion. Cancer Lett. 492, 1-10 


Arguello H, Estelle J, Leonard FC, Crispie F, Cotter PD, O'Sullivan O, Lynch H, Walia K, Duffy G, Lawlor PG, Gardiner GE. 2019. Influence of the intestinal microbiota on colonization resistance to Salmonella and the shedding pattern of naturally exposed pigs. mSystems. 4,e00021-19

Bernelin-Cottet C, Urien C, McCaffrey J, Collins D Donadei A, McDaid D, Jakob V, Barnier-Quer C, Collin N, Bouguyon E, Bordet E, Barc C, Boulesteix O, Leplat JJ, Blanc F, Contreras V, Bertho N, Moore AC, Schwartz-Cornil I. 2019. Electroporation of a nanoparticle-associated DNA vaccine induces higher inflammation and immunity compared to its delivery with microneedle patches in pigs. J Control Release. 308, 14-28

Bernelin-Cottet C, Urien C, Fretaud M, Langevin C, Trus I, Jouneau L, Blanc F, Leplat JJ, Barc C, Boulesteix O, Riou M, Dysart M, Mahé S, Studsrub E, Nauwynck H, Bertho N, Bourry O, Schwartz-Cornil I. 2019. A DNA prime immuno-potentiates a modified live vaccine against the porcine reproductive and respiratory syndrome virus but does not improve heterologous protection. Viruses. 11, pii: E576.

Bordet E, Fretaud M, Crisci E, Bouguyon E, Rault S, Pezant J, Pleau A, Renson P, Giuffra E, Larcher T, Bourge M, Bourry O, Boulesteix O, Langevin C, Schwartz-Cornil I, Bertho N. 2019. Macrophage-B cell interactions in the inverted porcine lymph node and their response to porcine reproductive and respiratory syndrome virus. Front Immunol. 10, 953

Cho IC, Park HB, Ahn JS, Han SH, Lee JB, Lim HT, Yoo CK, Jung EJ, Kim DH, Sun WS, Ramayo-Caldas Y, Kim SG, Kang YJ, Kim YK, Shin HS1, Seong PN, Hwang IS, Park BY, Hwang S, Lee SS, Ryu YC, Lee JH, Ko MS, Lee K, Andersson G, Pérez-Enciso M, Lee JW. 2019. A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs. PLoS Genet. 15, e1008279

Crespo-Piazuelo D, Migura-Garcia L, Estelle J, Criado-Mesas L, Revilla M, Castello A, Munoz M, Garcia-Casco JM, Fernandez AI, Ballester M, Folch JM. 2019. Association between the pig genome and its gut microbiota composition. Sci Rep. 9, 8791

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

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.

Giuffra E, Tuggle CK, FAANG Consortium. 2019. Functional annotation of animal genomes (FAANG): Current achievements and roadmap. Annu Rev Anim Biosci. 7, 65-88

Guillocheau GM, El Hou A, Meersseman C, Esquerré D, Rebours E, Letaief R, Simao M, Hypolite N, Bourneuf E, Bruneau N, Vaiman A, Vander Jagt CJ, Chamberlain  AJ, Rocha D. 2019. Survey of allele specific expression in bovine muscle. Sci Rep. 9, 4297

Massacci FR, Lovito C, Tofani S, Tentellini M, Genovese DA, De Leo AAP, Papa P, Magistrali CF, Manuali E, Trabalza-Marinucci M, Moscati L, Forte C. 2019. Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 positively affects performance and intestinal ecosystem in broilers during a Campylobacter jejuni infection. Microorganisms. 7, pii: E596

Massacci FR, Clark A, Ruet A, Lansade L, Costa M, Mach N. 2019. Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses. J Anim Breed Genet. in press

Muñoz M, Bozzi R, García-Casco J, Núñez Y, Ribani A, Franci O, García F, Škrlep M, Schiavo G, Bovo S, Utzeri VJ, Charneca R, Martins JM, Quintanilla R, Tibau J6, Margeta V, 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, Fernández AI, Fontanesi L, Óvilo C. 2019. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Sci Rep. 9, 13546

Munyaka PM, Kommadath A, Fouhse J, Wilkinson J, Diether N, Stothard P, Estellé J, Rogel-Gaillard C, Plastow G, Willing BP. 2019.  Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae.  Vaccine. in press

Larsen FT, Bed’Hom B, Guldbrandtsen B, Dalgaard TS. 2019. Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies. Mol Immunol. 114, 216-225

Larsen FT, Bed'Hom B, Naghizadeh M, Kjaerup RB, Zohari S, Dalgaard TS. 2019. Immunoprofiling of peripheral blood from infectious bronchitis virus vaccinated MHC-B chicken lines - Monocyte MHC-II expression as a potential correlate of protection. Dev Comp Immunol. 96, 93- 102

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

Peyraud JL, Aubin J, Barbier M, Baumont R, Berri C, Bidanel J P, Citti C, Cotinot C, Ducrot C, Dupraz P, Faverdin P, Friggens N, Houot S, Nozières-Petit MO, Rogel-Gaillard C, Sante-Lhoutellier V. 2019. Science for tomorrow’s livestock farming: A forward thinking conducted at INRA. Inra Prod Anim. 32, 323-338

Pitel F, Calenge F, Aigueperse N, Estelle-Fabrellas J, Coustham V, Calandreau F, Morisson M, Pascale Chavatte-Palmer P, Ginane C. 2019. Role of the early environment in phenotypic variability and adaptation of animals to their environment. INRA Prod Anim. 32, 247-262

Revilla M, Friggens NC, Broudiscou LP, Lemonnier G, Blanc F, Ravon L, Mercat MJ, Billon Y, Rogel-Gaillard C, Le Floch N, Estellé J, Muñoz-Tamayo R. 2019. Towards the quantitative characterisation of piglets’ robustness to weaning: a modelling approach. Animal. in press.

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


Argüello H, Estellé J, Zaldívar-López S, Jiménez-Marín Á, Carvajal A, López-Bascón MA, Crispie F, O'Sullivan O, Cotter PD, Priego-Capote F, Morera L, Garrido JJ. 2018. Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa. Sci Rep. 8, 7788.

Beauclercq S, Nadal-Desbarats L, Hennequet-Antier C, Gabriel I, Tesseraud S, Calenge F, Le Bihan-Duval  E, Mignon-Grasteau S. 2018. Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens. Sci Rep. 8, 6678.

Blanc F, Créchet F, Bruneau N, Piton G, Leplat JJ, Andréoletti F, Egidy G, Vincent-Naulleau S, Bourneuf E. 2018. Impact of a CD4 gene haplotype on the immune response in minipigs. Immunogenetics. 70, 209-222.

Bordet E, Blanc F, Tiret M, Crisci E, Bouguyon E, Renson P, Maisonnasse P, Bourge M, Leplat JJ, Giuffra E, Jouneau L, Schwartz-Cornil I, Bourry O, Bertho N. 2018. Porcine reproductive and respiratory syndrome virus type 1.3 Lena triggers conventional dendritic cells 1 activation and T helper 1 immune response without infecting dendritic cells. Front Immunol. 9, 2299

Bordet E, Maisonnasse P, Renson P, Bouguyon E, Crisci E, Tiret M, Descamps D, Bernelin-Cottet C, Urien C, Lefèvre F, Jouneau L, Bourry O, Leplat JJ, Schwartz-Cornil I, Bertho N. 2018. Porcine alveolar macrophage-like cells are pro-inflammatory pulmonary intravascular macrophages that produce large titers of porcine reproductive and respiratory syndrome virus. Sci Rep.  8, 10172

Bourneuf E, Estellé J, Blin A, Créchet F, del Pilar Schneider M,  Gilbert H,  Brossard M, Vaysse A, Lathrop M, Vincent-Naulleau S, Demenais F. 2018. New susceptibility loci for cutaneous melanoma risk and progression revealed using a porcine model. Oncotarget. 9, 27682-27697

Crespo-Piazuelo D, Estelle J, Revilla M Criado-Mesas L Ramayo-Caldas Y, Ovilo C, Fernandez AI, Ballester M, Folch JM. 2018. Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions. Sci Rep. 8, 12727

Lee C, Moroldo M, Perdomo-Sabogal A, Mach N, Marthey S, Lecardonnel J, Wahlberg P, Chong AY, Estellé J, Ho SYW, Rogel-Gaillard C, Gongora J. 2018. Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing. Immunogenetics. 70, 401-417.

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

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

Wragg D, Técher MA, Canale-Tabet K, Basso, B, Bidanel JP, Labarthe E, Bouchez O, Le Conte Y, Clémencet J, Delatte H, Vignal A. 2018. Autosomal and mitochondrial adaptation following admixture: a case study on the honeybees of Reunion Island. Genome Biol Evol. 10, 220-238.


Badaoui B, Fougeroux A, Petit F, Anselmo A, Gorni C, Cucurachi M, Cersini A, Granato A, Cardeti G, Formato G, Mutinelli F, Giuffra E, Williams JL, Botti S. 2017. RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae. PLoS One, 12- e0173438.

Ballester M, Ramayo-Caldas Y, Revilla M, Corominas J, Castello A, Estelle J, Fernandez AI, Folch JM. 2017. Integration of liver gene coexpression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs. Sci Rep. 7, 46539.        

Bourneuf E. 2017. The MeLiM minipig: An original spontaneous model to explore cutaneous melanoma genetic basis. Front Genet. 8, 148.

Bourneuf E, Otz P, Pausch H, Jagannathan V, Michot P,  Grohs C, Piton G, Ammermüller S, Deloche MC, Fritz S, Leclerc H, Péchoux C, Boukadiri A, Hozé C, Saintilan R, Créchet F,  Mosca M, Segelke D, Guillaume F, Bouet S, Baur A, Vasilescu A, Genestout L, Thomas A, Allais-Bonnet A, Rocha D, Colle MA, Klopp C,  Esquerré D, Wurmser C, Flisikowski K, Schwarzenbacher H, Burgstaller  J, Brügmann M, Dietschi E, Rudolph N, Fayolle G, Danchin-Burge C,  Schibler L, Bed’Hom B, Hayes BJ, Daetwyler HD, Fries R, Boichard  D, Pin D, Drögemüller C, Capitan A.  2017. Rapid discovery of de novo deleterious mutations in cattle enhances the value of livestock as model specie. Sci Rep. 7, 11466.

Campagne C, Reyes-Gomez E, Picco ME, Loiodice S, Salaun P, Ezagal J, Bernex F, Commère PH, Pons S, Esquerre D, Bourneuf E, Estellé J, Maskos U, Lopez-Bergami P, Aubin-Houzelstein G, Panthier JJ, Egidy G. 2017. RACK1 cooperates with NRASQ61K to promote melanoma in vivo. Cell Signal. pii: S0898-6568(17)30084-0.

Campagne C, Pons S, Esquerre D, Estellé J, Bourneuf E, Maskos U, Egidy G. 2017. Transcriptome of melanoma cells from two mouse models, Tyr:NRasQ61K and Tyr:Rack1-HA, Tyr:NRasQ61K. Data Brief.  14, 32-34.

Ducos A, Bed'Hom B, Acloque H, Pain B. 2017. Genome Editing: what impact for farm animal species ? INRA Prod Anim. 12, 3-18

Gilbert H, Billon Y, Brossard L, Faure J, Gatellier P, Gondret F, Labussière E, Lebret B, Lefaucheur L, Le Floch N, Louveau I, Merlot E, Meunier-Salaün MC, Montagne L, Mormede P, Renaudeau D, Riquet J, Rogel-Gaillard C, van Milgen J, Vincent A, Noblet J. 2017. Review: divergent selection for residual feed intake in the growing pig. Animal. ahead of print 

Muret K, Klopp C, Wucher V, Esquerre D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S. 2017. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol. 49, 6

Roselli M, Pieper R, Rogel-Gaillard C, de Vries H, Bailey M, Smidt H, Lauridsen C. 2017. Immunomodulating effects of probiotics for microbiota modulation, gut health and disease resistance in pigs. Anim Food Sci Technol. in press.  

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.  

Silalahi P, Tribout T,  Billon Y, Gogué J, Bidanel JP. 2017. Estimation of the effects of selection on French Large White sow and piglet performance during the suckling period. J Anim Sci. 95, 4333-4343  

Wragg D, Techer MA, Canale-Tabet K, Basso B, Bidanel JP, Labarthe E, Bouchez O, Le Conte Y, Clémencet J, Delatte H, Vignal A. 2017. Autosomal and mitochondrial adaptation following admixture: a case study on the honeybees of Reunion Island. Genome Biol Evol, in press



Campagne C, Reyes-Gomez E, Loiodice S, Gadin S, Ezagal J, Bernex F, Abitbol M, Louise A, Beermann F, Panthier JJ, Aubin-Houzelstein G, Egidy G.  2016. Haplosufficiency of PAX3 for melanoma development in Tyr::NRAS(Q61K); Cdkn2a(-/-) mice allows identification and sorting of melanoma cells using a Pax3(GFP) reporter allele. Melanoma Res. 26, 12-20

Désert C, Merlot E, Zerjal T, Bed'Hom B, Härtle S, Le Cam A, Roux,PF, Baeza E,  Gondret F, Duclos M, Lagarrigue S. 2016. Transcriptomes of whole blood and PBMC in chickens. Comp Biochem Physiol. in press

Fulton JE, McCarron AM, Lund AR, Pinegar KN, Wolc A, Chazara O, Bed'Hom B, Berres M, Miller MM. 2016. A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1. Genet Sel Evol. 48, 1

Jousselin E, Clamens AL, Galan M, Bernard M, Maman S, Gschloessl B, Duport MG, Meseguer A, Calevro F, Coeur D'Acier A. 2016. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. Molec Ecol Res. 16, 628-640

Maisonnasse P, Bouguyon E, Piton G, Ezquerra A, Urien C, Deloizy C, Bourge M, Leplat J-J , Simon G, Chevalier C, Vincent-Naulleau S, Crisci E, Montoya M, Schwartz-Cornil I, Bertho N. 2016. The respiratory DC/macrophage network at steady-state and upon influenza infection in the swine biomedical model. Mucosal Immunol. 9, 835-849

Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C, Lemonnier G, Leplat JJ, Billon Y, Berri M, Dore J, Rogel-Gaillard C, Estelllé J. 2016. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME Journal

Silalahi P, Tribout T,  Prunier A, Billon Y, Gogue J, Bidanel JP. 2016. Estimation of the effects of selection on French Large White reproductive performance using frozen semen. J Anim Sci. 94, 3655-3662

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

Wragg D, Marti-Marimon M, Basso B, Bidanel JP, Labarthe E, Bouchez O, Le Conte Y, Vignal A. 2016. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly. Sci Rep. 6, 27168

Xiao L, Estellé J, Kiilerich P, Ramayo-Caldas Y, Xia Z, Feng Q, Liang S, Pedersen A, Kjeldsen NJ, Liu C, Maguin E, Doré J, Pons N, Le Chatelier E, Prifti E, Li J, Jia H, Liu X, Xu X, Ehrlich SD, Madsen L, Kristiansen K, Rogel-Gaillard C, Wang J. 2016. A reference gene catalogue of the pig gut microbiome. Nat Microbiol. 1, 16161


Leif Andersson, Alan L Archibald, Cynthia D Bottema, Rudiger Brauning, Shane C Burgess, Dave W Burt, Eduardo Casas, Hans H Cheng, Laura Clarke, Christine Couldrey, Brian P Dalrymple, Christine G Elsik, Sylvain Foissac, Elisabetta Giuffra, Martien A Groenen, Ben J Hayes, LuSheng S Huang, Hassan Khatib, James W Kijas, Heebal Kim, Joan K Lunney, Fiona M McCarthy, John C McEwan, Stephen Moore, Bindu Nanduri, Cedric Notredame, Yniv Palti, Graham S Plastow, James M Reecy, Gary A Rohrer, Elena Sarropoulou, Carl J Schmidt, Jeffrey Silverstein, Ross L Tellam, Michele Tixier-Boichard, Gwenola Tosser-Klopp, Christopher K Tuggle, Johanna Vilkki, Stephen N White, Shuhong Zhao, Huaijun Zhou and The FAANG Consortium Coordinated international action to accelerate genome-to-phenome with FAAG. 2015. The Functional Annotation of ANimal Genomes project. Genome Biol, 16-57

Bacciu N, Bed'Hom B, Filangi O, Romé H, Gourichon D, Répérant JM, Le Roy P, Pinard-van der Laan MH, Demeure O. 2014. QTL detection for coccidiosis (Eimeria tenella) resistance in a Fayoumi × Leghorn F2 cross, using a medium-density SNP panel. Genet Sel Evol. 46, 14

Baco M., Chu C-Y, Bouet S., Rogel-Gaillard C., Bourneuf E., Le Provost F., Chu C-Y, Vincent-Naulleau S. 2014. Analysis of melanoma-related microRNAs expression during the spontaneous regression of cutaneous melanomas in MeLiM pigs. Pig Cell Melanoma Res. 27, 668-670

Baco M, Chu C, Chiang Y, Marthey S, Le Provost F, Chu C, Vincent-Naulleau S. 2013. Identification of microRNAs involved in the spontaneous regression of cutaneous melanoma in pigs. J Invest Dermatol. 133, S223. Meeting abstract. 
Baco M, Yang YT, Marthey S, Chiang YS, Chu CY, Leprovost F, Chu CY, Vincent-Naulleau S. 2013. miRNAs Profile of Cutaneous Melanoma Undergoing Complete Spontaneous Regression in MeLiM Pigs.    JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT. 11, 46-47. Meeting abstract

Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. 2014. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLoS ONE. 9, e91918

Bonnet-Garnier A, Veillard AC, Bed'Hom B, Hayes H, Britton-Davidian J. 2015. Assessing the quality of donor cells: karyotyping methods. Methods Mol Biol. 1222, 83-99

Calenge F, Martin C, Le Floch N, Phocas F, Morgavi D, Rogel-Gaillard C, Quere P. Integrating the characterization of digestive microbiota in phenotyping livestock animals: towards a new tool for animal health control? Inra Prod Anim. 27, 209-222

Calenge F, Mignon-Grasteau S, Chanteloup NK, Brée A, Lalmanach AC, Schouler C. 2014. Broiler lines divergently selected for digestive efficiency also differ in their susceptibility to colibacillosis. Avian Pathology. 43, 78- 81

Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson. 2014. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science. 345, 1074-1079

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

Corominas J, Marchesi JA, Puig-Oliveras A, Revilla M, Estellé J, Alves E, Folch JM, Ballester M. 2015. Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs. Genet Sel Evol. 47, 20

Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, Estelle J, Castello A, Alves, Pena RN, Ballester M, Folch JM. 2013. Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics. 14, 843

Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK. 2013. Structural and functional annotation of the porcine immunome. BMC Genomics 14, 332
Demeure O, Hamzic E, Juin H, Naciri M, Juul-Madsen HR, Okimoto R, Pinard-van der Laan MH, Bed'Hom B. 2013. Investigation of Immune Response to Eimeria maxima in Broilers. Scand J Immunol. 77,   276-277. Meeting abstract
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

Dhorne-Pollet S, Thélie A, Pollet N. 2013. Validation of novel reference genes for RT-qPCR studies of gene expression in Xenopus tropicalis during embryonic and post-embryonic development. Dev Dyn. 242, 709-717

Endale Ahanda ML, Zerjal T, Dhorne-Pollet S, Rau A, Cooksey A,  Giuffra E. 2015. Impact of the genetic background on the composition of the chicken plasma miRNome in response to a stress. PLoS One. 9, e114598

Endale Ahanda ML, Bienvenu T, Sermet-Gaudelus I, Mazzolini L, Edelman A, Zoorob R, Davezac N. 2015. The hsa-miR-125a/hsa-let-7e/hsa-miR-99b cluster is potentially implicated in Cystic Fibrosis pathogenesi. J Cyst Fibros. 14, 571-579

Fernández-Rodríguez A, Estellé J, Blin A, Muñoz M, Créchet F, Demenais F, Vincent-Naulleau S, Bourneuf E. 2014. KIT and melanoma predisposition in pigs: sequence variants and association analysis. Animal Genetics. 45, 445-448

Frésard L, Leroux S, Servin B, Gourichon D, Dehais P, San Cristobal M, Marsaud N, Bed'hom B, Hormozdiari F, Lusis AJ, Beaumont C, Zerjal T, Vignal A, Morisson M, Lagarrigue S,Pitel F. 2014. Transcriptome-wide investigation of genomic imprinting in chicken. Nucl Acids res. 42, 3768-3782

Galio L, Droineau S, Yeboah P, Boudiaf H, Bouet S, Truchet S, Devinoy E. 2013. MicroRNA in the ovine mammary gland during early pregnancy: spatial and temporal expression of miR-21, miR-205, and miR-200. Physiol Genom 45, 151-161

Gertz EM, Schäffer AA, Agarwala R, Bonnet-Garnier A, Rogel-Gaillard C, Hayes H, Mage RG. 2013. Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20. Immunogenetics 65, 749-762

Gourbeyre O, Berri M,  Lippi Y,  Meurens F, Vincent-Naulleau S, Laffitte J, Rogel-Gaillard C, Pinton P, Oswald I. 2015. Pattern recognition receptors in the gut: analysis of their expression along the intestinal tract and the crypt/villus axis. Physiol Rep. 3, e12225

Guignot F, Reigner F, Perreau C, Tartarin P, Babilliot JM, Bed’Hom B, Vidament M, Mermillod P, Duchamp G. 2015. Preimplantation genetic diagnosis in Welsh pony embryos after biopsy and cryopreservation. J Anim Sc. Ahead

Hamzic B, Bed'Hom B, Juin H, Hawken R, Abrahamsen MS, Elsen JM, Servin B, Pinard-van der Laan MH, Demeure O. 2015. Large-scale Investigation of Response to Eimeria maxima Challenge in Broilers. J Anim Sci. 93, 1830-1840

Hamzic E, Buitenhuis B, Hérault F, Hawken R, Abrahamsen MS, Servin B, Elsen JM, Pinard-van der Laan MH, Bed’Hom B. 2015. Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers. Genet Sel Evol. 47, 91

Hamzic E, Pinard-van der Laan MH, Bed'Hom B, Juul-Madsen H. 2015. Annotation and genetic diversity of the chicken collagenous lectins. Mol Immunol. 65, 277-286

Holm JB, Sorobetea D, Kiilerich P, Ramayo-Caldas Y, Estellé J, Ma T, Madsen L, Kristiansen K, Svensson-Frej M. 2015. Chronic Trichuris muris infection decreases diversity of the intestinal microbiota and concomitantly increases the abundance of Lactobacilli. PLoS One. 10, e0125495

Jacquier V, Estellé J, Schmaltz-Panneau B, Lecardonnel J, Moroldo M, Lemonnier G, Turner-Maier J, Duranthon V, Oswald IP, Gidenne T, Rogel-Gaillard C. 2015. Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-ionomycin. BMC Genomics. 16, 26

Jacquier V, Combes S, Oswald IP, C. Rogel-Gaillard, Gidenne T. 2014. Early modulation of the cecal microbial activity in the young rabbit with rapidly fermentable fiber: Impact on health and growth. Journal of Animal Science. 92, 5551-5559

Kjærup RM, Dalgaard TS, Norup LR, Hamzic E, Sørensen P, Juul-Madsen HR. 2014.  Characterization of cellular and humoral immune responses after IBV infection in chicken lLines differing in MBL serum concentration. Viral Immunol. 27, 529-542

Larzul C, Ducrocq V, Tudela F, Juin H, Garreau H. 2014. The length of productive life can be modified through selection: an experimental demonstration in the rabbit. J Anim Sci. 92, 2395-2401

Mach N, Berri M, Esquerré D, Chevaleyre C, Lemonnier G, Billon Y, Lepage P, Oswald IP, Doré J, Rogel-Gaillard C, Estellé J. 2014. Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing. PLoS ONE. 9, e88515

Mach N, Berri M, Estellé J, Leveneez F, Lemonnier G, Denis C, Leplat JJ, Chevaleyre C, Billon Y, Rogel-Gaillard C, Lepage P. 2015. Early life establishment of the swine gut microbiome and impact on host phenotypes. Environ Microbiol Rep. 7, 554-569

Mach N, Gao Y, Lemonnier G, Lecardonnel J, Oswald IP, Estelle J, Rogel-Gaillard C. 2013. The peripheral blood transcriptome reflects variations in immunity traits in swine: towards the identification of biomarkers. BMC Genomics. 14, 894

Mahjoub N, Dhorne-Pollet S, Fuchs X, Endale Ahanda ML, Lange E, Klupp B, Arya A, Loveland J, Lefevre F, Mettenleiter T,  Giuffra E. 2015. A 2.5 kb deletion contaning a cluster of nine microRNAs in the LAT locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency. J Virol. 89, 428-442

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

Miller I, Rogel-Gaillard C, Spina D, Fontanesi L, de Almeida AM. 2014. The rabbit as an experimental and production animal: from Genomics to Proteomics. Curr Prot Peptide Sci. 15, 134-135

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

Nie W, O'Brien PC, Fu B, Wang J, Su W, He K, Bed'Hom B, Volobouev V, Ferguson-Smith MA, Dobigny G, Yang F. 2015. Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes. BMC Evol Biol. 15, 205

Puig-Oliveras A, Ramayo-Caldas Y, Corominas J, Estellé J, Pérez-Montarelo D, Hudson NJ, Casellas J, Folch, Maria Ballester JM. 2014. Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition. PLoS ONE. 9, e99720

Ramayo-Caldas Y, Fortes MR, Hudson NJ, Porto-Neto LR, Bolormaa S, Barendse W, Kelly M, Moore SS, Goddard ME, Lehnert SA, Reverter A. 2014. A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle. J Anim Sci. 92, 2832-2845

Rostellato R, Bonfatti, V, Larzul C, Bidanel JP, Carnier P. 2015. Estimates of genetic parameters for content of boar taint compounds in adipose tissue of intact males at 160 and 220 days of age. J Anim Sci. 93, 4267-4276

Roux PF, Marthey S, Djari A, Moroldo M, Esquerré D, Estellé J, Klopp C, Lagarrigue S, Demeure O. 2015. Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings. Anim Genet. 46, 82-86

Ruscanu S, Jouneau L, Urien C, Bourge M, Lecardonnel J, Moroldo M, Loup B, Dalod M, Elhmouzi-Younes J, Bevilacqua C, Hope J, Vitour D, Zientara S, Meyer G, Schwartz-Cornil. 2013. Dendritic Cell Subtypes from Lymph Nodes and Blood Show Contrasted Gene Expression Programs upon Bluetongue Virus Infection. J Virol. 87, 9333-9343

Sanchez MP, Tribout T, Iannuccelli N, Bouffaud M, Servin B, Tenghe A, Dehais P, Muller N, Schneider MP, Mercat MJ, Rogel-Gaillard C, Milan D, Bidanel JP, Gilbert H. 2014. A genome-wide association study of production traits in a Large White commercial population: evidence of haplotypes affecting meat quality. Genetics Selection Evolution. 46, 12

Sintubin P,  Collin A , Bordas A,   Zerjal T,  Tesseraud S, Buyse J, Dridi S. 2014. Expression profile of hypothalamic neuropeptides in chicken lines selected for high or low residual feed intake. Neuropeptides. 48, 213-220

Tixier-Boichard M, Verrier E, Rognon X, Zerjal T. 2015. Farm animal genetic and genomic resources from an agroecological perspective. Front Genet. 6, 1-3

Tomas J, Wrzosek L, Bouznad N, Bouet S, Mayeur C, Noordine ML, Honvo-Houeto E, Langella P, Thomas M, Cherbuy C. 2013. Primocolonization is associated with colonic epithelial maturation during conventionalization. The FASEB J. 27, 645-655

Tran TS, Narcy A, Carré B, Gabriel I, Rideau N, Gilbert H, Demeure O, Bed'Hom B, Chantry-Darmon C, Boscher MY, Bastianelli D, Sellier N, Chabault M, Calenge F, Le Bihan-Duval E, Beaumont C, Mignon-Grasteau S. 2014. Detection of QTL controlling digestive efficiency and anatomy of the digestive tract in chicken fed a wheat-based diet. Genet Sel Evol. 46, 25

Wrzosek L, Miquel S, Noordine ML, Bouet S, Chevalier-Curt MJ, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M. 2013. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 11, 61