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Menu Logo Principal AgroParisTech Université Paris-Saclay

INRA GABI Unit

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

Publications

Recent publications

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

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.

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

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.

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.

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.

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.

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

Previous publications

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

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