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A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment
Li, Junhua; Zhong, Huanzi; Ramayo-Caldas, Yuliaxis; Terrapon, Nicolas; Lombard, Vincent; Potocki-Veronese, Gabrielle; Estelle, Jordi; Popova, Milka;...
10.1093/gigascience/giaa057
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A Co-Association Network Analysis of the Genetic Determination of Pig Conformation, Growth and Fatness
Puig-Oliveras, Anna; Ballester, Maria; Corominas, Jordi; Revilla, Manuel; Estelle, Jordi; Fernandez, Ana I; Ramayo-Caldas, Yuliaxis; Folch, Josep M
10.1371/journal.pone.0114862
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A Co-Association Network Analysis Reveals Putative Regulators for Health-Related Traits in Pigs
Crespo-Piazuelo, D; Ramayo-Caldas, Y; Gonzalez-Rodriguez, O; Pascual, M; Quintanilla, R; Ballester, M
10.3389/fimmu.2021.784978
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A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs
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, HS;...
10.1371/journal.pgen.1008279
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A gene co-association network regulating gut microbial communities in a Duroc pig population
Reverter, Antonio; Ballester, Maria; Alexandre, Pamela A; Marmol-Sanchez, Emilio; Dalmau, Antoni; Quintanilla, Raquel; Ramayo-Caldas, Yuliaxis
10.1186/s40168-020-00994-8
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A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle
Ramayo-Caldas; Y Fortes; M R S Hudson; N J Porto-Neto; L R Bolormaa; S Barendse; W Kelly; M Moore; S S Goddard; M E Lehnert; S A Reverter; A
10.2527/jas.2013-7484
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A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome
Godia, Marta; Ramayo-Caldas, Yuliaxis; Zingaretti, Laura M; Darwich, Laila; Lopez, Samantha; Rodriguez-Gil, Joan E; Yeste, Marc; Sanchez, Armand;...
10.1016/j.theriogenology.2020.08.001
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A quantitative real-time PCR method using an X-linked gene for sex typing in pigs
Ballester, Maria; Castello, Anna; Ramayo-Caldas, Yuliaxis; Folch, Josep M
10.1007/s12033-012-9589-5
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A reference gene catalogue of the pig gut microbiome
Xiao; Liang Estelle; Jordi Kiilerich; Pia Ramayo-Caldas; Yuliaxis Xia; Zhongkui Feng; Qiang Liang; Suisha Pedersen; Anni Oyan Kjeldsen; Niels Jorgen...
10.1038/NMICROBIOL.2016.161
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A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds
Marete; Andrew Lund; Mogens Sando Boichard; Didier Ramayo-Caldas; Yuliaxis
10.1371/journal.pone.0199931
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A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine
Godia, Marta; Reverter, Antonio; Gonzalez-Prendes, Rayner; Ramayo-Caldas, Yuliaxis; Castello, Anna; Rodriguez-Gil, Joan-Enric; Sanchez, Armand; Clop,...
10.1186/s12711-020-00592-0
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About the existence of common determinants of gene expression in the porcine liver and skeletal muscle
Gonzalez-Prendes, R; Marmol-Sanchez, E; Quintanilla, R; Castello, A; Zidi, A; Ramayo-Caldas, Y; Cardoso, TF; Manunza, A; Canovas, A; Amills, M
10.1186/s12864-019-5889-5
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Analyse génétique de la « fromageabilité » du lait de vache prédite par spectrométrie dans le moyen infrarouge en race Montbéliarde
Marie Pierre Sanchez; Valérie Wolf; Cécile Laithier; Mohammed El Jabri; Éric Beuvier; Odile Rolet Répécaud; Nicolas Gaudillière; Stéphanie...
10.20870/productions-animales.2019.32.3.2950
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Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition
Corominas, Jordi; Ramayo-Caldas, Yuliaxis; Puig-Oliveras, Anna; Estelle, Jordi; Castello, Anna; Alves, Estefania; Pena, Ramona N; Ballester, Maria;...
10.1186/1471-2164-14-843
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Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota
Velasco-Galilea, M; Guivernau, M; Piles, M; Vinas, M; Rafel, O; Sanchez, A; Ramayo-Caldas, Y; Gonzalez-Rodriguez, O; Sanchez, JP
10.1186/s42523-020-00059-z
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Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions
Crespo-Piazuelo, Daniel; Estelle, Jordi; Revilla, Manuel; Criado-Mesas, Lourdes; Ramayo-Caldas, Yuliaxis; Ovilo, Cristina; Fernandez, Ana I;...
10.1038/s41598-018-30932-6
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Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli
Holm; Jacob Bak Sorobetea; Daniel Kiilerich; Pia Ramayo-Caldas; Yuliaxis Estelle; Jordi Ma; Tao Madsen; Lise Kristiansen; Karsten Svensson-Frej;...
10.1371/journal.pone.0125495
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Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
Marmol-Sanchez, E; Ramayo-Caldas, Y; Quintanilla, R; Cardoso, TF; Gonzalez-Prendes, R; Tibau, J; Amills, M
10.1186/s40104-019-0412-z
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Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip
Ramayo-Caldas, Y; Castello, A; Pena, RN; Alves, E; Mercade, A; Souza, CA; Fernandez, AI; Perez-Enciso, M; Folch, JM
10.1186/1471-2164-11-593
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Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
Maroilley; T Lemonnier; G Lecardonnel; J Esquerre; D Ramayo-Caldas; Y Mercat; M J Rogel-Gaillard; C Estelle; J
10.1186/s12864-017-4354-6
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Detection of selection signatures in Limousin cattle using whole-genome resequencing
Mariadassou, M; Ramayo-Caldas, Y; Charles, M; Femenia, M; Renand, G; Rocha, D
10.1111/age.12982
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Diet, Immunity, and Microbiota Interactions: An Integrative Analysis of the Intestine Transcriptional Response and Microbiota Modulation in Gilthead Seabream (Sparus aurata) Fed an Essential Oils-Based Functional Diet
Firmino, Joana P; Vallejos-Vidal, Eva; Balebona, M Carmen; Ramayo-Caldas, Yuliaxis; Cerezo, Isabel M; Salomon, Ricardo; Tort, Lluis; Estevez, Alicia;...
10.3389/fimmu.2021.625297
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Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition
Puig-Oliveras, Anna; Ramayo-Caldas, Yuliaxis; Corominas, Jordi; Estelle, Jordi; Perez-Montarelo, Dafne; Hudson, Nicholas J; Casellas, Joaquim; Folch,...
10.1371/journal.pone.0099720
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Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition (vol 9, e99720, 2014)
Puig-Oliveras, A; Ramayo-Caldas, Y; Corominas, J; Estelle, J; Perez-Montarelo, D
10.1371/journal.pone.0103668
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Early socialization and environmental enrichment of lactating piglets affects the caecal microbiota and metabolomic response after weaning
Saladrigas-Garcia, M; D'Angelo, M; Ko, H L; Traserra, S; Nolis, P; Ramayo-Caldas, Y; Folch, J M; Vergara, P; Llonch, P; Perez, J F; Martin-Orue, S M
10.1038/s41598-021-85460-7
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Evaluation of the porcine ACSL4 gene as a candidate gene for meat quality traits in pigs
Corominas, J; Ramayo-Caldas, Y; Castello, A; Munoz, M; Ibanez-Escriche, N; Folch, J M; Ballester, M
10.1111/j.1365-2052.2012.02335.x
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From SNP co-association to RNA co-expression: Novel insights into gene networks for intramuscular fatty acid composition in porcine
Ramayo-Caldas, Yuliaxis; Ballester, Maria; Fortes, Marina R S; Esteve-Codina, Anna; Castello, Anna; Noguera, Jose L; Fernandez, Ana I; Perez-Enciso,...
10.1186/1471-2164-15-232
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Gene networks for three feed efficiency criteria reveal shared and specific biological processes
Taussat, Sebastien; Boussaha, Mekki; Ramayo-Caldas, Yuliaxis; Martin, Pauline; Venot, Eric; Cantalapiedra-Hijar, Gonzalo; Hoze, Chris; Fritz,...
10.1186/s12711-020-00585-z
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Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed
Rodriguez-Valera, Y; Renand, G; Naves, M; Fonseca-Jimenez, Y; Moreno-Probance, TI; Ramos-Onsins, S; Rocha, D; Ramayo-Caldas, Y
10.1038/s41598-018-29453-z
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Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs
Ballester, Maria; Ramayo-Caldas, Yuliaxis; Gonzalez-Rodriguez, Olga; Pascual, Mariam; Reixach, Josep; Diaz, Marta; Blanc, Fany; Lopez-Serrano, Sergi;...
10.1038/s41598-020-75417-7
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Genome-wide association study for intramuscular fatty acid composition in an Iberian x Landrace cross
Ramayo-Caldas, Y; Mercade, A; Castello, A; Yang, B; Rodriguez, C; Alves, E; Diaz, I; Ibanez-Escriche, N; Noguera, JL; Perez-Enciso, M; Fernandez, AI;...
10.2527/jas.2011-4900
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Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip
Fernandez, AI; Perez-Montarelo, D; Barragan, C; Ramayo-Caldas, Y; Ibanez-Escriche, N; Castello, A; Noguera, JL; Silio, L; Folch, JM; Rodriguez, MC
10.1186/1471-2156-13-41
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Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution
Ramayo-Caldas, Yuliaxis; Prenafeta-Boldu, Francesc; Zingaretti, Laura M.; Gonzalez-Rodriguez, Olga; Dalmau, Antoni; Quintanilla, Raquel; Ballester,...
10.1186/s42523-020-00038-4
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Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis
Valdes-Hernandez, J; Folch, JM; Crespo-Piazuelo, D; Passols, M; Sebastia, C; Criado-Mesas, L; Castello, A; Sanchez, A; Ramayo-Caldas, Y
10.1186/s12711-024-00882-x
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Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows
Ramayo-Caldas, Yuliaxis; Zingaretti, Laura; Popova, Milka; Estelle, Jordi; Bernard, Aurelien; Pons, Nicolas; Bellot, Pau; Mach, Nuria; Rau, Andrea;...
10.1111/jbg.12427
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Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs
Ramayo-Caldas, Yuliaxis; Marmol-Sanchez, Emilio; Ballester, Maria; Pablo Sanchez, Juan; Gonzalez-Prendes, Rayner; Amills, Marcel; Quintanilla, Raquel
10.1186/s12711-019-0490-6
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Integration of GWAS, pathway and network analyses reveals novel mechanistic insights into the synthesis of milk proteins in dairy cows
Pegolo, S; Mach, N; Ramayo-Caldas, Y; Schiavon, S; Bittante, G; Cecchinato, A
10.1038/s41598-017-18916-4
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Integration of liver gene coexpression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs
Ballester, Maria; Ramayo-Caldas, Yuliaxis; Revilla, Manuel; Corominas, Jordi; Castello, Anna; Estelle, Jordi; Fernandez, Ana I; Folch, Josep M
10.1038/srep46539
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Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency pigs
Ramayo-Caldas, Yuliaxis; Ballester, Maria; Pablo Sanchez, Juan; Gonzalez-Rodriguez, Olga; Revilla, Manuel; Reyer, Henry; Wimmers, Klaus;...
10.1038/s41598-017-19072-5
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kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets
Ramon, Elies; Belanche-Munoz, Lluis; Molist, Francesc; Quintanilla, Raquel; Perez-Enciso, Miguel; Ramayo-Caldas, Yuliaxis
10.3389/fmicb.2021.609048
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Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs
Ramayo-Caldas, Y; Zingaretti, LM; Perez-Pascual, D; Alexandre, PA; Reverter, A; Dalmau, A; Quintanilla, R; Ballester, M
10.1186/s42523-021-00138-9
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Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities
Zingaretti, Laura M; Renand, Gilles; Morgavi, Diego P; Ramayo-Caldas, Yuliaxis
10.1093/bioinformatics/btz862
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Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition
Ramayo-Caldas, Yuliaxis; Mach, Nuria; Esteve-Codina, Anna; Corominas, Jordi; Castello, Anna; Ballester, Maria; Estelle, Jordi; Ibanez-Escriche,...
10.1186/1471-2164-13-547
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Longitudinal modelling of performance and feed efficiency traits in growing Duroc pigs
Herrera-Caceres, W; Ramayo-Caldas, Y; Sanchez, JP
10.1016/j.livsci.2022.104824
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Mitochondrial DNA diversity in wild boar from the Primorsky Krai Region (East Russia)
Ramayo; Y Shemeret'eva; I N Perez-Enciso; M
10.1111/j.1365-2052.2010.02074.x
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Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs
Marmol-Sanchez, E; Cirera, S; Zingaretti, LM; Jacobsen, MJ; Ramayo-Caldas, Y; Jorgensen, CB; Fredholm, M; Cardoso, TF; Quintanilla, R; Amills, M
10.1111/age.13238
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Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota
Gonzalez-Prendes, R; Pena, RN; Sole, E; Seradj, AR; Estany, J; Ramayo-Caldas, Y
10.1038/s41598-019-51136-6
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Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds
Ramayo-Caldas, Yuliaxis; Renand, Gilles; Ballester, Maria; Saintilan, Romain; Rocha, Dominique
10.1186/s12711-016-0216-y
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New insight into the SSC8 genetic determination of fatty acid composition in pigs
Revilla, Manuel; Ramayo-Caldas, Yuliaxis; Castello, Anna; Corominas, Jordi; Puig-Oliveras, Anna; Ibanez-Escriche, Noelia; Munoz, Maria; Ballester,...
10.1186/1297-9686-46-28
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Opportunities and limits of combining microbiome and genome data for complex trait prediction
Perez-Enciso, M; Zingaretti, LM; Ramayo-Caldas, Y; de Los Campos, G
10.1186/s12711-021-00658-7
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Opportunities and limits of combining microbiome and genome data for complex trait prediction (vol 53, 65, 2021)
Perez-Enciso, Miguel; Zingaretti, Laura M.; Ramayo-Caldas, Yuliaxis; de los Campos, Gustavo;
10.1186/s12711-021-00691-6
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Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits
Ramayo-Caldas; Yuliaxis Mach; Nuria Lepage; Patricia Levenez; Florence Denis; Catherine Lemonnier; Gaetan Leplat; Jean-Jacques Billon; Yvon Berri;...
10.1038/ismej.2016.77
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Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs
Corominas, Jordi; Ramayo-Caldas, Yuliaxis; Puig-Oliveras, Anna; Perez-Montarelo, Dafne; Noguera, Jose L; Folch, Josep M; Ballester, Maria
10.1371/journal.pone.0053687
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Porcine colonization of the Americas: a 60k SNP story
Burgos-Paz, W; Souza, C A; Megens, H J; Ramayo-Caldas, Y; Melo, M; Lemus-Flores, C; Caal, E; Soto, H W; Martinez, R; Alvarez, L A; Aguirre, L;...
10.1038/hdy.2012.109
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Porcine Tissue-Specific Regulatory Networks Derived from Meta-Analysis of the Transcriptome
Perez-Montarelo; Dafne Hudson; Nicholas J Fernandez; Ana I Ramayo-Caldas; Yuliaxis Dalrymple; Brian P Reverter; Antonio
10.1371/journal.pone.0046159
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Priming for welfare: gut microbiota is associated with equitation conditions and behavior in horse athletes
Mach, Nuria; Ruet, Alice; Clark, Allison; Bars-Cortina, David; Ramayo-Caldas, Yuliaxis; Crisci, Elisa; Pennarun, Samuel; Dhorne-Pollet, Sophie;...
10.1038/s41598-020-65444-9
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Recombination rates across porcine autosomes inferred from high-density linkage maps
Munoz, M; Alves, E; Ramayo-Caldas, Y; Casellas, J; Rodriguez, C; Folch, JM; Silio, L; Fernandez, AI
10.1111/j.1365-2052.2011.02301.x
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Ruminant microbiota : research status and impacts of microbiota on animal performance and health
Zened, Asma; Forano, Evelyne; Delbes, Celine; Verdier-Metz, Isabelle; Morgavi, Diego; Popova, Milka; Ramayo-Caldas, Yuliaxis; Bergonier, Dominique;...
10.20870/productions-animales.2020.33.4.4597
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Sequence-based GWAS, network and pathway analyses reveal genes co-associated with milk cheese-making properties and milk composition in Montbeliarde cows
Sanchez, MP; Ramayo-Caldas, Y; Wolf, V; Laithier, C; El Jabri, M; Michenet, A; Boussaha, M; Taussat, S; Fritz, S; Delacroix-Buchet, A; Brochard, M;...
10.1186/s12711-019-0473-7
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Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs
Hong, Joon-Ki; Lee, Jae-Bong; Ramayo-Caldas, Yuliaxis; Kim, Si-Dong; Cho, Eun-Seok; Kim, Young-Sin; Cho, Kyu-Ho; Lee, Deuk-Hwan; Park, Hee-Bok
10.1038/s41598-020-71647-x
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SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile
Pegolo, S; Dadousis, C; Mach, N; Ramayo-Caldas, Y; Mele, M; Conte, G; Schiavon, S; Bittante, G; Cecchinato, A
10.1038/s41598-017-17434-7
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Supplementation of xylo-oligosaccharides to suckling piglets promotes the growth of fiber-degrading gut bacterial populations during the lactation and nursery periods
Gonzalez-Sole, F; Sola-Oriol, D; Ramayo-Caldas, Y; Rodriguez-Prado, M; Ortiz, GG; Bedford, MR; Perez, JF
10.1038/s41598-022-15963-4
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Systems biology approach provides novel insights into gene networks controlling tenderness and meat quality traits across French beef breeds
Ramayo-Caldas, Y.; Renand, G.; Ballester, M.; Saintilan, R.; Rocha, D.;
10.2527/jas2016.94supplement4118a
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The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle
Rodriguez-Valera, Yoel; Rocha, Dominique; Naves, Michel; Renand, Gilles; Perez-Pineda, Eliecer; Ramayo-Caldas, Yuliaxis; Ramos-Onsins, Sebastian E
10.3390/ani10122233
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The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes
Velasco-Galilea, M; Piles, M; Ramayo-Caldas, Y; Sanchez, JP
10.1038/s41598-021-99028-y
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Understanding host-microbiota interactions in the commercial piglet around weaning
Saladrigas-Garcia, M; D'Angelo, M; Ko, HL; Nolis, P; Ramayo-Caldas, Y; Folch, JM; Llonch, P; Sola-Oriol, D; Perez, JF; Martin-Orue, SM
10.1038/s41598-021-02754-6
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Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses
Mach; Nuria Ramayo-Caldas; Yuliaxis Clark; Allison Moroldo; Marco Robert; Celine Barrey; Eric Maria Lopez; Jesus Le Moyec; Laurence
10.1186/s12864-017-3571-3
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Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota
Velasco-Galilea, M; Piles, M; Ramayo-Caldas, Y; Varona, L; Sanchez, JP
10.1186/s12711-022-00738-2
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Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions
Ramirez-Ayala, Lino C; Rocha, Dominique; Ramos-Onsins, Sebas E; Leno-Colorado, Jordi; Charles, Mathieu; Bouchez, Olivier; Rodriguez-Valera, Yoel;...
10.1186/s12711-020-00597-9
