Research group

Amplicon Sequencing, Analysis packages (R, Python, etc.), Animal genomics, Bayesian statistics, Bioinformatics Software and Tools, Biological interpretation, Data Analysis, Data Visualization, Epigenomics, Experimental design, Expression Profiling, Frequentist analysis, Function prediction, Functional annotation, Functional genomics, Genomics, Integrative Analysis, Metabolome profiling, Metabolomics, Metagenomics, Microbial communities, Multivariate statistics, Network Biology, Non-parametric statistics, Omics, Pathway analysis, Pathway analysis, Regulatory biology, RNA Sequencing (RNA-seq), Sequence analysis, Statistical Methods for Biology, Systems Biology, Transcriptomics

Romero, M., Heras-Molina, A., Muñoz, M., Calvo, L., Morales, J. I., Rodríguez, A. I., Escudero, R., López-Bote, C., Óvilo, C., & Olivares, Á. (2025). Short- But Not Long-Term Effects of Creep Feeding Provided to Suckling Piglets. Animals, 15(2), 253. https://doi.org/10.3390/ani15020253

Fabbri, M. C., Arias, K. D., Rezende, M. P. G., Tiezzi, F., Biffani, S., Goyache, F., Schiavo, G., Bovo, S., Fontanesi, L., Čandek-Potokar, M., Muñoz, M., Ovilo, C., Poklukar, K., Škrlep, M., & Bozzi, R. (2025). Assessment of Heterozygosity in European Local and Cosmopolitan Pig Populations. Agriculture, 15(7), 761. https://doi.org/10.3390/agriculture15070761

Pérez-Díaz, J. L., del Álamo, C., Aranguren-Rivas, P., Peiró, S., Muñoz, M., Alcamí, A., Vázquez-Calvo, Á., Óvilo, C., Calvo, L., Morales, P., & Jiménez, B. (2025). Skin Aerosolization Predominance in a Pig Farm. Aerobiology, 3(3), 6. https://doi.org/10.3390/aerobiology3030006

Sebastià, C., Folch, J. M., Ballester, M., Estellé, J., Passols, M., Muñoz, M., García-Casco, J. M., Fernández, A. I., Castelló, A., Sánchez, A., & Crespo-Piazuelo, D. (2024). Interrelation between gut microbiota, SCFA, and fatty acid composition in pigs. MSystems, 9(1). https://doi.org/10.1128/msystems.01049-23

Gómez, G., Laviano, H. D., García-Casco, J., Muñoz, M., Gómez, F., Sánchez-Esquiliche, F., González-Bulnes, A., López-Bote, C., Óvilo, C., & Rey, A. I. (2024). Long-Term Effect of Maternal Antioxidant Supplementation on the Lipid Profile of the Progeny According to the Sow’s Parity Number. Antioxidants, 13(3), 379. https://doi.org/10.3390/antiox13030379

Gómez, G., Laviano, H. D., García-Casco, J., Muñoz, M., Gómez, F., Sánchez-Esquiliche, F., González-Bulnes, A., López-Bote, C., Óvilo, C., & Rey, A. I. (2024). Correction: Gómez et al. Long-Term Effect of Maternal Antioxidant Supplementation on the Lipid Profile of the Progeny According to the Sow’s Parity Number. Antioxidants 2024, 13, 379. Antioxidants, 13(8), 987. https://doi.org/10.3390/antiox13080987

Palma-Granados, P., García-Casco, J. M., Caraballo, C., Vázquez-Ortego, P., Gómez-Carballar, F., Sánchez-Esquiliche, F., Óvilo, C., & Muñoz, M. (2023). Design of a low-density SNP panel for intramuscular fat content and fatty acid composition of backfat in free-range Iberian pigs. Journal of Animal Science, 101. https://doi.org/10.1093/jas/skad079

Gómez, G., Laviano, H. D., García-Casco, J. M., Escudero, R., Muñoz, M., Heras-Molina, A., González-Bulnes, A., Óvilo, C., López-Bote, C., & Rey, A. I. (2023). Different Effect of Vitamin E or Hydroxytyrosol Supplementation to Sow’s Diet on Oxidative Status and Performances of Weaned Piglets. Antioxidants, 12(8), 1504. https://doi.org/10.3390/antiox12081504

Laviano, H. D., Gómez, G., Escudero, R., Nuñez, Y., García-Casco, J. M., Muñoz, M., Heras-Molina, A., López-Bote, C., González-Bulnes, A., Óvilo, C., & Rey, A. I. (2023). Maternal Supplementation of Vitamin E or Its Combination with Hydroxytyrosol Increases the Gut Health and Short Chain Fatty Acids of Piglets at Weaning. Antioxidants, 12(9), 1761. https://doi.org/10.3390/antiox12091761

Óvilo, C., Trakooljul, N., Núñez, Y., Hadlich, F., Murani, E., Ayuso, M., García-Contreras, C., Vázquez-Gómez, M., Rey, A. I., Garcia, F., García-Casco, J. M., López-Bote, C., Isabel, B., González-Bulnes, A., Wimmers, K., & Muñoz, M. (2022). SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-20817-0

Valle-Millares, D., Brochado-Kith, Ó., Gómez-Sanz, A., Martín-Carbonero, L., Ryan, P., De los Santos, I., Castro, J. M., Troya, J., Mayoral-Muñoz, M., Cuevas, G., Martínez-Román, P., Sanz-Sanz, J., Muñoz-Muñoz, M., Jiménez-Sousa, M. Á., Resino, S., Briz, V., & Fernández-Rodríguez, A. (2022). HCV eradication with DAAs differently affects HIV males and females: A whole miRNA sequencing characterization. Biomedicine & Pharmacotherapy, 145, 112405. https://doi.org/10.1016/j.biopha.2021.112405

Zorc, M., Škorput, D., Gvozdanović, K., Margeta, P., Karolyi, D., Luković, Z., Salajpal, K., Savić, R., Muñoz, M., Bovo, S., Djurkin Kušec, I., Radović, Č., Kušec, G., Čandek Potokar, M., & Dovč, P. (2022). Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. Genetics Selection Evolution, 54(1). https://doi.org/10.1186/s12711-022-00718-6

Dadousis, C., Muñoz, M., Óvilo, C., Fabbri, M. C., Araújo, J. P., Bovo, S., Potokar, M. Č., Charneca, R., Crovetti, A., Gallo, M., García-Casco, J. M., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M.-J., Pugliese, C., Quintanilla, R., Radović, Č., Razmaite, V., … Bozzi, R. (2022). Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-10698-8

Fernández‐Barroso, M. Á., García‐Casco, J. M., Núñez, Y., Ramírez‐Hidalgo, L., Matos, G., & Muñoz, M. (2022). Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile. Animal Genetics, 53(3), 352–367. Portico. https://doi.org/10.1111/age.13195

Martínez-Román, P., Crespo-Bermejo, C., Valle-Millares, D., Lara-Aguilar, V., Arca-Lafuente, S., Martín-Carbonero, L., Ryan, P., de los Santos, I., López-Huertas, M. R., Palladino, C., Muñoz-Muñoz, M., Fernández-Rodríguez, A., Coiras, M., & Briz, V. (2022). Dynamics of HIV Reservoir and HIV-1 Viral Splicing in HCV-Exposed Individuals after Elimination with DAAs or Spontaneous Clearance. Journal of Clinical Medicine, 11(13), 3579. https://doi.org/10.3390/jcm11133579

Muñoz, M., Fernández-Barroso, M. A., López-García, A., Caraballo, C., Nuñez, Y., Óvilo, C., González, E., & García-Casco, J. M. (2021). Consequences of a low protein diet on the liver and longissimus dorsi transcriptome of Duroc × Iberian crossbred pigs. Animal, 15(12), 100408. https://doi.org/10.1016/j.animal.2021.100408

Schiavo, G., Bovo, S., Muñoz, M., Ribani, A., Alves, E., Araújo, J. P., Bozzi, R., Čandek‐Potokar, M., Charneca, R., Fernandez, A. I., Gallo, M., García, F., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M. ‐J., Núñez, Y., Quintanilla, R., Radović, Č., … Fontanesi, L. (2021). Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. Animal Genetics, 52(2), 155–170. Portico. https://doi.org/10.1111/age.13045

Núñez, Y., Radović, Č., Savić, R., García-Casco, J. M., Čandek-Potokar, M., Benítez, R., Radojković, D., Lukić, M., Gogić, M., Muñoz, M., Fontanesi, L., & Óvilo, C. (2021). Muscle Transcriptome Analysis Reveals Molecular Pathways Related to Oxidative Phosphorylation, Antioxidant Defense, Fatness and Growth in Mangalitsa and Moravka Pigs. Animals, 11(3), 844. https://doi.org/10.3390/ani11030844

Fernández-Barroso, M. Á., Parrini, S., Muñoz, M., Palma-Granados, P., Matos, G., Ramírez, L., Crovetti, A., García-Casco, J. M., & Bozzi, R. (2021). Use of NIRS for the assessment of meat quality traits in open-air free-range Iberian pigs. Journal of Food Composition and Analysis, 102, 104018. https://doi.org/10.1016/j.jfca.2021.104018

Valle-Millares, D., Brochado-Kith, Ó., Martín-Carbonero, L., Domínguez-Domínguez, L., Ryan, P., De los Santos, I., De la Fuente, S., Castro, J., Lagarde, M., Cuevas, G., Mayoral-Muñoz, M., Matarranz, M., Díez, V., Gómez-Sanz, A., Martínez-Román, P., Crespo-Bermejo, C., Palladino, C., Muñoz-Muñoz, M., … Jiménez-Sousa, M. (2021). Different HCV Exposure Drives Specific miRNA Profile in PBMCs of HIV Patients. Biomedicines, 9(11), 1627. https://doi.org/10.3390/biomedicines9111627

Bovo, S., Ribani, A., Muñoz, M., Alves, E., Araujo, J. P., Bozzi, R., Charneca, R., Di Palma, F., Etherington, G., Fernandez, A. I., García, F., García‐Casco, J., Karolyi, D., Gallo, M., Gvozdanović, K., Martins, J. M., Mercat, M. J., Núñez, Y., Quintanilla, R., … Fontanesi, L. (2020). Genome‐wide detection of copy number variants in European autochthonous and commercial pig breeds by whole‐genome sequencing of DNA pools identified breed‐characterising copy number states. Animal Genetics, 51(4), 541–556. Portico. https://doi.org/10.1111/age.12954

Bovo, S., Schiavo, G., Ribani, A., Utzeri, V. J., Taurisano, V., Ballan, M., Muñoz, M., Alves, E., Araujo, J. P., Bozzi, R., Charneca, R., Palma, F. D., Djurkin, I., Etherington, G., Fernandez, A. I., García, F., García-Casco, J., Karolyi, D., Gallo, M., … Fontanesi, L. (2020). Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources. https://doi.org/10.21203/rs.3.rs-62420/v1

Muñoz, M., García-Casco, J. M., Alves, E., Benítez, R., Barragán, C., Caraballo, C., Fernández, A. I., García, F., Núñez, Y., Óvilo, C., Fernández, A., Rodríguez, C., & Silió, L. (2020). Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products. Meat Science, 167, 108152. https://doi.org/10.1016/j.meatsci.2020.108152

Fernández-Barroso, M. Á., Caraballo, C., Silió, L., Rodríguez, C., Nuñez, Y., Sánchez-Esquiliche, F., Matos, G., García-Casco, J. M., & Muñoz, M. (2020). Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile. Animals, 10(9), 1715. https://doi.org/10.3390/ani10091715

Bovo, S., Ribani, A., Muñoz, M., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Di Palma, F., Etherington, G., Fernandez, A. I., García, F., García-Casco, J., Karolyi, D., Gallo, M., Margeta, V., Martins, J. M., Mercat, M. J., Moscatelli, G., … Fontanesi, L. (2020). Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genetics Selection Evolution, 52(1). https://doi.org/10.1186/s12711-020-00553-7

Muñoz, M., Bozzi, R., García-Casco, J., Núñez, Y., Ribani, A., Franci, O., García, F., Škrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kušec, I., Mercat, M. J., Riquet, J., … Óvilo, C. (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-49830-6

Crespo-Piazuelo, D., Migura-Garcia, L., Estellé, J., Criado-Mesas, L., Revilla, M., Castelló, A., Muñoz, M., García-Casco, J. M., Fernández, A. I., Ballester, M., & Folch, J. M. (2019). Association between the pig genome and its gut microbiota composition. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-45066-6

Caraballo, C., Muñoz, M., Rodríguez, C., Silió, L., & García-Gasco, J. M. (2018). Verificación racial de jamones y paletas Ibéricos comercializados en supermercados españoles. Archivos de Zootecnia, 67(Supplement), 5–8. https://doi.org/10.21071/az.v67isupplement.3561

Muñoz, M., Sánchez-Esquiliche, F., Caraballo, C., Gómez, F., Pariente, J. M., Silió, L., Rodríguez, C., & García-Gasco, J. M. (2018). Programa de selección genética enfocada en la calidad de cerdos Ibéricos puros de montanera. Archivos de Zootecnia, 67(Supplement), 9–11. https://doi.org/10.21071/az.v67isupplement.3562

Martínez-Montes, Á. M., Fernández, A., Muñoz, M., Noguera, J. L., Folch, J. M., & Fernández, A. I. (2018). Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed. PLOS ONE, 13(3), e0190184. https://doi.org/10.1371/journal.pone.0190184

Muiños-Bühl, A., González-Recio, O., Muñoz, M., Óvilo, C., García-Casco, J., & Fernández, A. I. (2018). Evaluating Protocols for Porcine Faecal Microbiome Recollection, Storage and DNA Extraction: from the Farm to the Lab. Current Microbiology, 75(6), 651–657. https://doi.org/10.1007/s00284-017-1429-1

Muñoz, M., Bozzi, R., García, F., Núñez, Y., Geraci, C., Crovetti, A., García-Casco, J., Alves, E., Škrlep, M., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Kušec, G., Djurkin-Kušec, I., Mercat, M. J., Riquet, J., Estellé, J., Zimmer, C., … Óvilo, C. (2018). Diversity across major and candidate genes in European local pig breeds. PLOS ONE, 13(11), e0207475. https://doi.org/10.1371/journal.pone.0207475

Muñoz, M., García-Casco, J. M., Caraballo, C., Fernández-Barroso, M. Á., Sánchez-Esquiliche, F., Gómez, F., Rodríguez, M. del C., & Silió, L. (2018). Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs. Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00608

Muñoz, M., Rodríguez, M. C., García‐Cortes, L. A., González, A., García‐Casco, J. M., & Silió, L. (2017). Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality. Journal of Animal Breeding and Genetics, 134(6), 512–519. Portico. https://doi.org/10.1111/jbg.12298

Muñoz, M., Pong-Wong, R., Canela-Xandri, O., Rawlik, K., Haley, C. S., & Tenesa, A. (2016). Evaluating the contribution of genetics and familial shared environment to common disease using the UK Biobank. Nature Genetics, 48(9), 980–983. https://doi.org/10.1038/ng.3618

Fernández, A. I., Muñoz, M., Alves, E., Folch, J. M., Noguera, J. L., Enciso, M. P., Rodríguez, M. del C., & Silió, L. (2014). Recombination of the porcine X chromosome: a high density linkage map. BMC Genetics, 15(1). https://doi.org/10.1186/s12863-014-0148-x

Revilla, M., Ramayo-Caldas, Y., Castelló, A., Corominas, J., Puig-Oliveras, A., Ibáñez-Escriche, N., Muñoz, M., Ballester, M., & Folch, J. M. (2014). New insight into the SSC8 genetic determination of fatty acid composition in pigs. Genetics Selection Evolution, 46(1). https://doi.org/10.1186/1297-9686-46-28

Fernández‐Rodríguez, A., Estellé, J., Blin, A., Muñoz, M., Créchet, F., Demenais, F., Vincent‐Naulleau, S., & Bourneuf, E. (2014). <scp>KIT</scp> and melanoma predisposition in pigs: sequence variants and association analysis. Animal Genetics, 45(3), 445–448. Portico. https://doi.org/10.1111/age.12136

Fernández‐Rodríguez, A., Estellé, J., Blin, A., Muñoz, M., Créchet, F., Demenais, F., Vincent‐Naulleau, S., & Bourneuf, E. (2014). <scp>KIT</scp> and melanoma predisposition in pigs: sequence variants and association analysis. Animal Genetics, 45(3), 445–448. Portico. https://doi.org/10.1111/age.12136

Muñoz, M., Rodríguez, M. C., Alves, E., Folch, J. M., Ibañez-Escriche, N., Silió, L., & Fernández, A. I. (2013). Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics, 14(1), 845. https://doi.org/10.1186/1471-2164-14-845

Muñoz, M., Fernández, A. I., Benítez, R., Pena, R. N., Folch, J. M., Rodríguez, M. del C., Silió, L., & Alves, E. (2013). Disentangling Two QTL on Porcine Chromosome 12 for Backfat Fatty Acid Composition. Animal Biotechnology, 24(3), 168–186. https://doi.org/10.1080/10495398.2012.763130

Muñoz, M., Alves, E., Corominas, J., Folch, J. M., Casellas, J., Noguera, J. L., Silió, L., & Fernández, A. I. (2012). Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data. Frontiers in Genetics, 2. https://doi.org/10.3389/fgene.2011.00101

Corominas, J., Ramayo‐Caldas, Y., Castelló, A., Muñoz, M., Ibáñez‐Escriche, N., Folch, J. M., & Ballester, M. (2012). Evaluation of the porcine <scp>ACSL4</scp> gene as a candidate gene for meat quality traits in pigs. Animal Genetics, 43(6), 714–720. Portico. https://doi.org/10.1111/j.1365-2052.2012.02335.x

Corominas, J., Ramayo‐Caldas, Y., Castelló, A., Muñoz, M., Ibáñez‐Escriche, N., Folch, J. M., & Ballester, M. (2012). Evaluation of the porcine <scp>ACSL4</scp> gene as a candidate gene for meat quality traits in pigs. Animal Genetics, 43(6), 714–720. Portico. https://doi.org/10.1111/j.1365-2052.2012.02335.x

Muñoz, M., Alves, E., Ramayo‐Caldas, Y., Casellas, J., Rodríguez, C., Folch, J. M., Silió, L., & Fernández, A. I. (2011). Recombination rates across porcine autosomes inferred from high‐density linkage maps. Animal Genetics, 43(5), 620–623. Portico. https://doi.org/10.1111/j.1365-2052.2011.02301.x

Yang, B., Navarro, N., Noguera, J. L., Muñoz, M., Guo, T. F., Yang, K. X., Ma, J. W., Folch, J. M., Huang, L. S., & Pérez-Enciso, M. (2011). Building phenotype networks to improve QTL detection: a comparative analysis of fatty acid and fat traits in pigs. Journal of Animal Breeding and Genetics, 128(5), 329–343. https://doi.org/10.1111/j.1439-0388.2011.00928.x

Muñoz, M., Fernández, A. I., Óvilo, C., Muñoz, G., Rodriguez, C., Fernández, A., Alves, E., & Silió, L. (2010). Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line. Genetics Selection Evolution, 42(1). https://doi.org/10.1186/1297-9686-42-23

Fernandez-Rodriguez, A., Munoz, M., Fernandez, A., Pena, R. N., Tomas, A., Noguera, J. L., Ovilo, C., & Fernandez, A. I. (2010). Differential Gene Expression in Ovaries of Pregnant Pigs with High and Low Prolificacy Levels and Identification of Candidate Genes for Litter Size. Biology of Reproduction, 84(2), 299–307. https://doi.org/10.1095/biolreprod.110.085589

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