Research group

Analysis packages (R, Python, etc.), Bayesian statistics, Bioinformatics Software and Tools, Evolutionary modelling, Frequentist analysis, Genomics, Non-parametric statistics, Population genomics, Statistical Methods for Biology

Bazakos, C., Alexiou, K. G., Ramos‐Onsins, S., Koubouris, G., Tourvas, N., Xanthopoulou, A., Mellidou, I., Moysiadis, T., Vourlaki, I., Metzidakis, I., Sergentani, C., Manolikaki, I., Michailidis, M., Pistikoudi, A., Polidoros, A., Kostelenos, G., Aravanopoulos, F., Molassiotis, A., & Ganopoulos, I. (2023). Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology. The Plant Journal, 116(1), 303–319. Portico. https://doi.org/10.1111/tpj.16270

Ramayo-Caldas, Y., Crespo-Piazuelo, D., Morata, J., González-Rodríguez, O., Sebastià, C., Castello, A., Dalmau, A., Ramos-Onsins, S., Alexiou, K. G., Folch, J. M., Quintanilla, R., & Ballester, M. (2023). Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs. Microbiology Spectrum, 11(4). https://doi.org/10.1128/spectrum.05271-22

Duval, H., Coindre, E., Ramos-Onsins, S. E., Alexiou, K. G., Rubio-Cabetas, M. J., Martínez-García, P. J., Wirthensohn, M., Dhingra, A., Samarina, A., & Arús, P. (2023). Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis). Plants, 12(2), 242. https://doi.org/10.3390/plants12020242

Ramos-Onsins, S. E., Marmorini, G., Achaz, G., & Ferretti, L. (2023). A General Framework for Neutrality Tests Based on the Site Frequency Spectrum. Genes, 14(9), 1714. https://doi.org/10.3390/genes14091714

Vourlaki, I.-T., Castanera, R., Ramos-Onsins, S. E., Casacuberta, J. M., & Pérez-Enciso, M. (2022). Transposable element polymorphisms improve prediction of complex agronomic traits in rice. Theoretical and Applied Genetics, 135(9), 3211–3222. https://doi.org/10.1007/s00122-022-04180-2

Ramayo-Caldas, Y., Crespo-Piazuelo, D., Morata, J., González-Rodríguez, O., Sebastià, C., Castello, A., Dalmau, A., Ramos-Onsins, S., Alexiou, K. G., Folch, J. M., Quintanilla, R., & Ballester, M. (2022). Copy number variation onABCC2-DNMBP lociimpacts the diversity and composition of the gut microbiota in pigs. https://doi.org/10.1101/2022.10.06.510490

Castellano, D., Vourlaki, I.-T., Gutenkunst, R. N., & Ramos-Onsins, S. E. (2022). Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects. https://doi.org/10.1101/2022.08.24.505198

Wieters, B., Steige, K. A., He, F., Koch, E. M., Ramos-Onsins, S. E., Gu, H., Guo, Y.-L., Sunyaev, S., & de Meaux, J. (2021). Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLOS Genetics, 17(1), e1008748. https://doi.org/10.1371/journal.pgen.1008748

Ramírez-Ayala, L. C., Rocha, D., Ramos-Onsins, S. E., Leno-Colorado, J., Charles, M., Bouchez, O., Rodríguez-Valera, Y., Pérez-Enciso, M., & Ramayo-Caldas, Y. (2021). Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genetics Selection Evolution, 53(1). https://doi.org/10.1186/s12711-020-00597-9

Leno-Colorado, J., Guirao-Rico, S., Pérez-Enciso, M., & Ramos-Onsins, S. E. (2020). Pervasive selection pressure in wild and domestic pigs. https://doi.org/10.1101/2020.09.09.289439

Jadhav, A., Zhao, L., Liu, W., Ding, C., Nair, V., Ramos-Onsins, S. E., & Ferretti, L. (2020). Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections. Viruses, 12(11), 1305. https://doi.org/10.3390/v12111305

Rodríguez-Valera, Y., Rocha, D., Naves, M., Renand, G., Pérez-Pineda, E., Ramayo-Caldas, Y., & Ramos-Onsins, S. E. (2020). The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle. Animals, 10(12), 2233. https://doi.org/10.3390/ani10122233

Ferretti, L., Klassmann, A., Raineri, E., Ramos-Onsins, S. E., Wiehe, T., & Achaz, G. (2018). The neutral frequency spectrum of linked sites. Theoretical Population Biology, 123, 70–79. https://doi.org/10.1016/j.tpb.2018.06.001

Rodriguez-Valera, Y., Renand, G., Naves, M., Fonseca-Jiménez, Y., Moreno-Probance, T. I., Ramos-Onsins, S., Rocha, D., & Ramayo-Caldas, Y. (2018). Genetic diversity and selection signatures of the beef ‘Charolais de Cuba’ breed. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-29453-z

Morata, J., Tormo, M., Alexiou, K. G., Vives, C., Ramos-Onsins, S. E., Garcia-Mas, J., & Casacuberta, J. M. (2018). The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon. Genome Biology and Evolution, 10(6), 1584–1595. https://doi.org/10.1093/gbe/evy115

Ferretti, L., Ribeca, P., & Ramos-Onsins, S. E. (2018). The Site Frequency/Dosage Spectrum of Autopolyploid Populations. Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00480

Ferretti, L., Ledda, A., Wiehe, T., Achaz, G., & Ramos-Onsins, S. E. (2017). Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests. Genetics, 207(1), 229–240. https://doi.org/10.1534/genetics.116.188763

Stapley, J., Feulner, P. G. D., Johnston, S. E., Santure, A. W., & Smadja, C. M. (2017). Variation in recombination frequency and distribution across eukaryotes: patterns and processes. Philosophical Transactions of the Royal Society B: Biological Sciences, 372(1736), 20160455. https://doi.org/10.1098/rstb.2016.0455

Navarro, J., Nevado, B., Hernández, P., Vera, G., & Ramos-Onsins, S. E. (2017). Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis. Evolutionary Bioinformatics, 13. https://doi.org/10.1177/1176934317723884

Navarro, J., Vera, G., Ramos-Onsins, S., & Hernández, P. (2017). Improving Bioinformatics Analysis of Large Sequence Datasets Parallelizing Tools for Population Genomics. Euro-Par 2016: Parallel Processing Workshops, 457–467. https://doi.org/10.1007/978-3-319-58943-5_37

Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248

Guirao-Rico, S., Ramirez, O., Ojeda, A., Amills, M., & Ramos-Onsins, S. E. (2017). Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations. Heredity, 120(1), 63–76. https://doi.org/10.1038/s41437-017-0002-9

Clop, A., Sharaf, A., Castelló, A., Ramos-Onsins, S., Cirera, S., Mercadé, A., Derdak, S., Beltran, S., Huisman, A., Fredholm, M., van As, P., & Sánchez, A. (2016). Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2972-z

Montemuiño, C., Espinosa, A., Moure, J. C., Vera, G., Hernández, P., & Ramos-Onsins, S. (2016). Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS. Evolutionary Bioinformatics, 12. https://doi.org/10.4137/ebo.s40268

Argyris, J. M., Ruiz-Herrera, A., Madriz-Masis, P., Sanseverino, W., Morata, J., Pujol, M., Ramos-Onsins, S. E., & Garcia-Mas, J. (2015). Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-014-1196-3

Sanseverino, W., Hénaff, E., Vives, C., Pinosio, S., Burgos-Paz, W., Morgante, M., Ramos-Onsins, S. E., Garcia-Mas, J., & Casacuberta, J. M. (2015). Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome. Molecular Biology and Evolution, 32(10), 2760–2774. https://doi.org/10.1093/molbev/msv152

Pérez-Enciso, M., Burgos-Paz, W., & Ramos-Onsins, S. E. (2015). On genetic differentiation between domestic pigs and Tibetan wild boars. Nature Genetics, 47(3), 190–192. https://doi.org/10.1038/ng.3191

Ferretti, L., & Ramos-Onsins, S. E. (2015). A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids. Theoretical Population Biology, 100, 79–87. https://doi.org/10.1016/j.tpb.2015.01.001

Bianco, E., Nevado, B., Ramos-Onsins, S. E., & Pérez-Enciso, M. (2015). A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig. PLOS ONE, 10(3), e0118867. https://doi.org/10.1371/journal.pone.0118867

Ramos-Onsins, S. E., Burgos-Paz, W., Manunza, A., & Amills, M. (2014). Mining the pig genome to investigate the domestication process. Heredity, 113(6), 471–484. https://doi.org/10.1038/hdy.2014.68

Montemuiño, C., Espinosa, A., Moure, J.-C., Vera-Rodríguez, G., Ramos-Onsins, S., & Budé, P. H. (2014). msPar: A Parallel Coalescent Simulator. Euro-Par 2013: Parallel Processing Workshops, 321–330. https://doi.org/10.1007/978-3-642-54420-0_32

Nevado, B., Ramos‐Onsins, S. E., & Perez‐Enciso, M. (2014). Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics. Molecular Ecology, 23(7), 1764–1779. Portico. https://doi.org/10.1111/mec.12693

Pfeifer, B., Wittelsbürger, U., Ramos-Onsins, S. E., & Lercher, M. J. (2014). PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R. Molecular Biology and Evolution, 31(7), 1929–1936. https://doi.org/10.1093/molbev/msu136

Esteve-Codina, A., Paudel, Y., Ferretti, L., Raineri, E., Megens, H.-J., Silió, L., Rodríguez, M. C., Groenen, M. A., Ramos-Onsins, S. E., & Pérez-Enciso, M. (2013). Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics, 14(1), 148. https://doi.org/10.1186/1471-2164-14-148

Ferretti, L., Ramos‐Onsins, S. E., & Pérez‐Enciso, M. (2013). Population genomics from pool sequencing. Molecular Ecology, 22(22), 5561–5576. Portico. https://doi.org/10.1111/mec.12522

Segura, J., Ferretti, L., Ramos-Onsins, S., Capilla, L., Farré, M., Reis, F., Oliver-Bonet, M., Fernández-Bellón, H., Garcia, F., Garcia-Caldés, M., Robinson, T. J., & Ruiz-Herrera, A. (2013). Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference. Proceedings of the Royal Society B: Biological Sciences, 280(1771), 20131945. https://doi.org/10.1098/rspb.2013.1945

Ferretti, L., Raineri, E., & Ramos-Onsins, S. (2012). Neutrality Tests for Sequences with Missing Data. Genetics, 191(4), 1397–1401. https://doi.org/10.1534/genetics.112.139949

Burgos‐Paz, W., Souza, C. A., Castelló, A., Mercadé, A., Okumura, N., Sheremet’eva, I. N., Huang, L. S., Cho, I. C., Paiva, S. R., Ramos‐Onsins, S., & Pérez‐Enciso, M. (2012). Worldwide genetic relationships of pigs as inferred from X chromosome <scp>SNP</scp>s. Animal Genetics, 44(2), 130–138. Portico. https://doi.org/10.1111/j.1365-2052.2012.02374.x

Amaral, A. J., Ferretti, L., Megens, H.-J., Crooijmans, R. P. M. A., Nie, H., Ramos-Onsins, S. E., Perez-Enciso, M., Schook, L. B., & Groenen, M. A. M. (2011). Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA. PLoS ONE, 6(4), e14782. https://doi.org/10.1371/journal.pone.0014782

He, F., Chen, W.-H., Collins, S., Acquisti, C., Goebel, U., Ramos-Onsins, S., Lercher, M. J., & de Meaux, J. (2010). Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions inArabidopsis thaliana. Genetics, 185(2), 695–701. https://doi.org/10.1534/genetics.110.114629

HEIDEL, A. J., RAMOS-ONSINS, S. E., WANG, W.-K., CHIANG, T.-Y., & MITCHELL-OLDS, T. (2010). Population history in Arabidopsis halleri using multilocus analysis. Molecular Ecology, 19(16), 3364–3379. https://doi.org/10.1111/j.1365-294x.2010.04761.x

Ferretti, L., Perez-Enciso, M., & Ramos-Onsins, S. (2010). Optimal Neutrality Tests Based on the Frequency Spectrum. Genetics, 186(1), 353–365. https://doi.org/10.1534/genetics.110.118570

Ojeda, A., Ramos-Onsins, S. E., Marletta, D., Huang, L. S., Folch, J. M., & Pérez-Enciso, M. (2010). Evolutionary study of a potential selection target region in the pig. Heredity, 106(2), 330–338. https://doi.org/10.1038/hdy.2010.61

Song, B.-H., Windsor, A. J., Schmid, K. J., Ramos-Onsins, S., Schranz, M. E., Heidel, A. J., & Mitchell-Olds, T. (2009). Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium inBoechera stricta, a Wild Relative of Arabidopsis. Genetics, 181(3), 1021–1033. https://doi.org/10.1534/genetics.108.095364

RAMOS‐ONSINS, S. E., PUERMA, E., BALAÑÁ‐ALCAIDE, D., SALGUERO, D., & AGUADÉ, M. (2008). Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana. Molecular Ecology, 17(5), 1211–1223. Portico. https://doi.org/10.1111/j.1365-294x.2007.03633.x

Ramírez-Soriano, A., Ramos-Onsins, S. E., Rozas, J., Calafell, F., & Navarro, A. (2008). Statistical Power Analysis of Neutrality Tests Under Demographic Expansions, Contractions and Bottlenecks With Recombination. Genetics, 179(1), 555–567. https://doi.org/10.1534/genetics.107.083006

Ramos-Onsins, S. E., & Mitchell-Olds, T. (2007). Mlcoalsim: Multilocus Coalescent Simulations. Evolutionary Bioinformatics, 3. https://doi.org/10.1177/117693430700300020

RAMOS-ONSINS, S. E., MOUSSET, S., MITCHELL-OLDS, T., & STEPHAN, W. (2007). Population genetic inference using a fixed number of segregating sites: a reassessment. Genetical Research, 89(4), 231–244. https://doi.org/10.1017/s0016672307008877

BALAÑÁ‐ALCAIDE, D., RAMOS‐ONSINS, S. E., BOONE, Q., & AGUADÉ, M. (2006). Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions. Molecular Ecology, 15(8), 2059–2068. Portico. https://doi.org/10.1111/j.1365-294x.2006.02918.x

Quesada, H., Ramos-Onsins, S. E., Rozas, J., & Aguadé, M. (2006). Positive Selection Versus Demography: Evolutionary Inferences Based on an Unusual Haplotype Structure in Drosophila simulans. Molecular Biology and Evolution, 23(9), 1643–1647. https://doi.org/10.1093/molbev/msl031

Quesada, H., Ramos-Onsins, S. E., & Aguad�, M. (2005). Birth-and-Death Evolution of the Cecropin Multigene Family in Drosophila. Journal of Molecular Evolution, 60(1), 1–11. https://doi.org/10.1007/s00239-004-0053-4

Schmid, K. J., Ramos-Onsins, S., Ringys-Beckstein, H., Weisshaar, B., & Mitchell-Olds, T. (2005). A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism. Genetics, 169(3), 1601–1615. https://doi.org/10.1534/genetics.104.033795

Ramos-Onsins, S. E., Stranger, B. E., Mitchell-Olds, T., & Aguadé, M. (2004). Multilocus Analysis of Variation and Speciation in the Closely Related Species Arabidopsis halleri and A. lyrata. Genetics, 166(1), 373–388. https://doi.org/10.1534/genetics.166.1.373

Ramos-Onsins, S. E., & Rozas, J. (2002). Statistical Properties of New Neutrality Tests Against Population Growth. Molecular Biology and Evolution, 19(12), 2092–2100. https://doi.org/10.1093/oxfordjournals.molbev.a004034

Kuittinen, H., Aguadé, M., Charlesworth, D., Haan, A. D. E., Lauga, B., Mitchell‐Olds, T., Oikarinen, S., Ramos‐Onsins, S., Stranger, B., Van Tienderen, P., & Savolainen, O. (2002). Primers for 22 candidate genes for ecological adaptations in Brassicaceae. Molecular Ecology Notes, 2(3), 258–262. Portico. https://doi.org/10.1046/j.1471-8286.2002.00210.x

Zhao, Z., Jin, L., Fu, Y.-X., Ramsay, M., Jenkins, T., Leskinen, E., Pamilo, P., Trexler, M., Patthy, L., Jorde, L. B., Ramos-Onsins, S., Yu, N., & Li, W.-H. (2000). Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proceedings of the National Academy of Sciences, 97(21), 11354–11358. https://doi.org/10.1073/pnas.200348197

Ramos-Onsins, S., Segarra, C., Rozas, J., & Aguadé, M. (1998). Molecular and Chromosomal Phylogeny in theObscuraGroup ofDrosophilaInferred from Sequences of therp49Gene Region. Molecular Phylogenetics and Evolution, 9(1), 33–41. https://doi.org/10.1006/mpev.1997.0438

Amills, M., Megens, H.-J., Manunza, A., Ramos-Onsins, S. E., & Groenen, M. A. M. (n.d.). A Genomic Perspective on Wild Boar Demography and Evolution. Ecology, Conservation and Management of Wild Pigs and Peccaries, 376–387. https://doi.org/10.1017/9781316941232.036

• Development of Genomic tools for Population Analysis of Variability