Institution: CRAG
Research Groups: Statistical and population genomics
Position: Investigador CRAG
Home page: https://sites.google.com/view/sebas-ramos-onsins-lab
Contact email: sebastian.ramos@cragenomica.es
BCB Committee: Talent attraction and training
BCB Community: Bioinformatics tools, benchmarks and data visualization
BCB Tools: mstatspop
BCB Services:
Research topics: Evolutionary modelling, Statistical Methods for Biology, Bayesian statistics, Frequentist analysis, Non-parametric statistics, Genomics, Population genomics, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.)
Biography: I founded my own group in 2008 after obtaining the Ramon y Cajal position and developed my own lines of research: (i) analysis of nucleotide variability patterns, (ii) design of statistics and methods to detect different signals of evolutionary events, and (iii) software development to understand the causes of diversity. In the last 10 years, I have been the PI on three National Projects, PI on a competitive grant within CRAG, and have participated in five other competitive grants (National Thematic Network, Catalonia Quality Team).
My highest-impact contributions are related to software development and statistical development. I have developed significant code sections for DnaSP 6.0 (>3000 citations) and the R PopGenome library (>500 citations). In addition, my group has been developing statistical methods to analyze genomic variability data, others considering pools, missing data, autopolyploidy, and constructing statistical tests to detect evolutionary patterns (e.g., R2 >1000 citations). We have made relevant contributions in the study of variability in porcine and in melons, almonds, and olives.
Over the last 10 years, I have supervised four PhD students (a computer scientist, a physicist, an agricultural engineer, and a biochemist) and eight master's students (one mathematician, two biologists, and five bioinformaticians).
I have taught internships at the University of Barcelona in the core subject “Origin of Life and Evolution” and in the optional subject “Evolutionary Genetics” in 1996 and from 2004 to 2006. I have been a professor of the postgraduate course “DNA Phylogenies and Genealogies: Reconstruction and Applications” at the University of Barcelona from 2005 to 2023. I am a professor of the Master's Degree in Genetic Improvement and Reproductive Biotechnology at the Autonomous University of Barcelona since 2009 and of the Master's Degree in Bioinformatics at the Autonomous University of Barcelona since 2012. I have been accredited with 3 five-year periods by the General Secretariat of Research, Ministries of Science, Innovation and Universities (periods from 2008 to 2022).
Publications
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 SNPs. 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
Funding:
More info
Participation in:
Master Programs: Teaching at the "Master of Bioinformatics" (Universitat Autònoma de Barcelona) Teaching at the "Máster de Mejora Genética y Biotecnología de la Reproducción" (Universitat Autònoma de Barcelona)
Doctoral Programs: Member of the Doctoral Program in Genetics in the line of Comparative Genomics and Evolution at the Universitat Autònoma de Barcelona (https://www.uab.cat/en/phds/genetics#seccio-linies)
National Research Networks: Red temática AdaptNet (up to 2024)