Rodriguez-Valera Y, Renand G, Naves M, Fonseca-Jiménez Y, Moreno-Probance TI, Ramos-Onsins S, Rocha D, Ramayo-Caldas Y.
Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed.
Sci Rep. 2018 Jul 20;8(1):11005. doi: 10.1038/s41598-018-29453-z. [PubMed] [Journal]

Ferretti L, Klassmann A, Raineri E, Ramos-Onsins SE, Wiehe T, Achaz G.
The neutral frequency spectrum of linked sites.
Theor Popul Biol. 2018 Jun 28. pii: S0040-5809(17)30139-9. doi: 10.1016/j.tpb.2018.06.001. [PubMed] [Journal]

Morata J, Tormo M, Alexiou KG, Vives C, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM.
The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon.
Genome Biol Evol. 2018 Jun 1;10(6):1584-1595. doi: 10.1093/gbe/evy115. [PubMed] [Journal]

Sara Guirao-Rico, Oscar Ramirez, Ana Ojeda, Marcel Amills and Sebastian E. Ramos-Onsins
Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations
Heredity. 2018 120 (1): 63-76 [PubMed] [Journal]

Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio, Sara Guirao-Rico, Pablo Librado, Sebastián Ramos-Onsins and Alejandro Sánchez-Gracia
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
Molecular Biology and Evolution. 2017 1; 34 (12): 3299-3302 [PubMed] [Journal]

Marcel Amills, Hendrik-Jan Megens, Arianna Manunza, Sebastián E. Ramos-Onsins, and Martien Groenen.
A Genomic Perspective on Wild Boar Demography and Evolution.
Chapter book in "Ecology, Conservation and Management of Wild Pigs and Peccaries".
Editors Mario Meletti and Erik Meijaard.
Cambridge University Press 2017. [Book]

Navarro J, Nevado B, Hernández P, Vera G, Ramos-Onsins SE.
Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis.
Evol Bioinform Online. 2017 Aug 24;13:1176934317723884. doi: 10.1177/1176934317723884. eCollection 2017. [PubMed] [Journal]

Ferretti L, Ledda A, Wiehe T, Achaz G, Ramos-Onsins SE..
Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.
Genetics. 2017 Sep;207(1):229-240. doi: 10.1534/genetics.116.188763. Epub 2017 Jul 5. [PubMed] [Journal]

Montemuiño C, Espinosa A, Moure JC, Vera G, Hernández P, Ramos-Onsins S. Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS.
Evol Bioinform Online. 2016 Oct 2;12:223-228. eCollection 2016. Review. [PubMed] [Journal]

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.
Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes.
BMC Genomics. 2016 Aug 26;17:685. doi: 10.1186/s12864-016-2972-z. [PubMed] [Journal]

Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE*, Garcia-Mas J*, Casacuberta JM.* Transposon insertion, structural variations and SNPs contribute to the evolution of the melon genome.
Mol Biol Evol. 2015 Jul 14. pii: msv152. [PubMed] [Journal]

Bianco E, Nevado B, Ramos-Onsins SE, Pérez-Enciso M. A deep catalog of autosomal single nucleotide variation in the pig.
PLoS One. 2015 Mar 19;10(3):e0118867. doi: 10.1371/journal.pone.0118867. eCollection 2015. [PubMed] [Journal]

Ferretti L, Ramos-Onsins SE. A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids.
Theor. Popul. Biol. 2015 Jan 13;100C:79-87. doi: 10.1016/j.tpb.2015.01.001. [PubMed] [Journal][ArXiV]

Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J.
Use of targeted SNP selection for an improved anchoring of the melon ( Cucumis melo L.) scaffold genome assembly.
BMC Genomics. 2015 Jan 22;16(1):4. [PubMed] [Journal]

Pérez-Enciso M, Burgos-Paz W, Ramos-Onsins SE.
On genetic differentiation between domestic pigs and Tibetan wild boars.
Nat. Genet. 2015 Feb 25;47(3):190-2. doi: 10.1038/ng.3191. [PubMed] [Journal]

Ramos-Onsins SE, Burgos-Paz W, Manunza A, Amills M. (2014)
Mining the pig genome to investigate the domestication process.
Heredity (Edinb). 2014 Jul 30. doi: 10.1038/hdy.2014.68. [PubMed] [Journal]

Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher M. (2014)
An efficient swiss army knife for population genomic analyses in R.
Mol Biol Evol. 2014 Jul;31(7):1929-36 [PubMed] [Journal]

Montemuiño C, Espinosa A, Moure JC, Vera Rodriguez G, Ramos-Onsins SE, Hernández Budé P (2014)
mspar: A Parallel Coalescent Simulator.
D. an Mey et al. (Eds.): Euro-Par 2013 Workshops, LNCS 8374, pp. 321–330, 2014. © Springer-Verlag Berlin Heidelberg 2014 [Proocedings Book] [link to mspar software]

Nevado B, Ramos-Onsins SE, Perez-Enciso M (2014)
Re-sequencing studies of non-model organisms using closely-related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics
Mol Ecol. 2014 Apr;23(7):1764-79. [PubMed] [Journal]

Ferretti L, Ramos-Onsins SE, Pérez-Enciso M. (2013)
Population genomics from pool sequencing.

Mol Ecol. 2013 Sep 14; (22) 5561-5576.
[PubMed] [Journal].

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 TJ, Ruiz-Herrera A. (2013). Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference.
Proc Biol Sci. 2013 Sep 25;280(1771):20131945. Print 2013. [PubMed] [Journal].

Esteve-Codina A., Paudel Y., Ferretti L., Raineri E., Megens HJ, Silió L., Rodríguez MC, Groenen MA, Ramos-Onsins SE, Pérez-Enciso M. (2013)
Dissecting structural and nucleotide genome-wide variation in inbred iberian pigs.
BMC GENOMICS. 2013 Mar 5;14:148. doi: 10.1186/1471-2164-14-148. [PubMed] [Journal].

Ferretti L., Raineri E. and Ramos-Onsins SE., (2012) Neutrality tests for sequences with missing data.
GENETICS 2012 191(4), 1397-1401. [PubMed] [Journal].

Burgos-Paz W., Souza C.A., Castelló A., Mercadé A., Okumura N., Sheremt'eva I.N., Huang L.S., Cho I.C., Paiva S.R., Ramos-Onsins S.E. and Pérez-Enciso M. (2012).
Worldwide genetic relationships of pigs as inferred from X chromosome SNPs.
ANIMAL GENETICS 2012. doi: 10.1111/j.1365-2052.2012.02374.x [PubMed] [Journal]

Amaral, A. J., L. Ferretti, H.-J. Megens, R. P. M. A. Crooijmans, H. Nie, S. E. Ramos-Onsins, M. Perez-Enciso, L. B. Schook, and M. A. M. Groenen (2011, APR 4).
Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA.
PLOS ONE 2011 6(4). [PubMed] [Journal]

Ojeda, A., S. E. Ramos-Onsins*, D. Marletta, L. S. Huang, J. M. Folch, and M. Perez-Enciso* (2011, FEB).
Evolutionary study of a potential selection target region in the pig. (* corresponding authors)
HEREDITY 2011 106(2), 330–338. [PubMed] [Journal]

Ferretti, L., M. Perez-Enciso, and S. Ramos-Onsins (2010, SEP).
Optimal Neutrality Tests Based on the Frequency Spectrum.
GENETICS 2010 186(1), 353–U562. [PubMed] [Journal]

Heidel*, A. J., S. E. Ramos-Onsins*, W.-K. Wang, T.-Y. Chiang, and T. Mitchell-Olds (2010, AUG).
Population history in Arabidopsis halleri using multilocus analysis. (* first authors)
MOLECULAR ECOLOGY 2010 19(16), 3364–3379. [PubMed] [Journal]

He, F., W.-H. Chen, S. Collins, C. Acquisti, U. Goebel, S. Ramos-Onsins, M. J. Lercher, and J. de Meaux (2010, JUN).
Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions in Arabidopsis thaliana.
GENETICS 2010 185(2), 695–701. [PubMed] [Journal]

Song, B.-H., A. J. Windsor, K. J. Schmid, S. Ramos-Onsins, M. E. Schranz, A. J. Heidel, and T. Mitchell-Olds (2009, MAR).
Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis.
GENETICS 2009 181(3), 1021–1033. [PubMed] [Journal]

Ramos-Onsins, SE., E. Puerma, D. Balana-Alcaide, D. Salguero, and M. Aguade (2008, MAR).
Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana.
MOLECULAR ECOLOGY 2008 17(5), 1211–1223. [PubMed] [Journal]

Ramirez-Soriano, A., S. E. Ramos-Onsins, J. Rozas, F. Calafell, and A. Navarro (2008, MAY).
Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination.
GENETICS 2008 179(1), 555–567. [PubMed] [Journal]

Ramos-Onsins, S. E., S. Mousset, T. Mitchell-Olds, and W. Stephan (2007, AUG).
Population genetic inference using a fixed number of segregating sites: a re-assessment.
GENETICS RESEARCH 2007 89(4), 231–244. [PubMed] [Journal]

Ramos-Onsins, S. E. and T. Mitchell-Olds (2007).
Mlcoalsim: Multilocus Coalescent Simulations.
EVOLUTIONARY BIOINFORMATICS 2007 3, 41–44. [PubMed] [Journal]

Balana-Alcaide, D., S. Ramos-Onsins, Q. Boone, and M. Aguade (2006, JUL).
Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions.
MOLECULAR ECOLOGY 2006 15(8), 2059–2068. [PubMed] [Journal]

Quesada, H., S. E. Ramos-Onsins, J. Rozas, and M. Aguade (2006, SEP).
Positive selection versus demography: Evolutionary inferences based on an unusual haplotype structure in Drosophila simulans.
MOLECULAR BIOLOGY AND EVOLUTION 2006 23(9), 1643–1647. [PubMed] [Journal]

Schmid*, K., S. Ramos-Onsins*, H. Ringys-Beckstein, B. Weisshaar, and T. Mitchell-Olds (2005, MAR).
A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. (* first authors)
GENETICS 2005 169(3), 1601–1615. [PubMed] [Journal]

Quesada, H., S. Ramos-Onsins, and M. Aguade (2005, JAN).
Birth-and-death evolution of the Cecropin multigene family in Drosophila.
JOURNAL OF MOLECULAR EVOLUTION 2005 60(1), 1–11. [PubMed] [Journal]

Ramos-Onsins*, S., B. Stranger*, T. Mitchell-Olds, and M. Aguade (2004, JAN).
Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. (* first authors)
GENETICS 2004 166(1), 373–388. [PubMed] [Journal] [Corrigenda]

Ramos-Onsins, S. and J. Rozas (2002, DEC).
Statistical properties of new neutrality tests against population growth.
MOLECULAR BIOLOGY AND EVOLUTION 2002 19(12), 2092–2100. [PubMed] [Journal] [Corrigenda]

Kuittinen, H., M. Aguade, D. Charlesworth, A. Haan, B. Lauga, T. Mitchell-Olds, S. Oikarinen, S. Ramos-Onsins, B. Stranger, P. Van Tienderen, and O. Savolainen (2002, SEP).
Primers for 22 candidate genes for ecological adaptations in Brassicaceae.
MOLECULAR ECOLOGY NOTES 2002 2(3), 258–262. [PubMed] [Journal]

Zhao, Z., L. Jin, Y. Fu, M. Ramsay, T. Jenkins, E. Leskinen, P. Pamilo, M. Trexler, L. Patthy, L. Jorde, S. Ramos-Onsins, N. Yu, and W. Li (2000, OCT 10).
World-wide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22.

Ramos-Onsins, S. and M. Aguade (1998, SEP).
Molecular evolution of the Cecropin multigene family in Drosophila: Functional genes vs. pseudogenes.
GENETICS 1998 150(1), 157–171. [PubMed] [Journal]

Ramos-Onsins, S., C. Segarra, J. Rozas, and M. Aguade (1998, FEB).
Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region.
MOLECULAR PHYLOGENETICS AND EVOLUTION 1998 9(1), 33–41. [PubMed] [Journal]