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Items: 29

1.

The Site Frequency/Dosage Spectrum of Autopolyploid Populations.

Ferretti L, Ribeca P, Ramos-Onsins SE.

Front Genet. 2018 Oct 23;9:480. doi: 10.3389/fgene.2018.00480. eCollection 2018.

2.

The neutral frequency spectrum of linked sites.

Ferretti L, Klassmann A, Raineri E, Ramos-Onsins SE, Wiehe T, Achaz G.

Theor Popul Biol. 2018 Sep;123:70-79. doi: 10.1016/j.tpb.2018.06.001. Epub 2018 Jun 28.

PMID:
29964061
3.

The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon.

Morata J, Tormo M, Alexiou KG, Vives C, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM.

Genome Biol Evol. 2018 Jun 1;10(6):1584-1595. doi: 10.1093/gbe/evy115.

4.

Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations.

Guirao-Rico S, Ramirez O, Ojeda A, Amills M, Ramos-Onsins SE.

Heredity (Edinb). 2018 Jan;120(1):63-76. doi: 10.1038/s41437-017-0002-9. Epub 2017 Nov 20.

5.

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A.

Mol Biol Evol. 2017 Dec 1;34(12):3299-3302. doi: 10.1093/molbev/msx248.

PMID:
29029172
6.

Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis.

Navarro J, Nevado B, Hernández P, Vera G, Ramos-Onsins SE.

Evol Bioinform Online. 2017 Aug 24;13:1176934317723884. doi: 10.1177/1176934317723884. eCollection 2017.

7.

Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.

Ferretti L, Ledda A, Wiehe T, Achaz G, Ramos-Onsins SE.

Genetics. 2017 Sep;207(1):229-240. doi: 10.1534/genetics.116.188763. Epub 2017 Jul 5.

8.

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM.

Mol Biol Evol. 2015 Oct;32(10):2760-74. doi: 10.1093/molbev/msv152. Epub 2015 Jul 14.

PMID:
26174143
9.

A deep catalog of autosomal single nucleotide variation in the pig.

Bianco E, Nevado B, Ramos-Onsins SE, Pérez-Enciso M.

PLoS One. 2015 Mar 19;10(3):e0118867. doi: 10.1371/journal.pone.0118867. eCollection 2015.

10.

On genetic differentiation between domestic pigs and Tibetan wild boars.

Pérez-Enciso M, Burgos-Paz W, Ramos-Onsins SE.

Nat Genet. 2015 Mar;47(3):190-2. doi: 10.1038/ng.3191. No abstract available.

PMID:
25711861
11.

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly.

Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J.

BMC Genomics. 2015 Jan 22;16:4. doi: 10.1186/s12864-014-1196-3.

12.

A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids.

Ferretti L, Ramos-Onsins SE.

Theor Popul Biol. 2015 Mar;100C:79-87. doi: 10.1016/j.tpb.2015.01.001. Epub 2015 Jan 13.

PMID:
25595553
13.

Mining the pig genome to investigate the domestication process.

Ramos-Onsins SE, Burgos-Paz W, Manunza A, Amills M.

Heredity (Edinb). 2014 Dec;113(6):471-84. doi: 10.1038/hdy.2014.68. Epub 2014 Jul 30. Review.

15.

PopGenome: an efficient Swiss army knife for population genomic analyses in R.

Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ.

Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16.

16.

Population genomics from pool sequencing.

Ferretti L, Ramos-Onsins SE, Pérez-Enciso M.

Mol Ecol. 2013 Nov;22(22):5561-76. doi: 10.1111/mec.12522. Epub 2013 Oct 28.

PMID:
24102736
17.

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.

Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silió L, Rodríguez MC, Groenen MA, Ramos-Onsins SE, Pérez-Enciso M.

BMC Genomics. 2013 Mar 5;14:148. doi: 10.1186/1471-2164-14-148.

18.

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.

Amaral AJ, Ferretti L, Megens HJ, Crooijmans RP, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MA.

PLoS One. 2011 Apr 4;6(4):e14782. doi: 10.1371/journal.pone.0014782.

19.

Population history in Arabidopsis halleri using multilocus analysis.

Heidel AJ, Ramos-Onsins SE, Wang WK, Chiang TY, Mitchell-Olds T.

Mol Ecol. 2010 Aug;19(16):3364-79. doi: 10.1111/j.1365-294X.2010.04761.x. Epub 2010 Jul 28.

20.

Evolutionary study of a potential selection target region in the pig.

Ojeda A, Ramos-Onsins SE, Marletta D, Huang LS, Folch JM, Pérez-Enciso M.

Heredity (Edinb). 2011 Feb;106(2):330-8. doi: 10.1038/hdy.2010.61. Epub 2010 May 26.

21.

Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination.

Ramírez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A.

Genetics. 2008 May;179(1):555-67. doi: 10.1534/genetics.107.083006.

22.

Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana.

Ramos-Onsins SE, Puerma E, Balañá-Alcaide D, Salguero D, Aguadé M.

Mol Ecol. 2008 Mar;17(5):1211-23. doi: 10.1111/j.1365-294X.2007.03633.x. Epub 2008 Jan 21.

PMID:
18221273
23.

Population genetic inference using a fixed number of segregating sites: a reassessment.

Ramos-Onsins SE, Mousset S, Mitchell-Olds T, Stephan W.

Genet Res. 2007 Aug;89(4):231-44. doi: 10.1017/S0016672307008877.

PMID:
18208629
24.

Mlcoalsim: multilocus coalescent simulations.

Ramos-Onsins SE, Mitchell-Olds T.

Evol Bioinform Online. 2007 Mar 2;3:41-4.

25.

Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions.

Balañá-Alcaide D, Ramos-Onsins SE, Boone Q, Aguadé M.

Mol Ecol. 2006 Jul;15(8):2059-68.

PMID:
16780424
26.

Positive selection versus demography: evolutionary inferences based on an unusual haplotype structure in Drosophila simulans.

Quesada H, Ramos-Onsins SE, Rozas J, Aguadé M.

Mol Biol Evol. 2006 Sep;23(9):1643-7. Epub 2006 Jun 6.

PMID:
16757657
27.

Birth-and-death evolution of the Cecropin multigene family in Drosophila.

Quesada H, Ramos-Onsins SE, Aguadé M.

J Mol Evol. 2005 Jan;60(1):1-11.

PMID:
15696364
28.

Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata.

Ramos-Onsins SE, Stranger BE, Mitchell-Olds T, Aguadé M.

Genetics. 2004 Jan;166(1):373-88. Erratum in: Genetics. 2004 Aug;167(4):2143.

29.

Statistical properties of new neutrality tests against population growth.

Ramos-Onsins SE, Rozas J.

Mol Biol Evol. 2002 Dec;19(12):2092-100. Erratum in: Mol Biol Evol. 2006 Aug;23(8):1642.

PMID:
12446801

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