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Statistical and population genomics
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Overview
Our interests are to combine the development of methods / software with analysing real data, both from a population genetics point of view and QTL / association analysis. The research goals are the following:
Development of statisitcal methods and software. We study statistical methodologies to take advantage of the high throughput technologies, focusing on the search of the genetic causes of traits of interest (e.g., domestication traits). We develop statistical tests to detect extreme patterns of variation and software focus in the analysis of variability and in QTL /association analysis.
Analysis of genomic data in Sus scrofa. We have been interested in the study of empirical data, starting from single-locus strategies based on candidate genes to the analysis of genome-wide data using different sequencing and sampling strategies, in order to understand the patterns of the observed variability in Sus scrofa. We explore methods to combine external information (e.g., metabolic pathways, interactome) with nucleotide diversity statistics to explore potential selective sweeps using a holistic rather than gene by gene approach.
Selected Publications
Ferretti L, Ribeca P, Ramos-Onsins SE.
The Site Frequency/Dosage Spectrum of Autopolyploid Populations.
(2018) Front Genet. Oct 23;9:480. doi: 10.3389/fgene.2018.00480. eCollection
Morata, J., Tormo, M., Alexiou, K.G., Vives, C., Ramos-Onsins, S.E., Garcia-Mas, J., Casacuberta, J.M.
The evolutionary consequences of transposon-related pericentromer expansion in melon
(2018) Genome Biology and Evolution, vol. 10 (6), pp. 1584-1595
Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., Sanchez-Gracia, A.
DnaSP 6: DNA sequence polymorphism analysis of large data sets
(2017) Molecular Biology and Evolution, vol. 34 (12), pp. 3299-3302
Guirao-Rico, S., Ramirez, O., Ojeda, A., Amills, M., Ramos-Onsins, S.E.
Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations
(2018) Heredity, vol. 120 (1), pp. 63-76
Bellot, P., de los Campos, G., Pérez-Enciso, M.
Can deep learning improve genomic prediction of complex human traits?
(2018) Genetics, vol. 210 (3), pp. 809-819
Pérez-Enciso, M., Rincón, J.C., Legarra, A.
Sequence- vs. chip-assisted genomic selection: Accurate biological information is advised
(2015) Genetics Selection Evolution, vol. 47 (1), Art. number 43
Pérez-Enciso, M., Burgos-Paz, W., Ramos-Onsins, S.E.
On genetic differentiation between domestic pigs and Tibetan wild boars
(2015) Nature Genetics, vol. 47 (3), pp. 190-192
Ramírez, O., Burgos-Paz, W., Casas, E., Ballester, M., Bianco, E., Olalde, I., Santpere, G., Novella, V., Gut, M., Lalueza-Fox, C., Saña, M., Pérez-Enciso, M.
Genome data from a sixteenth century pig illuminate modern breed relationships
(2015) Heredity, vol. 114 (2), pp. 175-184
Groenen, M.A.M., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.-J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A.F., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.-H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P.M.A., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.-Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G.R., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.-L., Humphray, S.J., Hunt, T., Hornshoøj, H., Jeon, J.-T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.-H., Kim, K.-W., Kim, T.-H., Larson, G., Lee, K., Lee, K.-T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Nguyen, D.T., Ni, P., Oh, S.-J., Onteru, S., Panitz, F., Park, E.-W., Park, H.-S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L.B.
Analyses of pig genomes provide insight into porcine demography and evolution
(2012) Nature, vol. 491 (7424), pp. 393-398